diff --git a/CHANGES/v2.5.md b/CHANGES/v2.5.md
index f54c573032374302c21d6978cf0a8a036a59e508..109bbfd188737639e7d5c563956285031792ee54 100644
--- a/CHANGES/v2.5.md
+++ b/CHANGES/v2.5.md
@@ -35,6 +35,7 @@ Changes from version 2.4 which are relevant for users:
by matheval (easily writable as a function of the available ones).
- Implemented bash autocompletion, see \ref BashAutocompletion.
- \ref MOLINFO now allows selecting atoms from chains with a numeric ID (see \issue{320}).
+ - Removed the patch for GMX 5.0.4
Changes from version 2.4 which are relevant for developers:
- Code has been cleanup up replacing a number of pointers with `std::unique_ptr`.
diff --git a/patches/gromacs-5.1.4.config b/patches/gromacs-5.1.4.config
deleted file mode 100644
index ae65d400e7de4984db03a0a74349b1a50704db20..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.config
+++ /dev/null
@@ -1,35 +0,0 @@
-
-
-function plumed_preliminary_test(){
-# check if the README contains the word GROMACS and if gromacs has been already configured
- grep -q GROMACS README 1>/dev/null 2>/dev/null
-}
-
-function plumed_patch_info(){
-cat << EOF
-PLUMED can be incorporated into gromacs using the standard patching procedure.
-Patching must be done in the gromacs root directory _before_ the cmake command is invoked.
-
-On clusters you may want to patch gromacs using the static version of plumed, in this case
-building gromacs can result in multiple errors. One possible solution is to configure gromacs
-with these additional options:
-
-cmake -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON
-
-To enable PLUMED in a gromacs simulation one should use
-mdrun with an extra -plumed flag. The flag can be used to
-specify the name of the PLUMED input file, e.g.:
-
-gmx mdrun -plumed plumed.dat
-
-This patch also implements the -hrex keyword for gromacs. See \ref hrex
-
-For more information on gromacs you should visit http://www.gromacs.org
-
-EOF
-}
-
-plumed_before_patch(){
- plumed_patch_info
-}
-
diff --git a/patches/gromacs-5.1.4.diff/src/gromacs/CMakeLists.txt b/patches/gromacs-5.1.4.diff/src/gromacs/CMakeLists.txt
deleted file mode 100644
index 2af9fdf862dea3a884a4aaf07865bb85b43cc9ba..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/gromacs/CMakeLists.txt
+++ /dev/null
@@ -1,257 +0,0 @@
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-include(${CMAKE_SOURCE_DIR}/Plumed.cmake)
-
-set(LIBGROMACS_SOURCES)
-
-set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
-
-function (gmx_install_headers)
- if (NOT GMX_BUILD_MDRUN_ONLY)
- file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
- install(FILES ${ARGN}
- DESTINATION "${INCL_INSTALL_DIR}/${_dest}"
- COMPONENT development)
- endif()
- foreach (_file ${ARGN})
- if (IS_ABSOLUTE "${_file}")
- set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS ${_file})
- else()
- set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS
- ${CMAKE_CURRENT_LIST_DIR}/${_file})
- endif()
- endforeach()
-endfunction ()
-
-function (gmx_write_installed_header_list)
- get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
- string(REPLACE ";" "\n" _list "${_list}")
- # TODO: Make this only update the file timestamp if the contents actually change.
- file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
-endfunction()
-
-if(GMX_USE_TNG)
- option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS."
- OFF)
- # Detect TNG if GMX_EXTERNAL_TNG is explicitly ON
- if(GMX_EXTERNAL_TNG)
- find_package(TNG_IO 1.6.0)
- if(NOT TNG_IO_FOUND)
- message(FATAL_ERROR
- "TNG >= 1.6.0 not found. "
- "You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
- endif()
- include_directories(SYSTEM ${TNG_IO_INCLUDE_DIRS})
- endif()
- if(NOT GMX_EXTERNAL_TNG)
- include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
- tng_get_source_list(TNG_SOURCES TNG_IO_DEFINITIONS)
- list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
- tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
-
- if (HAVE_ZLIB)
- list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
- include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
- endif()
- endif()
-else()
- # We still need to get tng/tng_io_fwd.h from somewhere!
- include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
-endif()
-
-add_subdirectory(gmxlib)
-add_subdirectory(mdlib)
-add_subdirectory(listed-forces)
-add_subdirectory(commandline)
-add_subdirectory(domdec)
-add_subdirectory(ewald)
-add_subdirectory(fft)
-add_subdirectory(linearalgebra)
-add_subdirectory(math)
-add_subdirectory(mdrunutility)
-add_subdirectory(random)
-add_subdirectory(onlinehelp)
-add_subdirectory(options)
-add_subdirectory(pbcutil)
-add_subdirectory(timing)
-add_subdirectory(topology)
-add_subdirectory(utility)
-add_subdirectory(fileio)
-add_subdirectory(swap)
-add_subdirectory(essentialdynamics)
-add_subdirectory(pulling)
-add_subdirectory(simd)
-add_subdirectory(imd)
-if (NOT GMX_BUILD_MDRUN_ONLY)
- add_subdirectory(legacyheaders)
- add_subdirectory(gmxana)
- add_subdirectory(gmxpreprocess)
- add_subdirectory(correlationfunctions)
- add_subdirectory(statistics)
- add_subdirectory(analysisdata)
- add_subdirectory(selection)
- add_subdirectory(trajectoryanalysis)
- add_subdirectory(tools)
-endif()
-
-list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES})
-
-# This would be the standard way to include thread_mpi, but
-# we want libgromacs to link the functions directly
-#if(GMX_THREAD_MPI)
-# add_subdirectory(thread_mpi)
-#endif()
-#target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
-
-tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
-list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
-
-configure_file(version.h.cmakein version.h)
-gmx_install_headers(
- analysisdata.h
- commandline.h
- options.h
- selection.h
- trajectoryanalysis.h
- utility.h
- ${CMAKE_CURRENT_BINARY_DIR}/version.h
- )
-
-# This code is here instead of utility/CMakeLists.txt, because CMake
-# custom commands and source file properties can only be set in the directory
-# that contains the target that uses them.
-# TODO: Generate a header instead that can be included from baseversion.c.
-# That probably simplifies things somewhat.
-set(GENERATED_VERSION_FILE utility/baseversion-gen.c)
-gmx_configure_version_file(
- utility/baseversion-gen.c.cmakein ${GENERATED_VERSION_FILE}
- REMOTE_HASH SOURCE_FILE)
-list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
-
-# apply gcc 4.4.x bug workaround
-if(GMX_USE_GCC44_BUG_WORKAROUND)
- include(gmxGCC44O3BugWorkaround)
- gmx_apply_gcc44_bug_workaround("listed-forces/bonded.cpp")
- gmx_apply_gcc44_bug_workaround("mdlib/force.c")
- gmx_apply_gcc44_bug_workaround("mdlib/constr.c")
-endif()
-
-if (GMX_GPU AND NOT GMX_USE_OPENCL)
- cuda_add_library(libgromacs ${LIBGROMACS_SOURCES}
- OPTIONS
- RELWITHDEBINFO -g
- DEBUG -g -D_DEBUG_=1)
-else()
- add_library(libgromacs ${LIBGROMACS_SOURCES})
-endif()
-
-# Recent versions of gcc and clang give warnings on scanner.cpp, which
-# is a generated source file. These are awkward to suppress inline, so
-# we do it in the compilation command (after testing that the compiler
-# supports the suppressions). Setting the properties only works after
-# the related target has been created, e.g. after when the file is
-# used with add_library().
-include(CheckCXXCompilerFlag)
-check_cxx_compiler_flag(-Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
-if (HAS_NO_UNUSED_PARAMETER)
- set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-unused-parameter")
-endif()
-check_cxx_compiler_flag(-Wno-deprecated-register HAS_NO_DEPRECATED_REGISTER)
-if (HAS_NO_DEPRECATED_REGISTER)
- set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated-register")
-else()
- check_cxx_compiler_flag(-Wno-deprecated HAS_NO_DEPRECATED)
- if (HAS_NO_DEPRECATED)
- set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated")
- endif()
-endif()
-set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
-
-target_link_libraries(libgromacs ${PLUMED_LOAD})
-
-target_link_libraries(libgromacs
- ${EXTRAE_LIBRARIES}
- ${GMX_EXTRA_LIBRARIES}
- ${TNG_IO_LIBRARIES}
- ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
- ${XML_LIBRARIES}
- ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES})
-
-
-set_target_properties(libgromacs PROPERTIES
- OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
- SOVERSION ${LIBRARY_SOVERSION_MAJOR}
- VERSION ${LIBRARY_VERSION}
- COMPILE_FLAGS "${OpenMP_C_FLAGS}")
-
-gmx_write_installed_header_list()
-
-# Only install the library in mdrun-only mode if it is actually necessary
-# for the binary
-if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
- install(TARGETS libgromacs
- EXPORT libgromacs
- LIBRARY DESTINATION ${LIB_INSTALL_DIR}
- RUNTIME DESTINATION ${BIN_INSTALL_DIR}
- ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
- COMPONENT libraries)
-endif()
-
-if (NOT GMX_BUILD_MDRUN_ONLY)
- include(InstallLibInfo.cmake)
-endif()
-
-if (INSTALL_CUDART_LIB) #can be set manual by user
- if (GMX_GPU AND NOT GMX_USE_OPENCL)
- foreach(CUDA_LIB ${CUDA_LIBRARIES})
- string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
- if(IS_CUDART) #libcuda should not be installed
- #install also name-links (linker uses those)
- file(GLOB CUDA_LIBS ${CUDA_LIB}*)
- install(FILES ${CUDA_LIBS} DESTINATION
- ${LIB_INSTALL_DIR} COMPONENT libraries)
- endif()
- endforeach()
- else()
- message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
- endif()
-endif()
-
-if(GMX_GPU AND GMX_USE_OPENCL)
- set(OPENCL_KERNELS ${MDLIB_OPENCL_KERNELS})
-
- install(FILES ${OPENCL_KERNELS} DESTINATION
- ${OCL_INSTALL_DIR} COMPONENT libraries)
-endif()
diff --git a/patches/gromacs-5.1.4.diff/src/gromacs/CMakeLists.txt.preplumed b/patches/gromacs-5.1.4.diff/src/gromacs/CMakeLists.txt.preplumed
deleted file mode 100644
index 467b0be4c1abb18c0a53a96ed052353a608d4a0f..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/gromacs/CMakeLists.txt.preplumed
+++ /dev/null
@@ -1,251 +0,0 @@
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-set(LIBGROMACS_SOURCES)
-
-set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
-
-function (gmx_install_headers)
- if (NOT GMX_BUILD_MDRUN_ONLY)
- file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
- install(FILES ${ARGN}
- DESTINATION "${INCL_INSTALL_DIR}/${_dest}"
- COMPONENT development)
- endif()
- foreach (_file ${ARGN})
- if (IS_ABSOLUTE "${_file}")
- set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS ${_file})
- else()
- set_property(GLOBAL APPEND PROPERTY GMX_INSTALLED_HEADERS
- ${CMAKE_CURRENT_LIST_DIR}/${_file})
- endif()
- endforeach()
-endfunction ()
-
-function (gmx_write_installed_header_list)
- get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
- string(REPLACE ";" "\n" _list "${_list}")
- # TODO: Make this only update the file timestamp if the contents actually change.
- file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
-endfunction()
-
-if(GMX_USE_TNG)
- option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS."
- OFF)
- # Detect TNG if GMX_EXTERNAL_TNG is explicitly ON
- if(GMX_EXTERNAL_TNG)
- find_package(TNG_IO 1.6.0)
- if(NOT TNG_IO_FOUND)
- message(FATAL_ERROR
- "TNG >= 1.6.0 not found. "
- "You can set GMX_EXTERNAL_TNG=OFF to compile TNG.")
- endif()
- include_directories(SYSTEM ${TNG_IO_INCLUDE_DIRS})
- endif()
- if(NOT GMX_EXTERNAL_TNG)
- include(${CMAKE_SOURCE_DIR}/src/external/tng_io/BuildTNG.cmake)
- tng_get_source_list(TNG_SOURCES TNG_IO_DEFINITIONS)
- list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
- tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
-
- if (HAVE_ZLIB)
- list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
- include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
- endif()
- endif()
-else()
- # We still need to get tng/tng_io_fwd.h from somewhere!
- include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/tng_io/include)
-endif()
-
-add_subdirectory(gmxlib)
-add_subdirectory(mdlib)
-add_subdirectory(listed-forces)
-add_subdirectory(commandline)
-add_subdirectory(domdec)
-add_subdirectory(ewald)
-add_subdirectory(fft)
-add_subdirectory(linearalgebra)
-add_subdirectory(math)
-add_subdirectory(mdrunutility)
-add_subdirectory(random)
-add_subdirectory(onlinehelp)
-add_subdirectory(options)
-add_subdirectory(pbcutil)
-add_subdirectory(timing)
-add_subdirectory(topology)
-add_subdirectory(utility)
-add_subdirectory(fileio)
-add_subdirectory(swap)
-add_subdirectory(essentialdynamics)
-add_subdirectory(pulling)
-add_subdirectory(simd)
-add_subdirectory(imd)
-if (NOT GMX_BUILD_MDRUN_ONLY)
- add_subdirectory(legacyheaders)
- add_subdirectory(gmxana)
- add_subdirectory(gmxpreprocess)
- add_subdirectory(correlationfunctions)
- add_subdirectory(statistics)
- add_subdirectory(analysisdata)
- add_subdirectory(selection)
- add_subdirectory(trajectoryanalysis)
- add_subdirectory(tools)
-endif()
-
-list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES})
-
-# This would be the standard way to include thread_mpi, but
-# we want libgromacs to link the functions directly
-#if(GMX_THREAD_MPI)
-# add_subdirectory(thread_mpi)
-#endif()
-#target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
-
-tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
-list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
-
-configure_file(version.h.cmakein version.h)
-gmx_install_headers(
- analysisdata.h
- commandline.h
- options.h
- selection.h
- trajectoryanalysis.h
- utility.h
- ${CMAKE_CURRENT_BINARY_DIR}/version.h
- )
-
-# This code is here instead of utility/CMakeLists.txt, because CMake
-# custom commands and source file properties can only be set in the directory
-# that contains the target that uses them.
-# TODO: Generate a header instead that can be included from baseversion.c.
-# That probably simplifies things somewhat.
-set(GENERATED_VERSION_FILE utility/baseversion-gen.c)
-gmx_configure_version_file(
- utility/baseversion-gen.c.cmakein ${GENERATED_VERSION_FILE}
- REMOTE_HASH SOURCE_FILE)
-list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
-
-# apply gcc 4.4.x bug workaround
-if(GMX_USE_GCC44_BUG_WORKAROUND)
- include(gmxGCC44O3BugWorkaround)
- gmx_apply_gcc44_bug_workaround("listed-forces/bonded.cpp")
- gmx_apply_gcc44_bug_workaround("mdlib/force.c")
- gmx_apply_gcc44_bug_workaround("mdlib/constr.c")
-endif()
-
-if (GMX_GPU AND NOT GMX_USE_OPENCL)
- cuda_add_library(libgromacs ${LIBGROMACS_SOURCES}
- OPTIONS
- RELWITHDEBINFO -g
- DEBUG -g -D_DEBUG_=1)
-else()
- add_library(libgromacs ${LIBGROMACS_SOURCES})
-endif()
-
-# Recent versions of gcc and clang give warnings on scanner.cpp, which
-# is a generated source file. These are awkward to suppress inline, so
-# we do it in the compilation command (after testing that the compiler
-# supports the suppressions). Setting the properties only works after
-# the related target has been created, e.g. after when the file is
-# used with add_library().
-include(CheckCXXCompilerFlag)
-check_cxx_compiler_flag(-Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
-if (HAS_NO_UNUSED_PARAMETER)
- set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-unused-parameter")
-endif()
-check_cxx_compiler_flag(-Wno-deprecated-register HAS_NO_DEPRECATED_REGISTER)
-if (HAS_NO_DEPRECATED_REGISTER)
- set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated-register")
-else()
- check_cxx_compiler_flag(-Wno-deprecated HAS_NO_DEPRECATED)
- if (HAS_NO_DEPRECATED)
- set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-deprecated")
- endif()
-endif()
-set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
-
-target_link_libraries(libgromacs
- ${EXTRAE_LIBRARIES}
- ${GMX_EXTRA_LIBRARIES}
- ${TNG_IO_LIBRARIES}
- ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
- ${XML_LIBRARIES}
- ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES})
-set_target_properties(libgromacs PROPERTIES
- OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
- SOVERSION ${LIBRARY_SOVERSION_MAJOR}
- VERSION ${LIBRARY_VERSION}
- COMPILE_FLAGS "${OpenMP_C_FLAGS}")
-
-gmx_write_installed_header_list()
-
-# Only install the library in mdrun-only mode if it is actually necessary
-# for the binary
-if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
- install(TARGETS libgromacs
- EXPORT libgromacs
- LIBRARY DESTINATION ${LIB_INSTALL_DIR}
- RUNTIME DESTINATION ${BIN_INSTALL_DIR}
- ARCHIVE DESTINATION ${LIB_INSTALL_DIR}
- COMPONENT libraries)
-endif()
-
-if (NOT GMX_BUILD_MDRUN_ONLY)
- include(InstallLibInfo.cmake)
-endif()
-
-if (INSTALL_CUDART_LIB) #can be set manual by user
- if (GMX_GPU AND NOT GMX_USE_OPENCL)
- foreach(CUDA_LIB ${CUDA_LIBRARIES})
- string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
- if(IS_CUDART) #libcuda should not be installed
- #install also name-links (linker uses those)
- file(GLOB CUDA_LIBS ${CUDA_LIB}*)
- install(FILES ${CUDA_LIBS} DESTINATION
- ${LIB_INSTALL_DIR} COMPONENT libraries)
- endif()
- endforeach()
- else()
- message(WARNING "INSTALL_CUDART_LIB only makes sense with GMX_GPU")
- endif()
-endif()
-
-if(GMX_GPU AND GMX_USE_OPENCL)
- set(OPENCL_KERNELS ${MDLIB_OPENCL_KERNELS})
-
- install(FILES ${OPENCL_KERNELS} DESTINATION
- ${OCL_INSTALL_DIR} COMPONENT libraries)
-endif()
diff --git a/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/force.cpp b/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/force.cpp
deleted file mode 100644
index d06924cfa07c514f9a54e001be6a5b5fca2cc71f..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/force.cpp
+++ /dev/null
@@ -1,962 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "gromacs/legacyheaders/force.h"
-
-#include "config.h"
-
-#include <assert.h>
-#include <math.h>
-#include <string.h>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/ewald/ewald.h"
-#include "gromacs/ewald/long-range-correction.h"
-#include "gromacs/ewald/pme.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nonbonded.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/listed-forces/listed-forces.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/forcerec-threading.h"
-#include "gromacs/pbcutil/ishift.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-/* PLUMED */
-#include "../../../Plumed.h"
-int plumedswitch=0;
-plumed plumedmain;
-void(*plumedcmd)(plumed,const char*,const void*)=NULL;
-/* END PLUMED */
-
-
-void ns(FILE *fp,
- t_forcerec *fr,
- matrix box,
- gmx_groups_t *groups,
- gmx_localtop_t *top,
- t_mdatoms *md,
- t_commrec *cr,
- t_nrnb *nrnb,
- gmx_bool bFillGrid,
- gmx_bool bDoLongRangeNS)
-{
- 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, box, top, groups, cr, nrnb, md,
- bFillGrid, bDoLongRangeNS);
- 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_q, tensor vir_lj,
- real *Vcorr_q, real *Vcorr_lj,
- real *dvdl_q, real *dvdl_lj,
- int nthreads, f_thread_t *f_t)
-{
- int t, i;
- int nthreads_loop gmx_unused;
-
- // cppcheck-suppress unreadVariable
- nthreads_loop = gmx_omp_nthreads_get(emntBonded);
- /* This reduction can run over any number of threads */
-#pragma omp parallel for num_threads(nthreads_loop) private(t) schedule(static)
- for (i = 0; i < n; i++)
- {
- for (t = 1; t < nthreads; t++)
- {
- rvec_inc(f[i], f_t[t].f[i]);
- }
- }
- for (t = 1; t < nthreads; t++)
- {
- *Vcorr_q += f_t[t].Vcorr_q;
- *Vcorr_lj += f_t[t].Vcorr_lj;
- *dvdl_q += f_t[t].dvdl[efptCOUL];
- *dvdl_lj += f_t[t].dvdl[efptVDW];
- m_add(vir_q, f_t[t].vir_q, vir_q);
- m_add(vir_lj, f_t[t].vir_lj, vir_lj);
- }
-}
-
-void do_force_lowlevel(t_forcerec *fr, t_inputrec *ir,
- t_idef *idef, t_commrec *cr,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- t_mdatoms *md,
- rvec x[], history_t *hist,
- rvec f[],
- rvec f_longrange[],
- gmx_enerdata_t *enerd,
- t_fcdata *fcd,
- gmx_localtop_t *top,
- gmx_genborn_t *born,
- 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;
- int donb_flags;
- gmx_bool bSB;
- int pme_flags;
- matrix boxs;
- rvec box_size;
- t_pbc pbc;
- real dvdl_dum[efptNR], dvdl_nb[efptNR];
-
-#ifdef GMX_MPI
- double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
-#endif
-
- 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];
- }
-
- debug_gmx();
-
- /* do QMMM first if requested */
- if (fr->bQMMM)
- {
- enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
- }
-
- /* 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 */
- real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
- enerd->grpp.ener[egLJSR], nrnb);
- enerd->dvdl_lin[efptVDW] += dvdl_walls;
- }
-
- /* 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, 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;
-
- /* Currently all group scheme kernels always calculate (shift-)forces */
- if (flags & GMX_FORCE_FORCES)
- {
- donb_flags |= GMX_NONBONDED_DO_FORCE;
- }
- if (flags & GMX_FORCE_VIRIAL)
- {
- donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
- }
- 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(fr, x, f, f_longrange, md, excl,
- &enerd->grpp, 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++)
- {
- real lam_i[efptNR];
-
- 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(fr, x, f, f_longrange, md, excl,
- &(enerd->foreign_grpp), nrnb,
- lam_i, dvdl_dum, -1, -1,
- (donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
- sum_epot(&(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, ewcsLISTED);
- calc_gb_forces(cr, md, born, top, x, f, fr, idef,
- ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
- wallcycle_sub_stop(wcycle, ewcsLISTED);
- }
-
-#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];
- }
-
- debug_gmx();
-
-
- if (debug)
- {
- pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
- }
-
- /* Shift the coordinates. Must be done before listed forces and PPPM,
- * but is also necessary for SHAKE and update, therefore it can NOT
- * go when no listed forces have to be evaluated.
- *
- * The shifting and PBC code is deliberately not timed, since with
- * the Verlet scheme it only takes non-zero time with triclinic
- * boxes, and even then the time is around a factor of 100 less
- * than the next smallest counter.
- */
-
-
- /* 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 listed interactions or correct for exclusions */
- if (fr->bMolPBC &&
- ((flags & GMX_FORCE_LISTED)
- || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
- {
- /* TODO There are no electrostatics methods that require this
- transformation, when using the Verlet scheme, so update the
- above conditional. */
- /* 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();
-
- do_force_listed(wcycle, box, ir->fepvals, cr->ms,
- idef, (const rvec *) x, hist, f, fr,
- &pbc, graph, enerd, nrnb, lambda, md, fcd,
- DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
- flags);
-
- where();
-
- *cycles_pme = 0;
- clear_mat(fr->vir_el_recip);
- clear_mat(fr->vir_lj_recip);
-
- /* Do long-range electrostatics and/or LJ-PME, including related short-range
- * corrections.
- */
- if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
- {
- int status = 0;
- real Vlr_q = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
- real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
-
- bSB = (ir->nwall == 2);
- if (bSB)
- {
- copy_mat(box, boxs);
- svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
- box_size[ZZ] *= ir->wall_ewald_zfac;
- }
-
- if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
- {
- real dvdl_long_range_correction_q = 0;
- real dvdl_long_range_correction_lj = 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 i;
- rvec *fnv;
- tensor *vir_q, *vir_lj;
- real *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
- if (t == 0)
- {
- fnv = fr->f_novirsum;
- vir_q = &fr->vir_el_recip;
- vir_lj = &fr->vir_lj_recip;
- Vcorrt_q = &Vcorr_q;
- Vcorrt_lj = &Vcorr_lj;
- dvdlt_q = &dvdl_long_range_correction_q;
- dvdlt_lj = &dvdl_long_range_correction_lj;
- }
- else
- {
- fnv = fr->f_t[t].f;
- vir_q = &fr->f_t[t].vir_q;
- vir_lj = &fr->f_t[t].vir_lj;
- Vcorrt_q = &fr->f_t[t].Vcorr_q;
- Vcorrt_lj = &fr->f_t[t].Vcorr_lj;
- dvdlt_q = &fr->f_t[t].dvdl[efptCOUL];
- dvdlt_lj = &fr->f_t[t].dvdl[efptVDW];
- for (i = 0; i < fr->natoms_force; i++)
- {
- clear_rvec(fnv[i]);
- }
- clear_mat(*vir_q);
- clear_mat(*vir_lj);
- }
- *dvdlt_q = 0;
- *dvdlt_lj = 0;
-
- ewald_LRcorrection(md->homenr, cr, nthreads, t, fr,
- md->chargeA, md->chargeB,
- md->sqrt_c6A, md->sqrt_c6B,
- md->sigmaA, md->sigmaB,
- md->sigma3A, md->sigma3B,
- md->nChargePerturbed || md->nTypePerturbed,
- ir->cutoff_scheme != ecutsVERLET,
- excl, x, bSB ? boxs : box, mu_tot,
- ir->ewald_geometry,
- ir->epsilon_surface,
- fnv, *vir_q, *vir_lj,
- Vcorrt_q, Vcorrt_lj,
- lambda[efptCOUL], lambda[efptVDW],
- dvdlt_q, dvdlt_lj);
- }
- if (nthreads > 1)
- {
- reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
- fr->vir_el_recip, fr->vir_lj_recip,
- &Vcorr_q, &Vcorr_lj,
- &dvdl_long_range_correction_q,
- &dvdl_long_range_correction_lj,
- nthreads, fr->f_t);
- }
- wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
- }
-
- if (EEL_PME_EWALD(fr->eeltype) && fr->n_tpi == 0)
- {
- /* This is not in a subcounter because it takes a
- negligible and constant-sized amount of time */
- Vcorr_q += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
- &dvdl_long_range_correction_q,
- fr->vir_el_recip);
- }
-
- enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
- enerd->dvdl_lin[efptVDW] += dvdl_long_range_correction_lj;
-
- if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)) && (cr->duty & DUTY_PME))
- {
- /* Do reciprocal PME for Coulomb and/or LJ. */
- assert(fr->n_tpi >= 0);
- if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
- {
- pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
- if (EEL_PME(fr->eeltype))
- {
- pme_flags |= GMX_PME_DO_COULOMB;
- }
- if (EVDW_PME(fr->vdwtype))
- {
- pme_flags |= GMX_PME_DO_LJ;
- }
- if (flags & GMX_FORCE_FORCES)
- {
- pme_flags |= GMX_PME_CALC_F;
- }
- if (flags & GMX_FORCE_VIRIAL)
- {
- 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,
- 0, md->homenr - fr->n_tpi,
- x, fr->f_novirsum,
- md->chargeA, md->chargeB,
- md->sqrt_c6A, md->sqrt_c6B,
- md->sigmaA, md->sigmaB,
- 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_q,
- fr->vir_lj_recip, fr->ewaldcoeff_lj,
- &Vlr_q, &Vlr_lj,
- lambda[efptCOUL], lambda[efptVDW],
- &dvdl_long_range_q, &dvdl_long_range_lj, pme_flags);
- *cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
- if (status != 0)
- {
- gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
- }
- /* 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)
- {
- if (EVDW_PME(ir->vdwtype))
- {
-
- gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
- }
- /* 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_q);
- }
- }
- }
-
- if (!EEL_PME(fr->eeltype) && EEL_PME_EWALD(fr->eeltype))
- {
- Vlr_q = do_ewald(ir, x, fr->f_novirsum,
- md->chargeA, md->chargeB,
- box_size, cr, md->homenr,
- fr->vir_el_recip, fr->ewaldcoeff_q,
- lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
- }
-
- /* Note that with separate PME nodes we get the real energies later */
- enerd->dvdl_lin[efptCOUL] += dvdl_long_range_q;
- enerd->dvdl_lin[efptVDW] += dvdl_long_range_lj;
- enerd->term[F_COUL_RECIP] = Vlr_q + Vcorr_q;
- enerd->term[F_LJ_RECIP] = Vlr_lj + Vcorr_lj;
- if (debug)
- {
- fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
- Vlr_q, Vcorr_q, 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);
- fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
- Vlr_lj, Vcorr_lj, enerd->term[F_LJ_RECIP]);
- pr_rvecs(debug, 0, "vir_lj_recip after corr", fr->vir_lj_recip, DIM);
- }
- }
- else
- {
- /* Is there a reaction-field exclusion correction needed? */
- if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
- {
- /* With the Verlet scheme, exclusion forces are calculated
- * in the non-bonded kernel.
- */
- if (ir->cutoff_scheme != ecutsVERLET)
- {
- real dvdl_rf_excl = 0;
- enerd->term[F_RF_EXCL] =
- RF_excl_correction(fr, graph, md, excl, x, f,
- fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
-
- enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
- }
- }
- }
- 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)
- {
- char buf[22];
- fprintf(stderr, "* PP load balancing info: rank %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
- cr->nodeid, gmx_step_str(fr->timesteps, buf),
- 100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
- (fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
- }
- fr->timesteps++;
- }
-#endif
-
- if (debug)
- {
- pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
- }
-
- /* PLUMED */
- if(plumedswitch){
- int plumedNeedsEnergy;
- (*plumedcmd)(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
- if(!plumedNeedsEnergy) (*plumedcmd)(plumedmain,"performCalc",NULL);
- }
- /* END PLUMED */
-}
-
-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(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_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);
-}
diff --git a/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/force.cpp.preplumed b/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/force.cpp.preplumed
deleted file mode 100644
index c6d18a862ee109a32130b14b50c08caa66b9dcee..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/force.cpp.preplumed
+++ /dev/null
@@ -1,948 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "gromacs/legacyheaders/force.h"
-
-#include "config.h"
-
-#include <assert.h>
-#include <math.h>
-#include <string.h>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/ewald/ewald.h"
-#include "gromacs/ewald/long-range-correction.h"
-#include "gromacs/ewald/pme.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nonbonded.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/listed-forces/listed-forces.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/forcerec-threading.h"
-#include "gromacs/pbcutil/ishift.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
-void ns(FILE *fp,
- t_forcerec *fr,
- matrix box,
- gmx_groups_t *groups,
- gmx_localtop_t *top,
- t_mdatoms *md,
- t_commrec *cr,
- t_nrnb *nrnb,
- gmx_bool bFillGrid,
- gmx_bool bDoLongRangeNS)
-{
- 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, box, top, groups, cr, nrnb, md,
- bFillGrid, bDoLongRangeNS);
- 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_q, tensor vir_lj,
- real *Vcorr_q, real *Vcorr_lj,
- real *dvdl_q, real *dvdl_lj,
- int nthreads, f_thread_t *f_t)
-{
- int t, i;
- int nthreads_loop gmx_unused;
-
- // cppcheck-suppress unreadVariable
- nthreads_loop = gmx_omp_nthreads_get(emntBonded);
- /* This reduction can run over any number of threads */
-#pragma omp parallel for num_threads(nthreads_loop) private(t) schedule(static)
- for (i = 0; i < n; i++)
- {
- for (t = 1; t < nthreads; t++)
- {
- rvec_inc(f[i], f_t[t].f[i]);
- }
- }
- for (t = 1; t < nthreads; t++)
- {
- *Vcorr_q += f_t[t].Vcorr_q;
- *Vcorr_lj += f_t[t].Vcorr_lj;
- *dvdl_q += f_t[t].dvdl[efptCOUL];
- *dvdl_lj += f_t[t].dvdl[efptVDW];
- m_add(vir_q, f_t[t].vir_q, vir_q);
- m_add(vir_lj, f_t[t].vir_lj, vir_lj);
- }
-}
-
-void do_force_lowlevel(t_forcerec *fr, t_inputrec *ir,
- t_idef *idef, t_commrec *cr,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- t_mdatoms *md,
- rvec x[], history_t *hist,
- rvec f[],
- rvec f_longrange[],
- gmx_enerdata_t *enerd,
- t_fcdata *fcd,
- gmx_localtop_t *top,
- gmx_genborn_t *born,
- 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;
- int donb_flags;
- gmx_bool bSB;
- int pme_flags;
- matrix boxs;
- rvec box_size;
- t_pbc pbc;
- real dvdl_dum[efptNR], dvdl_nb[efptNR];
-
-#ifdef GMX_MPI
- double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
-#endif
-
- 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];
- }
-
- debug_gmx();
-
- /* do QMMM first if requested */
- if (fr->bQMMM)
- {
- enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr);
- }
-
- /* 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 */
- real dvdl_walls = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
- enerd->grpp.ener[egLJSR], nrnb);
- enerd->dvdl_lin[efptVDW] += dvdl_walls;
- }
-
- /* 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, 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;
-
- /* Currently all group scheme kernels always calculate (shift-)forces */
- if (flags & GMX_FORCE_FORCES)
- {
- donb_flags |= GMX_NONBONDED_DO_FORCE;
- }
- if (flags & GMX_FORCE_VIRIAL)
- {
- donb_flags |= GMX_NONBONDED_DO_SHIFTFORCE;
- }
- 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(fr, x, f, f_longrange, md, excl,
- &enerd->grpp, 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++)
- {
- real lam_i[efptNR];
-
- 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(fr, x, f, f_longrange, md, excl,
- &(enerd->foreign_grpp), nrnb,
- lam_i, dvdl_dum, -1, -1,
- (donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
- sum_epot(&(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, ewcsLISTED);
- calc_gb_forces(cr, md, born, top, x, f, fr, idef,
- ir->gb_algorithm, ir->sa_algorithm, nrnb, &pbc, graph, enerd);
- wallcycle_sub_stop(wcycle, ewcsLISTED);
- }
-
-#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];
- }
-
- debug_gmx();
-
-
- if (debug)
- {
- pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
- }
-
- /* Shift the coordinates. Must be done before listed forces and PPPM,
- * but is also necessary for SHAKE and update, therefore it can NOT
- * go when no listed forces have to be evaluated.
- *
- * The shifting and PBC code is deliberately not timed, since with
- * the Verlet scheme it only takes non-zero time with triclinic
- * boxes, and even then the time is around a factor of 100 less
- * than the next smallest counter.
- */
-
-
- /* 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 listed interactions or correct for exclusions */
- if (fr->bMolPBC &&
- ((flags & GMX_FORCE_LISTED)
- || EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype)))
- {
- /* TODO There are no electrostatics methods that require this
- transformation, when using the Verlet scheme, so update the
- above conditional. */
- /* 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();
-
- do_force_listed(wcycle, box, ir->fepvals, cr->ms,
- idef, (const rvec *) x, hist, f, fr,
- &pbc, graph, enerd, nrnb, lambda, md, fcd,
- DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
- flags);
-
- where();
-
- *cycles_pme = 0;
- clear_mat(fr->vir_el_recip);
- clear_mat(fr->vir_lj_recip);
-
- /* Do long-range electrostatics and/or LJ-PME, including related short-range
- * corrections.
- */
- if (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype))
- {
- int status = 0;
- real Vlr_q = 0, Vlr_lj = 0, Vcorr_q = 0, Vcorr_lj = 0;
- real dvdl_long_range_q = 0, dvdl_long_range_lj = 0;
-
- bSB = (ir->nwall == 2);
- if (bSB)
- {
- copy_mat(box, boxs);
- svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
- box_size[ZZ] *= ir->wall_ewald_zfac;
- }
-
- if (EEL_PME_EWALD(fr->eeltype) || EVDW_PME(fr->vdwtype))
- {
- real dvdl_long_range_correction_q = 0;
- real dvdl_long_range_correction_lj = 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 i;
- rvec *fnv;
- tensor *vir_q, *vir_lj;
- real *Vcorrt_q, *Vcorrt_lj, *dvdlt_q, *dvdlt_lj;
- if (t == 0)
- {
- fnv = fr->f_novirsum;
- vir_q = &fr->vir_el_recip;
- vir_lj = &fr->vir_lj_recip;
- Vcorrt_q = &Vcorr_q;
- Vcorrt_lj = &Vcorr_lj;
- dvdlt_q = &dvdl_long_range_correction_q;
- dvdlt_lj = &dvdl_long_range_correction_lj;
- }
- else
- {
- fnv = fr->f_t[t].f;
- vir_q = &fr->f_t[t].vir_q;
- vir_lj = &fr->f_t[t].vir_lj;
- Vcorrt_q = &fr->f_t[t].Vcorr_q;
- Vcorrt_lj = &fr->f_t[t].Vcorr_lj;
- dvdlt_q = &fr->f_t[t].dvdl[efptCOUL];
- dvdlt_lj = &fr->f_t[t].dvdl[efptVDW];
- for (i = 0; i < fr->natoms_force; i++)
- {
- clear_rvec(fnv[i]);
- }
- clear_mat(*vir_q);
- clear_mat(*vir_lj);
- }
- *dvdlt_q = 0;
- *dvdlt_lj = 0;
-
- ewald_LRcorrection(md->homenr, cr, nthreads, t, fr,
- md->chargeA, md->chargeB,
- md->sqrt_c6A, md->sqrt_c6B,
- md->sigmaA, md->sigmaB,
- md->sigma3A, md->sigma3B,
- md->nChargePerturbed || md->nTypePerturbed,
- ir->cutoff_scheme != ecutsVERLET,
- excl, x, bSB ? boxs : box, mu_tot,
- ir->ewald_geometry,
- ir->epsilon_surface,
- fnv, *vir_q, *vir_lj,
- Vcorrt_q, Vcorrt_lj,
- lambda[efptCOUL], lambda[efptVDW],
- dvdlt_q, dvdlt_lj);
- }
- if (nthreads > 1)
- {
- reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
- fr->vir_el_recip, fr->vir_lj_recip,
- &Vcorr_q, &Vcorr_lj,
- &dvdl_long_range_correction_q,
- &dvdl_long_range_correction_lj,
- nthreads, fr->f_t);
- }
- wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
- }
-
- if (EEL_PME_EWALD(fr->eeltype) && fr->n_tpi == 0)
- {
- /* This is not in a subcounter because it takes a
- negligible and constant-sized amount of time */
- Vcorr_q += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
- &dvdl_long_range_correction_q,
- fr->vir_el_recip);
- }
-
- enerd->dvdl_lin[efptCOUL] += dvdl_long_range_correction_q;
- enerd->dvdl_lin[efptVDW] += dvdl_long_range_correction_lj;
-
- if ((EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype)) && (cr->duty & DUTY_PME))
- {
- /* Do reciprocal PME for Coulomb and/or LJ. */
- assert(fr->n_tpi >= 0);
- if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
- {
- pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
- if (EEL_PME(fr->eeltype))
- {
- pme_flags |= GMX_PME_DO_COULOMB;
- }
- if (EVDW_PME(fr->vdwtype))
- {
- pme_flags |= GMX_PME_DO_LJ;
- }
- if (flags & GMX_FORCE_FORCES)
- {
- pme_flags |= GMX_PME_CALC_F;
- }
- if (flags & GMX_FORCE_VIRIAL)
- {
- 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,
- 0, md->homenr - fr->n_tpi,
- x, fr->f_novirsum,
- md->chargeA, md->chargeB,
- md->sqrt_c6A, md->sqrt_c6B,
- md->sigmaA, md->sigmaB,
- 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_q,
- fr->vir_lj_recip, fr->ewaldcoeff_lj,
- &Vlr_q, &Vlr_lj,
- lambda[efptCOUL], lambda[efptVDW],
- &dvdl_long_range_q, &dvdl_long_range_lj, pme_flags);
- *cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
- if (status != 0)
- {
- gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
- }
- /* 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)
- {
- if (EVDW_PME(ir->vdwtype))
- {
-
- gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
- }
- /* 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_q);
- }
- }
- }
-
- if (!EEL_PME(fr->eeltype) && EEL_PME_EWALD(fr->eeltype))
- {
- Vlr_q = do_ewald(ir, x, fr->f_novirsum,
- md->chargeA, md->chargeB,
- box_size, cr, md->homenr,
- fr->vir_el_recip, fr->ewaldcoeff_q,
- lambda[efptCOUL], &dvdl_long_range_q, fr->ewald_table);
- }
-
- /* Note that with separate PME nodes we get the real energies later */
- enerd->dvdl_lin[efptCOUL] += dvdl_long_range_q;
- enerd->dvdl_lin[efptVDW] += dvdl_long_range_lj;
- enerd->term[F_COUL_RECIP] = Vlr_q + Vcorr_q;
- enerd->term[F_LJ_RECIP] = Vlr_lj + Vcorr_lj;
- if (debug)
- {
- fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
- Vlr_q, Vcorr_q, 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);
- fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
- Vlr_lj, Vcorr_lj, enerd->term[F_LJ_RECIP]);
- pr_rvecs(debug, 0, "vir_lj_recip after corr", fr->vir_lj_recip, DIM);
- }
- }
- else
- {
- /* Is there a reaction-field exclusion correction needed? */
- if (EEL_RF(fr->eeltype) && eelRF_NEC != fr->eeltype)
- {
- /* With the Verlet scheme, exclusion forces are calculated
- * in the non-bonded kernel.
- */
- if (ir->cutoff_scheme != ecutsVERLET)
- {
- real dvdl_rf_excl = 0;
- enerd->term[F_RF_EXCL] =
- RF_excl_correction(fr, graph, md, excl, x, f,
- fr->fshift, &pbc, lambda[efptCOUL], &dvdl_rf_excl);
-
- enerd->dvdl_lin[efptCOUL] += dvdl_rf_excl;
- }
- }
- }
- 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)
- {
- char buf[22];
- fprintf(stderr, "* PP load balancing info: rank %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
- cr->nodeid, gmx_step_str(fr->timesteps, buf),
- 100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
- (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(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_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);
-}
diff --git a/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/minimize.cpp b/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/minimize.cpp
deleted file mode 100644
index 1caed3367c95d9113b08c558b304ccb2feafee0c..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/minimize.cpp
+++ /dev/null
@@ -1,2967 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-#include <string.h>
-#include <time.h>
-
-#include <algorithm>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/ewald/pme.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/mtxio.h"
-#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/linearalgebra/sparsematrix.h"
-#include "gromacs/listed-forces/manage-threading.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
-/* PLUMED */
-#include "../../../Plumed.h"
-extern int plumedswitch;
-extern plumed plumedmain;
-extern void(*plumedcmd)(plumed,const char*,const void*);
-/* END PLUMED */
-
-typedef struct {
- t_state s;
- rvec *f;
- real epot;
- real fnorm;
- real fmax;
- int a_fmax;
-} em_state_t;
-
-static em_state_t *init_em_state()
-{
- em_state_t *ems;
-
- snew(ems, 1);
-
- /* does this need to be here? Should the array be declared differently (staticaly)in the state definition? */
- snew(ems->s.lambda, efptNR);
-
- return ems;
-}
-
-static void print_em_start(FILE *fplog,
- t_commrec *cr,
- gmx_walltime_accounting_t walltime_accounting,
- gmx_wallcycle_t wcycle,
- const char *name)
-{
- walltime_accounting_start(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
- print_start(fplog, cr, walltime_accounting, name);
-}
-static void em_time_end(gmx_walltime_accounting_t walltime_accounting,
- gmx_wallcycle_t wcycle)
-{
- wallcycle_stop(wcycle, ewcRUN);
-
- walltime_accounting_end(walltime_accounting);
-}
-
-static void sp_header(FILE *out, const char *minimizer, real ftol, int nsteps)
-{
- fprintf(out, "\n");
- fprintf(out, "%s:\n", minimizer);
- fprintf(out, " Tolerance (Fmax) = %12.5e\n", ftol);
- fprintf(out, " Number of steps = %12d\n", nsteps);
-}
-
-static void warn_step(FILE *fp, real ftol, gmx_bool bLastStep, gmx_bool bConstrain)
-{
- char buffer[2048];
- if (bLastStep)
- {
- sprintf(buffer,
- "\nEnergy minimization reached the maximum number "
- "of steps before the forces reached the requested "
- "precision Fmax < %g.\n", ftol);
- }
- else
- {
- sprintf(buffer,
- "\nEnergy minimization has stopped, but the forces have "
- "not converged to the requested precision Fmax < %g (which "
- "may not be possible for your system). It stopped "
- "because the algorithm tried to make a new step whose size "
- "was too small, or there was no change in the energy since "
- "last step. Either way, we regard the minimization as "
- "converged to within the available machine precision, "
- "given your starting configuration and EM parameters.\n%s%s",
- ftol,
- sizeof(real) < sizeof(double) ?
- "\nDouble precision normally gives you higher accuracy, but "
- "this is often not needed for preparing to run molecular "
- "dynamics.\n" :
- "",
- bConstrain ?
- "You might need to increase your constraint accuracy, or turn\n"
- "off constraints altogether (set constraints = none in mdp file)\n" :
- "");
- }
- fputs(wrap_lines(buffer, 78, 0, FALSE), fp);
-}
-
-
-
-static void print_converged(FILE *fp, const char *alg, real ftol,
- gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
- real epot, real fmax, int nfmax, real fnorm)
-{
- char buf[STEPSTRSIZE];
-
- if (bDone)
- {
- fprintf(fp, "\n%s converged to Fmax < %g in %s steps\n",
- alg, ftol, gmx_step_str(count, buf));
- }
- else if (count < nsteps)
- {
- fprintf(fp, "\n%s converged to machine precision in %s steps,\n"
- "but did not reach the requested Fmax < %g.\n",
- alg, gmx_step_str(count, buf), ftol);
- }
- else
- {
- fprintf(fp, "\n%s did not converge to Fmax < %g in %s steps.\n",
- alg, ftol, gmx_step_str(count, buf));
- }
-
-#ifdef GMX_DOUBLE
- fprintf(fp, "Potential Energy = %21.14e\n", epot);
- fprintf(fp, "Maximum force = %21.14e on atom %d\n", fmax, nfmax+1);
- fprintf(fp, "Norm of force = %21.14e\n", fnorm);
-#else
- fprintf(fp, "Potential Energy = %14.7e\n", epot);
- fprintf(fp, "Maximum force = %14.7e on atom %d\n", fmax, nfmax+1);
- fprintf(fp, "Norm of force = %14.7e\n", fnorm);
-#endif
-}
-
-static void get_f_norm_max(t_commrec *cr,
- t_grpopts *opts, t_mdatoms *mdatoms, rvec *f,
- real *fnorm, real *fmax, int *a_fmax)
-{
- double fnorm2, *sum;
- real fmax2, fam;
- int la_max, a_max, start, end, i, m, gf;
-
- /* This routine finds the largest force and returns it.
- * On parallel machines the global max is taken.
- */
- fnorm2 = 0;
- fmax2 = 0;
- la_max = -1;
- start = 0;
- end = mdatoms->homenr;
- if (mdatoms->cFREEZE)
- {
- for (i = start; i < end; i++)
- {
- gf = mdatoms->cFREEZE[i];
- fam = 0;
- for (m = 0; m < DIM; m++)
- {
- if (!opts->nFreeze[gf][m])
- {
- fam += sqr(f[i][m]);
- }
- }
- fnorm2 += fam;
- if (fam > fmax2)
- {
- fmax2 = fam;
- la_max = i;
- }
- }
- }
- else
- {
- for (i = start; i < end; i++)
- {
- fam = norm2(f[i]);
- fnorm2 += fam;
- if (fam > fmax2)
- {
- fmax2 = fam;
- la_max = i;
- }
- }
- }
-
- if (la_max >= 0 && DOMAINDECOMP(cr))
- {
- a_max = cr->dd->gatindex[la_max];
- }
- else
- {
- a_max = la_max;
- }
- if (PAR(cr))
- {
- snew(sum, 2*cr->nnodes+1);
- sum[2*cr->nodeid] = fmax2;
- sum[2*cr->nodeid+1] = a_max;
- sum[2*cr->nnodes] = fnorm2;
- gmx_sumd(2*cr->nnodes+1, sum, cr);
- fnorm2 = sum[2*cr->nnodes];
- /* Determine the global maximum */
- for (i = 0; i < cr->nnodes; i++)
- {
- if (sum[2*i] > fmax2)
- {
- fmax2 = sum[2*i];
- a_max = (int)(sum[2*i+1] + 0.5);
- }
- }
- sfree(sum);
- }
-
- if (fnorm)
- {
- *fnorm = sqrt(fnorm2);
- }
- if (fmax)
- {
- *fmax = sqrt(fmax2);
- }
- if (a_fmax)
- {
- *a_fmax = a_max;
- }
-}
-
-static void get_state_f_norm_max(t_commrec *cr,
- t_grpopts *opts, t_mdatoms *mdatoms,
- em_state_t *ems)
-{
- get_f_norm_max(cr, opts, mdatoms, ems->f, &ems->fnorm, &ems->fmax, &ems->a_fmax);
-}
-
-void init_em(FILE *fplog, const char *title,
- t_commrec *cr, t_inputrec *ir,
- t_state *state_global, gmx_mtop_t *top_global,
- em_state_t *ems, gmx_localtop_t **top,
- rvec **f, rvec **f_global,
- t_nrnb *nrnb, rvec mu_tot,
- t_forcerec *fr, gmx_enerdata_t **enerd,
- t_graph **graph, t_mdatoms *mdatoms, gmx_global_stat_t *gstat,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int nfile, const t_filenm fnm[],
- gmx_mdoutf_t *outf, t_mdebin **mdebin,
- int imdport, unsigned long gmx_unused Flags,
- gmx_wallcycle_t wcycle)
-{
- int i;
- real dvdl_constr;
-
- if (fplog)
- {
- fprintf(fplog, "Initiating %s\n", title);
- }
-
- state_global->ngtc = 0;
-
- /* Initialize lambda variables */
- initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, NULL);
-
- init_nrnb(nrnb);
-
- /* Interactive molecular dynamics */
- init_IMD(ir, cr, top_global, fplog, 1, state_global->x,
- nfile, fnm, NULL, imdport, Flags);
-
- if (DOMAINDECOMP(cr))
- {
- *top = dd_init_local_top(top_global);
-
- dd_init_local_state(cr->dd, state_global, &ems->s);
-
- *f = NULL;
-
- /* 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,
- &ems->s, &ems->f, mdatoms, *top,
- fr, vsite, NULL, constr,
- nrnb, NULL, FALSE);
- dd_store_state(cr->dd, &ems->s);
-
- if (ir->nstfout)
- {
- snew(*f_global, top_global->natoms);
- }
- else
- {
- *f_global = NULL;
- }
- *graph = NULL;
- }
- else
- {
- snew(*f, top_global->natoms);
-
- /* Just copy the state */
- ems->s = *state_global;
- snew(ems->s.x, ems->s.nalloc);
- snew(ems->f, ems->s.nalloc);
- for (i = 0; i < state_global->natoms; i++)
- {
- copy_rvec(state_global->x[i], ems->s.x[i]);
- }
- copy_mat(state_global->box, ems->s.box);
-
- *top = gmx_mtop_generate_local_top(top_global, ir);
- *f_global = *f;
-
- setup_bonded_threading(fr, &(*top)->idef);
-
- if (ir->ePBC != epbcNONE && !fr->bMolPBC)
- {
- *graph = mk_graph(fplog, &((*top)->idef), 0, top_global->natoms, FALSE, FALSE);
- }
- else
- {
- *graph = NULL;
- }
-
- atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
- update_mdatoms(mdatoms, state_global->lambda[efptFEP]);
-
- if (vsite)
- {
- set_vsite_top(vsite, *top, mdatoms, cr);
- }
- }
-
- if (constr)
- {
- if (ir->eConstrAlg == econtSHAKE &&
- gmx_mtop_ftype_count(top_global, F_CONSTR) > 0)
- {
- gmx_fatal(FARGS, "Can not do energy minimization with %s, use %s\n",
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
- }
-
- if (!DOMAINDECOMP(cr))
- {
- set_constraints(constr, *top, ir, mdatoms, cr);
- }
-
- if (!ir->bContinuation)
- {
- /* Constrain the starting coordinates */
- dvdl_constr = 0;
- constrain(PAR(cr) ? NULL : fplog, TRUE, TRUE, constr, &(*top)->idef,
- ir, cr, -1, 0, 1.0, mdatoms,
- ems->s.x, ems->s.x, NULL, fr->bMolPBC, ems->s.box,
- ems->s.lambda[efptFEP], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
- }
- }
-
- if (PAR(cr))
- {
- *gstat = global_stat_init(ir);
- }
- else
- {
- *gstat = NULL;
- }
-
- *outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL, wcycle);
-
- snew(*enerd, 1);
- init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
- *enerd);
-
- if (mdebin != NULL)
- {
- /* Init bin for energy stuff */
- *mdebin = init_mdebin(mdoutf_get_fp_ene(*outf), top_global, ir, NULL);
- }
-
- clear_rvec(mu_tot);
- calc_shifts(ems->s.box, fr->shift_vec);
-
- /* PLUMED */
- if(plumedswitch){
- if(cr->ms && cr->ms->nsim>1) {
- if(MASTER(cr)) (*plumedcmd) (plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters);
- if(PAR(cr)){
- if(DOMAINDECOMP(cr)) {
- (*plumedcmd) (plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
- }else{
- (*plumedcmd) (plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
- }
- }
- (*plumedcmd) (plumedmain,"GREX init",NULL);
- }
- if(PAR(cr)){
- if(DOMAINDECOMP(cr)) {
- (*plumedcmd) (plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
- }else{
- (*plumedcmd) (plumedmain,"setMPIComm",&cr->mpi_comm_mysim);
- }
- }
- (*plumedcmd) (plumedmain,"setNatoms",&top_global->natoms);
- (*plumedcmd) (plumedmain,"setMDEngine","gromacs");
- (*plumedcmd) (plumedmain,"setLog",fplog);
- real real_delta_t;
- real_delta_t=ir->delta_t;
- (*plumedcmd) (plumedmain,"setTimestep",&real_delta_t);
- (*plumedcmd) (plumedmain,"init",NULL);
-
- if(PAR(cr)){
- if(DOMAINDECOMP(cr)) {
- (*plumedcmd) (plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
- (*plumedcmd) (plumedmain,"setAtomsGatindex",cr->dd->gatindex);
- }
- }
- }
- /* END PLUMED */
-}
-
-static void finish_em(t_commrec *cr, gmx_mdoutf_t outf,
- gmx_walltime_accounting_t walltime_accounting,
- gmx_wallcycle_t wcycle)
-{
- if (!(cr->duty & DUTY_PME))
- {
- /* Tell the PME only node to finish */
- gmx_pme_send_finish(cr);
- }
-
- done_mdoutf(outf);
-
- em_time_end(walltime_accounting, wcycle);
-}
-
-static void swap_em_state(em_state_t *ems1, em_state_t *ems2)
-{
- em_state_t tmp;
-
- tmp = *ems1;
- *ems1 = *ems2;
- *ems2 = tmp;
-}
-
-static void copy_em_coords(em_state_t *ems, t_state *state)
-{
- int i;
-
- for (i = 0; (i < state->natoms); i++)
- {
- copy_rvec(ems->s.x[i], state->x[i]);
- }
-}
-
-static void write_em_traj(FILE *fplog, t_commrec *cr,
- gmx_mdoutf_t outf,
- gmx_bool bX, gmx_bool bF, const char *confout,
- gmx_mtop_t *top_global,
- t_inputrec *ir, gmx_int64_t step,
- em_state_t *state,
- t_state *state_global, rvec *f_global)
-{
- int mdof_flags;
- gmx_bool bIMDout = FALSE;
-
-
- /* Shall we do IMD output? */
- if (ir->bIMD)
- {
- bIMDout = do_per_step(step, IMD_get_step(ir->imd->setup));
- }
-
- if ((bX || bF || bIMDout || confout != NULL) && !DOMAINDECOMP(cr))
- {
- copy_em_coords(state, state_global);
- f_global = state->f;
- }
-
- mdof_flags = 0;
- if (bX)
- {
- mdof_flags |= MDOF_X;
- }
- if (bF)
- {
- mdof_flags |= MDOF_F;
- }
-
- /* If we want IMD output, set appropriate MDOF flag */
- if (ir->bIMD)
- {
- mdof_flags |= MDOF_IMD;
- }
-
- mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
- top_global, step, (double)step,
- &state->s, state_global, state->f, f_global);
-
- if (confout != NULL && MASTER(cr))
- {
- if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
- {
- /* Make molecules whole only for confout writing */
- do_pbc_mtop(fplog, ir->ePBC, state_global->box, top_global,
- state_global->x);
- }
-
- write_sto_conf_mtop(confout,
- *top_global->name, top_global,
- state_global->x, NULL, ir->ePBC, state_global->box);
- }
-}
-
-static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
- gmx_bool bMolPBC,
- em_state_t *ems1, real a, rvec *f, em_state_t *ems2,
- gmx_constr_t constr, gmx_localtop_t *top,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_int64_t count)
-
-{
- t_state *s1, *s2;
- int start, end;
- real dvdl_constr;
- int nthreads gmx_unused;
-
- s1 = &ems1->s;
- s2 = &ems2->s;
-
- if (DOMAINDECOMP(cr) && s1->ddp_count != cr->dd->ddp_count)
- {
- gmx_incons("state mismatch in do_em_step");
- }
-
- s2->flags = s1->flags;
-
- if (s2->nalloc != s1->nalloc)
- {
- s2->nalloc = s1->nalloc;
- srenew(s2->x, s1->nalloc);
- srenew(ems2->f, s1->nalloc);
- if (s2->flags & (1<<estCGP))
- {
- srenew(s2->cg_p, s1->nalloc);
- }
- }
-
- s2->natoms = s1->natoms;
- copy_mat(s1->box, s2->box);
- /* Copy free energy state */
- for (int i = 0; i < efptNR; i++)
- {
- s2->lambda[i] = s1->lambda[i];
- }
- copy_mat(s1->box, s2->box);
-
- start = 0;
- end = md->homenr;
-
- // cppcheck-suppress unreadVariable
- nthreads = gmx_omp_nthreads_get(emntUpdate);
-#pragma omp parallel num_threads(nthreads)
- {
- rvec *x1 = s1->x;
- rvec *x2 = s2->x;
-
- int gf = 0;
-#pragma omp for schedule(static) nowait
- for (int i = start; i < end; i++)
- {
- if (md->cFREEZE)
- {
- gf = md->cFREEZE[i];
- }
- for (int m = 0; m < DIM; m++)
- {
- if (ir->opts.nFreeze[gf][m])
- {
- x2[i][m] = x1[i][m];
- }
- else
- {
- x2[i][m] = x1[i][m] + a*f[i][m];
- }
- }
- }
-
- if (s2->flags & (1<<estCGP))
- {
- /* Copy the CG p vector */
- rvec *p1 = s1->cg_p;
- rvec *p2 = s2->cg_p;
-#pragma omp for schedule(static) nowait
- for (int i = start; i < end; i++)
- {
- copy_rvec(p1[i], p2[i]);
- }
- }
-
- if (DOMAINDECOMP(cr))
- {
- s2->ddp_count = s1->ddp_count;
- if (s2->cg_gl_nalloc < s1->cg_gl_nalloc)
- {
-#pragma omp barrier
- s2->cg_gl_nalloc = s1->cg_gl_nalloc;
- srenew(s2->cg_gl, s2->cg_gl_nalloc);
-#pragma omp barrier
- }
- s2->ncg_gl = s1->ncg_gl;
-#pragma omp for schedule(static) nowait
- for (int i = 0; i < s2->ncg_gl; i++)
- {
- s2->cg_gl[i] = s1->cg_gl[i];
- }
- s2->ddp_count_cg_gl = s1->ddp_count_cg_gl;
- }
- }
-
- if (constr)
- {
- wallcycle_start(wcycle, ewcCONSTR);
- dvdl_constr = 0;
- constrain(NULL, TRUE, TRUE, constr, &top->idef,
- ir, cr, count, 0, 1.0, md,
- s1->x, s2->x, NULL, bMolPBC, s2->box,
- s2->lambda[efptBONDED], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
- wallcycle_stop(wcycle, ewcCONSTR);
- }
-}
-
-static void em_dd_partition_system(FILE *fplog, int step, t_commrec *cr,
- gmx_mtop_t *top_global, t_inputrec *ir,
- em_state_t *ems, gmx_localtop_t *top,
- t_mdatoms *mdatoms, t_forcerec *fr,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle)
-{
- /* Repartition the domain decomposition */
- dd_partition_system(fplog, step, cr, FALSE, 1,
- NULL, top_global, ir,
- &ems->s, &ems->f,
- mdatoms, top, fr, vsite, NULL, constr,
- nrnb, wcycle, FALSE);
- dd_store_state(cr->dd, &ems->s);
-}
-
-static void evaluate_energy(FILE *fplog, t_commrec *cr,
- gmx_mtop_t *top_global,
- em_state_t *ems, gmx_localtop_t *top,
- t_inputrec *inputrec,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_global_stat_t gstat,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- t_fcdata *fcd,
- t_graph *graph, t_mdatoms *mdatoms,
- t_forcerec *fr, rvec mu_tot,
- gmx_enerdata_t *enerd, tensor vir, tensor pres,
- gmx_int64_t count, gmx_bool bFirst)
-{
- real t;
- gmx_bool bNS;
- tensor force_vir, shake_vir, ekin;
- real dvdl_constr, prescorr, enercorr, dvdlcorr;
- real terminate = 0;
-
- /* Set the time to the initial time, the time does not change during EM */
- t = inputrec->init_t;
-
- if (bFirst ||
- (DOMAINDECOMP(cr) && ems->s.ddp_count < cr->dd->ddp_count))
- {
- /* This is the first state or an old state used before the last ns */
- bNS = TRUE;
- }
- else
- {
- bNS = FALSE;
- if (inputrec->nstlist > 0)
- {
- bNS = TRUE;
- }
- }
-
- if (vsite)
- {
- construct_vsites(vsite, ems->s.x, 1, NULL,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, ems->s.box);
- }
-
- if (DOMAINDECOMP(cr) && bNS)
- {
- /* Repartition the domain decomposition */
- em_dd_partition_system(fplog, count, cr, top_global, inputrec,
- ems, top, mdatoms, fr, vsite, constr,
- nrnb, wcycle);
- /* PLUMED */
- if(plumedswitch){
- (*plumedcmd) (plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
- (*plumedcmd) (plumedmain,"setAtomsGatindex",cr->dd->gatindex);
- }
- /* END PLUMED */
- }
-
- /* Calc force & energy on new trial position */
- /* do_force always puts the charge groups in the box and shifts again
- * We do not unshift, so molecules are always whole in congrad.c
- */
- /* PLUMED */
- int plumedNeedsEnergy=0;
- matrix plumed_vir;
- if(plumedswitch){
- long int lstep=count; (*plumedcmd)(plumedmain,"setStepLong",&lstep);
- (*plumedcmd) (plumedmain,"setPositions",&ems->s.x[0][0]);
- (*plumedcmd) (plumedmain,"setMasses",&mdatoms->massT[0]);
- (*plumedcmd) (plumedmain,"setCharges",&mdatoms->chargeA[0]);
- (*plumedcmd) (plumedmain,"setBox",&ems->s.box[0][0]);
- (*plumedcmd) (plumedmain,"prepareCalc",NULL);
- (*plumedcmd) (plumedmain,"setForces",&ems->f[0][0]);
- (*plumedcmd) (plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
- clear_mat(plumed_vir);
- (*plumedcmd) (plumedmain,"setVirial",&plumed_vir[0][0]);
- }
- /* END PLUMED */
- do_force(fplog, cr, inputrec,
- count, nrnb, wcycle, top, &top_global->groups,
- ems->s.box, ems->s.x, &ems->s.hist,
- ems->f, force_vir, mdatoms, enerd, fcd,
- ems->s.lambda, graph, fr, vsite, mu_tot, t, NULL, NULL, TRUE,
- GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
- GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
- (bNS ? GMX_FORCE_NS | GMX_FORCE_DO_LR : 0));
- /* PLUMED */
- if(plumedswitch){
- if(plumedNeedsEnergy) {
- msmul(force_vir,2.0,plumed_vir);
- (*plumedcmd) (plumedmain,"setEnergy",&enerd->term[F_EPOT]);
- (*plumedcmd) (plumedmain,"performCalc",NULL);
- msmul(plumed_vir,0.5,force_vir);
- } else {
- msmul(plumed_vir,0.5,plumed_vir);
- m_add(force_vir,plumed_vir,force_vir);
- }
- }
- /* END PLUMED */
-
- /* Clear the unused shake virial and pressure */
- clear_mat(shake_vir);
- clear_mat(pres);
-
- /* Communicate stuff when parallel */
- if (PAR(cr) && inputrec->eI != eiNM)
- {
- wallcycle_start(wcycle, ewcMoveE);
-
- global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
- inputrec, NULL, NULL, NULL, 1, &terminate,
- top_global, &ems->s, FALSE,
- CGLO_ENERGY |
- CGLO_PRESSURE |
- CGLO_CONSTRAINT);
-
- wallcycle_stop(wcycle, ewcMoveE);
- }
-
- /* Calculate long range corrections to pressure and energy */
- calc_dispcorr(inputrec, fr, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
- pres, force_vir, &prescorr, &enercorr, &dvdlcorr);
- enerd->term[F_DISPCORR] = enercorr;
- enerd->term[F_EPOT] += enercorr;
- enerd->term[F_PRES] += prescorr;
- enerd->term[F_DVDL] += dvdlcorr;
-
- ems->epot = enerd->term[F_EPOT];
-
- if (constr)
- {
- /* Project out the constraint components of the force */
- wallcycle_start(wcycle, ewcCONSTR);
- dvdl_constr = 0;
- constrain(NULL, FALSE, FALSE, constr, &top->idef,
- inputrec, cr, count, 0, 1.0, mdatoms,
- ems->s.x, ems->f, ems->f, fr->bMolPBC, ems->s.box,
- ems->s.lambda[efptBONDED], &dvdl_constr,
- NULL, &shake_vir, nrnb, econqForceDispl);
- enerd->term[F_DVDL_CONSTR] += dvdl_constr;
- m_add(force_vir, shake_vir, vir);
- wallcycle_stop(wcycle, ewcCONSTR);
- }
- else
- {
- copy_mat(force_vir, vir);
- }
-
- clear_mat(ekin);
- enerd->term[F_PRES] =
- calc_pres(fr->ePBC, inputrec->nwall, ems->s.box, ekin, vir, pres);
-
- sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
-
- if (EI_ENERGY_MINIMIZATION(inputrec->eI))
- {
- get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, ems);
- }
-}
-
-static double reorder_partsum(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
- gmx_mtop_t *mtop,
- em_state_t *s_min, em_state_t *s_b)
-{
- rvec *fm, *fb, *fmg;
- t_block *cgs_gl;
- int ncg, *cg_gl, *index, c, cg, i, a0, a1, a, gf, m;
- double partsum;
- unsigned char *grpnrFREEZE;
-
- if (debug)
- {
- fprintf(debug, "Doing reorder_partsum\n");
- }
-
- fm = s_min->f;
- fb = s_b->f;
-
- cgs_gl = dd_charge_groups_global(cr->dd);
- index = cgs_gl->index;
-
- /* Collect fm in a global vector fmg.
- * This conflicts with the spirit of domain decomposition,
- * but to fully optimize this a much more complicated algorithm is required.
- */
- snew(fmg, mtop->natoms);
-
- ncg = s_min->s.ncg_gl;
- cg_gl = s_min->s.cg_gl;
- i = 0;
- for (c = 0; c < ncg; c++)
- {
- cg = cg_gl[c];
- a0 = index[cg];
- a1 = index[cg+1];
- for (a = a0; a < a1; a++)
- {
- copy_rvec(fm[i], fmg[a]);
- i++;
- }
- }
- gmx_sum(mtop->natoms*3, fmg[0], cr);
-
- /* Now we will determine the part of the sum for the cgs in state s_b */
- ncg = s_b->s.ncg_gl;
- cg_gl = s_b->s.cg_gl;
- partsum = 0;
- i = 0;
- gf = 0;
- grpnrFREEZE = mtop->groups.grpnr[egcFREEZE];
- for (c = 0; c < ncg; c++)
- {
- cg = cg_gl[c];
- a0 = index[cg];
- a1 = index[cg+1];
- for (a = a0; a < a1; a++)
- {
- if (mdatoms->cFREEZE && grpnrFREEZE)
- {
- gf = grpnrFREEZE[i];
- }
- for (m = 0; m < DIM; m++)
- {
- if (!opts->nFreeze[gf][m])
- {
- partsum += (fb[i][m] - fmg[a][m])*fb[i][m];
- }
- }
- i++;
- }
- }
-
- sfree(fmg);
-
- return partsum;
-}
-
-static real pr_beta(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
- gmx_mtop_t *mtop,
- em_state_t *s_min, em_state_t *s_b)
-{
- rvec *fm, *fb;
- double sum;
- int gf, i, m;
-
- /* This is just the classical Polak-Ribiere calculation of beta;
- * it looks a bit complicated since we take freeze groups into account,
- * and might have to sum it in parallel runs.
- */
-
- if (!DOMAINDECOMP(cr) ||
- (s_min->s.ddp_count == cr->dd->ddp_count &&
- s_b->s.ddp_count == cr->dd->ddp_count))
- {
- fm = s_min->f;
- fb = s_b->f;
- sum = 0;
- gf = 0;
- /* This part of code can be incorrect with DD,
- * since the atom ordering in s_b and s_min might differ.
- */
- for (i = 0; i < mdatoms->homenr; i++)
- {
- if (mdatoms->cFREEZE)
- {
- gf = mdatoms->cFREEZE[i];
- }
- for (m = 0; m < DIM; m++)
- {
- if (!opts->nFreeze[gf][m])
- {
- sum += (fb[i][m] - fm[i][m])*fb[i][m];
- }
- }
- }
- }
- else
- {
- /* We need to reorder cgs while summing */
- sum = reorder_partsum(cr, opts, mdatoms, mtop, s_min, s_b);
- }
- if (PAR(cr))
- {
- gmx_sumd(1, &sum, cr);
- }
-
- return sum/sqr(s_min->fnorm);
-}
-
-double do_cg(FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
- int gmx_unused nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
- t_inputrec *inputrec,
- 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 gmx_unused ed,
- t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- const char *CG = "Polak-Ribiere Conjugate Gradients";
-
- em_state_t *s_min, *s_a, *s_b, *s_c;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- rvec *f_global, *p, *sf;
- double gpa, gpb, gpc, tmp, minstep;
- real fnormn;
- real stepsize;
- real a, b, c, beta = 0.0;
- real epot_repl = 0;
- real pnorm;
- t_mdebin *mdebin;
- gmx_bool converged, foundlower;
- rvec mu_tot;
- gmx_bool do_log = FALSE, do_ene = FALSE, do_x, do_f;
- tensor vir, pres;
- int number_steps, neval = 0, nstcg = inputrec->nstcgsteep;
- gmx_mdoutf_t outf;
- int i, m, gf, step, nminstep;
-
- step = 0;
-
- s_min = init_em_state();
- s_a = init_em_state();
- s_b = init_em_state();
- s_c = init_em_state();
-
- /* Init em and store the local state in s_min */
- init_em(fplog, CG, cr, inputrec,
- state_global, top_global, s_min, &top, &f, &f_global,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
-
- /* Print to log file */
- print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
-
- /* Max number of steps */
- number_steps = inputrec->nsteps;
-
- if (MASTER(cr))
- {
- sp_header(stderr, CG, inputrec->em_tol, number_steps);
- }
- if (fplog)
- {
- sp_header(fplog, CG, inputrec->em_tol, number_steps);
- }
-
- /* Call the force routine and some auxiliary (neighboursearching etc.) */
- /* do_force always puts the charge groups in the box and shifts again
- * We do not unshift, so molecules are always whole in congrad.c
- */
- evaluate_energy(fplog, cr,
- top_global, s_min, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, TRUE);
- where();
-
- if (MASTER(cr))
- {
- /* Copy stuff to the energy bin for easy printing etc. */
- upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
-
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
- print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
- where();
-
- /* Estimate/guess the initial stepsize */
- stepsize = inputrec->em_stepsize/s_min->fnorm;
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fprintf(stderr, " F-max = %12.5e on atom %d\n",
- s_min->fmax, s_min->a_fmax+1);
- fprintf(stderr, " F-Norm = %12.5e\n",
- s_min->fnorm/sqrtNumAtoms);
- fprintf(stderr, "\n");
- /* and copy to the log file too... */
- fprintf(fplog, " F-max = %12.5e on atom %d\n",
- s_min->fmax, s_min->a_fmax+1);
- fprintf(fplog, " F-Norm = %12.5e\n",
- s_min->fnorm/sqrtNumAtoms);
- fprintf(fplog, "\n");
- }
- /* Start the loop over CG steps.
- * Each successful step is counted, and we continue until
- * we either converge or reach the max number of steps.
- */
- converged = FALSE;
- for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
- {
-
- /* start taking steps in a new direction
- * First time we enter the routine, beta=0, and the direction is
- * simply the negative gradient.
- */
-
- /* Calculate the new direction in p, and the gradient in this direction, gpa */
- p = s_min->s.cg_p;
- sf = s_min->f;
- gpa = 0;
- gf = 0;
- for (i = 0; i < mdatoms->homenr; i++)
- {
- if (mdatoms->cFREEZE)
- {
- gf = mdatoms->cFREEZE[i];
- }
- for (m = 0; m < DIM; m++)
- {
- if (!inputrec->opts.nFreeze[gf][m])
- {
- p[i][m] = sf[i][m] + beta*p[i][m];
- gpa -= p[i][m]*sf[i][m];
- /* f is negative gradient, thus the sign */
- }
- else
- {
- p[i][m] = 0;
- }
- }
- }
-
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpa, cr);
- }
-
- /* Calculate the norm of the search vector */
- get_f_norm_max(cr, &(inputrec->opts), mdatoms, p, &pnorm, NULL, NULL);
-
- /* Just in case stepsize reaches zero due to numerical precision... */
- if (stepsize <= 0)
- {
- stepsize = inputrec->em_stepsize/pnorm;
- }
-
- /*
- * Double check the value of the derivative in the search direction.
- * If it is positive it must be due to the old information in the
- * CG formula, so just remove that and start over with beta=0.
- * This corresponds to a steepest descent step.
- */
- if (gpa > 0)
- {
- beta = 0;
- step--; /* Don't count this step since we are restarting */
- continue; /* Go back to the beginning of the big for-loop */
- }
-
- /* Calculate minimum allowed stepsize, before the average (norm)
- * relative change in coordinate is smaller than precision
- */
- minstep = 0;
- for (i = 0; i < mdatoms->homenr; i++)
- {
- for (m = 0; m < DIM; m++)
- {
- tmp = fabs(s_min->s.x[i][m]);
- if (tmp < 1.0)
- {
- tmp = 1.0;
- }
- tmp = p[i][m]/tmp;
- minstep += tmp*tmp;
- }
- }
- /* Add up from all CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &minstep, cr);
- }
-
- minstep = GMX_REAL_EPS/sqrt(minstep/(3*state_global->natoms));
-
- if (stepsize < minstep)
- {
- converged = TRUE;
- break;
- }
-
- /* Write coordinates if necessary */
- do_x = do_per_step(step, inputrec->nstxout);
- do_f = do_per_step(step, inputrec->nstfout);
-
- write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
- top_global, inputrec, step,
- s_min, state_global, f_global);
-
- /* Take a step downhill.
- * In theory, we should minimize the function along this direction.
- * That is quite possible, but it turns out to take 5-10 function evaluations
- * for each line. However, we dont really need to find the exact minimum -
- * it is much better to start a new CG step in a modified direction as soon
- * as we are close to it. This will save a lot of energy evaluations.
- *
- * In practice, we just try to take a single step.
- * If it worked (i.e. lowered the energy), we increase the stepsize but
- * the continue straight to the next CG step without trying to find any minimum.
- * If it didn't work (higher energy), there must be a minimum somewhere between
- * the old position and the new one.
- *
- * Due to the finite numerical accuracy, it turns out that it is a good idea
- * to even accept a SMALL increase in energy, if the derivative is still downhill.
- * This leads to lower final energies in the tests I've done. / Erik
- */
- s_a->epot = s_min->epot;
- a = 0.0;
- c = a + stepsize; /* reference position along line is zero */
-
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count < cr->dd->ddp_count)
- {
- em_dd_partition_system(fplog, step, cr, top_global, inputrec,
- s_min, top, mdatoms, fr, vsite, constr,
- nrnb, wcycle);
- }
-
- /* Take a trial step (new coords in s_c) */
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, c, s_min->s.cg_p, s_c,
- constr, top, nrnb, wcycle, -1);
-
- neval++;
- /* Calculate energy for the trial step */
- evaluate_energy(fplog, cr,
- top_global, s_c, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, FALSE);
-
- /* Calc derivative along line */
- p = s_c->s.cg_p;
- sf = s_c->f;
- gpc = 0;
- for (i = 0; i < mdatoms->homenr; i++)
- {
- for (m = 0; m < DIM; m++)
- {
- gpc -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
- }
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpc, cr);
- }
-
- /* This is the max amount of increase in energy we tolerate */
- tmp = sqrt(GMX_REAL_EPS)*fabs(s_a->epot);
-
- /* Accept the step if the energy is lower, or if it is not significantly higher
- * and the line derivative is still negative.
- */
- if (s_c->epot < s_a->epot || (gpc < 0 && s_c->epot < (s_a->epot + tmp)))
- {
- foundlower = TRUE;
- /* Great, we found a better energy. Increase step for next iteration
- * if we are still going down, decrease it otherwise
- */
- if (gpc < 0)
- {
- stepsize *= 1.618034; /* The golden section */
- }
- else
- {
- stepsize *= 0.618034; /* 1/golden section */
- }
- }
- else
- {
- /* New energy is the same or higher. We will have to do some work
- * to find a smaller value in the interval. Take smaller step next time!
- */
- foundlower = FALSE;
- stepsize *= 0.618034;
- }
-
-
-
-
- /* OK, if we didn't find a lower value we will have to locate one now - there must
- * be one in the interval [a=0,c].
- * The same thing is valid here, though: Don't spend dozens of iterations to find
- * the line minimum. We try to interpolate based on the derivative at the endpoints,
- * and only continue until we find a lower value. In most cases this means 1-2 iterations.
- *
- * I also have a safeguard for potentially really pathological functions so we never
- * take more than 20 steps before we give up ...
- *
- * If we already found a lower value we just skip this step and continue to the update.
- */
- if (!foundlower)
- {
- nminstep = 0;
-
- do
- {
- /* Select a new trial point.
- * If the derivatives at points a & c have different sign we interpolate to zero,
- * otherwise just do a bisection.
- */
- if (gpa < 0 && gpc > 0)
- {
- b = a + gpa*(a-c)/(gpc-gpa);
- }
- else
- {
- b = 0.5*(a+c);
- }
-
- /* safeguard if interpolation close to machine accuracy causes errors:
- * never go outside the interval
- */
- if (b <= a || b >= c)
- {
- b = 0.5*(a+c);
- }
-
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
- {
- /* Reload the old state */
- em_dd_partition_system(fplog, -1, cr, top_global, inputrec,
- s_min, top, mdatoms, fr, vsite, constr,
- nrnb, wcycle);
- }
-
- /* Take a trial step to this new point - new coords in s_b */
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, b, s_min->s.cg_p, s_b,
- constr, top, nrnb, wcycle, -1);
-
- neval++;
- /* Calculate energy for the trial step */
- evaluate_energy(fplog, cr,
- top_global, s_b, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, FALSE);
-
- /* p does not change within a step, but since the domain decomposition
- * might change, we have to use cg_p of s_b here.
- */
- p = s_b->s.cg_p;
- sf = s_b->f;
- gpb = 0;
- for (i = 0; i < mdatoms->homenr; i++)
- {
- for (m = 0; m < DIM; m++)
- {
- gpb -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
- }
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpb, cr);
- }
-
- if (debug)
- {
- fprintf(debug, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
- s_a->epot, s_b->epot, s_c->epot, gpb);
- }
-
- epot_repl = s_b->epot;
-
- /* Keep one of the intervals based on the value of the derivative at the new point */
- if (gpb > 0)
- {
- /* Replace c endpoint with b */
- swap_em_state(s_b, s_c);
- c = b;
- gpc = gpb;
- }
- else
- {
- /* Replace a endpoint with b */
- swap_em_state(s_b, s_a);
- a = b;
- gpa = gpb;
- }
-
- /*
- * Stop search as soon as we find a value smaller than the endpoints.
- * Never run more than 20 steps, no matter what.
- */
- nminstep++;
- }
- while ((epot_repl > s_a->epot || epot_repl > s_c->epot) &&
- (nminstep < 20));
-
- if (fabs(epot_repl - s_min->epot) < fabs(s_min->epot)*GMX_REAL_EPS ||
- nminstep >= 20)
- {
- /* OK. We couldn't find a significantly lower energy.
- * If beta==0 this was steepest descent, and then we give up.
- * If not, set beta=0 and restart with steepest descent before quitting.
- */
- if (beta == 0.0)
- {
- /* Converged */
- converged = TRUE;
- break;
- }
- else
- {
- /* Reset memory before giving up */
- beta = 0.0;
- continue;
- }
- }
-
- /* Select min energy state of A & C, put the best in B.
- */
- if (s_c->epot < s_a->epot)
- {
- if (debug)
- {
- fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n",
- s_c->epot, s_a->epot);
- }
- swap_em_state(s_b, s_c);
- gpb = gpc;
- }
- else
- {
- if (debug)
- {
- fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n",
- s_a->epot, s_c->epot);
- }
- swap_em_state(s_b, s_a);
- gpb = gpa;
- }
-
- }
- else
- {
- if (debug)
- {
- fprintf(debug, "CGE: Found a lower energy %f, moving C to B\n",
- s_c->epot);
- }
- swap_em_state(s_b, s_c);
- gpb = gpc;
- }
-
- /* new search direction */
- /* beta = 0 means forget all memory and restart with steepest descents. */
- if (nstcg && ((step % nstcg) == 0))
- {
- beta = 0.0;
- }
- else
- {
- /* s_min->fnorm cannot be zero, because then we would have converged
- * and broken out.
- */
-
- /* Polak-Ribiere update.
- * Change to fnorm2/fnorm2_old for Fletcher-Reeves
- */
- beta = pr_beta(cr, &inputrec->opts, mdatoms, top_global, s_min, s_b);
- }
- /* Limit beta to prevent oscillations */
- if (fabs(beta) > 5.0)
- {
- beta = 0.0;
- }
-
-
- /* update positions */
- swap_em_state(s_min, s_b);
- gpa = gpb;
-
- /* Print it if necessary */
- if (MASTER(cr))
- {
- if (bVerbose)
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step, s_min->epot, s_min->fnorm/sqrtNumAtoms,
- s_min->fmax, s_min->a_fmax+1);
- }
- /* Store the new (lower) energies */
- upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
-
- do_log = do_per_step(step, inputrec->nstlog);
- do_ene = do_per_step(step, inputrec->nstenergy);
-
- /* Prepare IMD energy record, if bIMD is TRUE. */
- IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, step, TRUE);
-
- if (do_log)
- {
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
- }
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
-
- /* Send energies and positions to the IMD client if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
- {
- IMD_send_positions(inputrec->imd);
- }
-
- /* Stop when the maximum force lies below tolerance.
- * If we have reached machine precision, converged is already set to true.
- */
- converged = converged || (s_min->fmax < inputrec->em_tol);
-
- } /* End of the loop */
-
- /* IMD cleanup, if bIMD is TRUE. */
- IMD_finalize(inputrec->bIMD, inputrec->imd);
-
- if (converged)
- {
- step--; /* we never took that last step in this case */
-
- }
- if (s_min->fmax > inputrec->em_tol)
- {
- if (MASTER(cr))
- {
- warn_step(stderr, inputrec->em_tol, step-1 == number_steps, FALSE);
- warn_step(fplog, inputrec->em_tol, step-1 == number_steps, FALSE);
- }
- converged = FALSE;
- }
-
- if (MASTER(cr))
- {
- /* If we printed energy and/or logfile last step (which was the last step)
- * we don't have to do it again, but otherwise print the final values.
- */
- if (!do_log)
- {
- /* Write final value to log since we didn't do anything the last step */
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
- }
- if (!do_ene || !do_log)
- {
- /* Write final energy file entries */
- print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
- }
-
- /* Print some stuff... */
- if (MASTER(cr))
- {
- fprintf(stderr, "\nwriting lowest energy coordinates.\n");
- }
-
- /* IMPORTANT!
- * For accurate normal mode calculation it is imperative that we
- * store the last conformation into the full precision binary trajectory.
- *
- * However, we should only do it if we did NOT already write this step
- * above (which we did if do_x or do_f was true).
- */
- do_x = !do_per_step(step, inputrec->nstxout);
- do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
-
- write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
- top_global, inputrec, step,
- s_min, state_global, f_global);
-
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fnormn = s_min->fnorm/sqrtNumAtoms;
- print_converged(stderr, CG, inputrec->em_tol, step, converged, number_steps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
- print_converged(fplog, CG, inputrec->em_tol, step, converged, number_steps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
-
- fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
- }
-
- finish_em(cr, outf, walltime_accounting, wcycle);
-
- /* To print the actual number of steps we needed somewhere */
- walltime_accounting_set_nsteps_done(walltime_accounting, step);
-
- return 0;
-} /* That's all folks */
-
-
-double do_lbfgs(FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
- int gmx_unused nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
- t_inputrec *inputrec,
- gmx_mtop_t *top_global, t_fcdata *fcd,
- t_state *state,
- t_mdatoms *mdatoms,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t gmx_unused ed,
- t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- static const char *LBFGS = "Low-Memory BFGS Minimizer";
- em_state_t ems;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- rvec *f_global;
- int ncorr, nmaxcorr, point, cp, neval, nminstep;
- double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
- real *rho, *alpha, *ff, *xx, *p, *s, *lastx, *lastf, **dx, **dg;
- real *xa, *xb, *xc, *fa, *fb, *fc, *xtmp, *ftmp;
- real a, b, c, maxdelta, delta;
- real diag, Epot0, Epot, EpotA, EpotB, EpotC;
- real dgdx, dgdg, sq, yr, beta;
- t_mdebin *mdebin;
- gmx_bool converged;
- rvec mu_tot;
- real fnorm, fmax;
- gmx_bool do_log, do_ene, do_x, do_f, foundlower, *frozen;
- tensor vir, pres;
- int start, end, number_steps;
- gmx_mdoutf_t outf;
- int i, k, m, n, nfmax, gf, step;
- int mdof_flags;
-
- if (PAR(cr))
- {
- gmx_fatal(FARGS, "Cannot do parallel L-BFGS Minimization - yet.\n");
- }
-
- if (NULL != constr)
- {
- gmx_fatal(FARGS, "The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent).");
- }
-
- n = 3*state->natoms;
- nmaxcorr = inputrec->nbfgscorr;
-
- /* Allocate memory */
- /* Use pointers to real so we dont have to loop over both atoms and
- * dimensions all the time...
- * x/f are allocated as rvec *, so make new x0/f0 pointers-to-real
- * that point to the same memory.
- */
- snew(xa, n);
- snew(xb, n);
- snew(xc, n);
- snew(fa, n);
- snew(fb, n);
- snew(fc, n);
- snew(frozen, n);
-
- snew(p, n);
- snew(lastx, n);
- snew(lastf, n);
- snew(rho, nmaxcorr);
- snew(alpha, nmaxcorr);
-
- snew(dx, nmaxcorr);
- for (i = 0; i < nmaxcorr; i++)
- {
- snew(dx[i], n);
- }
-
- snew(dg, nmaxcorr);
- for (i = 0; i < nmaxcorr; i++)
- {
- snew(dg[i], n);
- }
-
- step = 0;
- neval = 0;
-
- /* Init em */
- init_em(fplog, LBFGS, cr, inputrec,
- state, top_global, &ems, &top, &f, &f_global,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
- /* Do_lbfgs is not completely updated like do_steep and do_cg,
- * so we free some memory again.
- */
- sfree(ems.s.x);
- sfree(ems.f);
-
- xx = (real *)state->x;
- ff = (real *)f;
-
- start = 0;
- end = mdatoms->homenr;
-
- /* Print to log file */
- print_em_start(fplog, cr, walltime_accounting, wcycle, LBFGS);
-
- do_log = do_ene = do_x = do_f = TRUE;
-
- /* Max number of steps */
- number_steps = inputrec->nsteps;
-
- /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
- gf = 0;
- for (i = start; i < end; i++)
- {
- if (mdatoms->cFREEZE)
- {
- gf = mdatoms->cFREEZE[i];
- }
- for (m = 0; m < DIM; m++)
- {
- frozen[3*i+m] = inputrec->opts.nFreeze[gf][m];
- }
- }
- if (MASTER(cr))
- {
- sp_header(stderr, LBFGS, inputrec->em_tol, number_steps);
- }
- if (fplog)
- {
- sp_header(fplog, LBFGS, inputrec->em_tol, number_steps);
- }
-
- if (vsite)
- {
- construct_vsites(vsite, state->x, 1, NULL,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
- }
-
- /* Call the force routine and some auxiliary (neighboursearching etc.) */
- /* do_force always puts the charge groups in the box and shifts again
- * We do not unshift, so molecules are always whole
- */
- neval++;
- ems.s.x = state->x;
- ems.f = f;
- evaluate_energy(fplog, cr,
- top_global, &ems, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, TRUE);
- where();
-
- if (MASTER(cr))
- {
- /* Copy stuff to the energy bin for easy printing etc. */
- upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
-
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
- print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
- where();
-
- /* This is the starting energy */
- Epot = enerd->term[F_EPOT];
-
- fnorm = ems.fnorm;
- fmax = ems.fmax;
- nfmax = ems.a_fmax;
-
- /* Set the initial step.
- * since it will be multiplied by the non-normalized search direction
- * vector (force vector the first time), we scale it by the
- * norm of the force.
- */
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
- fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
- fprintf(stderr, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
- fprintf(stderr, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
- fprintf(stderr, "\n");
- /* and copy to the log file too... */
- fprintf(fplog, "Using %d BFGS correction steps.\n\n", nmaxcorr);
- fprintf(fplog, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
- fprintf(fplog, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
- fprintf(fplog, "\n");
- }
-
- // Point is an index to the memory of search directions, where 0 is the first one.
- point = 0;
-
- // Set initial search direction to the force (-gradient), or 0 for frozen particles.
- for (i = 0; i < n; i++)
- {
- if (!frozen[i])
- {
- dx[point][i] = ff[i]; /* Initial search direction */
- }
- else
- {
- dx[point][i] = 0;
- }
- }
-
- // Stepsize will be modified during the search, and actually it is not critical
- // (the main efficiency in the algorithm comes from changing directions), but
- // we still need an initial value, so estimate it as the inverse of the norm
- // so we take small steps where the potential fluctuates a lot.
- stepsize = 1.0/fnorm;
-
- /* Start the loop over BFGS steps.
- * Each successful step is counted, and we continue until
- * we either converge or reach the max number of steps.
- */
-
- ncorr = 0;
-
- /* Set the gradient from the force */
- converged = FALSE;
- for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
- {
-
- /* Write coordinates if necessary */
- do_x = do_per_step(step, inputrec->nstxout);
- do_f = do_per_step(step, inputrec->nstfout);
-
- mdof_flags = 0;
- if (do_x)
- {
- mdof_flags |= MDOF_X;
- }
-
- if (do_f)
- {
- mdof_flags |= MDOF_F;
- }
-
- if (inputrec->bIMD)
- {
- mdof_flags |= MDOF_IMD;
- }
-
- mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
- top_global, step, (real)step, state, state, f, f);
-
- /* Do the linesearching in the direction dx[point][0..(n-1)] */
-
- /* make s a pointer to current search direction - point=0 first time we get here */
- s = dx[point];
-
- // calculate line gradient in position A
- for (gpa = 0, i = 0; i < n; i++)
- {
- gpa -= s[i]*ff[i];
- }
-
- /* Calculate minimum allowed stepsize along the line, before the average (norm)
- * relative change in coordinate is smaller than precision
- */
- for (minstep = 0, i = 0; i < n; i++)
- {
- tmp = fabs(xx[i]);
- if (tmp < 1.0)
- {
- tmp = 1.0;
- }
- tmp = s[i]/tmp;
- minstep += tmp*tmp;
- }
- minstep = GMX_REAL_EPS/sqrt(minstep/n);
-
- if (stepsize < minstep)
- {
- converged = TRUE;
- break;
- }
-
- // Before taking any steps along the line, store the old position
- for (i = 0; i < n; i++)
- {
- lastx[i] = xx[i];
- lastf[i] = ff[i];
- }
- Epot0 = Epot;
-
- for (i = 0; i < n; i++)
- {
- xa[i] = xx[i];
- }
-
- /* Take a step downhill.
- * In theory, we should find the actual minimum of the function in this
- * direction, somewhere along the line.
- * That is quite possible, but it turns out to take 5-10 function evaluations
- * for each line. However, we dont really need to find the exact minimum -
- * it is much better to start a new BFGS step in a modified direction as soon
- * as we are close to it. This will save a lot of energy evaluations.
- *
- * In practice, we just try to take a single step.
- * If it worked (i.e. lowered the energy), we increase the stepsize but
- * continue straight to the next BFGS step without trying to find any minimum,
- * i.e. we change the search direction too. If the line was smooth, it is
- * likely we are in a smooth region, and then it makes sense to take longer
- * steps in the modified search direction too.
- *
- * If it didn't work (higher energy), there must be a minimum somewhere between
- * the old position and the new one. Then we need to start by finding a lower
- * value before we change search direction. Since the energy was apparently
- * quite rough, we need to decrease the step size.
- *
- * Due to the finite numerical accuracy, it turns out that it is a good idea
- * to accept a SMALL increase in energy, if the derivative is still downhill.
- * This leads to lower final energies in the tests I've done. / Erik
- */
-
- // State "A" is the first position along the line.
- // reference position along line is initially zero
- EpotA = Epot0;
- a = 0.0;
-
- // Check stepsize first. We do not allow displacements
- // larger than emstep.
- //
- do
- {
- // Pick a new position C by adding stepsize to A.
- c = a + stepsize;
-
- // Calculate what the largest change in any individual coordinate
- // would be (translation along line * gradient along line)
- maxdelta = 0;
- for (i = 0; i < n; i++)
- {
- delta = c*s[i];
- if (delta > maxdelta)
- {
- maxdelta = delta;
- }
- }
- // If any displacement is larger than the stepsize limit, reduce the step
- if (maxdelta > inputrec->em_stepsize)
- {
- stepsize *= 0.1;
- }
- }
- while (maxdelta > inputrec->em_stepsize);
-
- // Take a trial step and move the coordinate array xc[] to position C
- for (i = 0; i < n; i++)
- {
- xc[i] = lastx[i] + c*s[i];
- }
-
- neval++;
- // Calculate energy for the trial step in position C
- ems.s.x = (rvec *)xc;
- ems.f = (rvec *)fc;
- evaluate_energy(fplog, cr,
- top_global, &ems, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, step, FALSE);
- EpotC = ems.epot;
-
- // Calc line gradient in position C
- for (gpc = 0, i = 0; i < n; i++)
- {
- gpc -= s[i]*fc[i]; /* f is negative gradient, thus the sign */
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpc, cr);
- }
-
- // This is the max amount of increase in energy we tolerate.
- // By allowing VERY small changes (close to numerical precision) we
- // frequently find even better (lower) final energies.
- tmp = sqrt(GMX_REAL_EPS)*fabs(EpotA);
-
- // Accept the step if the energy is lower in the new position C (compared to A),
- // or if it is not significantly higher and the line derivative is still negative.
- if (EpotC < EpotA || (gpc < 0 && EpotC < (EpotA+tmp)))
- {
- // Great, we found a better energy. We no longer try to alter the
- // stepsize, but simply accept this new better position. The we select a new
- // search direction instead, which will be much more efficient than continuing
- // to take smaller steps along a line. Set fnorm based on the new C position,
- // which will be used to update the stepsize to 1/fnorm further down.
- foundlower = TRUE;
- fnorm = ems.fnorm;
- }
- else
- {
- // If we got here, the energy is NOT lower in point C, i.e. it will be the same
- // or higher than in point A. In this case it is pointless to move to point C,
- // so we will have to do more iterations along the same line to find a smaller
- // value in the interval [A=0.0,C].
- // Here, A is still 0.0, but that will change when we do a search in the interval
- // [0.0,C] below. That search we will do by interpolation or bisection rather
- // than with the stepsize, so no need to modify it. For the next search direction
- // it will be reset to 1/fnorm anyway.
- foundlower = FALSE;
- }
-
- if (!foundlower)
- {
- // OK, if we didn't find a lower value we will have to locate one now - there must
- // be one in the interval [a,c].
- // The same thing is valid here, though: Don't spend dozens of iterations to find
- // the line minimum. We try to interpolate based on the derivative at the endpoints,
- // and only continue until we find a lower value. In most cases this means 1-2 iterations.
- // I also have a safeguard for potentially really pathological functions so we never
- // take more than 20 steps before we give up.
- // If we already found a lower value we just skip this step and continue to the update.
- nminstep = 0;
- do
- {
- // Select a new trial point B in the interval [A,C].
- // If the derivatives at points a & c have different sign we interpolate to zero,
- // otherwise just do a bisection since there might be multiple minima/maxima
- // inside the interval.
- if (gpa < 0 && gpc > 0)
- {
- b = a + gpa*(a-c)/(gpc-gpa);
- }
- else
- {
- b = 0.5*(a+c);
- }
-
- /* safeguard if interpolation close to machine accuracy causes errors:
- * never go outside the interval
- */
- if (b <= a || b >= c)
- {
- b = 0.5*(a+c);
- }
-
- // Take a trial step to point B
- for (i = 0; i < n; i++)
- {
- xb[i] = lastx[i] + b*s[i];
- }
-
- neval++;
- // Calculate energy for the trial step in point B
- ems.s.x = (rvec *)xb;
- ems.f = (rvec *)fb;
- evaluate_energy(fplog, cr,
- top_global, &ems, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, step, FALSE);
- EpotB = ems.epot;
- fnorm = ems.fnorm;
-
- // Calculate gradient in point B
- for (gpb = 0, i = 0; i < n; i++)
- {
- gpb -= s[i]*fb[i]; /* f is negative gradient, thus the sign */
-
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpb, cr);
- }
-
- // Keep one of the intervals [A,B] or [B,C] based on the value of the derivative
- // at the new point B, and rename the endpoints of this new interval A and C.
- if (gpb > 0)
- {
- /* Replace c endpoint with b */
- EpotC = EpotB;
- c = b;
- gpc = gpb;
- /* swap coord pointers b/c */
- xtmp = xb;
- ftmp = fb;
- xb = xc;
- fb = fc;
- xc = xtmp;
- fc = ftmp;
- }
- else
- {
- /* Replace a endpoint with b */
- EpotA = EpotB;
- a = b;
- gpa = gpb;
- /* swap coord pointers a/b */
- xtmp = xb;
- ftmp = fb;
- xb = xa;
- fb = fa;
- xa = xtmp;
- fa = ftmp;
- }
-
- /*
- * Stop search as soon as we find a value smaller than the endpoints,
- * or if the tolerance is below machine precision.
- * Never run more than 20 steps, no matter what.
- */
- nminstep++;
- }
- while ((EpotB > EpotA || EpotB > EpotC) && (nminstep < 20));
-
- if (fabs(EpotB-Epot0) < GMX_REAL_EPS || nminstep >= 20)
- {
- /* OK. We couldn't find a significantly lower energy.
- * If ncorr==0 this was steepest descent, and then we give up.
- * If not, reset memory to restart as steepest descent before quitting.
- */
- if (ncorr == 0)
- {
- /* Converged */
- converged = TRUE;
- break;
- }
- else
- {
- /* Reset memory */
- ncorr = 0;
- /* Search in gradient direction */
- for (i = 0; i < n; i++)
- {
- dx[point][i] = ff[i];
- }
- /* Reset stepsize */
- stepsize = 1.0/fnorm;
- continue;
- }
- }
-
- /* Select min energy state of A & C, put the best in xx/ff/Epot
- */
- if (EpotC < EpotA)
- {
- Epot = EpotC;
- /* Use state C */
- for (i = 0; i < n; i++)
- {
- xx[i] = xc[i];
- ff[i] = fc[i];
- }
- step_taken = c;
- }
- else
- {
- Epot = EpotA;
- /* Use state A */
- for (i = 0; i < n; i++)
- {
- xx[i] = xa[i];
- ff[i] = fa[i];
- }
- step_taken = a;
- }
-
- }
- else
- {
- /* found lower */
- Epot = EpotC;
- /* Use state C */
- for (i = 0; i < n; i++)
- {
- xx[i] = xc[i];
- ff[i] = fc[i];
- }
- step_taken = c;
- }
-
- /* Update the memory information, and calculate a new
- * approximation of the inverse hessian
- */
-
- /* Have new data in Epot, xx, ff */
- if (ncorr < nmaxcorr)
- {
- ncorr++;
- }
-
- for (i = 0; i < n; i++)
- {
- dg[point][i] = lastf[i]-ff[i];
- dx[point][i] *= step_taken;
- }
-
- dgdg = 0;
- dgdx = 0;
- for (i = 0; i < n; i++)
- {
- dgdg += dg[point][i]*dg[point][i];
- dgdx += dg[point][i]*dx[point][i];
- }
-
- diag = dgdx/dgdg;
-
- rho[point] = 1.0/dgdx;
- point++;
-
- if (point >= nmaxcorr)
- {
- point = 0;
- }
-
- /* Update */
- for (i = 0; i < n; i++)
- {
- p[i] = ff[i];
- }
-
- cp = point;
-
- /* Recursive update. First go back over the memory points */
- for (k = 0; k < ncorr; k++)
- {
- cp--;
- if (cp < 0)
- {
- cp = ncorr-1;
- }
-
- sq = 0;
- for (i = 0; i < n; i++)
- {
- sq += dx[cp][i]*p[i];
- }
-
- alpha[cp] = rho[cp]*sq;
-
- for (i = 0; i < n; i++)
- {
- p[i] -= alpha[cp]*dg[cp][i];
- }
- }
-
- for (i = 0; i < n; i++)
- {
- p[i] *= diag;
- }
-
- /* And then go forward again */
- for (k = 0; k < ncorr; k++)
- {
- yr = 0;
- for (i = 0; i < n; i++)
- {
- yr += p[i]*dg[cp][i];
- }
-
- beta = rho[cp]*yr;
- beta = alpha[cp]-beta;
-
- for (i = 0; i < n; i++)
- {
- p[i] += beta*dx[cp][i];
- }
-
- cp++;
- if (cp >= ncorr)
- {
- cp = 0;
- }
- }
-
- for (i = 0; i < n; i++)
- {
- if (!frozen[i])
- {
- dx[point][i] = p[i];
- }
- else
- {
- dx[point][i] = 0;
- }
- }
-
- /* Test whether the convergence criterion is met */
- get_f_norm_max(cr, &(inputrec->opts), mdatoms, f, &fnorm, &fmax, &nfmax);
-
- /* Print it if necessary */
- if (MASTER(cr))
- {
- if (bVerbose)
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
- fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step, Epot, fnorm/sqrtNumAtoms, fmax, nfmax+1);
- }
- /* Store the new (lower) energies */
- upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
- do_log = do_per_step(step, inputrec->nstlog);
- do_ene = do_per_step(step, inputrec->nstenergy);
- if (do_log)
- {
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
- }
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
-
- /* Send x and E to IMD client, if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state->box, state->x, inputrec, 0, wcycle) && MASTER(cr))
- {
- IMD_send_positions(inputrec->imd);
- }
-
- // Reset stepsize in we are doing more iterations
- stepsize = 1.0/fnorm;
-
- /* Stop when the maximum force lies below tolerance.
- * If we have reached machine precision, converged is already set to true.
- */
- converged = converged || (fmax < inputrec->em_tol);
-
- } /* End of the loop */
-
- /* IMD cleanup, if bIMD is TRUE. */
- IMD_finalize(inputrec->bIMD, inputrec->imd);
-
- if (converged)
- {
- step--; /* we never took that last step in this case */
-
- }
- if (fmax > inputrec->em_tol)
- {
- if (MASTER(cr))
- {
- warn_step(stderr, inputrec->em_tol, step-1 == number_steps, FALSE);
- warn_step(fplog, inputrec->em_tol, step-1 == number_steps, FALSE);
- }
- converged = FALSE;
- }
-
- /* If we printed energy and/or logfile last step (which was the last step)
- * we don't have to do it again, but otherwise print the final values.
- */
- if (!do_log) /* Write final value to log since we didn't do anythin last step */
- {
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
- }
- if (!do_ene || !do_log) /* Write final energy file entries */
- {
- print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
-
- /* Print some stuff... */
- if (MASTER(cr))
- {
- fprintf(stderr, "\nwriting lowest energy coordinates.\n");
- }
-
- /* IMPORTANT!
- * For accurate normal mode calculation it is imperative that we
- * store the last conformation into the full precision binary trajectory.
- *
- * However, we should only do it if we did NOT already write this step
- * above (which we did if do_x or do_f was true).
- */
- do_x = !do_per_step(step, inputrec->nstxout);
- do_f = !do_per_step(step, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
- top_global, inputrec, step,
- &ems, state, f);
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
- print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
- number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
- print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
- number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
-
- fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
- }
-
- finish_em(cr, outf, walltime_accounting, wcycle);
-
- /* To print the actual number of steps we needed somewhere */
- walltime_accounting_set_nsteps_done(walltime_accounting, step);
-
- return 0;
-} /* That's all folks */
-
-
-double do_steep(FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
- int gmx_unused nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
- t_inputrec *inputrec,
- 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 gmx_unused ed,
- t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- const char *SD = "Steepest Descents";
- em_state_t *s_min, *s_try;
- rvec *f_global;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- real stepsize;
- real ustep, fnormn;
- gmx_mdoutf_t outf;
- t_mdebin *mdebin;
- gmx_bool bDone, bAbort, do_x, do_f;
- tensor vir, pres;
- rvec mu_tot;
- int nsteps;
- int count = 0;
- int steps_accepted = 0;
-
- s_min = init_em_state();
- s_try = init_em_state();
-
- /* Init em and store the local state in s_try */
- init_em(fplog, SD, cr, inputrec,
- state_global, top_global, s_try, &top, &f, &f_global,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
-
- /* Print to log file */
- print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
-
- /* Set variables for stepsize (in nm). This is the largest
- * step that we are going to make in any direction.
- */
- ustep = inputrec->em_stepsize;
- stepsize = 0;
-
- /* Max number of steps */
- nsteps = inputrec->nsteps;
-
- if (MASTER(cr))
- {
- /* Print to the screen */
- sp_header(stderr, SD, inputrec->em_tol, nsteps);
- }
- if (fplog)
- {
- sp_header(fplog, SD, inputrec->em_tol, nsteps);
- }
-
- /**** HERE STARTS THE LOOP ****
- * count is the counter for the number of steps
- * bDone will be TRUE when the minimization has converged
- * bAbort will be TRUE when nsteps steps have been performed or when
- * the stepsize becomes smaller than is reasonable for machine precision
- */
- count = 0;
- bDone = FALSE;
- bAbort = FALSE;
- while (!bDone && !bAbort)
- {
- bAbort = (nsteps >= 0) && (count == nsteps);
-
- /* set new coordinates, except for first step */
- if (count > 0)
- {
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
- s_min, stepsize, s_min->f, s_try,
- constr, top, nrnb, wcycle, count);
- }
-
- evaluate_energy(fplog, cr,
- top_global, s_try, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, count, count == 0);
-
- if (MASTER(cr))
- {
- print_ebin_header(fplog, count, count, s_try->s.lambda[efptFEP]);
- }
-
- if (count == 0)
- {
- s_min->epot = s_try->epot;
- }
-
- /* Print it if necessary */
- if (MASTER(cr))
- {
- if (bVerbose)
- {
- fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
- count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax+1,
- ( (count == 0) || (s_try->epot < s_min->epot) ) ? '\n' : '\r');
- }
-
- if ( (count == 0) || (s_try->epot < s_min->epot) )
- {
- /* Store the new (lower) energies */
- upd_mdebin(mdebin, FALSE, FALSE, (double)count,
- mdatoms->tmass, enerd, &s_try->s, inputrec->fepvals, inputrec->expandedvals,
- s_try->s.box, NULL, NULL, vir, pres, NULL, mu_tot, constr);
-
- /* Prepare IMD energy record, if bIMD is TRUE. */
- IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE);
-
- print_ebin(mdoutf_get_fp_ene(outf), TRUE,
- do_per_step(steps_accepted, inputrec->nstdisreout),
- do_per_step(steps_accepted, inputrec->nstorireout),
- fplog, count, count, eprNORMAL, TRUE,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- fflush(fplog);
- }
- }
-
- /* Now if the new energy is smaller than the previous...
- * or if this is the first step!
- * or if we did random steps!
- */
-
- if ( (count == 0) || (s_try->epot < s_min->epot) )
- {
- steps_accepted++;
-
- /* Test whether the convergence criterion is met... */
- bDone = (s_try->fmax < inputrec->em_tol);
-
- /* Copy the arrays for force, positions and energy */
- /* The 'Min' array always holds the coords and forces of the minimal
- sampled energy */
- swap_em_state(s_min, s_try);
- if (count > 0)
- {
- ustep *= 1.2;
- }
-
- /* Write to trn, if necessary */
- do_x = do_per_step(steps_accepted, inputrec->nstxout);
- do_f = do_per_step(steps_accepted, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
- top_global, inputrec, count,
- s_min, state_global, f_global);
- }
- else
- {
- /* If energy is not smaller make the step smaller... */
- ustep *= 0.5;
-
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
- {
- /* Reload the old state */
- em_dd_partition_system(fplog, count, cr, top_global, inputrec,
- s_min, top, mdatoms, fr, vsite, constr,
- nrnb, wcycle);
- }
- }
-
- /* Determine new step */
- stepsize = ustep/s_min->fmax;
-
- /* Check if stepsize is too small, with 1 nm as a characteristic length */
-#ifdef GMX_DOUBLE
- if (count == nsteps || ustep < 1e-12)
-#else
- if (count == nsteps || ustep < 1e-6)
-#endif
- {
- if (MASTER(cr))
- {
- warn_step(stderr, inputrec->em_tol, count == nsteps, constr != NULL);
- warn_step(fplog, inputrec->em_tol, count == nsteps, constr != NULL);
- }
- bAbort = TRUE;
- }
-
- /* Send IMD energies and positions, if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, count, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
- {
- IMD_send_positions(inputrec->imd);
- }
-
- count++;
- } /* End of the loop */
-
- /* IMD cleanup, if bIMD is TRUE. */
- IMD_finalize(inputrec->bIMD, inputrec->imd);
-
- /* Print some data... */
- if (MASTER(cr))
- {
- fprintf(stderr, "\nwriting lowest energy coordinates.\n");
- }
- write_em_traj(fplog, cr, outf, TRUE, inputrec->nstfout, ftp2fn(efSTO, nfile, fnm),
- top_global, inputrec, count,
- s_min, state_global, f_global);
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fnormn = s_min->fnorm/sqrtNumAtoms;
-
- print_converged(stderr, SD, inputrec->em_tol, count, bDone, nsteps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
- print_converged(fplog, SD, inputrec->em_tol, count, bDone, nsteps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
- }
-
- finish_em(cr, outf, walltime_accounting, wcycle);
-
- /* To print the actual number of steps we needed somewhere */
- inputrec->nsteps = count;
-
- walltime_accounting_set_nsteps_done(walltime_accounting, count);
-
- return 0;
-} /* That's all folks */
-
-
-double do_nm(FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
- int gmx_unused nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
- t_inputrec *inputrec,
- 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 gmx_unused ed,
- t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- const char *NM = "Normal Mode Analysis";
- gmx_mdoutf_t outf;
- int natoms, atom, d;
- int nnodes, node;
- rvec *f_global;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- tensor vir, pres;
- rvec mu_tot;
- rvec *fneg, *dfdx;
- gmx_bool bSparse; /* use sparse matrix storage format */
- size_t sz = 0;
- gmx_sparsematrix_t * sparse_matrix = NULL;
- real * full_matrix = NULL;
- em_state_t * state_work;
-
- /* added with respect to mdrun */
- int i, j, k, row, col;
- real der_range = 10.0*sqrt(GMX_REAL_EPS);
- real x_min;
- bool bIsMaster = MASTER(cr);
-
- if (constr != NULL)
- {
- gmx_fatal(FARGS, "Constraints present with Normal Mode Analysis, this combination is not supported");
- }
-
- state_work = init_em_state();
-
- /* Init em and store the local state in state_minimum */
- init_em(fplog, NM, cr, inputrec,
- state_global, top_global, state_work, &top,
- &f, &f_global,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, NULL, imdport, Flags, wcycle);
-
- natoms = top_global->natoms;
- snew(fneg, natoms);
- snew(dfdx, natoms);
-
-#ifndef GMX_DOUBLE
- if (bIsMaster)
- {
- fprintf(stderr,
- "NOTE: This version of GROMACS has been compiled in single precision,\n"
- " which MIGHT not be accurate enough for normal mode analysis.\n"
- " GROMACS now uses sparse matrix storage, so the memory requirements\n"
- " are fairly modest even if you recompile in double precision.\n\n");
- }
-#endif
-
- /* Check if we can/should use sparse storage format.
- *
- * Sparse format is only useful when the Hessian itself is sparse, which it
- * will be when we use a cutoff.
- * For small systems (n<1000) it is easier to always use full matrix format, though.
- */
- if (EEL_FULL(fr->eeltype) || fr->rlist == 0.0)
- {
- md_print_info(cr, fplog, "Non-cutoff electrostatics used, forcing full Hessian format.\n");
- bSparse = FALSE;
- }
- else if (top_global->natoms < 1000)
- {
- md_print_info(cr, fplog, "Small system size (N=%d), using full Hessian format.\n", top_global->natoms);
- bSparse = FALSE;
- }
- else
- {
- md_print_info(cr, fplog, "Using compressed symmetric sparse Hessian format.\n");
- bSparse = TRUE;
- }
-
- if (bIsMaster)
- {
- sz = DIM*top_global->natoms;
-
- fprintf(stderr, "Allocating Hessian memory...\n\n");
-
- if (bSparse)
- {
- sparse_matrix = gmx_sparsematrix_init(sz);
- sparse_matrix->compressed_symmetric = TRUE;
- }
- else
- {
- snew(full_matrix, sz*sz);
- }
- }
-
- init_nrnb(nrnb);
-
- where();
-
- /* Write start time and temperature */
- print_em_start(fplog, cr, walltime_accounting, wcycle, NM);
-
- /* fudge nr of steps to nr of atoms */
- inputrec->nsteps = natoms*2;
-
- if (bIsMaster)
- {
- fprintf(stderr, "starting normal mode calculation '%s'\n%d steps.\n\n",
- *(top_global->name), (int)inputrec->nsteps);
- }
-
- nnodes = cr->nnodes;
-
- /* Make evaluate_energy do a single node force calculation */
- cr->nnodes = 1;
- evaluate_energy(fplog, cr,
- top_global, state_work, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, TRUE);
- cr->nnodes = nnodes;
-
- /* if forces are not small, warn user */
- get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, state_work);
-
- md_print_info(cr, fplog, "Maximum force:%12.5e\n", state_work->fmax);
- if (state_work->fmax > 1.0e-3)
- {
- md_print_info(cr, fplog,
- "The force is probably not small enough to "
- "ensure that you are at a minimum.\n"
- "Be aware that negative eigenvalues may occur\n"
- "when the resulting matrix is diagonalized.\n\n");
- }
-
- /***********************************************************
- *
- * Loop over all pairs in matrix
- *
- * do_force called twice. Once with positive and
- * once with negative displacement
- *
- ************************************************************/
-
- /* Steps are divided one by one over the nodes */
- for (atom = cr->nodeid; atom < natoms; atom += nnodes)
- {
-
- for (d = 0; d < DIM; d++)
- {
- x_min = state_work->s.x[atom][d];
-
- state_work->s.x[atom][d] = x_min - der_range;
-
- /* Make evaluate_energy do a single node force calculation */
- cr->nnodes = 1;
- evaluate_energy(fplog, cr,
- top_global, state_work, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, atom*2, FALSE);
-
- for (i = 0; i < natoms; i++)
- {
- copy_rvec(state_work->f[i], fneg[i]);
- }
-
- state_work->s.x[atom][d] = x_min + der_range;
-
- evaluate_energy(fplog, cr,
- top_global, state_work, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, atom*2+1, FALSE);
- cr->nnodes = nnodes;
-
- /* x is restored to original */
- state_work->s.x[atom][d] = x_min;
-
- for (j = 0; j < natoms; j++)
- {
- for (k = 0; (k < DIM); k++)
- {
- dfdx[j][k] =
- -(state_work->f[j][k] - fneg[j][k])/(2*der_range);
- }
- }
-
- if (!bIsMaster)
- {
-#ifdef GMX_MPI
-#ifdef GMX_DOUBLE
-#define mpi_type MPI_DOUBLE
-#else
-#define mpi_type MPI_FLOAT
-#endif
- MPI_Send(dfdx[0], natoms*DIM, mpi_type, MASTERNODE(cr), cr->nodeid,
- cr->mpi_comm_mygroup);
-#endif
- }
- else
- {
- for (node = 0; (node < nnodes && atom+node < natoms); node++)
- {
- if (node > 0)
- {
-#ifdef GMX_MPI
- MPI_Status stat;
- MPI_Recv(dfdx[0], natoms*DIM, mpi_type, node, node,
- cr->mpi_comm_mygroup, &stat);
-#undef mpi_type
-#endif
- }
-
- row = (atom + node)*DIM + d;
-
- for (j = 0; j < natoms; j++)
- {
- for (k = 0; k < DIM; k++)
- {
- col = j*DIM + k;
-
- if (bSparse)
- {
- if (col >= row && dfdx[j][k] != 0.0)
- {
- gmx_sparsematrix_increment_value(sparse_matrix,
- row, col, dfdx[j][k]);
- }
- }
- else
- {
- full_matrix[row*sz+col] = dfdx[j][k];
- }
- }
- }
- }
- }
-
- if (bVerbose && fplog)
- {
- fflush(fplog);
- }
- }
- /* write progress */
- if (bIsMaster && bVerbose)
- {
- fprintf(stderr, "\rFinished step %d out of %d",
- std::min(atom+nnodes, natoms), natoms);
- fflush(stderr);
- }
- }
-
- if (bIsMaster)
- {
- fprintf(stderr, "\n\nWriting Hessian...\n");
- gmx_mtxio_write(ftp2fn(efMTX, nfile, fnm), sz, sz, full_matrix, sparse_matrix);
- }
-
- finish_em(cr, outf, walltime_accounting, wcycle);
-
- walltime_accounting_set_nsteps_done(walltime_accounting, natoms*2);
-
- return 0;
-}
diff --git a/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/minimize.cpp.preplumed b/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/minimize.cpp.preplumed
deleted file mode 100644
index a6ffb5c793f445ef6779c929ac1548b8888f1648..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/gromacs/mdlib/minimize.cpp.preplumed
+++ /dev/null
@@ -1,2888 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-#include <string.h>
-#include <time.h>
-
-#include <algorithm>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/ewald/pme.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/mtxio.h"
-#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/linearalgebra/sparsematrix.h"
-#include "gromacs/listed-forces/manage-threading.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
-typedef struct {
- t_state s;
- rvec *f;
- real epot;
- real fnorm;
- real fmax;
- int a_fmax;
-} em_state_t;
-
-static em_state_t *init_em_state()
-{
- em_state_t *ems;
-
- snew(ems, 1);
-
- /* does this need to be here? Should the array be declared differently (staticaly)in the state definition? */
- snew(ems->s.lambda, efptNR);
-
- return ems;
-}
-
-static void print_em_start(FILE *fplog,
- t_commrec *cr,
- gmx_walltime_accounting_t walltime_accounting,
- gmx_wallcycle_t wcycle,
- const char *name)
-{
- walltime_accounting_start(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
- print_start(fplog, cr, walltime_accounting, name);
-}
-static void em_time_end(gmx_walltime_accounting_t walltime_accounting,
- gmx_wallcycle_t wcycle)
-{
- wallcycle_stop(wcycle, ewcRUN);
-
- walltime_accounting_end(walltime_accounting);
-}
-
-static void sp_header(FILE *out, const char *minimizer, real ftol, int nsteps)
-{
- fprintf(out, "\n");
- fprintf(out, "%s:\n", minimizer);
- fprintf(out, " Tolerance (Fmax) = %12.5e\n", ftol);
- fprintf(out, " Number of steps = %12d\n", nsteps);
-}
-
-static void warn_step(FILE *fp, real ftol, gmx_bool bLastStep, gmx_bool bConstrain)
-{
- char buffer[2048];
- if (bLastStep)
- {
- sprintf(buffer,
- "\nEnergy minimization reached the maximum number "
- "of steps before the forces reached the requested "
- "precision Fmax < %g.\n", ftol);
- }
- else
- {
- sprintf(buffer,
- "\nEnergy minimization has stopped, but the forces have "
- "not converged to the requested precision Fmax < %g (which "
- "may not be possible for your system). It stopped "
- "because the algorithm tried to make a new step whose size "
- "was too small, or there was no change in the energy since "
- "last step. Either way, we regard the minimization as "
- "converged to within the available machine precision, "
- "given your starting configuration and EM parameters.\n%s%s",
- ftol,
- sizeof(real) < sizeof(double) ?
- "\nDouble precision normally gives you higher accuracy, but "
- "this is often not needed for preparing to run molecular "
- "dynamics.\n" :
- "",
- bConstrain ?
- "You might need to increase your constraint accuracy, or turn\n"
- "off constraints altogether (set constraints = none in mdp file)\n" :
- "");
- }
- fputs(wrap_lines(buffer, 78, 0, FALSE), fp);
-}
-
-
-
-static void print_converged(FILE *fp, const char *alg, real ftol,
- gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
- real epot, real fmax, int nfmax, real fnorm)
-{
- char buf[STEPSTRSIZE];
-
- if (bDone)
- {
- fprintf(fp, "\n%s converged to Fmax < %g in %s steps\n",
- alg, ftol, gmx_step_str(count, buf));
- }
- else if (count < nsteps)
- {
- fprintf(fp, "\n%s converged to machine precision in %s steps,\n"
- "but did not reach the requested Fmax < %g.\n",
- alg, gmx_step_str(count, buf), ftol);
- }
- else
- {
- fprintf(fp, "\n%s did not converge to Fmax < %g in %s steps.\n",
- alg, ftol, gmx_step_str(count, buf));
- }
-
-#ifdef GMX_DOUBLE
- fprintf(fp, "Potential Energy = %21.14e\n", epot);
- fprintf(fp, "Maximum force = %21.14e on atom %d\n", fmax, nfmax+1);
- fprintf(fp, "Norm of force = %21.14e\n", fnorm);
-#else
- fprintf(fp, "Potential Energy = %14.7e\n", epot);
- fprintf(fp, "Maximum force = %14.7e on atom %d\n", fmax, nfmax+1);
- fprintf(fp, "Norm of force = %14.7e\n", fnorm);
-#endif
-}
-
-static void get_f_norm_max(t_commrec *cr,
- t_grpopts *opts, t_mdatoms *mdatoms, rvec *f,
- real *fnorm, real *fmax, int *a_fmax)
-{
- double fnorm2, *sum;
- real fmax2, fam;
- int la_max, a_max, start, end, i, m, gf;
-
- /* This routine finds the largest force and returns it.
- * On parallel machines the global max is taken.
- */
- fnorm2 = 0;
- fmax2 = 0;
- la_max = -1;
- start = 0;
- end = mdatoms->homenr;
- if (mdatoms->cFREEZE)
- {
- for (i = start; i < end; i++)
- {
- gf = mdatoms->cFREEZE[i];
- fam = 0;
- for (m = 0; m < DIM; m++)
- {
- if (!opts->nFreeze[gf][m])
- {
- fam += sqr(f[i][m]);
- }
- }
- fnorm2 += fam;
- if (fam > fmax2)
- {
- fmax2 = fam;
- la_max = i;
- }
- }
- }
- else
- {
- for (i = start; i < end; i++)
- {
- fam = norm2(f[i]);
- fnorm2 += fam;
- if (fam > fmax2)
- {
- fmax2 = fam;
- la_max = i;
- }
- }
- }
-
- if (la_max >= 0 && DOMAINDECOMP(cr))
- {
- a_max = cr->dd->gatindex[la_max];
- }
- else
- {
- a_max = la_max;
- }
- if (PAR(cr))
- {
- snew(sum, 2*cr->nnodes+1);
- sum[2*cr->nodeid] = fmax2;
- sum[2*cr->nodeid+1] = a_max;
- sum[2*cr->nnodes] = fnorm2;
- gmx_sumd(2*cr->nnodes+1, sum, cr);
- fnorm2 = sum[2*cr->nnodes];
- /* Determine the global maximum */
- for (i = 0; i < cr->nnodes; i++)
- {
- if (sum[2*i] > fmax2)
- {
- fmax2 = sum[2*i];
- a_max = (int)(sum[2*i+1] + 0.5);
- }
- }
- sfree(sum);
- }
-
- if (fnorm)
- {
- *fnorm = sqrt(fnorm2);
- }
- if (fmax)
- {
- *fmax = sqrt(fmax2);
- }
- if (a_fmax)
- {
- *a_fmax = a_max;
- }
-}
-
-static void get_state_f_norm_max(t_commrec *cr,
- t_grpopts *opts, t_mdatoms *mdatoms,
- em_state_t *ems)
-{
- get_f_norm_max(cr, opts, mdatoms, ems->f, &ems->fnorm, &ems->fmax, &ems->a_fmax);
-}
-
-void init_em(FILE *fplog, const char *title,
- t_commrec *cr, t_inputrec *ir,
- t_state *state_global, gmx_mtop_t *top_global,
- em_state_t *ems, gmx_localtop_t **top,
- rvec **f, rvec **f_global,
- t_nrnb *nrnb, rvec mu_tot,
- t_forcerec *fr, gmx_enerdata_t **enerd,
- t_graph **graph, t_mdatoms *mdatoms, gmx_global_stat_t *gstat,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int nfile, const t_filenm fnm[],
- gmx_mdoutf_t *outf, t_mdebin **mdebin,
- int imdport, unsigned long gmx_unused Flags,
- gmx_wallcycle_t wcycle)
-{
- int i;
- real dvdl_constr;
-
- if (fplog)
- {
- fprintf(fplog, "Initiating %s\n", title);
- }
-
- state_global->ngtc = 0;
-
- /* Initialize lambda variables */
- initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, NULL);
-
- init_nrnb(nrnb);
-
- /* Interactive molecular dynamics */
- init_IMD(ir, cr, top_global, fplog, 1, state_global->x,
- nfile, fnm, NULL, imdport, Flags);
-
- if (DOMAINDECOMP(cr))
- {
- *top = dd_init_local_top(top_global);
-
- dd_init_local_state(cr->dd, state_global, &ems->s);
-
- *f = NULL;
-
- /* 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,
- &ems->s, &ems->f, mdatoms, *top,
- fr, vsite, NULL, constr,
- nrnb, NULL, FALSE);
- dd_store_state(cr->dd, &ems->s);
-
- if (ir->nstfout)
- {
- snew(*f_global, top_global->natoms);
- }
- else
- {
- *f_global = NULL;
- }
- *graph = NULL;
- }
- else
- {
- snew(*f, top_global->natoms);
-
- /* Just copy the state */
- ems->s = *state_global;
- snew(ems->s.x, ems->s.nalloc);
- snew(ems->f, ems->s.nalloc);
- for (i = 0; i < state_global->natoms; i++)
- {
- copy_rvec(state_global->x[i], ems->s.x[i]);
- }
- copy_mat(state_global->box, ems->s.box);
-
- *top = gmx_mtop_generate_local_top(top_global, ir);
- *f_global = *f;
-
- setup_bonded_threading(fr, &(*top)->idef);
-
- if (ir->ePBC != epbcNONE && !fr->bMolPBC)
- {
- *graph = mk_graph(fplog, &((*top)->idef), 0, top_global->natoms, FALSE, FALSE);
- }
- else
- {
- *graph = NULL;
- }
-
- atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
- update_mdatoms(mdatoms, state_global->lambda[efptFEP]);
-
- if (vsite)
- {
- set_vsite_top(vsite, *top, mdatoms, cr);
- }
- }
-
- if (constr)
- {
- if (ir->eConstrAlg == econtSHAKE &&
- gmx_mtop_ftype_count(top_global, F_CONSTR) > 0)
- {
- gmx_fatal(FARGS, "Can not do energy minimization with %s, use %s\n",
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
- }
-
- if (!DOMAINDECOMP(cr))
- {
- set_constraints(constr, *top, ir, mdatoms, cr);
- }
-
- if (!ir->bContinuation)
- {
- /* Constrain the starting coordinates */
- dvdl_constr = 0;
- constrain(PAR(cr) ? NULL : fplog, TRUE, TRUE, constr, &(*top)->idef,
- ir, cr, -1, 0, 1.0, mdatoms,
- ems->s.x, ems->s.x, NULL, fr->bMolPBC, ems->s.box,
- ems->s.lambda[efptFEP], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
- }
- }
-
- if (PAR(cr))
- {
- *gstat = global_stat_init(ir);
- }
- else
- {
- *gstat = NULL;
- }
-
- *outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL, wcycle);
-
- snew(*enerd, 1);
- init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
- *enerd);
-
- if (mdebin != NULL)
- {
- /* Init bin for energy stuff */
- *mdebin = init_mdebin(mdoutf_get_fp_ene(*outf), top_global, ir, NULL);
- }
-
- clear_rvec(mu_tot);
- calc_shifts(ems->s.box, fr->shift_vec);
-}
-
-static void finish_em(t_commrec *cr, gmx_mdoutf_t outf,
- gmx_walltime_accounting_t walltime_accounting,
- gmx_wallcycle_t wcycle)
-{
- if (!(cr->duty & DUTY_PME))
- {
- /* Tell the PME only node to finish */
- gmx_pme_send_finish(cr);
- }
-
- done_mdoutf(outf);
-
- em_time_end(walltime_accounting, wcycle);
-}
-
-static void swap_em_state(em_state_t *ems1, em_state_t *ems2)
-{
- em_state_t tmp;
-
- tmp = *ems1;
- *ems1 = *ems2;
- *ems2 = tmp;
-}
-
-static void copy_em_coords(em_state_t *ems, t_state *state)
-{
- int i;
-
- for (i = 0; (i < state->natoms); i++)
- {
- copy_rvec(ems->s.x[i], state->x[i]);
- }
-}
-
-static void write_em_traj(FILE *fplog, t_commrec *cr,
- gmx_mdoutf_t outf,
- gmx_bool bX, gmx_bool bF, const char *confout,
- gmx_mtop_t *top_global,
- t_inputrec *ir, gmx_int64_t step,
- em_state_t *state,
- t_state *state_global, rvec *f_global)
-{
- int mdof_flags;
- gmx_bool bIMDout = FALSE;
-
-
- /* Shall we do IMD output? */
- if (ir->bIMD)
- {
- bIMDout = do_per_step(step, IMD_get_step(ir->imd->setup));
- }
-
- if ((bX || bF || bIMDout || confout != NULL) && !DOMAINDECOMP(cr))
- {
- copy_em_coords(state, state_global);
- f_global = state->f;
- }
-
- mdof_flags = 0;
- if (bX)
- {
- mdof_flags |= MDOF_X;
- }
- if (bF)
- {
- mdof_flags |= MDOF_F;
- }
-
- /* If we want IMD output, set appropriate MDOF flag */
- if (ir->bIMD)
- {
- mdof_flags |= MDOF_IMD;
- }
-
- mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
- top_global, step, (double)step,
- &state->s, state_global, state->f, f_global);
-
- if (confout != NULL && MASTER(cr))
- {
- if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
- {
- /* Make molecules whole only for confout writing */
- do_pbc_mtop(fplog, ir->ePBC, state_global->box, top_global,
- state_global->x);
- }
-
- write_sto_conf_mtop(confout,
- *top_global->name, top_global,
- state_global->x, NULL, ir->ePBC, state_global->box);
- }
-}
-
-static void do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
- gmx_bool bMolPBC,
- em_state_t *ems1, real a, rvec *f, em_state_t *ems2,
- gmx_constr_t constr, gmx_localtop_t *top,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_int64_t count)
-
-{
- t_state *s1, *s2;
- int start, end;
- real dvdl_constr;
- int nthreads gmx_unused;
-
- s1 = &ems1->s;
- s2 = &ems2->s;
-
- if (DOMAINDECOMP(cr) && s1->ddp_count != cr->dd->ddp_count)
- {
- gmx_incons("state mismatch in do_em_step");
- }
-
- s2->flags = s1->flags;
-
- if (s2->nalloc != s1->nalloc)
- {
- s2->nalloc = s1->nalloc;
- srenew(s2->x, s1->nalloc);
- srenew(ems2->f, s1->nalloc);
- if (s2->flags & (1<<estCGP))
- {
- srenew(s2->cg_p, s1->nalloc);
- }
- }
-
- s2->natoms = s1->natoms;
- copy_mat(s1->box, s2->box);
- /* Copy free energy state */
- for (int i = 0; i < efptNR; i++)
- {
- s2->lambda[i] = s1->lambda[i];
- }
- copy_mat(s1->box, s2->box);
-
- start = 0;
- end = md->homenr;
-
- // cppcheck-suppress unreadVariable
- nthreads = gmx_omp_nthreads_get(emntUpdate);
-#pragma omp parallel num_threads(nthreads)
- {
- rvec *x1 = s1->x;
- rvec *x2 = s2->x;
-
- int gf = 0;
-#pragma omp for schedule(static) nowait
- for (int i = start; i < end; i++)
- {
- if (md->cFREEZE)
- {
- gf = md->cFREEZE[i];
- }
- for (int m = 0; m < DIM; m++)
- {
- if (ir->opts.nFreeze[gf][m])
- {
- x2[i][m] = x1[i][m];
- }
- else
- {
- x2[i][m] = x1[i][m] + a*f[i][m];
- }
- }
- }
-
- if (s2->flags & (1<<estCGP))
- {
- /* Copy the CG p vector */
- rvec *p1 = s1->cg_p;
- rvec *p2 = s2->cg_p;
-#pragma omp for schedule(static) nowait
- for (int i = start; i < end; i++)
- {
- copy_rvec(p1[i], p2[i]);
- }
- }
-
- if (DOMAINDECOMP(cr))
- {
- s2->ddp_count = s1->ddp_count;
- if (s2->cg_gl_nalloc < s1->cg_gl_nalloc)
- {
-#pragma omp barrier
- s2->cg_gl_nalloc = s1->cg_gl_nalloc;
- srenew(s2->cg_gl, s2->cg_gl_nalloc);
-#pragma omp barrier
- }
- s2->ncg_gl = s1->ncg_gl;
-#pragma omp for schedule(static) nowait
- for (int i = 0; i < s2->ncg_gl; i++)
- {
- s2->cg_gl[i] = s1->cg_gl[i];
- }
- s2->ddp_count_cg_gl = s1->ddp_count_cg_gl;
- }
- }
-
- if (constr)
- {
- wallcycle_start(wcycle, ewcCONSTR);
- dvdl_constr = 0;
- constrain(NULL, TRUE, TRUE, constr, &top->idef,
- ir, cr, count, 0, 1.0, md,
- s1->x, s2->x, NULL, bMolPBC, s2->box,
- s2->lambda[efptBONDED], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
- wallcycle_stop(wcycle, ewcCONSTR);
- }
-}
-
-static void em_dd_partition_system(FILE *fplog, int step, t_commrec *cr,
- gmx_mtop_t *top_global, t_inputrec *ir,
- em_state_t *ems, gmx_localtop_t *top,
- t_mdatoms *mdatoms, t_forcerec *fr,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle)
-{
- /* Repartition the domain decomposition */
- dd_partition_system(fplog, step, cr, FALSE, 1,
- NULL, top_global, ir,
- &ems->s, &ems->f,
- mdatoms, top, fr, vsite, NULL, constr,
- nrnb, wcycle, FALSE);
- dd_store_state(cr->dd, &ems->s);
-}
-
-static void evaluate_energy(FILE *fplog, t_commrec *cr,
- gmx_mtop_t *top_global,
- em_state_t *ems, gmx_localtop_t *top,
- t_inputrec *inputrec,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_global_stat_t gstat,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- t_fcdata *fcd,
- t_graph *graph, t_mdatoms *mdatoms,
- t_forcerec *fr, rvec mu_tot,
- gmx_enerdata_t *enerd, tensor vir, tensor pres,
- gmx_int64_t count, gmx_bool bFirst)
-{
- real t;
- gmx_bool bNS;
- tensor force_vir, shake_vir, ekin;
- real dvdl_constr, prescorr, enercorr, dvdlcorr;
- real terminate = 0;
-
- /* Set the time to the initial time, the time does not change during EM */
- t = inputrec->init_t;
-
- if (bFirst ||
- (DOMAINDECOMP(cr) && ems->s.ddp_count < cr->dd->ddp_count))
- {
- /* This is the first state or an old state used before the last ns */
- bNS = TRUE;
- }
- else
- {
- bNS = FALSE;
- if (inputrec->nstlist > 0)
- {
- bNS = TRUE;
- }
- }
-
- if (vsite)
- {
- construct_vsites(vsite, ems->s.x, 1, NULL,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, ems->s.box);
- }
-
- if (DOMAINDECOMP(cr) && bNS)
- {
- /* Repartition the domain decomposition */
- em_dd_partition_system(fplog, count, cr, top_global, inputrec,
- ems, top, mdatoms, fr, vsite, constr,
- nrnb, wcycle);
- }
-
- /* Calc force & energy on new trial position */
- /* do_force always puts the charge groups in the box and shifts again
- * We do not unshift, so molecules are always whole in congrad.c
- */
- do_force(fplog, cr, inputrec,
- count, nrnb, wcycle, top, &top_global->groups,
- ems->s.box, ems->s.x, &ems->s.hist,
- ems->f, force_vir, mdatoms, enerd, fcd,
- ems->s.lambda, graph, fr, vsite, mu_tot, t, NULL, NULL, TRUE,
- GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
- GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
- (bNS ? GMX_FORCE_NS | GMX_FORCE_DO_LR : 0));
-
- /* Clear the unused shake virial and pressure */
- clear_mat(shake_vir);
- clear_mat(pres);
-
- /* Communicate stuff when parallel */
- if (PAR(cr) && inputrec->eI != eiNM)
- {
- wallcycle_start(wcycle, ewcMoveE);
-
- global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
- inputrec, NULL, NULL, NULL, 1, &terminate,
- top_global, &ems->s, FALSE,
- CGLO_ENERGY |
- CGLO_PRESSURE |
- CGLO_CONSTRAINT);
-
- wallcycle_stop(wcycle, ewcMoveE);
- }
-
- /* Calculate long range corrections to pressure and energy */
- calc_dispcorr(inputrec, fr, top_global->natoms, ems->s.box, ems->s.lambda[efptVDW],
- pres, force_vir, &prescorr, &enercorr, &dvdlcorr);
- enerd->term[F_DISPCORR] = enercorr;
- enerd->term[F_EPOT] += enercorr;
- enerd->term[F_PRES] += prescorr;
- enerd->term[F_DVDL] += dvdlcorr;
-
- ems->epot = enerd->term[F_EPOT];
-
- if (constr)
- {
- /* Project out the constraint components of the force */
- wallcycle_start(wcycle, ewcCONSTR);
- dvdl_constr = 0;
- constrain(NULL, FALSE, FALSE, constr, &top->idef,
- inputrec, cr, count, 0, 1.0, mdatoms,
- ems->s.x, ems->f, ems->f, fr->bMolPBC, ems->s.box,
- ems->s.lambda[efptBONDED], &dvdl_constr,
- NULL, &shake_vir, nrnb, econqForceDispl);
- enerd->term[F_DVDL_CONSTR] += dvdl_constr;
- m_add(force_vir, shake_vir, vir);
- wallcycle_stop(wcycle, ewcCONSTR);
- }
- else
- {
- copy_mat(force_vir, vir);
- }
-
- clear_mat(ekin);
- enerd->term[F_PRES] =
- calc_pres(fr->ePBC, inputrec->nwall, ems->s.box, ekin, vir, pres);
-
- sum_dhdl(enerd, ems->s.lambda, inputrec->fepvals);
-
- if (EI_ENERGY_MINIMIZATION(inputrec->eI))
- {
- get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, ems);
- }
-}
-
-static double reorder_partsum(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
- gmx_mtop_t *mtop,
- em_state_t *s_min, em_state_t *s_b)
-{
- rvec *fm, *fb, *fmg;
- t_block *cgs_gl;
- int ncg, *cg_gl, *index, c, cg, i, a0, a1, a, gf, m;
- double partsum;
- unsigned char *grpnrFREEZE;
-
- if (debug)
- {
- fprintf(debug, "Doing reorder_partsum\n");
- }
-
- fm = s_min->f;
- fb = s_b->f;
-
- cgs_gl = dd_charge_groups_global(cr->dd);
- index = cgs_gl->index;
-
- /* Collect fm in a global vector fmg.
- * This conflicts with the spirit of domain decomposition,
- * but to fully optimize this a much more complicated algorithm is required.
- */
- snew(fmg, mtop->natoms);
-
- ncg = s_min->s.ncg_gl;
- cg_gl = s_min->s.cg_gl;
- i = 0;
- for (c = 0; c < ncg; c++)
- {
- cg = cg_gl[c];
- a0 = index[cg];
- a1 = index[cg+1];
- for (a = a0; a < a1; a++)
- {
- copy_rvec(fm[i], fmg[a]);
- i++;
- }
- }
- gmx_sum(mtop->natoms*3, fmg[0], cr);
-
- /* Now we will determine the part of the sum for the cgs in state s_b */
- ncg = s_b->s.ncg_gl;
- cg_gl = s_b->s.cg_gl;
- partsum = 0;
- i = 0;
- gf = 0;
- grpnrFREEZE = mtop->groups.grpnr[egcFREEZE];
- for (c = 0; c < ncg; c++)
- {
- cg = cg_gl[c];
- a0 = index[cg];
- a1 = index[cg+1];
- for (a = a0; a < a1; a++)
- {
- if (mdatoms->cFREEZE && grpnrFREEZE)
- {
- gf = grpnrFREEZE[i];
- }
- for (m = 0; m < DIM; m++)
- {
- if (!opts->nFreeze[gf][m])
- {
- partsum += (fb[i][m] - fmg[a][m])*fb[i][m];
- }
- }
- i++;
- }
- }
-
- sfree(fmg);
-
- return partsum;
-}
-
-static real pr_beta(t_commrec *cr, t_grpopts *opts, t_mdatoms *mdatoms,
- gmx_mtop_t *mtop,
- em_state_t *s_min, em_state_t *s_b)
-{
- rvec *fm, *fb;
- double sum;
- int gf, i, m;
-
- /* This is just the classical Polak-Ribiere calculation of beta;
- * it looks a bit complicated since we take freeze groups into account,
- * and might have to sum it in parallel runs.
- */
-
- if (!DOMAINDECOMP(cr) ||
- (s_min->s.ddp_count == cr->dd->ddp_count &&
- s_b->s.ddp_count == cr->dd->ddp_count))
- {
- fm = s_min->f;
- fb = s_b->f;
- sum = 0;
- gf = 0;
- /* This part of code can be incorrect with DD,
- * since the atom ordering in s_b and s_min might differ.
- */
- for (i = 0; i < mdatoms->homenr; i++)
- {
- if (mdatoms->cFREEZE)
- {
- gf = mdatoms->cFREEZE[i];
- }
- for (m = 0; m < DIM; m++)
- {
- if (!opts->nFreeze[gf][m])
- {
- sum += (fb[i][m] - fm[i][m])*fb[i][m];
- }
- }
- }
- }
- else
- {
- /* We need to reorder cgs while summing */
- sum = reorder_partsum(cr, opts, mdatoms, mtop, s_min, s_b);
- }
- if (PAR(cr))
- {
- gmx_sumd(1, &sum, cr);
- }
-
- return sum/sqr(s_min->fnorm);
-}
-
-double do_cg(FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
- int gmx_unused nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
- t_inputrec *inputrec,
- 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 gmx_unused ed,
- t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- const char *CG = "Polak-Ribiere Conjugate Gradients";
-
- em_state_t *s_min, *s_a, *s_b, *s_c;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- rvec *f_global, *p, *sf;
- double gpa, gpb, gpc, tmp, minstep;
- real fnormn;
- real stepsize;
- real a, b, c, beta = 0.0;
- real epot_repl = 0;
- real pnorm;
- t_mdebin *mdebin;
- gmx_bool converged, foundlower;
- rvec mu_tot;
- gmx_bool do_log = FALSE, do_ene = FALSE, do_x, do_f;
- tensor vir, pres;
- int number_steps, neval = 0, nstcg = inputrec->nstcgsteep;
- gmx_mdoutf_t outf;
- int i, m, gf, step, nminstep;
-
- step = 0;
-
- s_min = init_em_state();
- s_a = init_em_state();
- s_b = init_em_state();
- s_c = init_em_state();
-
- /* Init em and store the local state in s_min */
- init_em(fplog, CG, cr, inputrec,
- state_global, top_global, s_min, &top, &f, &f_global,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
-
- /* Print to log file */
- print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
-
- /* Max number of steps */
- number_steps = inputrec->nsteps;
-
- if (MASTER(cr))
- {
- sp_header(stderr, CG, inputrec->em_tol, number_steps);
- }
- if (fplog)
- {
- sp_header(fplog, CG, inputrec->em_tol, number_steps);
- }
-
- /* Call the force routine and some auxiliary (neighboursearching etc.) */
- /* do_force always puts the charge groups in the box and shifts again
- * We do not unshift, so molecules are always whole in congrad.c
- */
- evaluate_energy(fplog, cr,
- top_global, s_min, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, TRUE);
- where();
-
- if (MASTER(cr))
- {
- /* Copy stuff to the energy bin for easy printing etc. */
- upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
-
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
- print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
- where();
-
- /* Estimate/guess the initial stepsize */
- stepsize = inputrec->em_stepsize/s_min->fnorm;
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fprintf(stderr, " F-max = %12.5e on atom %d\n",
- s_min->fmax, s_min->a_fmax+1);
- fprintf(stderr, " F-Norm = %12.5e\n",
- s_min->fnorm/sqrtNumAtoms);
- fprintf(stderr, "\n");
- /* and copy to the log file too... */
- fprintf(fplog, " F-max = %12.5e on atom %d\n",
- s_min->fmax, s_min->a_fmax+1);
- fprintf(fplog, " F-Norm = %12.5e\n",
- s_min->fnorm/sqrtNumAtoms);
- fprintf(fplog, "\n");
- }
- /* Start the loop over CG steps.
- * Each successful step is counted, and we continue until
- * we either converge or reach the max number of steps.
- */
- converged = FALSE;
- for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
- {
-
- /* start taking steps in a new direction
- * First time we enter the routine, beta=0, and the direction is
- * simply the negative gradient.
- */
-
- /* Calculate the new direction in p, and the gradient in this direction, gpa */
- p = s_min->s.cg_p;
- sf = s_min->f;
- gpa = 0;
- gf = 0;
- for (i = 0; i < mdatoms->homenr; i++)
- {
- if (mdatoms->cFREEZE)
- {
- gf = mdatoms->cFREEZE[i];
- }
- for (m = 0; m < DIM; m++)
- {
- if (!inputrec->opts.nFreeze[gf][m])
- {
- p[i][m] = sf[i][m] + beta*p[i][m];
- gpa -= p[i][m]*sf[i][m];
- /* f is negative gradient, thus the sign */
- }
- else
- {
- p[i][m] = 0;
- }
- }
- }
-
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpa, cr);
- }
-
- /* Calculate the norm of the search vector */
- get_f_norm_max(cr, &(inputrec->opts), mdatoms, p, &pnorm, NULL, NULL);
-
- /* Just in case stepsize reaches zero due to numerical precision... */
- if (stepsize <= 0)
- {
- stepsize = inputrec->em_stepsize/pnorm;
- }
-
- /*
- * Double check the value of the derivative in the search direction.
- * If it is positive it must be due to the old information in the
- * CG formula, so just remove that and start over with beta=0.
- * This corresponds to a steepest descent step.
- */
- if (gpa > 0)
- {
- beta = 0;
- step--; /* Don't count this step since we are restarting */
- continue; /* Go back to the beginning of the big for-loop */
- }
-
- /* Calculate minimum allowed stepsize, before the average (norm)
- * relative change in coordinate is smaller than precision
- */
- minstep = 0;
- for (i = 0; i < mdatoms->homenr; i++)
- {
- for (m = 0; m < DIM; m++)
- {
- tmp = fabs(s_min->s.x[i][m]);
- if (tmp < 1.0)
- {
- tmp = 1.0;
- }
- tmp = p[i][m]/tmp;
- minstep += tmp*tmp;
- }
- }
- /* Add up from all CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &minstep, cr);
- }
-
- minstep = GMX_REAL_EPS/sqrt(minstep/(3*state_global->natoms));
-
- if (stepsize < minstep)
- {
- converged = TRUE;
- break;
- }
-
- /* Write coordinates if necessary */
- do_x = do_per_step(step, inputrec->nstxout);
- do_f = do_per_step(step, inputrec->nstfout);
-
- write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
- top_global, inputrec, step,
- s_min, state_global, f_global);
-
- /* Take a step downhill.
- * In theory, we should minimize the function along this direction.
- * That is quite possible, but it turns out to take 5-10 function evaluations
- * for each line. However, we dont really need to find the exact minimum -
- * it is much better to start a new CG step in a modified direction as soon
- * as we are close to it. This will save a lot of energy evaluations.
- *
- * In practice, we just try to take a single step.
- * If it worked (i.e. lowered the energy), we increase the stepsize but
- * the continue straight to the next CG step without trying to find any minimum.
- * If it didn't work (higher energy), there must be a minimum somewhere between
- * the old position and the new one.
- *
- * Due to the finite numerical accuracy, it turns out that it is a good idea
- * to even accept a SMALL increase in energy, if the derivative is still downhill.
- * This leads to lower final energies in the tests I've done. / Erik
- */
- s_a->epot = s_min->epot;
- a = 0.0;
- c = a + stepsize; /* reference position along line is zero */
-
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count < cr->dd->ddp_count)
- {
- em_dd_partition_system(fplog, step, cr, top_global, inputrec,
- s_min, top, mdatoms, fr, vsite, constr,
- nrnb, wcycle);
- }
-
- /* Take a trial step (new coords in s_c) */
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, c, s_min->s.cg_p, s_c,
- constr, top, nrnb, wcycle, -1);
-
- neval++;
- /* Calculate energy for the trial step */
- evaluate_energy(fplog, cr,
- top_global, s_c, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, FALSE);
-
- /* Calc derivative along line */
- p = s_c->s.cg_p;
- sf = s_c->f;
- gpc = 0;
- for (i = 0; i < mdatoms->homenr; i++)
- {
- for (m = 0; m < DIM; m++)
- {
- gpc -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
- }
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpc, cr);
- }
-
- /* This is the max amount of increase in energy we tolerate */
- tmp = sqrt(GMX_REAL_EPS)*fabs(s_a->epot);
-
- /* Accept the step if the energy is lower, or if it is not significantly higher
- * and the line derivative is still negative.
- */
- if (s_c->epot < s_a->epot || (gpc < 0 && s_c->epot < (s_a->epot + tmp)))
- {
- foundlower = TRUE;
- /* Great, we found a better energy. Increase step for next iteration
- * if we are still going down, decrease it otherwise
- */
- if (gpc < 0)
- {
- stepsize *= 1.618034; /* The golden section */
- }
- else
- {
- stepsize *= 0.618034; /* 1/golden section */
- }
- }
- else
- {
- /* New energy is the same or higher. We will have to do some work
- * to find a smaller value in the interval. Take smaller step next time!
- */
- foundlower = FALSE;
- stepsize *= 0.618034;
- }
-
-
-
-
- /* OK, if we didn't find a lower value we will have to locate one now - there must
- * be one in the interval [a=0,c].
- * The same thing is valid here, though: Don't spend dozens of iterations to find
- * the line minimum. We try to interpolate based on the derivative at the endpoints,
- * and only continue until we find a lower value. In most cases this means 1-2 iterations.
- *
- * I also have a safeguard for potentially really pathological functions so we never
- * take more than 20 steps before we give up ...
- *
- * If we already found a lower value we just skip this step and continue to the update.
- */
- if (!foundlower)
- {
- nminstep = 0;
-
- do
- {
- /* Select a new trial point.
- * If the derivatives at points a & c have different sign we interpolate to zero,
- * otherwise just do a bisection.
- */
- if (gpa < 0 && gpc > 0)
- {
- b = a + gpa*(a-c)/(gpc-gpa);
- }
- else
- {
- b = 0.5*(a+c);
- }
-
- /* safeguard if interpolation close to machine accuracy causes errors:
- * never go outside the interval
- */
- if (b <= a || b >= c)
- {
- b = 0.5*(a+c);
- }
-
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
- {
- /* Reload the old state */
- em_dd_partition_system(fplog, -1, cr, top_global, inputrec,
- s_min, top, mdatoms, fr, vsite, constr,
- nrnb, wcycle);
- }
-
- /* Take a trial step to this new point - new coords in s_b */
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, b, s_min->s.cg_p, s_b,
- constr, top, nrnb, wcycle, -1);
-
- neval++;
- /* Calculate energy for the trial step */
- evaluate_energy(fplog, cr,
- top_global, s_b, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, FALSE);
-
- /* p does not change within a step, but since the domain decomposition
- * might change, we have to use cg_p of s_b here.
- */
- p = s_b->s.cg_p;
- sf = s_b->f;
- gpb = 0;
- for (i = 0; i < mdatoms->homenr; i++)
- {
- for (m = 0; m < DIM; m++)
- {
- gpb -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
- }
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpb, cr);
- }
-
- if (debug)
- {
- fprintf(debug, "CGE: EpotA %f EpotB %f EpotC %f gpb %f\n",
- s_a->epot, s_b->epot, s_c->epot, gpb);
- }
-
- epot_repl = s_b->epot;
-
- /* Keep one of the intervals based on the value of the derivative at the new point */
- if (gpb > 0)
- {
- /* Replace c endpoint with b */
- swap_em_state(s_b, s_c);
- c = b;
- gpc = gpb;
- }
- else
- {
- /* Replace a endpoint with b */
- swap_em_state(s_b, s_a);
- a = b;
- gpa = gpb;
- }
-
- /*
- * Stop search as soon as we find a value smaller than the endpoints.
- * Never run more than 20 steps, no matter what.
- */
- nminstep++;
- }
- while ((epot_repl > s_a->epot || epot_repl > s_c->epot) &&
- (nminstep < 20));
-
- if (fabs(epot_repl - s_min->epot) < fabs(s_min->epot)*GMX_REAL_EPS ||
- nminstep >= 20)
- {
- /* OK. We couldn't find a significantly lower energy.
- * If beta==0 this was steepest descent, and then we give up.
- * If not, set beta=0 and restart with steepest descent before quitting.
- */
- if (beta == 0.0)
- {
- /* Converged */
- converged = TRUE;
- break;
- }
- else
- {
- /* Reset memory before giving up */
- beta = 0.0;
- continue;
- }
- }
-
- /* Select min energy state of A & C, put the best in B.
- */
- if (s_c->epot < s_a->epot)
- {
- if (debug)
- {
- fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n",
- s_c->epot, s_a->epot);
- }
- swap_em_state(s_b, s_c);
- gpb = gpc;
- }
- else
- {
- if (debug)
- {
- fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n",
- s_a->epot, s_c->epot);
- }
- swap_em_state(s_b, s_a);
- gpb = gpa;
- }
-
- }
- else
- {
- if (debug)
- {
- fprintf(debug, "CGE: Found a lower energy %f, moving C to B\n",
- s_c->epot);
- }
- swap_em_state(s_b, s_c);
- gpb = gpc;
- }
-
- /* new search direction */
- /* beta = 0 means forget all memory and restart with steepest descents. */
- if (nstcg && ((step % nstcg) == 0))
- {
- beta = 0.0;
- }
- else
- {
- /* s_min->fnorm cannot be zero, because then we would have converged
- * and broken out.
- */
-
- /* Polak-Ribiere update.
- * Change to fnorm2/fnorm2_old for Fletcher-Reeves
- */
- beta = pr_beta(cr, &inputrec->opts, mdatoms, top_global, s_min, s_b);
- }
- /* Limit beta to prevent oscillations */
- if (fabs(beta) > 5.0)
- {
- beta = 0.0;
- }
-
-
- /* update positions */
- swap_em_state(s_min, s_b);
- gpa = gpb;
-
- /* Print it if necessary */
- if (MASTER(cr))
- {
- if (bVerbose)
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step, s_min->epot, s_min->fnorm/sqrtNumAtoms,
- s_min->fmax, s_min->a_fmax+1);
- }
- /* Store the new (lower) energies */
- upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
-
- do_log = do_per_step(step, inputrec->nstlog);
- do_ene = do_per_step(step, inputrec->nstenergy);
-
- /* Prepare IMD energy record, if bIMD is TRUE. */
- IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, step, TRUE);
-
- if (do_log)
- {
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
- }
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
-
- /* Send energies and positions to the IMD client if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
- {
- IMD_send_positions(inputrec->imd);
- }
-
- /* Stop when the maximum force lies below tolerance.
- * If we have reached machine precision, converged is already set to true.
- */
- converged = converged || (s_min->fmax < inputrec->em_tol);
-
- } /* End of the loop */
-
- /* IMD cleanup, if bIMD is TRUE. */
- IMD_finalize(inputrec->bIMD, inputrec->imd);
-
- if (converged)
- {
- step--; /* we never took that last step in this case */
-
- }
- if (s_min->fmax > inputrec->em_tol)
- {
- if (MASTER(cr))
- {
- warn_step(stderr, inputrec->em_tol, step-1 == number_steps, FALSE);
- warn_step(fplog, inputrec->em_tol, step-1 == number_steps, FALSE);
- }
- converged = FALSE;
- }
-
- if (MASTER(cr))
- {
- /* If we printed energy and/or logfile last step (which was the last step)
- * we don't have to do it again, but otherwise print the final values.
- */
- if (!do_log)
- {
- /* Write final value to log since we didn't do anything the last step */
- print_ebin_header(fplog, step, step, s_min->s.lambda[efptFEP]);
- }
- if (!do_ene || !do_log)
- {
- /* Write final energy file entries */
- print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
- }
-
- /* Print some stuff... */
- if (MASTER(cr))
- {
- fprintf(stderr, "\nwriting lowest energy coordinates.\n");
- }
-
- /* IMPORTANT!
- * For accurate normal mode calculation it is imperative that we
- * store the last conformation into the full precision binary trajectory.
- *
- * However, we should only do it if we did NOT already write this step
- * above (which we did if do_x or do_f was true).
- */
- do_x = !do_per_step(step, inputrec->nstxout);
- do_f = (inputrec->nstfout > 0 && !do_per_step(step, inputrec->nstfout));
-
- write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
- top_global, inputrec, step,
- s_min, state_global, f_global);
-
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fnormn = s_min->fnorm/sqrtNumAtoms;
- print_converged(stderr, CG, inputrec->em_tol, step, converged, number_steps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
- print_converged(fplog, CG, inputrec->em_tol, step, converged, number_steps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
-
- fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
- }
-
- finish_em(cr, outf, walltime_accounting, wcycle);
-
- /* To print the actual number of steps we needed somewhere */
- walltime_accounting_set_nsteps_done(walltime_accounting, step);
-
- return 0;
-} /* That's all folks */
-
-
-double do_lbfgs(FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
- int gmx_unused nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
- t_inputrec *inputrec,
- gmx_mtop_t *top_global, t_fcdata *fcd,
- t_state *state,
- t_mdatoms *mdatoms,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t gmx_unused ed,
- t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- static const char *LBFGS = "Low-Memory BFGS Minimizer";
- em_state_t ems;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- rvec *f_global;
- int ncorr, nmaxcorr, point, cp, neval, nminstep;
- double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
- real *rho, *alpha, *ff, *xx, *p, *s, *lastx, *lastf, **dx, **dg;
- real *xa, *xb, *xc, *fa, *fb, *fc, *xtmp, *ftmp;
- real a, b, c, maxdelta, delta;
- real diag, Epot0, Epot, EpotA, EpotB, EpotC;
- real dgdx, dgdg, sq, yr, beta;
- t_mdebin *mdebin;
- gmx_bool converged;
- rvec mu_tot;
- real fnorm, fmax;
- gmx_bool do_log, do_ene, do_x, do_f, foundlower, *frozen;
- tensor vir, pres;
- int start, end, number_steps;
- gmx_mdoutf_t outf;
- int i, k, m, n, nfmax, gf, step;
- int mdof_flags;
-
- if (PAR(cr))
- {
- gmx_fatal(FARGS, "Cannot do parallel L-BFGS Minimization - yet.\n");
- }
-
- if (NULL != constr)
- {
- gmx_fatal(FARGS, "The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent).");
- }
-
- n = 3*state->natoms;
- nmaxcorr = inputrec->nbfgscorr;
-
- /* Allocate memory */
- /* Use pointers to real so we dont have to loop over both atoms and
- * dimensions all the time...
- * x/f are allocated as rvec *, so make new x0/f0 pointers-to-real
- * that point to the same memory.
- */
- snew(xa, n);
- snew(xb, n);
- snew(xc, n);
- snew(fa, n);
- snew(fb, n);
- snew(fc, n);
- snew(frozen, n);
-
- snew(p, n);
- snew(lastx, n);
- snew(lastf, n);
- snew(rho, nmaxcorr);
- snew(alpha, nmaxcorr);
-
- snew(dx, nmaxcorr);
- for (i = 0; i < nmaxcorr; i++)
- {
- snew(dx[i], n);
- }
-
- snew(dg, nmaxcorr);
- for (i = 0; i < nmaxcorr; i++)
- {
- snew(dg[i], n);
- }
-
- step = 0;
- neval = 0;
-
- /* Init em */
- init_em(fplog, LBFGS, cr, inputrec,
- state, top_global, &ems, &top, &f, &f_global,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
- /* Do_lbfgs is not completely updated like do_steep and do_cg,
- * so we free some memory again.
- */
- sfree(ems.s.x);
- sfree(ems.f);
-
- xx = (real *)state->x;
- ff = (real *)f;
-
- start = 0;
- end = mdatoms->homenr;
-
- /* Print to log file */
- print_em_start(fplog, cr, walltime_accounting, wcycle, LBFGS);
-
- do_log = do_ene = do_x = do_f = TRUE;
-
- /* Max number of steps */
- number_steps = inputrec->nsteps;
-
- /* Create a 3*natoms index to tell whether each degree of freedom is frozen */
- gf = 0;
- for (i = start; i < end; i++)
- {
- if (mdatoms->cFREEZE)
- {
- gf = mdatoms->cFREEZE[i];
- }
- for (m = 0; m < DIM; m++)
- {
- frozen[3*i+m] = inputrec->opts.nFreeze[gf][m];
- }
- }
- if (MASTER(cr))
- {
- sp_header(stderr, LBFGS, inputrec->em_tol, number_steps);
- }
- if (fplog)
- {
- sp_header(fplog, LBFGS, inputrec->em_tol, number_steps);
- }
-
- if (vsite)
- {
- construct_vsites(vsite, state->x, 1, NULL,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
- }
-
- /* Call the force routine and some auxiliary (neighboursearching etc.) */
- /* do_force always puts the charge groups in the box and shifts again
- * We do not unshift, so molecules are always whole
- */
- neval++;
- ems.s.x = state->x;
- ems.f = f;
- evaluate_energy(fplog, cr,
- top_global, &ems, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, TRUE);
- where();
-
- if (MASTER(cr))
- {
- /* Copy stuff to the energy bin for easy printing etc. */
- upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
-
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
- print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
- where();
-
- /* This is the starting energy */
- Epot = enerd->term[F_EPOT];
-
- fnorm = ems.fnorm;
- fmax = ems.fmax;
- nfmax = ems.a_fmax;
-
- /* Set the initial step.
- * since it will be multiplied by the non-normalized search direction
- * vector (force vector the first time), we scale it by the
- * norm of the force.
- */
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
- fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
- fprintf(stderr, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
- fprintf(stderr, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
- fprintf(stderr, "\n");
- /* and copy to the log file too... */
- fprintf(fplog, "Using %d BFGS correction steps.\n\n", nmaxcorr);
- fprintf(fplog, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
- fprintf(fplog, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
- fprintf(fplog, "\n");
- }
-
- // Point is an index to the memory of search directions, where 0 is the first one.
- point = 0;
-
- // Set initial search direction to the force (-gradient), or 0 for frozen particles.
- for (i = 0; i < n; i++)
- {
- if (!frozen[i])
- {
- dx[point][i] = ff[i]; /* Initial search direction */
- }
- else
- {
- dx[point][i] = 0;
- }
- }
-
- // Stepsize will be modified during the search, and actually it is not critical
- // (the main efficiency in the algorithm comes from changing directions), but
- // we still need an initial value, so estimate it as the inverse of the norm
- // so we take small steps where the potential fluctuates a lot.
- stepsize = 1.0/fnorm;
-
- /* Start the loop over BFGS steps.
- * Each successful step is counted, and we continue until
- * we either converge or reach the max number of steps.
- */
-
- ncorr = 0;
-
- /* Set the gradient from the force */
- converged = FALSE;
- for (step = 0; (number_steps < 0 || (number_steps >= 0 && step <= number_steps)) && !converged; step++)
- {
-
- /* Write coordinates if necessary */
- do_x = do_per_step(step, inputrec->nstxout);
- do_f = do_per_step(step, inputrec->nstfout);
-
- mdof_flags = 0;
- if (do_x)
- {
- mdof_flags |= MDOF_X;
- }
-
- if (do_f)
- {
- mdof_flags |= MDOF_F;
- }
-
- if (inputrec->bIMD)
- {
- mdof_flags |= MDOF_IMD;
- }
-
- mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
- top_global, step, (real)step, state, state, f, f);
-
- /* Do the linesearching in the direction dx[point][0..(n-1)] */
-
- /* make s a pointer to current search direction - point=0 first time we get here */
- s = dx[point];
-
- // calculate line gradient in position A
- for (gpa = 0, i = 0; i < n; i++)
- {
- gpa -= s[i]*ff[i];
- }
-
- /* Calculate minimum allowed stepsize along the line, before the average (norm)
- * relative change in coordinate is smaller than precision
- */
- for (minstep = 0, i = 0; i < n; i++)
- {
- tmp = fabs(xx[i]);
- if (tmp < 1.0)
- {
- tmp = 1.0;
- }
- tmp = s[i]/tmp;
- minstep += tmp*tmp;
- }
- minstep = GMX_REAL_EPS/sqrt(minstep/n);
-
- if (stepsize < minstep)
- {
- converged = TRUE;
- break;
- }
-
- // Before taking any steps along the line, store the old position
- for (i = 0; i < n; i++)
- {
- lastx[i] = xx[i];
- lastf[i] = ff[i];
- }
- Epot0 = Epot;
-
- for (i = 0; i < n; i++)
- {
- xa[i] = xx[i];
- }
-
- /* Take a step downhill.
- * In theory, we should find the actual minimum of the function in this
- * direction, somewhere along the line.
- * That is quite possible, but it turns out to take 5-10 function evaluations
- * for each line. However, we dont really need to find the exact minimum -
- * it is much better to start a new BFGS step in a modified direction as soon
- * as we are close to it. This will save a lot of energy evaluations.
- *
- * In practice, we just try to take a single step.
- * If it worked (i.e. lowered the energy), we increase the stepsize but
- * continue straight to the next BFGS step without trying to find any minimum,
- * i.e. we change the search direction too. If the line was smooth, it is
- * likely we are in a smooth region, and then it makes sense to take longer
- * steps in the modified search direction too.
- *
- * If it didn't work (higher energy), there must be a minimum somewhere between
- * the old position and the new one. Then we need to start by finding a lower
- * value before we change search direction. Since the energy was apparently
- * quite rough, we need to decrease the step size.
- *
- * Due to the finite numerical accuracy, it turns out that it is a good idea
- * to accept a SMALL increase in energy, if the derivative is still downhill.
- * This leads to lower final energies in the tests I've done. / Erik
- */
-
- // State "A" is the first position along the line.
- // reference position along line is initially zero
- EpotA = Epot0;
- a = 0.0;
-
- // Check stepsize first. We do not allow displacements
- // larger than emstep.
- //
- do
- {
- // Pick a new position C by adding stepsize to A.
- c = a + stepsize;
-
- // Calculate what the largest change in any individual coordinate
- // would be (translation along line * gradient along line)
- maxdelta = 0;
- for (i = 0; i < n; i++)
- {
- delta = c*s[i];
- if (delta > maxdelta)
- {
- maxdelta = delta;
- }
- }
- // If any displacement is larger than the stepsize limit, reduce the step
- if (maxdelta > inputrec->em_stepsize)
- {
- stepsize *= 0.1;
- }
- }
- while (maxdelta > inputrec->em_stepsize);
-
- // Take a trial step and move the coordinate array xc[] to position C
- for (i = 0; i < n; i++)
- {
- xc[i] = lastx[i] + c*s[i];
- }
-
- neval++;
- // Calculate energy for the trial step in position C
- ems.s.x = (rvec *)xc;
- ems.f = (rvec *)fc;
- evaluate_energy(fplog, cr,
- top_global, &ems, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, step, FALSE);
- EpotC = ems.epot;
-
- // Calc line gradient in position C
- for (gpc = 0, i = 0; i < n; i++)
- {
- gpc -= s[i]*fc[i]; /* f is negative gradient, thus the sign */
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpc, cr);
- }
-
- // This is the max amount of increase in energy we tolerate.
- // By allowing VERY small changes (close to numerical precision) we
- // frequently find even better (lower) final energies.
- tmp = sqrt(GMX_REAL_EPS)*fabs(EpotA);
-
- // Accept the step if the energy is lower in the new position C (compared to A),
- // or if it is not significantly higher and the line derivative is still negative.
- if (EpotC < EpotA || (gpc < 0 && EpotC < (EpotA+tmp)))
- {
- // Great, we found a better energy. We no longer try to alter the
- // stepsize, but simply accept this new better position. The we select a new
- // search direction instead, which will be much more efficient than continuing
- // to take smaller steps along a line. Set fnorm based on the new C position,
- // which will be used to update the stepsize to 1/fnorm further down.
- foundlower = TRUE;
- fnorm = ems.fnorm;
- }
- else
- {
- // If we got here, the energy is NOT lower in point C, i.e. it will be the same
- // or higher than in point A. In this case it is pointless to move to point C,
- // so we will have to do more iterations along the same line to find a smaller
- // value in the interval [A=0.0,C].
- // Here, A is still 0.0, but that will change when we do a search in the interval
- // [0.0,C] below. That search we will do by interpolation or bisection rather
- // than with the stepsize, so no need to modify it. For the next search direction
- // it will be reset to 1/fnorm anyway.
- foundlower = FALSE;
- }
-
- if (!foundlower)
- {
- // OK, if we didn't find a lower value we will have to locate one now - there must
- // be one in the interval [a,c].
- // The same thing is valid here, though: Don't spend dozens of iterations to find
- // the line minimum. We try to interpolate based on the derivative at the endpoints,
- // and only continue until we find a lower value. In most cases this means 1-2 iterations.
- // I also have a safeguard for potentially really pathological functions so we never
- // take more than 20 steps before we give up.
- // If we already found a lower value we just skip this step and continue to the update.
- nminstep = 0;
- do
- {
- // Select a new trial point B in the interval [A,C].
- // If the derivatives at points a & c have different sign we interpolate to zero,
- // otherwise just do a bisection since there might be multiple minima/maxima
- // inside the interval.
- if (gpa < 0 && gpc > 0)
- {
- b = a + gpa*(a-c)/(gpc-gpa);
- }
- else
- {
- b = 0.5*(a+c);
- }
-
- /* safeguard if interpolation close to machine accuracy causes errors:
- * never go outside the interval
- */
- if (b <= a || b >= c)
- {
- b = 0.5*(a+c);
- }
-
- // Take a trial step to point B
- for (i = 0; i < n; i++)
- {
- xb[i] = lastx[i] + b*s[i];
- }
-
- neval++;
- // Calculate energy for the trial step in point B
- ems.s.x = (rvec *)xb;
- ems.f = (rvec *)fb;
- evaluate_energy(fplog, cr,
- top_global, &ems, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, step, FALSE);
- EpotB = ems.epot;
- fnorm = ems.fnorm;
-
- // Calculate gradient in point B
- for (gpb = 0, i = 0; i < n; i++)
- {
- gpb -= s[i]*fb[i]; /* f is negative gradient, thus the sign */
-
- }
- /* Sum the gradient along the line across CPUs */
- if (PAR(cr))
- {
- gmx_sumd(1, &gpb, cr);
- }
-
- // Keep one of the intervals [A,B] or [B,C] based on the value of the derivative
- // at the new point B, and rename the endpoints of this new interval A and C.
- if (gpb > 0)
- {
- /* Replace c endpoint with b */
- EpotC = EpotB;
- c = b;
- gpc = gpb;
- /* swap coord pointers b/c */
- xtmp = xb;
- ftmp = fb;
- xb = xc;
- fb = fc;
- xc = xtmp;
- fc = ftmp;
- }
- else
- {
- /* Replace a endpoint with b */
- EpotA = EpotB;
- a = b;
- gpa = gpb;
- /* swap coord pointers a/b */
- xtmp = xb;
- ftmp = fb;
- xb = xa;
- fb = fa;
- xa = xtmp;
- fa = ftmp;
- }
-
- /*
- * Stop search as soon as we find a value smaller than the endpoints,
- * or if the tolerance is below machine precision.
- * Never run more than 20 steps, no matter what.
- */
- nminstep++;
- }
- while ((EpotB > EpotA || EpotB > EpotC) && (nminstep < 20));
-
- if (fabs(EpotB-Epot0) < GMX_REAL_EPS || nminstep >= 20)
- {
- /* OK. We couldn't find a significantly lower energy.
- * If ncorr==0 this was steepest descent, and then we give up.
- * If not, reset memory to restart as steepest descent before quitting.
- */
- if (ncorr == 0)
- {
- /* Converged */
- converged = TRUE;
- break;
- }
- else
- {
- /* Reset memory */
- ncorr = 0;
- /* Search in gradient direction */
- for (i = 0; i < n; i++)
- {
- dx[point][i] = ff[i];
- }
- /* Reset stepsize */
- stepsize = 1.0/fnorm;
- continue;
- }
- }
-
- /* Select min energy state of A & C, put the best in xx/ff/Epot
- */
- if (EpotC < EpotA)
- {
- Epot = EpotC;
- /* Use state C */
- for (i = 0; i < n; i++)
- {
- xx[i] = xc[i];
- ff[i] = fc[i];
- }
- step_taken = c;
- }
- else
- {
- Epot = EpotA;
- /* Use state A */
- for (i = 0; i < n; i++)
- {
- xx[i] = xa[i];
- ff[i] = fa[i];
- }
- step_taken = a;
- }
-
- }
- else
- {
- /* found lower */
- Epot = EpotC;
- /* Use state C */
- for (i = 0; i < n; i++)
- {
- xx[i] = xc[i];
- ff[i] = fc[i];
- }
- step_taken = c;
- }
-
- /* Update the memory information, and calculate a new
- * approximation of the inverse hessian
- */
-
- /* Have new data in Epot, xx, ff */
- if (ncorr < nmaxcorr)
- {
- ncorr++;
- }
-
- for (i = 0; i < n; i++)
- {
- dg[point][i] = lastf[i]-ff[i];
- dx[point][i] *= step_taken;
- }
-
- dgdg = 0;
- dgdx = 0;
- for (i = 0; i < n; i++)
- {
- dgdg += dg[point][i]*dg[point][i];
- dgdx += dg[point][i]*dx[point][i];
- }
-
- diag = dgdx/dgdg;
-
- rho[point] = 1.0/dgdx;
- point++;
-
- if (point >= nmaxcorr)
- {
- point = 0;
- }
-
- /* Update */
- for (i = 0; i < n; i++)
- {
- p[i] = ff[i];
- }
-
- cp = point;
-
- /* Recursive update. First go back over the memory points */
- for (k = 0; k < ncorr; k++)
- {
- cp--;
- if (cp < 0)
- {
- cp = ncorr-1;
- }
-
- sq = 0;
- for (i = 0; i < n; i++)
- {
- sq += dx[cp][i]*p[i];
- }
-
- alpha[cp] = rho[cp]*sq;
-
- for (i = 0; i < n; i++)
- {
- p[i] -= alpha[cp]*dg[cp][i];
- }
- }
-
- for (i = 0; i < n; i++)
- {
- p[i] *= diag;
- }
-
- /* And then go forward again */
- for (k = 0; k < ncorr; k++)
- {
- yr = 0;
- for (i = 0; i < n; i++)
- {
- yr += p[i]*dg[cp][i];
- }
-
- beta = rho[cp]*yr;
- beta = alpha[cp]-beta;
-
- for (i = 0; i < n; i++)
- {
- p[i] += beta*dx[cp][i];
- }
-
- cp++;
- if (cp >= ncorr)
- {
- cp = 0;
- }
- }
-
- for (i = 0; i < n; i++)
- {
- if (!frozen[i])
- {
- dx[point][i] = p[i];
- }
- else
- {
- dx[point][i] = 0;
- }
- }
-
- /* Test whether the convergence criterion is met */
- get_f_norm_max(cr, &(inputrec->opts), mdatoms, f, &fnorm, &fmax, &nfmax);
-
- /* Print it if necessary */
- if (MASTER(cr))
- {
- if (bVerbose)
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
- fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step, Epot, fnorm/sqrtNumAtoms, fmax, nfmax+1);
- }
- /* Store the new (lower) energies */
- upd_mdebin(mdebin, FALSE, FALSE, (double)step,
- mdatoms->tmass, enerd, state, inputrec->fepvals, inputrec->expandedvals, state->box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
- do_log = do_per_step(step, inputrec->nstlog);
- do_ene = do_per_step(step, inputrec->nstenergy);
- if (do_log)
- {
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
- }
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
-
- /* Send x and E to IMD client, if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state->box, state->x, inputrec, 0, wcycle) && MASTER(cr))
- {
- IMD_send_positions(inputrec->imd);
- }
-
- // Reset stepsize in we are doing more iterations
- stepsize = 1.0/fnorm;
-
- /* Stop when the maximum force lies below tolerance.
- * If we have reached machine precision, converged is already set to true.
- */
- converged = converged || (fmax < inputrec->em_tol);
-
- } /* End of the loop */
-
- /* IMD cleanup, if bIMD is TRUE. */
- IMD_finalize(inputrec->bIMD, inputrec->imd);
-
- if (converged)
- {
- step--; /* we never took that last step in this case */
-
- }
- if (fmax > inputrec->em_tol)
- {
- if (MASTER(cr))
- {
- warn_step(stderr, inputrec->em_tol, step-1 == number_steps, FALSE);
- warn_step(fplog, inputrec->em_tol, step-1 == number_steps, FALSE);
- }
- converged = FALSE;
- }
-
- /* If we printed energy and/or logfile last step (which was the last step)
- * we don't have to do it again, but otherwise print the final values.
- */
- if (!do_log) /* Write final value to log since we didn't do anythin last step */
- {
- print_ebin_header(fplog, step, step, state->lambda[efptFEP]);
- }
- if (!do_ene || !do_log) /* Write final energy file entries */
- {
- print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : NULL, step, step, eprNORMAL,
- TRUE, mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- }
-
- /* Print some stuff... */
- if (MASTER(cr))
- {
- fprintf(stderr, "\nwriting lowest energy coordinates.\n");
- }
-
- /* IMPORTANT!
- * For accurate normal mode calculation it is imperative that we
- * store the last conformation into the full precision binary trajectory.
- *
- * However, we should only do it if we did NOT already write this step
- * above (which we did if do_x or do_f was true).
- */
- do_x = !do_per_step(step, inputrec->nstxout);
- do_f = !do_per_step(step, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
- top_global, inputrec, step,
- &ems, state, f);
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state->natoms));
- print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
- number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
- print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
- number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
-
- fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
- }
-
- finish_em(cr, outf, walltime_accounting, wcycle);
-
- /* To print the actual number of steps we needed somewhere */
- walltime_accounting_set_nsteps_done(walltime_accounting, step);
-
- return 0;
-} /* That's all folks */
-
-
-double do_steep(FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
- int gmx_unused nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
- t_inputrec *inputrec,
- 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 gmx_unused ed,
- t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- const char *SD = "Steepest Descents";
- em_state_t *s_min, *s_try;
- rvec *f_global;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- real stepsize;
- real ustep, fnormn;
- gmx_mdoutf_t outf;
- t_mdebin *mdebin;
- gmx_bool bDone, bAbort, do_x, do_f;
- tensor vir, pres;
- rvec mu_tot;
- int nsteps;
- int count = 0;
- int steps_accepted = 0;
-
- s_min = init_em_state();
- s_try = init_em_state();
-
- /* Init em and store the local state in s_try */
- init_em(fplog, SD, cr, inputrec,
- state_global, top_global, s_try, &top, &f, &f_global,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
-
- /* Print to log file */
- print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
-
- /* Set variables for stepsize (in nm). This is the largest
- * step that we are going to make in any direction.
- */
- ustep = inputrec->em_stepsize;
- stepsize = 0;
-
- /* Max number of steps */
- nsteps = inputrec->nsteps;
-
- if (MASTER(cr))
- {
- /* Print to the screen */
- sp_header(stderr, SD, inputrec->em_tol, nsteps);
- }
- if (fplog)
- {
- sp_header(fplog, SD, inputrec->em_tol, nsteps);
- }
-
- /**** HERE STARTS THE LOOP ****
- * count is the counter for the number of steps
- * bDone will be TRUE when the minimization has converged
- * bAbort will be TRUE when nsteps steps have been performed or when
- * the stepsize becomes smaller than is reasonable for machine precision
- */
- count = 0;
- bDone = FALSE;
- bAbort = FALSE;
- while (!bDone && !bAbort)
- {
- bAbort = (nsteps >= 0) && (count == nsteps);
-
- /* set new coordinates, except for first step */
- if (count > 0)
- {
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
- s_min, stepsize, s_min->f, s_try,
- constr, top, nrnb, wcycle, count);
- }
-
- evaluate_energy(fplog, cr,
- top_global, s_try, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, count, count == 0);
-
- if (MASTER(cr))
- {
- print_ebin_header(fplog, count, count, s_try->s.lambda[efptFEP]);
- }
-
- if (count == 0)
- {
- s_min->epot = s_try->epot;
- }
-
- /* Print it if necessary */
- if (MASTER(cr))
- {
- if (bVerbose)
- {
- fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
- count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax+1,
- ( (count == 0) || (s_try->epot < s_min->epot) ) ? '\n' : '\r');
- }
-
- if ( (count == 0) || (s_try->epot < s_min->epot) )
- {
- /* Store the new (lower) energies */
- upd_mdebin(mdebin, FALSE, FALSE, (double)count,
- mdatoms->tmass, enerd, &s_try->s, inputrec->fepvals, inputrec->expandedvals,
- s_try->s.box, NULL, NULL, vir, pres, NULL, mu_tot, constr);
-
- /* Prepare IMD energy record, if bIMD is TRUE. */
- IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE);
-
- print_ebin(mdoutf_get_fp_ene(outf), TRUE,
- do_per_step(steps_accepted, inputrec->nstdisreout),
- do_per_step(steps_accepted, inputrec->nstorireout),
- fplog, count, count, eprNORMAL, TRUE,
- mdebin, fcd, &(top_global->groups), &(inputrec->opts));
- fflush(fplog);
- }
- }
-
- /* Now if the new energy is smaller than the previous...
- * or if this is the first step!
- * or if we did random steps!
- */
-
- if ( (count == 0) || (s_try->epot < s_min->epot) )
- {
- steps_accepted++;
-
- /* Test whether the convergence criterion is met... */
- bDone = (s_try->fmax < inputrec->em_tol);
-
- /* Copy the arrays for force, positions and energy */
- /* The 'Min' array always holds the coords and forces of the minimal
- sampled energy */
- swap_em_state(s_min, s_try);
- if (count > 0)
- {
- ustep *= 1.2;
- }
-
- /* Write to trn, if necessary */
- do_x = do_per_step(steps_accepted, inputrec->nstxout);
- do_f = do_per_step(steps_accepted, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
- top_global, inputrec, count,
- s_min, state_global, f_global);
- }
- else
- {
- /* If energy is not smaller make the step smaller... */
- ustep *= 0.5;
-
- if (DOMAINDECOMP(cr) && s_min->s.ddp_count != cr->dd->ddp_count)
- {
- /* Reload the old state */
- em_dd_partition_system(fplog, count, cr, top_global, inputrec,
- s_min, top, mdatoms, fr, vsite, constr,
- nrnb, wcycle);
- }
- }
-
- /* Determine new step */
- stepsize = ustep/s_min->fmax;
-
- /* Check if stepsize is too small, with 1 nm as a characteristic length */
-#ifdef GMX_DOUBLE
- if (count == nsteps || ustep < 1e-12)
-#else
- if (count == nsteps || ustep < 1e-6)
-#endif
- {
- if (MASTER(cr))
- {
- warn_step(stderr, inputrec->em_tol, count == nsteps, constr != NULL);
- warn_step(fplog, inputrec->em_tol, count == nsteps, constr != NULL);
- }
- bAbort = TRUE;
- }
-
- /* Send IMD energies and positions, if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, count, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
- {
- IMD_send_positions(inputrec->imd);
- }
-
- count++;
- } /* End of the loop */
-
- /* IMD cleanup, if bIMD is TRUE. */
- IMD_finalize(inputrec->bIMD, inputrec->imd);
-
- /* Print some data... */
- if (MASTER(cr))
- {
- fprintf(stderr, "\nwriting lowest energy coordinates.\n");
- }
- write_em_traj(fplog, cr, outf, TRUE, inputrec->nstfout, ftp2fn(efSTO, nfile, fnm),
- top_global, inputrec, count,
- s_min, state_global, f_global);
-
- if (MASTER(cr))
- {
- double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fnormn = s_min->fnorm/sqrtNumAtoms;
-
- print_converged(stderr, SD, inputrec->em_tol, count, bDone, nsteps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
- print_converged(fplog, SD, inputrec->em_tol, count, bDone, nsteps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
- }
-
- finish_em(cr, outf, walltime_accounting, wcycle);
-
- /* To print the actual number of steps we needed somewhere */
- inputrec->nsteps = count;
-
- walltime_accounting_set_nsteps_done(walltime_accounting, count);
-
- return 0;
-} /* That's all folks */
-
-
-double do_nm(FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const output_env_t gmx_unused oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
- int gmx_unused nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
- t_inputrec *inputrec,
- 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 gmx_unused ed,
- t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
- gmx_membed_t gmx_unused membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- const char *NM = "Normal Mode Analysis";
- gmx_mdoutf_t outf;
- int natoms, atom, d;
- int nnodes, node;
- rvec *f_global;
- gmx_localtop_t *top;
- gmx_enerdata_t *enerd;
- rvec *f;
- gmx_global_stat_t gstat;
- t_graph *graph;
- tensor vir, pres;
- rvec mu_tot;
- rvec *fneg, *dfdx;
- gmx_bool bSparse; /* use sparse matrix storage format */
- size_t sz = 0;
- gmx_sparsematrix_t * sparse_matrix = NULL;
- real * full_matrix = NULL;
- em_state_t * state_work;
-
- /* added with respect to mdrun */
- int i, j, k, row, col;
- real der_range = 10.0*sqrt(GMX_REAL_EPS);
- real x_min;
- bool bIsMaster = MASTER(cr);
-
- if (constr != NULL)
- {
- gmx_fatal(FARGS, "Constraints present with Normal Mode Analysis, this combination is not supported");
- }
-
- state_work = init_em_state();
-
- /* Init em and store the local state in state_minimum */
- init_em(fplog, NM, cr, inputrec,
- state_global, top_global, state_work, &top,
- &f, &f_global,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, NULL, imdport, Flags, wcycle);
-
- natoms = top_global->natoms;
- snew(fneg, natoms);
- snew(dfdx, natoms);
-
-#ifndef GMX_DOUBLE
- if (bIsMaster)
- {
- fprintf(stderr,
- "NOTE: This version of GROMACS has been compiled in single precision,\n"
- " which MIGHT not be accurate enough for normal mode analysis.\n"
- " GROMACS now uses sparse matrix storage, so the memory requirements\n"
- " are fairly modest even if you recompile in double precision.\n\n");
- }
-#endif
-
- /* Check if we can/should use sparse storage format.
- *
- * Sparse format is only useful when the Hessian itself is sparse, which it
- * will be when we use a cutoff.
- * For small systems (n<1000) it is easier to always use full matrix format, though.
- */
- if (EEL_FULL(fr->eeltype) || fr->rlist == 0.0)
- {
- md_print_info(cr, fplog, "Non-cutoff electrostatics used, forcing full Hessian format.\n");
- bSparse = FALSE;
- }
- else if (top_global->natoms < 1000)
- {
- md_print_info(cr, fplog, "Small system size (N=%d), using full Hessian format.\n", top_global->natoms);
- bSparse = FALSE;
- }
- else
- {
- md_print_info(cr, fplog, "Using compressed symmetric sparse Hessian format.\n");
- bSparse = TRUE;
- }
-
- if (bIsMaster)
- {
- sz = DIM*top_global->natoms;
-
- fprintf(stderr, "Allocating Hessian memory...\n\n");
-
- if (bSparse)
- {
- sparse_matrix = gmx_sparsematrix_init(sz);
- sparse_matrix->compressed_symmetric = TRUE;
- }
- else
- {
- snew(full_matrix, sz*sz);
- }
- }
-
- init_nrnb(nrnb);
-
- where();
-
- /* Write start time and temperature */
- print_em_start(fplog, cr, walltime_accounting, wcycle, NM);
-
- /* fudge nr of steps to nr of atoms */
- inputrec->nsteps = natoms*2;
-
- if (bIsMaster)
- {
- fprintf(stderr, "starting normal mode calculation '%s'\n%d steps.\n\n",
- *(top_global->name), (int)inputrec->nsteps);
- }
-
- nnodes = cr->nnodes;
-
- /* Make evaluate_energy do a single node force calculation */
- cr->nnodes = 1;
- evaluate_energy(fplog, cr,
- top_global, state_work, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, -1, TRUE);
- cr->nnodes = nnodes;
-
- /* if forces are not small, warn user */
- get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, state_work);
-
- md_print_info(cr, fplog, "Maximum force:%12.5e\n", state_work->fmax);
- if (state_work->fmax > 1.0e-3)
- {
- md_print_info(cr, fplog,
- "The force is probably not small enough to "
- "ensure that you are at a minimum.\n"
- "Be aware that negative eigenvalues may occur\n"
- "when the resulting matrix is diagonalized.\n\n");
- }
-
- /***********************************************************
- *
- * Loop over all pairs in matrix
- *
- * do_force called twice. Once with positive and
- * once with negative displacement
- *
- ************************************************************/
-
- /* Steps are divided one by one over the nodes */
- for (atom = cr->nodeid; atom < natoms; atom += nnodes)
- {
-
- for (d = 0; d < DIM; d++)
- {
- x_min = state_work->s.x[atom][d];
-
- state_work->s.x[atom][d] = x_min - der_range;
-
- /* Make evaluate_energy do a single node force calculation */
- cr->nnodes = 1;
- evaluate_energy(fplog, cr,
- top_global, state_work, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, atom*2, FALSE);
-
- for (i = 0; i < natoms; i++)
- {
- copy_rvec(state_work->f[i], fneg[i]);
- }
-
- state_work->s.x[atom][d] = x_min + der_range;
-
- evaluate_energy(fplog, cr,
- top_global, state_work, top,
- inputrec, nrnb, wcycle, gstat,
- vsite, constr, fcd, graph, mdatoms, fr,
- mu_tot, enerd, vir, pres, atom*2+1, FALSE);
- cr->nnodes = nnodes;
-
- /* x is restored to original */
- state_work->s.x[atom][d] = x_min;
-
- for (j = 0; j < natoms; j++)
- {
- for (k = 0; (k < DIM); k++)
- {
- dfdx[j][k] =
- -(state_work->f[j][k] - fneg[j][k])/(2*der_range);
- }
- }
-
- if (!bIsMaster)
- {
-#ifdef GMX_MPI
-#ifdef GMX_DOUBLE
-#define mpi_type MPI_DOUBLE
-#else
-#define mpi_type MPI_FLOAT
-#endif
- MPI_Send(dfdx[0], natoms*DIM, mpi_type, MASTERNODE(cr), cr->nodeid,
- cr->mpi_comm_mygroup);
-#endif
- }
- else
- {
- for (node = 0; (node < nnodes && atom+node < natoms); node++)
- {
- if (node > 0)
- {
-#ifdef GMX_MPI
- MPI_Status stat;
- MPI_Recv(dfdx[0], natoms*DIM, mpi_type, node, node,
- cr->mpi_comm_mygroup, &stat);
-#undef mpi_type
-#endif
- }
-
- row = (atom + node)*DIM + d;
-
- for (j = 0; j < natoms; j++)
- {
- for (k = 0; k < DIM; k++)
- {
- col = j*DIM + k;
-
- if (bSparse)
- {
- if (col >= row && dfdx[j][k] != 0.0)
- {
- gmx_sparsematrix_increment_value(sparse_matrix,
- row, col, dfdx[j][k]);
- }
- }
- else
- {
- full_matrix[row*sz+col] = dfdx[j][k];
- }
- }
- }
- }
- }
-
- if (bVerbose && fplog)
- {
- fflush(fplog);
- }
- }
- /* write progress */
- if (bIsMaster && bVerbose)
- {
- fprintf(stderr, "\rFinished step %d out of %d",
- std::min(atom+nnodes, natoms), natoms);
- fflush(stderr);
- }
- }
-
- if (bIsMaster)
- {
- fprintf(stderr, "\n\nWriting Hessian...\n");
- gmx_mtxio_write(ftp2fn(efMTX, nfile, fnm), sz, sz, full_matrix, sparse_matrix);
- }
-
- finish_em(cr, outf, walltime_accounting, wcycle);
-
- walltime_accounting_set_nsteps_done(walltime_accounting, natoms*2);
-
- return 0;
-}
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp b/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp
deleted file mode 100644
index d4bb5960fb564e760c7372ebb56cce5d280a3cd2..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp
+++ /dev/null
@@ -1,2038 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-#include "thread_mpi/threads.h"
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/domdec/domdec_network.h"
-#include "gromacs/ewald/pme-load-balancing.h"
-#include "gromacs/ewald/pme.h"
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/fileio/mdoutf.h"
-#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/fileio/trx.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/ebin.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/shellfc.h"
-#include "gromacs/legacyheaders/sighandler.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/types/constr.h"
-#include "gromacs/legacyheaders/types/enums.h"
-#include "gromacs/legacyheaders/types/fcdata.h"
-#include "gromacs/legacyheaders/types/force_flags.h"
-#include "gromacs/legacyheaders/types/forcerec.h"
-#include "gromacs/legacyheaders/types/group.h"
-#include "gromacs/legacyheaders/types/inputrec.h"
-#include "gromacs/legacyheaders/types/interaction_const.h"
-#include "gromacs/legacyheaders/types/mdatom.h"
-#include "gromacs/legacyheaders/types/membedt.h"
-#include "gromacs/legacyheaders/types/nrnb.h"
-#include "gromacs/legacyheaders/types/oenv.h"
-#include "gromacs/legacyheaders/types/shellfc.h"
-#include "gromacs/legacyheaders/types/state.h"
-#include "gromacs/listed-forces/manage-threading.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/compute_io.h"
-#include "gromacs/mdlib/mdrun_signalling.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/swap/swapcoords.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
-#include "gromacs/topology/atoms.h"
-#include "gromacs/topology/idef.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/real.h"
-#include "gromacs/utility/smalloc.h"
-
-#include "deform.h"
-#include "membed.h"
-#include "repl_ex.h"
-
-/* PLUMED */
-#include "../../../Plumed.h"
-extern int plumedswitch;
-extern plumed plumedmain;
-/* END PLUMED */
-
-/* PLUMED HREX */
-extern int plumed_hrex;
-/* END PLUMED HREX */
-
-#ifdef GMX_FAHCORE
-#include "corewrap.h"
-#endif
-
-static void reset_all_counters(FILE *fplog, t_commrec *cr,
- gmx_int64_t step,
- gmx_int64_t *step_rel, t_inputrec *ir,
- gmx_wallcycle_t wcycle, t_nrnb *nrnb,
- gmx_walltime_accounting_t walltime_accounting,
- struct nonbonded_verlet_t *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 (use_GPU(nbv))
- {
- nbnxn_gpu_reset_timings(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);
- walltime_accounting_start(walltime_accounting);
- print_date_and_time(fplog, cr->nodeid, "Restarted time", gmx_gettime());
-}
-
-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,
- int imdport,
- unsigned long Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- gmx_mdoutf_t outf = NULL;
- gmx_int64_t step, step_rel;
- double elapsed_time;
- double t, t0, lam0[efptNR];
- gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, 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;
- 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;
- matrix pcoupl_mu, M;
- t_trxframe rerun_fr;
- gmx_repl_ex_t repl_ex = NULL;
- int nchkpt = 1;
- gmx_localtop_t *top;
- t_mdebin *mdebin = NULL;
- t_state *state = NULL;
- rvec *f_global = NULL;
- gmx_enerdata_t *enerd;
- rvec *f = NULL;
- gmx_global_stat_t gstat;
- gmx_update_t upd = NULL;
- t_graph *graph = NULL;
- gmx_signalling_t gs;
- gmx_groups_t *groups;
- gmx_ekindata_t *ekind;
- gmx_shellfc_t shellfc;
- int count, nconverged = 0;
- double tcount = 0;
- gmx_bool bConverged = TRUE, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
- gmx_bool bResetCountersHalfMaxH = FALSE;
- gmx_bool bVV, bTemp, bPres, bTrotter;
- gmx_bool bUpdateDoLR;
- real dvdl_constr;
- rvec *cbuf = NULL;
- int cbuf_nalloc = 0;
- matrix lastbox;
- int lamnew = 0;
- /* for FEP */
- int nstfep = 0;
- double cycles;
- real saved_conserved_quantity = 0;
- real last_ekin = 0;
- 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_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
- simulation stops. If equal to zero, don't
- communicate any more between multisims.*/
- /* PME load balancing data for GPU kernels */
- pme_load_balancing_t *pme_loadbal = NULL;
- gmx_bool bPMETune = FALSE;
- gmx_bool bPMETunePrinting = FALSE;
-
- /* Interactive MD */
- gmx_bool bIMDstep = FALSE;
-
- /* PLUMED */
- int plumedNeedsEnergy=0;
- int plumedWantsToStop=0;
- matrix plumed_vir;
- /* END PLUMED */
-
-#ifdef GMX_FAHCORE
- /* Temporary addition for FAHCORE checkpointing */
- int chkpt_ret;
-#endif
-
- /* Check for special mdrun options */
- bRerunMD = (Flags & MD_RERUN);
- 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);
- 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 (bRerunMD)
- {
- ir->nstxout_compressed = 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, Flags, wcycle);
-
- 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);
- }
-
- /* Kinetic energy data */
- snew(ekind, 1);
- init_ekindata(fplog, top_global, &(ir->opts), ekind);
- /* 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 (shellfc && ir->nstcalcenergy != 1)
- {
- gmx_fatal(FARGS, "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is not supported in combinations with shell particles.\nPlease make a new tpr file.", ir->nstcalcenergy);
- }
- if (shellfc && DOMAINDECOMP(cr))
- {
- gmx_fatal(FARGS, "Shell particles are not implemented with domain decomposition, use a single rank");
- }
- if (shellfc && ir->eI == eiNM)
- {
- /* Currently shells don't work with Normal Modes */
- gmx_fatal(FARGS, "Normal Mode analysis is not supported with shells.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
- }
-
- if (vsite && ir->eI == eiNM)
- {
- /* Currently virtual sites don't work with Normal Modes */
- gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
- }
-
- if (DEFORM(*ir))
- {
- tMPI_Thread_mutex_lock(&deform_init_box_mutex);
- set_deform_reference_box(upd,
- deform_init_init_step_tpx,
- deform_init_box_tpx);
- tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
- }
-
- {
- 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
- {
- top = gmx_mtop_generate_local_top(top_global, ir);
-
- state = serial_init_local_state(state_global);
- f_global = f;
-
- atoms2md(top_global, ir, 0, NULL, top_global->natoms, 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);
- }
-
- setup_bonded_threading(fr, &top->idef);
- }
-
- /* Set up interactive MD (IMD) */
- init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, state_global->x,
- nfile, fnm, oenv, imdport, Flags);
-
- 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, NULL, 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 (ir->bExpanded)
- {
- init_expanded_ensemble(bStateFromCP, ir, &state->dfhist);
- }
-
- 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);
- }
-
- /* Initialize constraints */
- if (constr && !DOMAINDECOMP(cr))
- {
- set_constraints(constr, top, ir, mdatoms, cr);
- }
-
- 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 PME for Coulomb. Is is not supported
- * with only LJ PME, or for reruns.
- */
- bPMETune = ((Flags & MD_TUNEPME) && EEL_PME(fr->eeltype) && !bRerunMD &&
- !(Flags & MD_REPRODUCIBLE));
- if (bPMETune)
- {
- pme_loadbal_init(&pme_loadbal, cr, fplog, ir, state->box,
- fr->ic, fr->pmedata, use_GPU(fr->nbv),
- &bPMETunePrinting);
- }
-
- if (!ir->bContinuation && !bRerunMD)
- {
- if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
- {
- /* Set the velocities of frozen particles to zero */
- for (i = 0; i < 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,
- cr, nrnb, fr, top);
- }
- if (vsite)
- {
- /* Construct the virtual sites for the initial configuration */
- construct_vsites(vsite, state->x, ir->delta_t, NULL,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
- }
- }
-
- debug_gmx();
-
- if (IR_TWINRANGE(*ir) && repl_ex_nst % ir->nstcalclr != 0)
- {
- /* We should exchange at nstcalclr steps to get correct integration */
- gmx_fatal(FARGS, "The replica exchange period (%d) is not divisible by nstcalclr (%d)", repl_ex_nst, ir->nstcalclr);
- }
-
- if (ir->efep != efepNO)
- {
- /* Set free energy calculation frequency as the greatest common
- * denominator of nstdhdl and repl_ex_nst.
- * Check for nstcalclr with twin-range, since we need the long-range
- * contribution to the free-energy at the correct (nstcalclr) steps.
- */
- nstfep = ir->fepvals->nstdhdl;
- if (ir->bExpanded)
- {
- if (IR_TWINRANGE(*ir) &&
- ir->expandedvals->nstexpanded % ir->nstcalclr != 0)
- {
- gmx_fatal(FARGS, "nstexpanded should be divisible by nstcalclr");
- }
- nstfep = gmx_greatest_common_divisor(ir->expandedvals->nstexpanded, nstfep);
- }
- if (repl_ex_nst > 0)
- {
- nstfep = gmx_greatest_common_divisor(repl_ex_nst, nstfep);
- }
- /* We checked divisibility of repl_ex_nst and nstcalclr above */
- if (IR_TWINRANGE(*ir) && nstfep % ir->nstcalclr != 0)
- {
- gmx_incons("nstfep not divisible by nstcalclr");
- }
- }
-
- /* Be REALLY careful about what flags you set here. You CANNOT assume
- * this is the first step, since we might be restarting from a checkpoint,
- * and in that case we should not do any modifications to the state.
- */
- bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
-
- cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
- | (bStopCM ? 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, &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, &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 */
- }
-
- /* 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");
- }
-
- /* PLUMED */
- if(plumedswitch){
- /* detect plumed API version */
- int pversion=0;
- plumed_cmd(plumedmain,"getApiVersion",&pversion);
- /* setting kbT is only implemented with api>1) */
- real kbT=ir->opts.ref_t[0]*BOLTZ;
- if(pversion>1) plumed_cmd(plumedmain,"setKbT",&kbT);
- if(pversion>2){
- int res=1;
- if( (Flags & MD_STARTFROMCPT) ) plumed_cmd(plumedmain,"setRestart",&res);
- }
-
- if(cr->ms && cr->ms->nsim>1) {
- if(MASTER(cr)) plumed_cmd(plumedmain,"GREX setMPIIntercomm",&cr->ms->mpi_comm_masters);
- if(PAR(cr)){
- if(DOMAINDECOMP(cr)) {
- plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->dd->mpi_comm_all);
- }else{
- plumed_cmd(plumedmain,"GREX setMPIIntracomm",&cr->mpi_comm_mysim);
- }
- }
- plumed_cmd(plumedmain,"GREX init",NULL);
- }
- if(PAR(cr)){
- if(DOMAINDECOMP(cr)) {
- plumed_cmd(plumedmain,"setMPIComm",&cr->dd->mpi_comm_all);
- }
- }
- plumed_cmd(plumedmain,"setNatoms",&top_global->natoms);
- plumed_cmd(plumedmain,"setMDEngine","gromacs");
- plumed_cmd(plumedmain,"setLog",fplog);
- real real_delta_t;
- real_delta_t=ir->delta_t;
- plumed_cmd(plumedmain,"setTimestep",&real_delta_t);
- plumed_cmd(plumedmain,"init",NULL);
-
- if(PAR(cr)){
- if(DOMAINDECOMP(cr)) {
- plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
- plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
- }
- }
- }
- /* END PLUMED */
-
- walltime_accounting_start(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
- print_start(fplog, cr, walltime_accounting, "mdrun");
-
- /* 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;
- bSumEkinhOld = FALSE;
- bExchanged = FALSE;
- bNeedRepartition = FALSE;
-
- init_global_signals(&gs, cr, ir, repl_ex_nst);
-
- step = ir->init_step;
- step_rel = 0;
-
- if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
- {
- /* check how many steps are left in other sims */
- multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
- }
- /* PLUMED */
- // we reenable this because it is useful with Metainference
- //if (MULTISIM(cr) && max_hours > 0)
- //{
- // gmx_fatal(FARGS, "The combination of mdrun -maxh and mdrun -multi is not supported. Please use the nsteps .mdp field.");
- //}
- /* PLUMED */
-
- /* 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))
- {
-
- /* Determine if this is a neighbor search step */
- bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
-
- if (bPMETune && bNStList)
- {
- /* PME grid + cut-off optimization with GPUs or PME nodes */
- pme_loadbal_do(pme_loadbal, cr,
- (bVerbose && MASTER(cr)) ? stderr : NULL,
- fplog,
- ir, fr, state, wcycle,
- step, step_rel,
- &bPMETunePrinting);
- }
-
- 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 = ((ir->efep != efepNO) && do_per_step(step, nstfep));
- bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded)
- && (ir->bExpanded) && (step > 0) && (!bStartingFromCpt));
- }
-
- bDoReplEx = ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
- do_per_step(step, repl_ex_nst));
-
- 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 with domain decomposition, use a single rank");
- }
- 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(vsite, state->x, ir->delta_t, state->v,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, 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));
-
- 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 */
- bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
- }
-
- /* 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) && (bNStList || 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 triggers energy and virial calculation. Because this leads
- * to different code paths, forces can be different. Thus for exact
- * continuation we should avoid extra log output.
- * Note that the || bLastStep can result in non-exact continuation
- * beyond the last step. But we don't consider that to be an issue.
- */
- do_log = do_per_step(step, ir->nstlog) || (bFirstStep && !bStateFromCP) || 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 */
- 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 && !bPMETunePrinting);
-
- /* PLUMED */
- if(plumedswitch){
- plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
- plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
- }
- /* END PLUMED */
- }
- }
-
- if (MASTER(cr) && do_log)
- {
- 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, &bSumEkinhOld,
- CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
- }
- clear_mat(force_vir);
-
-/* PLUMED HREX */
- gmx_bool bHREX;
- bHREX = bDoReplEx && plumed_hrex;
-
- if(plumedswitch) if(bHREX){
- gmx_enerdata_t *hrex_enerd;
- snew(hrex_enerd,1);
- init_enerdata(top_global->groups.grps[egcENER].nr,ir->fepvals->n_lambda,hrex_enerd);
- int repl=-1;
- int nrepl=-1;
- if(MASTER(cr)){
- repl=replica_exchange_get_repl(repl_ex);
- nrepl=replica_exchange_get_nrepl(repl_ex);
- }
- if (DOMAINDECOMP(cr))
- dd_collect_state(cr->dd,state,state_global);
- else
- copy_state_nonatomdata(state, state_global);
- if(MASTER(cr)){
- if(repl%2==step/repl_ex_nst%2){
- if(repl-1>=0) exchange_state(cr->ms,repl-1,state_global);
- }else{
- if(repl+1<nrepl) exchange_state(cr->ms,repl+1,state_global);
- }
- }
- if (!DOMAINDECOMP(cr))
- copy_state_nonatomdata(state_global, state);
- if(PAR(cr)){
- if (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);
- }
- }
- do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
- state->box, state->x, &state->hist,
- f, force_vir, mdatoms, hrex_enerd, fcd,
- state->lambda, graph,
- fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
- GMX_FORCE_STATECHANGED |
- ((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
- GMX_FORCE_ALLFORCES |
- GMX_FORCE_SEPLRF |
- GMX_FORCE_VIRIAL |
- GMX_FORCE_ENERGY |
- GMX_FORCE_DHDL |
- GMX_FORCE_NS |
- ( ( fr->bTwinRange && do_per_step(step, ir->nstcalclr) ) ? GMX_FORCE_DO_LR :0) );
- plumed_cmd(plumedmain,"GREX cacheLocalUSwap",&hrex_enerd->term[F_EPOT]);
- sfree(hrex_enerd);
-
-/* exchange back */
- if (DOMAINDECOMP(cr))
- dd_collect_state(cr->dd,state,state_global);
- else
- copy_state_nonatomdata(state, state_global);
- if(MASTER(cr)){
- if(repl%2==step/repl_ex_nst%2){
- if(repl-1>=0) exchange_state(cr->ms,repl-1,state_global);
- }else{
- if(repl+1<nrepl) exchange_state(cr->ms,repl+1,state_global);
- }
- }
- if (!DOMAINDECOMP(cr))
- copy_state_nonatomdata(state_global, state);
- if(PAR(cr)){
- if (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);
- if(plumedswitch){
- plumed_cmd(plumedmain,"setAtomsNlocal",&cr->dd->nat_home);
- plumed_cmd(plumedmain,"setAtomsGatindex",cr->dd->gatindex);
- }
- }
- }
-
- }
-/* END PLUMED HREX */
-
- /* 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. */
-
- /* TODO: This is probably not what we want, we will write to energy file one step after nstcalcenergy steps. */
- bCalcEnerStep = do_per_step(step - 1, ir->nstcalcenergy);
- bCalcVir = bCalcEnerStep ||
- (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
- }
- else
- {
- bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
- bCalcVir = bCalcEnerStep ||
- (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
- }
- bCalcEner = bCalcEnerStep;
-
- do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
-
- if (do_ene || do_log || bDoReplEx)
- {
- bCalcVir = TRUE;
- bCalcEner = TRUE;
- }
-
- /* 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)));
-
- /* 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, step,
- ir, bNS, force_flags,
- top,
- constr, enerd, fcd,
- state, f, force_vir, mdatoms,
- nrnb, wcycle, graph, groups,
- shellfc, fr, bBornRadii, t, mu_tot,
- &bConverged, vsite,
- mdoutf_get_fp_field(outf));
- 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
- */
-
- /* PLUMED */
- plumedNeedsEnergy=0;
- if(plumedswitch){
- int pversion=0;
- plumed_cmd(plumedmain,"getApiVersion",&pversion);
- long int lstep=step; plumed_cmd(plumedmain,"setStepLong",&lstep);
- plumed_cmd(plumedmain,"setPositions",&state->x[0][0]);
- plumed_cmd(plumedmain,"setMasses",&mdatoms->massT[0]);
- plumed_cmd(plumedmain,"setCharges",&mdatoms->chargeA[0]);
- plumed_cmd(plumedmain,"setBox",&state->box[0][0]);
- plumed_cmd(plumedmain,"prepareCalc",NULL);
- plumed_cmd(plumedmain,"setStopFlag",&plumedWantsToStop);
- int checkp=0; if(bCPT) checkp=1;
- if(pversion>3) plumed_cmd(plumedmain,"doCheckPoint",&checkp);
- plumed_cmd(plumedmain,"setForces",&f[0][0]);
- plumed_cmd(plumedmain,"isEnergyNeeded",&plumedNeedsEnergy);
- if(plumedNeedsEnergy) force_flags |= (GMX_FORCE_ENERGY | GMX_FORCE_VIRIAL);
- clear_mat(plumed_vir);
- plumed_cmd(plumedmain,"setVirial",&plumed_vir[0][0]);
- }
- /* END PLUMED */
- do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
- state->box, state->x, &state->hist,
- f, force_vir, mdatoms, enerd, fcd,
- state->lambda, graph,
- fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
- (bNS ? GMX_FORCE_NS : 0) | force_flags);
- /* PLUMED */
- if(plumedswitch){
- if(plumedNeedsEnergy){
- msmul(force_vir,2.0,plumed_vir);
- plumed_cmd(plumedmain,"setEnergy",&enerd->term[F_EPOT]);
- plumed_cmd(plumedmain,"performCalc",NULL);
- msmul(plumed_vir,0.5,force_vir);
- } else {
- msmul(plumed_vir,0.5,plumed_vir);
- m_add(force_vir,plumed_vir,force_vir);
- }
- if(bDoReplEx) plumed_cmd(plumedmain,"GREX savePositions",NULL);
- if(plumedWantsToStop) ir->nsteps=step_rel+1;
- if(bHREX) plumed_cmd(plumedmain,"GREX cacheLocalUNow",&enerd->term[F_EPOT]);
- }
- /* END PLUMED */
- }
-
- if (bVV && !bStartingFromCpt && !bRerunMD)
- /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
- {
- rvec *vbuf = NULL;
-
- wallcycle_start(wcycle, ewcUPDATE);
- 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.
- */
- snew(vbuf, state->natoms);
- copy_rvecn(state->v, vbuf, 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.
- *
- * TODO Remove various aspects of VV+twin-range in master
- * branch, because VV integrators did not ever support
- * twin-range multiple time stepping with constraints.
- */
- bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
-
- update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
- f, bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, upd, bInitStep, etrtVELOCITY1,
- cr, nrnb, constr, &top->idef);
-
- if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- update_constraints(fplog, step, NULL, ir, mdatoms,
- state, fr->bMolPBC, graph, f,
- &top->idef, shake_vir,
- cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir);
- wallcycle_start(wcycle, ewcUPDATE);
- if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
- {
- /* Correct the virial for multiple time stepping */
- m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
- }
- }
- 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)
- {
- 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))
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- 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, &bSumEkinhOld,
- cglo_flags
- | CGLO_ENERGY
- | (bTemp ? CGLO_TEMPERATURE : 0)
- | (bPres ? CGLO_PRESSURE : 0)
- | (bPres ? CGLO_CONSTRAINT : 0)
- | (bStopCM ? CGLO_STOPCM : 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 */
- wallcycle_start(wcycle, ewcUPDATE);
- }
- /* 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)
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- /* 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, &bSumEkinhOld,
- CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
- wallcycle_start(wcycle, ewcUPDATE);
- }
- }
- }
- 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);
- 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 (ir->eI == eiVV && bInitStep)
- {
- copy_rvecn(vbuf, state->v, 0, state->natoms);
- sfree(vbuf);
- }
- wallcycle_stop(wcycle, ewcUPDATE);
- }
-
- /* 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 (ir->efep != efepNO && !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, state->fep_state, &state->dfhist, step, state->v, mdatoms);
- /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
- copy_df_history(&state_global->dfhist, &state->dfhist);
- }
-
- /* Now we have the energies and forces corresponding to the
- * coordinates at time t. We must output all of this before
- * the update.
- */
- do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
- ir, state, state_global, top_global, fr,
- outf, mdebin, ekind, f, f_global,
- &nchkpt,
- bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT),
- bSumEkinhOld);
- /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
- bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
-
- /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
- if (bStartingFromCpt && bTrotter)
- {
- copy_mat(state->svir_prev, shake_vir);
- copy_mat(state->fvir_prev, force_vir);
- }
-
- elapsed_time = walltime_accounting_get_current_elapsed_time(walltime_accounting);
-
- /* 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 && elapsed_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) &&
- elapsed_time > max_hours*60.0*60.0*0.495)
- {
- /* Set flag that will communicate the signal to all ranks in the simulation */
- gs.sig[eglsRESETCOUNTERS] = 1;
- }
-
- /* 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 ||
- elapsed_time >= nchkpt*cpt_period*60.0)) &&
- gs.set[eglsCHKPT] == 0)
- {
- gs.sig[eglsCHKPT] = 1;
- }
-
- /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen controlled
- in preprocessing */
-
- 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, cr, mdatoms, state, upd, 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, mdatoms,
- state, fr->bMolPBC, graph, f,
- &top->idef, tmp_vir,
- cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir);
- }
- }
- /* ######### 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);
-
- dvdl_constr = 0;
-
- if (!bRerunMD || rerun_fr.bV || bForceUpdate)
- {
- wallcycle_start(wcycle, ewcUPDATE);
- /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
- if (bTrotter)
- {
- 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(step, ir, state, ekind, &MassQ, mdatoms);
- update_pcouple(fplog, step, ir, state, pcoupl_mu, M, 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, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, 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)
- {
- /* We probably only need md->homenr, not state->natoms */
- if (state->natoms > cbuf_nalloc)
- {
- cbuf_nalloc = state->natoms;
- srenew(cbuf, cbuf_nalloc);
- }
- 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, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
- wallcycle_stop(wcycle, ewcUPDATE);
-
- update_constraints(fplog, step, &dvdl_constr, ir, mdatoms, state,
- fr->bMolPBC, graph, f,
- &top->idef, shake_vir,
- cr, nrnb, wcycle, upd, constr,
- FALSE, bCalcVir);
-
- if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
- {
- /* Correct the virial for multiple time stepping */
- m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
- }
-
- 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, &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, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, 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, mdatoms,
- state, fr->bMolPBC, graph, f,
- &top->idef, tmp_vir,
- cr, nrnb, wcycle, upd, NULL,
- FALSE, bCalcVir);
- }
- 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(vsite, state->x, ir->delta_t, state->v,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
-
- if (graph != NULL)
- {
- unshift_self(graph, state->box, state->x);
- }
- wallcycle_stop(wcycle, ewcVSITECONSTR);
- }
-
- /* ############## IF NOT VV, Calculate globals HERE ############ */
- /* 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)))
- {
- 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, &gs,
- (step_rel % gs.nstms == 0) &&
- (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
- lastbox,
- top_global, &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)
- | CGLO_CONSTRAINT
- );
- }
-
- /* ############# 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 (ir->efep != efepNO && (!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, f,
- pcoupl_mu, nrnb, upd);
-
- /* ################# END UPDATE STEP 2 ################# */
- /* #### We now have r(t+dt) and v(t+dt/2) ############# */
-
- /* The coordinates (x) were unshifted in update */
- if (!bGStat)
- {
- /* We will not sum ekinh_old,
- * so signal that we still have to do it.
- */
- bSumEkinhOld = TRUE;
- }
-
- /* ######### 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);
- }
- /* ######### END PREPARING EDR OUTPUT ########### */
-
- /* Output stuff */
- if (MASTER(cr))
- {
- if (fplog && do_log && bDoExpanded)
- {
- /* only needed if doing expanded ensemble */
- PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
- &state_global->dfhist, state->fep_state, ir->nstlog, step);
- }
- if (bCalcEner)
- {
- upd_mdebin(mdebin, bDoDHDL, bCalcEnerStep,
- 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);
- }
-
- gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
- gmx_bool do_or = do_per_step(step, ir->nstorireout);
-
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
- step, t,
- eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
-
- if (ir->bPull)
- {
- pull_print_output(ir->pull_work, 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 */
- /* Gets written into the state at the beginning of next loop*/
- state->fep_state = lamnew;
- }
- /* Print the remaining wall clock time for the run */
- if (MULTIMASTER(cr) &&
- (do_verbose || gmx_got_usr_signal()) &&
- !bPMETunePrinting)
- {
- if (shellfc)
- {
- fprintf(stderr, "\n");
- }
- print_time(stderr, walltime_accounting, step, ir, cr);
- }
-
- /* Ion/water position swapping.
- * Not done in last step since trajectory writing happens before this call
- * in the MD loop and exchanges would be lost anyway. */
- bNeedRepartition = FALSE;
- if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep &&
- do_per_step(step, ir->swap->nstswap))
- {
- bNeedRepartition = do_swapcoords(cr, step, t, ir, wcycle,
- bRerunMD ? rerun_fr.x : state->x,
- bRerunMD ? rerun_fr.box : state->box,
- top_global, MASTER(cr) && bVerbose, bRerunMD);
-
- if (bNeedRepartition && DOMAINDECOMP(cr))
- {
- dd_collect_state(cr->dd, state, state_global);
- }
- }
-
- /* Replica exchange */
- bExchanged = FALSE;
- if (bDoReplEx)
- {
- bExchanged = replica_exchange(fplog, cr, repl_ex,
- state_global, enerd,
- state, step, t);
- }
-
- if ( (bExchanged || bNeedRepartition) && 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);
- }
- }
-
- cycles = wallcycle_stop(wcycle, ewcSTEP);
- if (DOMAINDECOMP(cr) && wcycle)
- {
- dd_cycles_add(cr->dd, cycles, ddCyclStep);
- }
-
- if (!bRerunMD || !rerun_fr.bStep)
- {
- /* increase the MD step number */
- step++;
- step_rel++;
- }
-
- /* TODO make a counter-reset module */
- /* If it is time to reset counters, set a flag that remains
- true until counters actually get reset */
- if (step_rel == wcycle_get_reset_counters(wcycle) ||
- gs.set[eglsRESETCOUNTERS] != 0)
- {
- if (pme_loadbal_is_active(pme_loadbal))
- {
- /* Do not permit counter reset while PME load
- * balancing is active. The only purpose for resetting
- * counters is to measure reliable performance data,
- * and that can't be done before balancing
- * completes.
- *
- * TODO consider fixing this by delaying the reset
- * until after load balancing completes,
- * e.g. https://gerrit.gromacs.org/#/c/4964/2 */
- gmx_fatal(FARGS, "PME tuning was still active when attempting to "
- "reset mdrun counters at step %" GMX_PRId64 ". Try "
- "resetting counters later in the run, e.g. with gmx "
- "mdrun -resetstep.", step);
- }
- reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
- use_GPU(fr->nbv) ? fr->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 -= elapsed_time/(60.0*60.0);
- /* If mdrun -maxh -resethway was active, it can only trigger once */
- bResetCountersHalfMaxH = FALSE; /* TODO move this to where gs.sig[eglsRESETCOUNTERS] is set */
- /* Reset can only happen once, so clear the triggering flag. */
- gs.set[eglsRESETCOUNTERS] = 0;
- }
-
- /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
- IMD_prep_energies_send_positions(ir->bIMD && MASTER(cr), bIMDstep, ir->imd, enerd, step, bCalcEner, wcycle);
-
- }
- /* End of main MD loop */
- debug_gmx();
-
- /* Closing TNG files can include compressing data. Therefore it is good to do that
- * before stopping the time measurements. */
- mdoutf_tng_close(outf);
-
- /* Stop measuring walltime */
- walltime_accounting_end(walltime_accounting);
-
- 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(mdoutf_get_fp_ene(outf), FALSE, FALSE, FALSE, fplog, step, t,
- eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
- }
- }
-
- done_mdoutf(outf);
- debug_gmx();
-
- if (bPMETune)
- {
- pme_loadbal_done(pme_loadbal, cr, fplog, use_GPU(fr->nbv));
- }
-
- 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);
- }
-
- /* IMD cleanup, if bIMD is TRUE. */
- IMD_finalize(ir->bIMD, ir->imd);
-
- walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
-
- return 0;
-}
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp.preplumed b/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp.preplumed
deleted file mode 100644
index afa3d62a75a4e225841c05283444184851e8fa20..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/md.cpp.preplumed
+++ /dev/null
@@ -1,1846 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-
-#include "thread_mpi/threads.h"
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/domdec/domdec_network.h"
-#include "gromacs/ewald/pme-load-balancing.h"
-#include "gromacs/ewald/pme.h"
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/fileio/mdoutf.h"
-#include "gromacs/fileio/trajectory_writing.h"
-#include "gromacs/fileio/trx.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/ebin.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/shellfc.h"
-#include "gromacs/legacyheaders/sighandler.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/tgroup.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/vcm.h"
-#include "gromacs/legacyheaders/vsite.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/types/constr.h"
-#include "gromacs/legacyheaders/types/enums.h"
-#include "gromacs/legacyheaders/types/fcdata.h"
-#include "gromacs/legacyheaders/types/force_flags.h"
-#include "gromacs/legacyheaders/types/forcerec.h"
-#include "gromacs/legacyheaders/types/group.h"
-#include "gromacs/legacyheaders/types/inputrec.h"
-#include "gromacs/legacyheaders/types/interaction_const.h"
-#include "gromacs/legacyheaders/types/mdatom.h"
-#include "gromacs/legacyheaders/types/membedt.h"
-#include "gromacs/legacyheaders/types/nrnb.h"
-#include "gromacs/legacyheaders/types/oenv.h"
-#include "gromacs/legacyheaders/types/shellfc.h"
-#include "gromacs/legacyheaders/types/state.h"
-#include "gromacs/listed-forces/manage-threading.h"
-#include "gromacs/math/utilities.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/compute_io.h"
-#include "gromacs/mdlib/mdrun_signalling.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
-#include "gromacs/pbcutil/mshift.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/swap/swapcoords.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/timing/walltime_accounting.h"
-#include "gromacs/topology/atoms.h"
-#include "gromacs/topology/idef.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/real.h"
-#include "gromacs/utility/smalloc.h"
-
-#include "deform.h"
-#include "membed.h"
-#include "repl_ex.h"
-
-#ifdef GMX_FAHCORE
-#include "corewrap.h"
-#endif
-
-static void reset_all_counters(FILE *fplog, t_commrec *cr,
- gmx_int64_t step,
- gmx_int64_t *step_rel, t_inputrec *ir,
- gmx_wallcycle_t wcycle, t_nrnb *nrnb,
- gmx_walltime_accounting_t walltime_accounting,
- struct nonbonded_verlet_t *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 (use_GPU(nbv))
- {
- nbnxn_gpu_reset_timings(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);
- walltime_accounting_start(walltime_accounting);
- print_date_and_time(fplog, cr->nodeid, "Restarted time", gmx_gettime());
-}
-
-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,
- int imdport,
- unsigned long Flags,
- gmx_walltime_accounting_t walltime_accounting)
-{
- gmx_mdoutf_t outf = NULL;
- gmx_int64_t step, step_rel;
- double elapsed_time;
- double t, t0, lam0[efptNR];
- gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, 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;
- 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;
- matrix pcoupl_mu, M;
- t_trxframe rerun_fr;
- gmx_repl_ex_t repl_ex = NULL;
- int nchkpt = 1;
- gmx_localtop_t *top;
- t_mdebin *mdebin = NULL;
- t_state *state = NULL;
- rvec *f_global = NULL;
- gmx_enerdata_t *enerd;
- rvec *f = NULL;
- gmx_global_stat_t gstat;
- gmx_update_t upd = NULL;
- t_graph *graph = NULL;
- gmx_signalling_t gs;
- gmx_groups_t *groups;
- gmx_ekindata_t *ekind;
- gmx_shellfc_t shellfc;
- int count, nconverged = 0;
- double tcount = 0;
- gmx_bool bConverged = TRUE, bSumEkinhOld, bDoReplEx, bExchanged, bNeedRepartition;
- gmx_bool bResetCountersHalfMaxH = FALSE;
- gmx_bool bVV, bTemp, bPres, bTrotter;
- gmx_bool bUpdateDoLR;
- real dvdl_constr;
- rvec *cbuf = NULL;
- int cbuf_nalloc = 0;
- matrix lastbox;
- int lamnew = 0;
- /* for FEP */
- int nstfep = 0;
- double cycles;
- real saved_conserved_quantity = 0;
- real last_ekin = 0;
- 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_int64_t multisim_nsteps = -1; /* number of steps to do before first multisim
- simulation stops. If equal to zero, don't
- communicate any more between multisims.*/
- /* PME load balancing data for GPU kernels */
- pme_load_balancing_t *pme_loadbal = NULL;
- gmx_bool bPMETune = FALSE;
- gmx_bool bPMETunePrinting = FALSE;
-
- /* Interactive MD */
- gmx_bool bIMDstep = FALSE;
-
-#ifdef GMX_FAHCORE
- /* Temporary addition for FAHCORE checkpointing */
- int chkpt_ret;
-#endif
-
- /* Check for special mdrun options */
- bRerunMD = (Flags & MD_RERUN);
- 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);
- 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 (bRerunMD)
- {
- ir->nstxout_compressed = 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, Flags, wcycle);
-
- 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);
- }
-
- /* Kinetic energy data */
- snew(ekind, 1);
- init_ekindata(fplog, top_global, &(ir->opts), ekind);
- /* 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 (shellfc && ir->nstcalcenergy != 1)
- {
- gmx_fatal(FARGS, "You have nstcalcenergy set to a value (%d) that is different from 1.\nThis is not supported in combinations with shell particles.\nPlease make a new tpr file.", ir->nstcalcenergy);
- }
- if (shellfc && DOMAINDECOMP(cr))
- {
- gmx_fatal(FARGS, "Shell particles are not implemented with domain decomposition, use a single rank");
- }
- if (shellfc && ir->eI == eiNM)
- {
- /* Currently shells don't work with Normal Modes */
- gmx_fatal(FARGS, "Normal Mode analysis is not supported with shells.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
- }
-
- if (vsite && ir->eI == eiNM)
- {
- /* Currently virtual sites don't work with Normal Modes */
- gmx_fatal(FARGS, "Normal Mode analysis is not supported with virtual sites.\nIf you'd like to help with adding support, we have an open discussion at http://redmine.gromacs.org/issues/879\n");
- }
-
- if (DEFORM(*ir))
- {
- tMPI_Thread_mutex_lock(&deform_init_box_mutex);
- set_deform_reference_box(upd,
- deform_init_init_step_tpx,
- deform_init_box_tpx);
- tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
- }
-
- {
- 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
- {
- top = gmx_mtop_generate_local_top(top_global, ir);
-
- state = serial_init_local_state(state_global);
- f_global = f;
-
- atoms2md(top_global, ir, 0, NULL, top_global->natoms, 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);
- }
-
- setup_bonded_threading(fr, &top->idef);
- }
-
- /* Set up interactive MD (IMD) */
- init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, state_global->x,
- nfile, fnm, oenv, imdport, Flags);
-
- 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, NULL, 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 (ir->bExpanded)
- {
- init_expanded_ensemble(bStateFromCP, ir, &state->dfhist);
- }
-
- 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);
- }
-
- /* Initialize constraints */
- if (constr && !DOMAINDECOMP(cr))
- {
- set_constraints(constr, top, ir, mdatoms, cr);
- }
-
- 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 PME for Coulomb. Is is not supported
- * with only LJ PME, or for reruns.
- */
- bPMETune = ((Flags & MD_TUNEPME) && EEL_PME(fr->eeltype) && !bRerunMD &&
- !(Flags & MD_REPRODUCIBLE));
- if (bPMETune)
- {
- pme_loadbal_init(&pme_loadbal, cr, fplog, ir, state->box,
- fr->ic, fr->pmedata, use_GPU(fr->nbv),
- &bPMETunePrinting);
- }
-
- if (!ir->bContinuation && !bRerunMD)
- {
- if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
- {
- /* Set the velocities of frozen particles to zero */
- for (i = 0; i < 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,
- cr, nrnb, fr, top);
- }
- if (vsite)
- {
- /* Construct the virtual sites for the initial configuration */
- construct_vsites(vsite, state->x, ir->delta_t, NULL,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
- }
- }
-
- debug_gmx();
-
- if (IR_TWINRANGE(*ir) && repl_ex_nst % ir->nstcalclr != 0)
- {
- /* We should exchange at nstcalclr steps to get correct integration */
- gmx_fatal(FARGS, "The replica exchange period (%d) is not divisible by nstcalclr (%d)", repl_ex_nst, ir->nstcalclr);
- }
-
- if (ir->efep != efepNO)
- {
- /* Set free energy calculation frequency as the greatest common
- * denominator of nstdhdl and repl_ex_nst.
- * Check for nstcalclr with twin-range, since we need the long-range
- * contribution to the free-energy at the correct (nstcalclr) steps.
- */
- nstfep = ir->fepvals->nstdhdl;
- if (ir->bExpanded)
- {
- if (IR_TWINRANGE(*ir) &&
- ir->expandedvals->nstexpanded % ir->nstcalclr != 0)
- {
- gmx_fatal(FARGS, "nstexpanded should be divisible by nstcalclr");
- }
- nstfep = gmx_greatest_common_divisor(ir->expandedvals->nstexpanded, nstfep);
- }
- if (repl_ex_nst > 0)
- {
- nstfep = gmx_greatest_common_divisor(repl_ex_nst, nstfep);
- }
- /* We checked divisibility of repl_ex_nst and nstcalclr above */
- if (IR_TWINRANGE(*ir) && nstfep % ir->nstcalclr != 0)
- {
- gmx_incons("nstfep not divisible by nstcalclr");
- }
- }
-
- /* Be REALLY careful about what flags you set here. You CANNOT assume
- * this is the first step, since we might be restarting from a checkpoint,
- * and in that case we should not do any modifications to the state.
- */
- bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
-
- cglo_flags = (CGLO_TEMPERATURE | CGLO_GSTAT
- | (bStopCM ? 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, &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, &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 */
- }
-
- /* 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");
- }
-
- walltime_accounting_start(walltime_accounting);
- wallcycle_start(wcycle, ewcRUN);
- print_start(fplog, cr, walltime_accounting, "mdrun");
-
- /* 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;
- bSumEkinhOld = FALSE;
- bExchanged = FALSE;
- bNeedRepartition = FALSE;
-
- init_global_signals(&gs, cr, ir, repl_ex_nst);
-
- step = ir->init_step;
- step_rel = 0;
-
- if (MULTISIM(cr) && (repl_ex_nst <= 0 ))
- {
- /* check how many steps are left in other sims */
- multisim_nsteps = get_multisim_nsteps(cr, ir->nsteps);
- }
- if (MULTISIM(cr) && max_hours > 0)
- {
- gmx_fatal(FARGS, "The combination of mdrun -maxh and mdrun -multi is not supported. Please use the nsteps .mdp field.");
- }
-
- /* 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))
- {
-
- /* Determine if this is a neighbor search step */
- bNStList = (ir->nstlist > 0 && step % ir->nstlist == 0);
-
- if (bPMETune && bNStList)
- {
- /* PME grid + cut-off optimization with GPUs or PME nodes */
- pme_loadbal_do(pme_loadbal, cr,
- (bVerbose && MASTER(cr)) ? stderr : NULL,
- fplog,
- ir, fr, state, wcycle,
- step, step_rel,
- &bPMETunePrinting);
- }
-
- 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 = ((ir->efep != efepNO) && do_per_step(step, nstfep));
- bDoExpanded = (do_per_step(step, ir->expandedvals->nstexpanded)
- && (ir->bExpanded) && (step > 0) && (!bStartingFromCpt));
- }
-
- bDoReplEx = ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
- do_per_step(step, repl_ex_nst));
-
- 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 with domain decomposition, use a single rank");
- }
- 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(vsite, state->x, ir->delta_t, state->v,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, 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));
-
- 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 */
- bNS = (bFirstStep || bNStList || bExchanged || bNeedRepartition);
- }
-
- /* 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) && (bNStList || 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 triggers energy and virial calculation. Because this leads
- * to different code paths, forces can be different. Thus for exact
- * continuation we should avoid extra log output.
- * Note that the || bLastStep can result in non-exact continuation
- * beyond the last step. But we don't consider that to be an issue.
- */
- do_log = do_per_step(step, ir->nstlog) || (bFirstStep && !bStateFromCP) || 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 */
- 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 && !bPMETunePrinting);
- }
- }
-
- if (MASTER(cr) && do_log)
- {
- 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, &bSumEkinhOld,
- CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
- }
- clear_mat(force_vir);
-
- /* 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. */
-
- /* TODO: This is probably not what we want, we will write to energy file one step after nstcalcenergy steps. */
- bCalcEnerStep = do_per_step(step - 1, ir->nstcalcenergy);
- bCalcVir = bCalcEnerStep ||
- (ir->epc != epcNO && (do_per_step(step, ir->nstpcouple) || do_per_step(step-1, ir->nstpcouple)));
- }
- else
- {
- bCalcEnerStep = do_per_step(step, ir->nstcalcenergy);
- bCalcVir = bCalcEnerStep ||
- (ir->epc != epcNO && do_per_step(step, ir->nstpcouple));
- }
- bCalcEner = bCalcEnerStep;
-
- do_ene = (do_per_step(step, ir->nstenergy) || bLastStep);
-
- if (do_ene || do_log || bDoReplEx)
- {
- bCalcVir = TRUE;
- bCalcEner = TRUE;
- }
-
- /* 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)));
-
- /* 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, step,
- ir, bNS, force_flags,
- top,
- constr, enerd, fcd,
- state, f, force_vir, mdatoms,
- nrnb, wcycle, graph, groups,
- shellfc, fr, bBornRadii, t, mu_tot,
- &bConverged, vsite,
- mdoutf_get_fp_field(outf));
- 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, groups,
- state->box, state->x, &state->hist,
- f, force_vir, mdatoms, enerd, fcd,
- state->lambda, graph,
- fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
- (bNS ? GMX_FORCE_NS : 0) | force_flags);
- }
-
- if (bVV && !bStartingFromCpt && !bRerunMD)
- /* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
- {
- rvec *vbuf = NULL;
-
- wallcycle_start(wcycle, ewcUPDATE);
- 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.
- */
- snew(vbuf, state->natoms);
- copy_rvecn(state->v, vbuf, 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.
- *
- * TODO Remove various aspects of VV+twin-range in master
- * branch, because VV integrators did not ever support
- * twin-range multiple time stepping with constraints.
- */
- bUpdateDoLR = (fr->bTwinRange && do_per_step(step, ir->nstcalclr));
-
- update_coords(fplog, step, ir, mdatoms, state, fr->bMolPBC,
- f, bUpdateDoLR, fr->f_twin, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, upd, bInitStep, etrtVELOCITY1,
- cr, nrnb, constr, &top->idef);
-
- if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- update_constraints(fplog, step, NULL, ir, mdatoms,
- state, fr->bMolPBC, graph, f,
- &top->idef, shake_vir,
- cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir);
- wallcycle_start(wcycle, ewcUPDATE);
- if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
- {
- /* Correct the virial for multiple time stepping */
- m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
- }
- }
- 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)
- {
- 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))
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- 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, &bSumEkinhOld,
- cglo_flags
- | CGLO_ENERGY
- | (bTemp ? CGLO_TEMPERATURE : 0)
- | (bPres ? CGLO_PRESSURE : 0)
- | (bPres ? CGLO_CONSTRAINT : 0)
- | (bStopCM ? CGLO_STOPCM : 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 */
- wallcycle_start(wcycle, ewcUPDATE);
- }
- /* 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)
- {
- wallcycle_stop(wcycle, ewcUPDATE);
- /* 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, &bSumEkinhOld,
- CGLO_RERUNMD | CGLO_GSTAT | CGLO_TEMPERATURE);
- wallcycle_start(wcycle, ewcUPDATE);
- }
- }
- }
- 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);
- 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 (ir->eI == eiVV && bInitStep)
- {
- copy_rvecn(vbuf, state->v, 0, state->natoms);
- sfree(vbuf);
- }
- wallcycle_stop(wcycle, ewcUPDATE);
- }
-
- /* 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 (ir->efep != efepNO && !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, state->fep_state, &state->dfhist, step, state->v, mdatoms);
- /* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
- copy_df_history(&state_global->dfhist, &state->dfhist);
- }
-
- /* Now we have the energies and forces corresponding to the
- * coordinates at time t. We must output all of this before
- * the update.
- */
- do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
- ir, state, state_global, top_global, fr,
- outf, mdebin, ekind, f, f_global,
- &nchkpt,
- bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT),
- bSumEkinhOld);
- /* Check if IMD step and do IMD communication, if bIMD is TRUE. */
- bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
-
- /* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
- if (bStartingFromCpt && bTrotter)
- {
- copy_mat(state->svir_prev, shake_vir);
- copy_mat(state->fvir_prev, force_vir);
- }
-
- elapsed_time = walltime_accounting_get_current_elapsed_time(walltime_accounting);
-
- /* 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 && elapsed_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) &&
- elapsed_time > max_hours*60.0*60.0*0.495)
- {
- /* Set flag that will communicate the signal to all ranks in the simulation */
- gs.sig[eglsRESETCOUNTERS] = 1;
- }
-
- /* 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 ||
- elapsed_time >= nchkpt*cpt_period*60.0)) &&
- gs.set[eglsCHKPT] == 0)
- {
- gs.sig[eglsCHKPT] = 1;
- }
-
- /* at the start of step, randomize or scale the velocities ((if vv. Restriction of Andersen controlled
- in preprocessing */
-
- 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, cr, mdatoms, state, upd, 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, mdatoms,
- state, fr->bMolPBC, graph, f,
- &top->idef, tmp_vir,
- cr, nrnb, wcycle, upd, constr,
- TRUE, bCalcVir);
- }
- }
- /* ######### 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);
-
- dvdl_constr = 0;
-
- if (!bRerunMD || rerun_fr.bV || bForceUpdate)
- {
- wallcycle_start(wcycle, ewcUPDATE);
- /* UPDATE PRESSURE VARIABLES IN TROTTER FORMULATION WITH CONSTRAINTS */
- if (bTrotter)
- {
- 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(step, ir, state, ekind, &MassQ, mdatoms);
- update_pcouple(fplog, step, ir, state, pcoupl_mu, M, 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, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, 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)
- {
- /* We probably only need md->homenr, not state->natoms */
- if (state->natoms > cbuf_nalloc)
- {
- cbuf_nalloc = state->natoms;
- srenew(cbuf, cbuf_nalloc);
- }
- 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, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, upd, bInitStep, etrtPOSITION, cr, nrnb, constr, &top->idef);
- wallcycle_stop(wcycle, ewcUPDATE);
-
- update_constraints(fplog, step, &dvdl_constr, ir, mdatoms, state,
- fr->bMolPBC, graph, f,
- &top->idef, shake_vir,
- cr, nrnb, wcycle, upd, constr,
- FALSE, bCalcVir);
-
- if (bCalcVir && bUpdateDoLR && ir->nstcalclr > 1)
- {
- /* Correct the virial for multiple time stepping */
- m_sub(shake_vir, fr->vir_twin_constr, shake_vir);
- }
-
- 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, &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, bCalcVir ? &fr->vir_twin_constr : NULL, fcd,
- ekind, M, 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, mdatoms,
- state, fr->bMolPBC, graph, f,
- &top->idef, tmp_vir,
- cr, nrnb, wcycle, upd, NULL,
- FALSE, bCalcVir);
- }
- 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(vsite, state->x, ir->delta_t, state->v,
- top->idef.iparams, top->idef.il,
- fr->ePBC, fr->bMolPBC, cr, state->box);
-
- if (graph != NULL)
- {
- unshift_self(graph, state->box, state->x);
- }
- wallcycle_stop(wcycle, ewcVSITECONSTR);
- }
-
- /* ############## IF NOT VV, Calculate globals HERE ############ */
- /* 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)))
- {
- 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, &gs,
- (step_rel % gs.nstms == 0) &&
- (multisim_nsteps < 0 || (step_rel < multisim_nsteps)),
- lastbox,
- top_global, &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)
- | CGLO_CONSTRAINT
- );
- }
-
- /* ############# 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 (ir->efep != efepNO && (!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, f,
- pcoupl_mu, nrnb, upd);
-
- /* ################# END UPDATE STEP 2 ################# */
- /* #### We now have r(t+dt) and v(t+dt/2) ############# */
-
- /* The coordinates (x) were unshifted in update */
- if (!bGStat)
- {
- /* We will not sum ekinh_old,
- * so signal that we still have to do it.
- */
- bSumEkinhOld = TRUE;
- }
-
- /* ######### 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);
- }
- /* ######### END PREPARING EDR OUTPUT ########### */
-
- /* Output stuff */
- if (MASTER(cr))
- {
- if (fplog && do_log && bDoExpanded)
- {
- /* only needed if doing expanded ensemble */
- PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
- &state_global->dfhist, state->fep_state, ir->nstlog, step);
- }
- if (bCalcEner)
- {
- upd_mdebin(mdebin, bDoDHDL, bCalcEnerStep,
- 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);
- }
-
- gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
- gmx_bool do_or = do_per_step(step, ir->nstorireout);
-
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
- step, t,
- eprNORMAL, bCompact, mdebin, fcd, groups, &(ir->opts));
-
- if (ir->bPull)
- {
- pull_print_output(ir->pull_work, 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 */
- /* Gets written into the state at the beginning of next loop*/
- state->fep_state = lamnew;
- }
- /* Print the remaining wall clock time for the run */
- if (MULTIMASTER(cr) &&
- (do_verbose || gmx_got_usr_signal()) &&
- !bPMETunePrinting)
- {
- if (shellfc)
- {
- fprintf(stderr, "\n");
- }
- print_time(stderr, walltime_accounting, step, ir, cr);
- }
-
- /* Ion/water position swapping.
- * Not done in last step since trajectory writing happens before this call
- * in the MD loop and exchanges would be lost anyway. */
- bNeedRepartition = FALSE;
- if ((ir->eSwapCoords != eswapNO) && (step > 0) && !bLastStep &&
- do_per_step(step, ir->swap->nstswap))
- {
- bNeedRepartition = do_swapcoords(cr, step, t, ir, wcycle,
- bRerunMD ? rerun_fr.x : state->x,
- bRerunMD ? rerun_fr.box : state->box,
- top_global, MASTER(cr) && bVerbose, bRerunMD);
-
- if (bNeedRepartition && DOMAINDECOMP(cr))
- {
- dd_collect_state(cr->dd, state, state_global);
- }
- }
-
- /* Replica exchange */
- bExchanged = FALSE;
- if (bDoReplEx)
- {
- bExchanged = replica_exchange(fplog, cr, repl_ex,
- state_global, enerd,
- state, step, t);
- }
-
- if ( (bExchanged || bNeedRepartition) && 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);
- }
- }
-
- cycles = wallcycle_stop(wcycle, ewcSTEP);
- if (DOMAINDECOMP(cr) && wcycle)
- {
- dd_cycles_add(cr->dd, cycles, ddCyclStep);
- }
-
- if (!bRerunMD || !rerun_fr.bStep)
- {
- /* increase the MD step number */
- step++;
- step_rel++;
- }
-
- /* TODO make a counter-reset module */
- /* If it is time to reset counters, set a flag that remains
- true until counters actually get reset */
- if (step_rel == wcycle_get_reset_counters(wcycle) ||
- gs.set[eglsRESETCOUNTERS] != 0)
- {
- if (pme_loadbal_is_active(pme_loadbal))
- {
- /* Do not permit counter reset while PME load
- * balancing is active. The only purpose for resetting
- * counters is to measure reliable performance data,
- * and that can't be done before balancing
- * completes.
- *
- * TODO consider fixing this by delaying the reset
- * until after load balancing completes,
- * e.g. https://gerrit.gromacs.org/#/c/4964/2 */
- gmx_fatal(FARGS, "PME tuning was still active when attempting to "
- "reset mdrun counters at step %" GMX_PRId64 ". Try "
- "resetting counters later in the run, e.g. with gmx "
- "mdrun -resetstep.", step);
- }
- reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
- use_GPU(fr->nbv) ? fr->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 -= elapsed_time/(60.0*60.0);
- /* If mdrun -maxh -resethway was active, it can only trigger once */
- bResetCountersHalfMaxH = FALSE; /* TODO move this to where gs.sig[eglsRESETCOUNTERS] is set */
- /* Reset can only happen once, so clear the triggering flag. */
- gs.set[eglsRESETCOUNTERS] = 0;
- }
-
- /* If bIMD is TRUE, the master updates the IMD energy record and sends positions to VMD client */
- IMD_prep_energies_send_positions(ir->bIMD && MASTER(cr), bIMDstep, ir->imd, enerd, step, bCalcEner, wcycle);
-
- }
- /* End of main MD loop */
- debug_gmx();
-
- /* Closing TNG files can include compressing data. Therefore it is good to do that
- * before stopping the time measurements. */
- mdoutf_tng_close(outf);
-
- /* Stop measuring walltime */
- walltime_accounting_end(walltime_accounting);
-
- 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(mdoutf_get_fp_ene(outf), FALSE, FALSE, FALSE, fplog, step, t,
- eprAVER, FALSE, mdebin, fcd, groups, &(ir->opts));
- }
- }
-
- done_mdoutf(outf);
- debug_gmx();
-
- if (bPMETune)
- {
- pme_loadbal_done(pme_loadbal, cr, fplog, use_GPU(fr->nbv));
- }
-
- 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);
- }
-
- /* IMD cleanup, if bIMD is TRUE. */
- IMD_finalize(ir->bIMD, ir->imd);
-
- walltime_accounting_set_nsteps_done(walltime_accounting, step_rel);
-
- return 0;
-}
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/mdrun.cpp b/patches/gromacs-5.1.4.diff/src/programs/mdrun/mdrun.cpp
deleted file mode 100644
index 1ef58aedc6e29dbcccf927e349d8597b2293c3ec..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/mdrun.cpp
+++ /dev/null
@@ -1,602 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \defgroup module_mdrun Implementation of mdrun
- * \ingroup group_mdrun
- *
- * \brief This module contains code that implements mdrun.
- */
-/*! \internal \file
- *
- * \brief This file implements mdrun
- *
- * \author Berk Hess <hess@kth.se>
- * \author David van der Spoel <david.vanderspoel@icm.uu.se>
- * \author Erik Lindahl <erik@kth.se>
- * \author Mark Abraham <mark.j.abraham@gmail.com>
- *
- * \ingroup module_mdrun
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <stdio.h>
-#include <string.h>
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/mdrunutility/handlerestart.h"
-#include "gromacs/utility/fatalerror.h"
-
-#include "mdrun_main.h"
-
-/* PLUMED */
-#include "../../../Plumed.h"
-extern int plumedswitch;
-extern plumed plumedmain;
-extern void(*plumedcmd)(plumed,const char*,const void*);
-/* END PLUMED */
-
-/* PLUMED HREX */
-int plumed_hrex;
-/* END PLUMED HREX */
-
-/*! \brief Return whether either of the command-line parameters that
- * will trigger a multi-simulation is set */
-static bool is_multisim_option_set(int argc, const char *const argv[])
-{
- for (int i = 0; i < argc; ++i)
- {
- if (strcmp(argv[i], "-multi") == 0 || strcmp(argv[i], "-multidir") == 0)
- {
- return true;
- }
- }
- return false;
-}
-
-//! Implements C-style main function for mdrun
-int gmx_mdrun(int argc, char *argv[])
-{
- const char *desc[] = {
- "[THISMODULE] is the main computational chemistry engine",
- "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
- "but it can also perform Stochastic Dynamics, Energy Minimization,",
- "test particle insertion or (re)calculation of energies.",
- "Normal mode analysis is another option. In this case [TT]mdrun[tt]",
- "builds a Hessian matrix from single conformation.",
- "For usual Normal Modes-like calculations, make sure that",
- "the structure provided is properly energy-minimized.",
- "The generated matrix can be diagonalized by [gmx-nmeig].[PAR]",
- "The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
- "and distributes the topology over ranks if needed.",
- "[TT]mdrun[tt] produces at least four output files.",
- "A single log file ([TT]-g[tt]) is written.",
- "The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
- "optionally forces.",
- "The structure file ([TT]-c[tt]) contains the coordinates and",
- "velocities of the last step.",
- "The energy file ([TT]-e[tt]) contains energies, the temperature,",
- "pressure, etc, a lot of these things are also printed in the log file.",
- "Optionally coordinates can be written to a compressed trajectory file",
- "([TT]-x[tt]).[PAR]",
- "The option [TT]-dhdl[tt] is only used when free energy calculation is",
- "turned on.[PAR]",
- "Running mdrun efficiently in parallel is a complex topic topic,",
- "many aspects of which are covered in the online User Guide. You",
- "should look there for practical advice on using many of the options",
- "available in mdrun.[PAR]",
- "ED (essential dynamics) sampling and/or additional flooding potentials",
- "are switched on by using the [TT]-ei[tt] flag followed by an [REF].edi[ref]",
- "file. The [REF].edi[ref] file can be produced with the [TT]make_edi[tt] tool",
- "or by using options in the essdyn menu of the WHAT IF program.",
- "[TT]mdrun[tt] produces a [REF].xvg[ref] output file that",
- "contains projections of positions, velocities and forces onto selected",
- "eigenvectors.[PAR]",
- "When user-defined potential functions have been selected in the",
- "[REF].mdp[ref] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
- "a formatted table with potential functions. The file is read from",
- "either the current directory or from the [TT]GMXLIB[tt] directory.",
- "A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
- "for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
- "normal Coulomb.",
- "When pair interactions are present, a separate table for pair interaction",
- "functions is read using the [TT]-tablep[tt] option.[PAR]",
- "When tabulated bonded functions are present in the topology,",
- "interaction functions are read using the [TT]-tableb[tt] option.",
- "For each different tabulated interaction type used, a table file name must",
- "be given. For the topology to work, a file name given here must match a",
- "character sequence before the file extension. That sequence is: an underscore,",
- "then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals,",
- "and finally the matching table number index used in the topology.[PAR]",
- "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
- "coordinates and forces when pulling is selected",
- "in the [REF].mdp[ref] file.[PAR]",
- "Finally some experimental algorithms can be tested when the",
- "appropriate options have been given. Currently under",
- "investigation are: polarizability.",
- "[PAR]",
- "The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
- "a protein into a membrane. This module requires a number of settings",
- "that are provided in a data file that is the argument of this option.",
- "For more details in membrane embedding, see the documentation in the",
- "user guide. The options [TT]-mn[tt] and [TT]-mp[tt] are used to provide",
- "the index and topology files used for the embedding.",
- "[PAR]",
- "The option [TT]-pforce[tt] is useful when you suspect a simulation",
- "crashes due to too large forces. With this option coordinates and",
- "forces of atoms with a force larger than a certain value will",
- "be printed to stderr.",
- "[PAR]",
- "Checkpoints containing the complete state of the system are written",
- "at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
- "unless option [TT]-cpt[tt] is set to -1.",
- "The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
- "make sure that a recent state of the system is always available,",
- "even when the simulation is terminated while writing a checkpoint.",
- "With [TT]-cpnum[tt] all checkpoint files are kept and appended",
- "with the step number.",
- "A simulation can be continued by reading the full state from file",
- "with option [TT]-cpi[tt]. This option is intelligent in the way that",
- "if no checkpoint file is found, GROMACS just assumes a normal run and",
- "starts from the first step of the [REF].tpr[ref] file. By default the output",
- "will be appending to the existing output files. The checkpoint file",
- "contains checksums of all output files, such that you will never",
- "loose data when some output files are modified, corrupt or removed.",
- "There are three scenarios with [TT]-cpi[tt]:[PAR]",
- "[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
- "[TT]*[tt] all files are present with names and checksums matching those stored",
- "in the checkpoint file: files are appended[PAR]",
- "[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
- "With [TT]-noappend[tt] new output files are opened and the simulation",
- "part number is added to all output file names.",
- "Note that in all cases the checkpoint file itself is not renamed",
- "and will be overwritten, unless its name does not match",
- "the [TT]-cpo[tt] option.",
- "[PAR]",
- "With checkpointing the output is appended to previously written",
- "output files, unless [TT]-noappend[tt] is used or none of the previous",
- "output files are present (except for the checkpoint file).",
- "The integrity of the files to be appended is verified using checksums",
- "which are stored in the checkpoint file. This ensures that output can",
- "not be mixed up or corrupted due to file appending. When only some",
- "of the previous output files are present, a fatal error is generated",
- "and no old output files are modified and no new output files are opened.",
- "The result with appending will be the same as from a single run.",
- "The contents will be binary identical, unless you use a different number",
- "of ranks or dynamic load balancing or the FFT library uses optimizations",
- "through timing.",
- "[PAR]",
- "With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
- "file is written at the first neighbor search step where the run time",
- "exceeds [TT]-maxh[tt]\\*0.99 hours. This option is particularly useful in",
- "combination with setting [TT]nsteps[tt] to -1 either in the mdp or using the",
- "similarly named command line option. This results in an infinite run,",
- "terminated only when the time limit set by [TT]-maxh[tt] is reached (if any)"
- "or upon receiving a signal."
- "[PAR]",
- "When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
- "step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
- "pressed), it will stop after the next neighbor search step ",
- "(with nstlist=0 at the next step).",
- "In both cases all the usual output will be written to file.",
- "When running with MPI, a signal to one of the [TT]mdrun[tt] ranks",
- "is sufficient, this signal should not be sent to mpirun or",
- "the [TT]mdrun[tt] process that is the parent of the others.",
- "[PAR]",
- "Interactive molecular dynamics (IMD) can be activated by using at least one",
- "of the three IMD switches: The [TT]-imdterm[tt] switch allows to terminate",
- "the simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
- "[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
- "IMD remote can be turned on by [TT]-imdpull[tt].",
- "The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
- "file pointed to by [TT]-if[tt] contains atom indices and forces if IMD",
- "pulling is used."
- "[PAR]",
- "When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
- };
- t_commrec *cr;
- t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efTRN, "-o", NULL, ffWRITE },
- { efCOMPRESSED, "-x", NULL, ffOPTWR },
- { efCPT, "-cpi", NULL, ffOPTRD | ffALLOW_MISSING },
- { efCPT, "-cpo", NULL, ffOPTWR },
- { efSTO, "-c", "confout", ffWRITE },
- { efEDR, "-e", "ener", ffWRITE },
- { efLOG, "-g", "md", ffWRITE },
- { efXVG, "-dhdl", "dhdl", ffOPTWR },
- { efXVG, "-field", "field", ffOPTWR },
- { efXVG, "-table", "table", ffOPTRD },
- { efXVG, "-tabletf", "tabletf", ffOPTRD },
- { efXVG, "-tablep", "tablep", ffOPTRD },
- { efXVG, "-tableb", "table", ffOPTRDMULT },
- { efTRX, "-rerun", "rerun", ffOPTRD },
- { efXVG, "-tpi", "tpi", ffOPTWR },
- { efXVG, "-tpid", "tpidist", ffOPTWR },
- { efEDI, "-ei", "sam", ffOPTRD },
- { efXVG, "-eo", "edsam", ffOPTWR },
- { efXVG, "-devout", "deviatie", ffOPTWR },
- { efXVG, "-runav", "runaver", ffOPTWR },
- { efXVG, "-px", "pullx", ffOPTWR },
- { efXVG, "-pf", "pullf", ffOPTWR },
- { efXVG, "-ro", "rotation", ffOPTWR },
- { efLOG, "-ra", "rotangles", ffOPTWR },
- { efLOG, "-rs", "rotslabs", ffOPTWR },
- { efLOG, "-rt", "rottorque", ffOPTWR },
- { efMTX, "-mtx", "nm", ffOPTWR },
- { efNDX, "-dn", "dipole", ffOPTWR },
- { efRND, "-multidir", NULL, ffOPTRDMULT},
- { efDAT, "-plumed", "plumed", ffOPTRD }, /* PLUMED */
- { efDAT, "-membed", "membed", ffOPTRD },
- { efTOP, "-mp", "membed", ffOPTRD },
- { efNDX, "-mn", "membed", ffOPTRD },
- { efXVG, "-if", "imdforces", ffOPTWR },
- { efXVG, "-swap", "swapions", ffOPTWR }
- };
- const int NFILE = asize(fnm);
-
- /* Command line options ! */
- gmx_bool bDDBondCheck = TRUE;
- gmx_bool bDDBondComm = TRUE;
- gmx_bool bTunePME = TRUE;
- gmx_bool bVerbose = FALSE;
- gmx_bool bCompact = TRUE;
- gmx_bool bRerunVSite = FALSE;
- gmx_bool bConfout = TRUE;
- gmx_bool bReproducible = FALSE;
- gmx_bool bIMDwait = FALSE;
- gmx_bool bIMDterm = FALSE;
- gmx_bool bIMDpull = FALSE;
-
- int npme = -1;
- int nstlist = 0;
- int nmultisim = 0;
- int nstglobalcomm = -1;
- int repl_ex_nst = 0;
- int repl_ex_seed = -1;
- int repl_ex_nex = 0;
- int nstepout = 100;
- int resetstep = -1;
- gmx_int64_t nsteps = -2; /* the value -2 means that the mdp option will be used */
- int imdport = 8888; /* can be almost anything, 8888 is easy to remember */
-
- rvec realddxyz = {0, 0, 0};
- const char *ddno_opt[ddnoNR+1] =
- { NULL, "interleave", "pp_pme", "cartesian", NULL };
- const char *dddlb_opt[] =
- { NULL, "auto", "no", "yes", NULL };
- const char *thread_aff_opt[threadaffNR+1] =
- { NULL, "auto", "on", "off", NULL };
- const char *nbpu_opt[] =
- { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
- real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
- char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
- real cpt_period = 15.0, max_hours = -1;
- gmx_bool bTryToAppendFiles = TRUE;
- gmx_bool bKeepAndNumCPT = FALSE;
- gmx_bool bResetCountersHalfWay = FALSE;
- output_env_t oenv = NULL;
-
- /* Non transparent initialization of a complex gmx_hw_opt_t struct.
- * But unfortunately we are not allowed to call a function here,
- * since declarations follow below.
- */
- gmx_hw_opt_t hw_opt = {
- 0, 0, 0, 0, threadaffSEL, 0, 0,
- { NULL, FALSE, 0, NULL }
- };
-
- t_pargs pa[] = {
-
- { "-dd", FALSE, etRVEC, {&realddxyz},
- "Domain decomposition grid, 0 is optimize" },
- { "-ddorder", FALSE, etENUM, {ddno_opt},
- "DD rank order" },
- { "-npme", FALSE, etINT, {&npme},
- "Number of separate ranks to be used for PME, -1 is guess" },
- { "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
- "Total number of threads to start (0 is guess)" },
- { "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
- "Number of thread-MPI threads to start (0 is guess)" },
- { "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
- "Number of OpenMP threads per MPI rank to start (0 is guess)" },
- { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
- "Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
- { "-pin", FALSE, etENUM, {thread_aff_opt},
- "Whether mdrun should try to set thread affinities" },
- { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
- "The lowest logical core number to which mdrun should pin the first thread" },
- { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
- "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
- { "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
- "List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping" },
- { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
- "Check for all bonded interactions with DD" },
- { "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
- "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
- { "-rdd", FALSE, etREAL, {&rdd},
- "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
- { "-rcon", FALSE, etREAL, {&rconstr},
- "Maximum distance for P-LINCS (nm), 0 is estimate" },
- { "-dlb", FALSE, etENUM, {dddlb_opt},
- "Dynamic load balancing (with DD)" },
- { "-dds", FALSE, etREAL, {&dlb_scale},
- "Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
- "provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
- { "-ddcsx", FALSE, etSTR, {&ddcsx},
- "HIDDENA string containing a vector of the relative sizes in the x "
- "direction of the corresponding DD cells. Only effective with static "
- "load balancing." },
- { "-ddcsy", FALSE, etSTR, {&ddcsy},
- "HIDDENA string containing a vector of the relative sizes in the y "
- "direction of the corresponding DD cells. Only effective with static "
- "load balancing." },
- { "-ddcsz", FALSE, etSTR, {&ddcsz},
- "HIDDENA string containing a vector of the relative sizes in the z "
- "direction of the corresponding DD cells. Only effective with static "
- "load balancing." },
- { "-gcom", FALSE, etINT, {&nstglobalcomm},
- "Global communication frequency" },
- { "-nb", FALSE, etENUM, {&nbpu_opt},
- "Calculate non-bonded interactions on" },
- { "-nstlist", FALSE, etINT, {&nstlist},
- "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
- { "-tunepme", FALSE, etBOOL, {&bTunePME},
- "Optimize PME load between PP/PME ranks or GPU/CPU" },
- { "-v", FALSE, etBOOL, {&bVerbose},
- "Be loud and noisy" },
- { "-compact", FALSE, etBOOL, {&bCompact},
- "Write a compact log file" },
- { "-pforce", FALSE, etREAL, {&pforce},
- "Print all forces larger than this (kJ/mol nm)" },
- { "-reprod", FALSE, etBOOL, {&bReproducible},
- "Try to avoid optimizations that affect binary reproducibility" },
- { "-cpt", FALSE, etREAL, {&cpt_period},
- "Checkpoint interval (minutes)" },
- { "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
- "Keep and number checkpoint files" },
- { "-append", FALSE, etBOOL, {&bTryToAppendFiles},
- "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
- { "-nsteps", FALSE, etINT64, {&nsteps},
- "Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
- { "-maxh", FALSE, etREAL, {&max_hours},
- "Terminate after 0.99 times this time (hours)" },
- { "-multi", FALSE, etINT, {&nmultisim},
- "Do multiple simulations in parallel" },
- { "-replex", FALSE, etINT, {&repl_ex_nst},
- "Attempt replica exchange periodically with this period (steps)" },
- { "-nex", FALSE, etINT, {&repl_ex_nex},
- "Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
- { "-reseed", FALSE, etINT, {&repl_ex_seed},
- "Seed for replica exchange, -1 is generate a seed" },
- { "-hrex", FALSE, etBOOL, {&plumed_hrex},
- "Enable hamiltonian replica exchange" },
- { "-imdport", FALSE, etINT, {&imdport},
- "HIDDENIMD listening port" },
- { "-imdwait", FALSE, etBOOL, {&bIMDwait},
- "HIDDENPause the simulation while no IMD client is connected" },
- { "-imdterm", FALSE, etBOOL, {&bIMDterm},
- "HIDDENAllow termination of the simulation from IMD client" },
- { "-imdpull", FALSE, etBOOL, {&bIMDpull},
- "HIDDENAllow pulling in the simulation from IMD client" },
- { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
- "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
- { "-confout", FALSE, etBOOL, {&bConfout},
- "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
- { "-stepout", FALSE, etINT, {&nstepout},
- "HIDDENFrequency of writing the remaining wall clock time for the run" },
- { "-resetstep", FALSE, etINT, {&resetstep},
- "HIDDENReset cycle counters after these many time steps" },
- { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
- "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
- };
- unsigned long Flags;
- ivec ddxyz;
- int dd_node_order;
- gmx_bool bDoAppendFiles, bStartFromCpt;
- FILE *fplog;
- int rc;
- char **multidir = NULL;
-
- cr = init_commrec();
-
- unsigned long PCA_Flags = PCA_CAN_SET_DEFFNM;
- // With -multi or -multidir, the file names are going to get processed
- // further (or the working directory changed), so we can't check for their
- // existence during parsing. It isn't useful to do any completion based on
- // file system contents, either.
- if (is_multisim_option_set(argc, argv))
- {
- PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
- }
-
- /* Comment this in to do fexist calls only on master
- * works not with rerun or tables at the moment
- * also comment out the version of init_forcerec in md.c
- * with NULL instead of opt2fn
- */
- /*
- if (!MASTER(cr))
- {
- PCA_Flags |= PCA_NOT_READ_NODE;
- }
- */
-
- if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
- {
- return 0;
- }
-
-
- /* we set these early because they might be used in init_multisystem()
- Note that there is the potential for npme>nnodes until the number of
- threads is set later on, if there's thread parallelization. That shouldn't
- lead to problems. */
- dd_node_order = nenum(ddno_opt);
- cr->npmenodes = npme;
-
- hw_opt.thread_affinity = nenum(thread_aff_opt);
-
- /* now check the -multi and -multidir option */
- if (opt2bSet("-multidir", NFILE, fnm))
- {
- if (nmultisim > 0)
- {
- gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
- }
- nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
- }
-
-
- if (repl_ex_nst != 0 && nmultisim < 2)
- {
- gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
- }
-
- if (repl_ex_nex < 0)
- {
- gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
- }
-
- if (nmultisim >= 1)
- {
-#ifndef GMX_THREAD_MPI
- gmx_bool bParFn = (multidir == NULL);
- init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
-#else
- gmx_fatal(FARGS, "mdrun -multi or -multidir are not supported with the thread-MPI library. "
- "Please compile GROMACS with a proper external MPI library.");
-#endif
- }
-
- handleRestart(cr, bTryToAppendFiles, NFILE, fnm,
- &bDoAppendFiles, &bStartFromCpt);
-
- Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
- Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
- Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
- Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
- Flags = Flags | (bConfout ? MD_CONFOUT : 0);
- Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
- Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
- Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
- Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
- Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
- Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
- Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
- Flags = Flags | (opt2parg_bSet("-ntomp", asize(pa), pa) ? MD_NTOMPSET : 0);
- Flags = Flags | (bIMDwait ? MD_IMDWAIT : 0);
- Flags = Flags | (bIMDterm ? MD_IMDTERM : 0);
- Flags = Flags | (bIMDpull ? MD_IMDPULL : 0);
-
- /* We postpone opening the log file if we are appending, so we can
- first truncate the old log file and append to the correct position
- there instead. */
- if (MASTER(cr) && !bDoAppendFiles)
- {
- gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
- Flags & MD_APPENDFILES, &fplog);
- }
- else
- {
- fplog = NULL;
- }
-
- ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
- ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
- ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
-
- /* PLUMED */
- plumedswitch=0;
- if (opt2bSet("-plumed",NFILE,fnm)) plumedswitch=1;
- if(plumedswitch){
- plumedcmd=plumed_cmd;
- int real_precision=sizeof(real);
- real energyUnits=1.0;
- real lengthUnits=1.0;
- real timeUnits=1.0;
-
- if(!plumed_installed()){
- gmx_fatal(FARGS,"Plumed is not available. Check your PLUMED_KERNEL variable.");
- }
- plumedmain=plumed_create();
- plumed_cmd(plumedmain,"setRealPrecision",&real_precision);
- // this is not necessary for gromacs units:
- plumed_cmd(plumedmain,"setMDEnergyUnits",&energyUnits);
- plumed_cmd(plumedmain,"setMDLengthUnits",&lengthUnits);
- plumed_cmd(plumedmain,"setMDTimeUnits",&timeUnits);
- //
- plumed_cmd(plumedmain,"setPlumedDat",ftp2fn(efDAT,NFILE,fnm));
- plumedswitch=1;
- }
- /* PLUMED HREX*/
- if(getenv("PLUMED_HREX")) plumed_hrex=1;
- if(plumed_hrex){
- if(!plumedswitch) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) requires -plumed");
- if(repl_ex_nst==0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) replica exchange");
- if(repl_ex_nex!=0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) not compatible with -nex");
- }
- /* END PLUMED HREX */
-
- /* END PLUMED */
-
- rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
- nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
- dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
- nbpu_opt[0], nstlist,
- nsteps, nstepout, resetstep,
- nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
- pforce, cpt_period, max_hours, imdport, Flags);
-
- /* Log file has to be closed in mdrunner if we are appending to it
- (fplog not set here) */
- if (MASTER(cr) && !bDoAppendFiles)
- {
- gmx_log_close(fplog);
- }
-
- return rc;
-}
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/mdrun.cpp.preplumed b/patches/gromacs-5.1.4.diff/src/programs/mdrun/mdrun.cpp.preplumed
deleted file mode 100644
index fcdc36952adcd0d2e1ad0dcf25c5c997e1a2dd72..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/mdrun.cpp.preplumed
+++ /dev/null
@@ -1,554 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \defgroup module_mdrun Implementation of mdrun
- * \ingroup group_mdrun
- *
- * \brief This module contains code that implements mdrun.
- */
-/*! \internal \file
- *
- * \brief This file implements mdrun
- *
- * \author Berk Hess <hess@kth.se>
- * \author David van der Spoel <david.vanderspoel@icm.uu.se>
- * \author Erik Lindahl <erik@kth.se>
- * \author Mark Abraham <mark.j.abraham@gmail.com>
- *
- * \ingroup module_mdrun
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <stdio.h>
-#include <string.h>
-
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/readinp.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/mdrunutility/handlerestart.h"
-#include "gromacs/utility/fatalerror.h"
-
-#include "mdrun_main.h"
-
-/*! \brief Return whether either of the command-line parameters that
- * will trigger a multi-simulation is set */
-static bool is_multisim_option_set(int argc, const char *const argv[])
-{
- for (int i = 0; i < argc; ++i)
- {
- if (strcmp(argv[i], "-multi") == 0 || strcmp(argv[i], "-multidir") == 0)
- {
- return true;
- }
- }
- return false;
-}
-
-//! Implements C-style main function for mdrun
-int gmx_mdrun(int argc, char *argv[])
-{
- const char *desc[] = {
- "[THISMODULE] is the main computational chemistry engine",
- "within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
- "but it can also perform Stochastic Dynamics, Energy Minimization,",
- "test particle insertion or (re)calculation of energies.",
- "Normal mode analysis is another option. In this case [TT]mdrun[tt]",
- "builds a Hessian matrix from single conformation.",
- "For usual Normal Modes-like calculations, make sure that",
- "the structure provided is properly energy-minimized.",
- "The generated matrix can be diagonalized by [gmx-nmeig].[PAR]",
- "The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
- "and distributes the topology over ranks if needed.",
- "[TT]mdrun[tt] produces at least four output files.",
- "A single log file ([TT]-g[tt]) is written.",
- "The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
- "optionally forces.",
- "The structure file ([TT]-c[tt]) contains the coordinates and",
- "velocities of the last step.",
- "The energy file ([TT]-e[tt]) contains energies, the temperature,",
- "pressure, etc, a lot of these things are also printed in the log file.",
- "Optionally coordinates can be written to a compressed trajectory file",
- "([TT]-x[tt]).[PAR]",
- "The option [TT]-dhdl[tt] is only used when free energy calculation is",
- "turned on.[PAR]",
- "Running mdrun efficiently in parallel is a complex topic topic,",
- "many aspects of which are covered in the online User Guide. You",
- "should look there for practical advice on using many of the options",
- "available in mdrun.[PAR]",
- "ED (essential dynamics) sampling and/or additional flooding potentials",
- "are switched on by using the [TT]-ei[tt] flag followed by an [REF].edi[ref]",
- "file. The [REF].edi[ref] file can be produced with the [TT]make_edi[tt] tool",
- "or by using options in the essdyn menu of the WHAT IF program.",
- "[TT]mdrun[tt] produces a [REF].xvg[ref] output file that",
- "contains projections of positions, velocities and forces onto selected",
- "eigenvectors.[PAR]",
- "When user-defined potential functions have been selected in the",
- "[REF].mdp[ref] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
- "a formatted table with potential functions. The file is read from",
- "either the current directory or from the [TT]GMXLIB[tt] directory.",
- "A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
- "for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
- "normal Coulomb.",
- "When pair interactions are present, a separate table for pair interaction",
- "functions is read using the [TT]-tablep[tt] option.[PAR]",
- "When tabulated bonded functions are present in the topology,",
- "interaction functions are read using the [TT]-tableb[tt] option.",
- "For each different tabulated interaction type used, a table file name must",
- "be given. For the topology to work, a file name given here must match a",
- "character sequence before the file extension. That sequence is: an underscore,",
- "then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals,",
- "and finally the matching table number index used in the topology.[PAR]",
- "The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
- "coordinates and forces when pulling is selected",
- "in the [REF].mdp[ref] file.[PAR]",
- "Finally some experimental algorithms can be tested when the",
- "appropriate options have been given. Currently under",
- "investigation are: polarizability.",
- "[PAR]",
- "The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
- "a protein into a membrane. This module requires a number of settings",
- "that are provided in a data file that is the argument of this option.",
- "For more details in membrane embedding, see the documentation in the",
- "user guide. The options [TT]-mn[tt] and [TT]-mp[tt] are used to provide",
- "the index and topology files used for the embedding.",
- "[PAR]",
- "The option [TT]-pforce[tt] is useful when you suspect a simulation",
- "crashes due to too large forces. With this option coordinates and",
- "forces of atoms with a force larger than a certain value will",
- "be printed to stderr.",
- "[PAR]",
- "Checkpoints containing the complete state of the system are written",
- "at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
- "unless option [TT]-cpt[tt] is set to -1.",
- "The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
- "make sure that a recent state of the system is always available,",
- "even when the simulation is terminated while writing a checkpoint.",
- "With [TT]-cpnum[tt] all checkpoint files are kept and appended",
- "with the step number.",
- "A simulation can be continued by reading the full state from file",
- "with option [TT]-cpi[tt]. This option is intelligent in the way that",
- "if no checkpoint file is found, GROMACS just assumes a normal run and",
- "starts from the first step of the [REF].tpr[ref] file. By default the output",
- "will be appending to the existing output files. The checkpoint file",
- "contains checksums of all output files, such that you will never",
- "loose data when some output files are modified, corrupt or removed.",
- "There are three scenarios with [TT]-cpi[tt]:[PAR]",
- "[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
- "[TT]*[tt] all files are present with names and checksums matching those stored",
- "in the checkpoint file: files are appended[PAR]",
- "[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
- "With [TT]-noappend[tt] new output files are opened and the simulation",
- "part number is added to all output file names.",
- "Note that in all cases the checkpoint file itself is not renamed",
- "and will be overwritten, unless its name does not match",
- "the [TT]-cpo[tt] option.",
- "[PAR]",
- "With checkpointing the output is appended to previously written",
- "output files, unless [TT]-noappend[tt] is used or none of the previous",
- "output files are present (except for the checkpoint file).",
- "The integrity of the files to be appended is verified using checksums",
- "which are stored in the checkpoint file. This ensures that output can",
- "not be mixed up or corrupted due to file appending. When only some",
- "of the previous output files are present, a fatal error is generated",
- "and no old output files are modified and no new output files are opened.",
- "The result with appending will be the same as from a single run.",
- "The contents will be binary identical, unless you use a different number",
- "of ranks or dynamic load balancing or the FFT library uses optimizations",
- "through timing.",
- "[PAR]",
- "With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
- "file is written at the first neighbor search step where the run time",
- "exceeds [TT]-maxh[tt]\\*0.99 hours. This option is particularly useful in",
- "combination with setting [TT]nsteps[tt] to -1 either in the mdp or using the",
- "similarly named command line option. This results in an infinite run,",
- "terminated only when the time limit set by [TT]-maxh[tt] is reached (if any)"
- "or upon receiving a signal."
- "[PAR]",
- "When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
- "step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
- "pressed), it will stop after the next neighbor search step ",
- "(with nstlist=0 at the next step).",
- "In both cases all the usual output will be written to file.",
- "When running with MPI, a signal to one of the [TT]mdrun[tt] ranks",
- "is sufficient, this signal should not be sent to mpirun or",
- "the [TT]mdrun[tt] process that is the parent of the others.",
- "[PAR]",
- "Interactive molecular dynamics (IMD) can be activated by using at least one",
- "of the three IMD switches: The [TT]-imdterm[tt] switch allows to terminate",
- "the simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
- "[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
- "IMD remote can be turned on by [TT]-imdpull[tt].",
- "The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
- "file pointed to by [TT]-if[tt] contains atom indices and forces if IMD",
- "pulling is used."
- "[PAR]",
- "When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
- };
- t_commrec *cr;
- t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efTRN, "-o", NULL, ffWRITE },
- { efCOMPRESSED, "-x", NULL, ffOPTWR },
- { efCPT, "-cpi", NULL, ffOPTRD | ffALLOW_MISSING },
- { efCPT, "-cpo", NULL, ffOPTWR },
- { efSTO, "-c", "confout", ffWRITE },
- { efEDR, "-e", "ener", ffWRITE },
- { efLOG, "-g", "md", ffWRITE },
- { efXVG, "-dhdl", "dhdl", ffOPTWR },
- { efXVG, "-field", "field", ffOPTWR },
- { efXVG, "-table", "table", ffOPTRD },
- { efXVG, "-tabletf", "tabletf", ffOPTRD },
- { efXVG, "-tablep", "tablep", ffOPTRD },
- { efXVG, "-tableb", "table", ffOPTRDMULT },
- { efTRX, "-rerun", "rerun", ffOPTRD },
- { efXVG, "-tpi", "tpi", ffOPTWR },
- { efXVG, "-tpid", "tpidist", ffOPTWR },
- { efEDI, "-ei", "sam", ffOPTRD },
- { efXVG, "-eo", "edsam", ffOPTWR },
- { efXVG, "-devout", "deviatie", ffOPTWR },
- { efXVG, "-runav", "runaver", ffOPTWR },
- { efXVG, "-px", "pullx", ffOPTWR },
- { efXVG, "-pf", "pullf", ffOPTWR },
- { efXVG, "-ro", "rotation", ffOPTWR },
- { efLOG, "-ra", "rotangles", ffOPTWR },
- { efLOG, "-rs", "rotslabs", ffOPTWR },
- { efLOG, "-rt", "rottorque", ffOPTWR },
- { efMTX, "-mtx", "nm", ffOPTWR },
- { efNDX, "-dn", "dipole", ffOPTWR },
- { efRND, "-multidir", NULL, ffOPTRDMULT},
- { efDAT, "-membed", "membed", ffOPTRD },
- { efTOP, "-mp", "membed", ffOPTRD },
- { efNDX, "-mn", "membed", ffOPTRD },
- { efXVG, "-if", "imdforces", ffOPTWR },
- { efXVG, "-swap", "swapions", ffOPTWR }
- };
- const int NFILE = asize(fnm);
-
- /* Command line options ! */
- gmx_bool bDDBondCheck = TRUE;
- gmx_bool bDDBondComm = TRUE;
- gmx_bool bTunePME = TRUE;
- gmx_bool bVerbose = FALSE;
- gmx_bool bCompact = TRUE;
- gmx_bool bRerunVSite = FALSE;
- gmx_bool bConfout = TRUE;
- gmx_bool bReproducible = FALSE;
- gmx_bool bIMDwait = FALSE;
- gmx_bool bIMDterm = FALSE;
- gmx_bool bIMDpull = FALSE;
-
- int npme = -1;
- int nstlist = 0;
- int nmultisim = 0;
- int nstglobalcomm = -1;
- int repl_ex_nst = 0;
- int repl_ex_seed = -1;
- int repl_ex_nex = 0;
- int nstepout = 100;
- int resetstep = -1;
- gmx_int64_t nsteps = -2; /* the value -2 means that the mdp option will be used */
- int imdport = 8888; /* can be almost anything, 8888 is easy to remember */
-
- rvec realddxyz = {0, 0, 0};
- const char *ddno_opt[ddnoNR+1] =
- { NULL, "interleave", "pp_pme", "cartesian", NULL };
- const char *dddlb_opt[] =
- { NULL, "auto", "no", "yes", NULL };
- const char *thread_aff_opt[threadaffNR+1] =
- { NULL, "auto", "on", "off", NULL };
- const char *nbpu_opt[] =
- { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
- real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
- char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
- real cpt_period = 15.0, max_hours = -1;
- gmx_bool bTryToAppendFiles = TRUE;
- gmx_bool bKeepAndNumCPT = FALSE;
- gmx_bool bResetCountersHalfWay = FALSE;
- output_env_t oenv = NULL;
-
- /* Non transparent initialization of a complex gmx_hw_opt_t struct.
- * But unfortunately we are not allowed to call a function here,
- * since declarations follow below.
- */
- gmx_hw_opt_t hw_opt = {
- 0, 0, 0, 0, threadaffSEL, 0, 0,
- { NULL, FALSE, 0, NULL }
- };
-
- t_pargs pa[] = {
-
- { "-dd", FALSE, etRVEC, {&realddxyz},
- "Domain decomposition grid, 0 is optimize" },
- { "-ddorder", FALSE, etENUM, {ddno_opt},
- "DD rank order" },
- { "-npme", FALSE, etINT, {&npme},
- "Number of separate ranks to be used for PME, -1 is guess" },
- { "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
- "Total number of threads to start (0 is guess)" },
- { "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
- "Number of thread-MPI threads to start (0 is guess)" },
- { "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
- "Number of OpenMP threads per MPI rank to start (0 is guess)" },
- { "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
- "Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
- { "-pin", FALSE, etENUM, {thread_aff_opt},
- "Whether mdrun should try to set thread affinities" },
- { "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
- "The lowest logical core number to which mdrun should pin the first thread" },
- { "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
- "Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
- { "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
- "List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping" },
- { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
- "Check for all bonded interactions with DD" },
- { "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
- "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
- { "-rdd", FALSE, etREAL, {&rdd},
- "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
- { "-rcon", FALSE, etREAL, {&rconstr},
- "Maximum distance for P-LINCS (nm), 0 is estimate" },
- { "-dlb", FALSE, etENUM, {dddlb_opt},
- "Dynamic load balancing (with DD)" },
- { "-dds", FALSE, etREAL, {&dlb_scale},
- "Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
- "provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
- { "-ddcsx", FALSE, etSTR, {&ddcsx},
- "HIDDENA string containing a vector of the relative sizes in the x "
- "direction of the corresponding DD cells. Only effective with static "
- "load balancing." },
- { "-ddcsy", FALSE, etSTR, {&ddcsy},
- "HIDDENA string containing a vector of the relative sizes in the y "
- "direction of the corresponding DD cells. Only effective with static "
- "load balancing." },
- { "-ddcsz", FALSE, etSTR, {&ddcsz},
- "HIDDENA string containing a vector of the relative sizes in the z "
- "direction of the corresponding DD cells. Only effective with static "
- "load balancing." },
- { "-gcom", FALSE, etINT, {&nstglobalcomm},
- "Global communication frequency" },
- { "-nb", FALSE, etENUM, {&nbpu_opt},
- "Calculate non-bonded interactions on" },
- { "-nstlist", FALSE, etINT, {&nstlist},
- "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
- { "-tunepme", FALSE, etBOOL, {&bTunePME},
- "Optimize PME load between PP/PME ranks or GPU/CPU" },
- { "-v", FALSE, etBOOL, {&bVerbose},
- "Be loud and noisy" },
- { "-compact", FALSE, etBOOL, {&bCompact},
- "Write a compact log file" },
- { "-pforce", FALSE, etREAL, {&pforce},
- "Print all forces larger than this (kJ/mol nm)" },
- { "-reprod", FALSE, etBOOL, {&bReproducible},
- "Try to avoid optimizations that affect binary reproducibility" },
- { "-cpt", FALSE, etREAL, {&cpt_period},
- "Checkpoint interval (minutes)" },
- { "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
- "Keep and number checkpoint files" },
- { "-append", FALSE, etBOOL, {&bTryToAppendFiles},
- "Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
- { "-nsteps", FALSE, etINT64, {&nsteps},
- "Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
- { "-maxh", FALSE, etREAL, {&max_hours},
- "Terminate after 0.99 times this time (hours)" },
- { "-multi", FALSE, etINT, {&nmultisim},
- "Do multiple simulations in parallel" },
- { "-replex", FALSE, etINT, {&repl_ex_nst},
- "Attempt replica exchange periodically with this period (steps)" },
- { "-nex", FALSE, etINT, {&repl_ex_nex},
- "Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
- { "-reseed", FALSE, etINT, {&repl_ex_seed},
- "Seed for replica exchange, -1 is generate a seed" },
- { "-imdport", FALSE, etINT, {&imdport},
- "HIDDENIMD listening port" },
- { "-imdwait", FALSE, etBOOL, {&bIMDwait},
- "HIDDENPause the simulation while no IMD client is connected" },
- { "-imdterm", FALSE, etBOOL, {&bIMDterm},
- "HIDDENAllow termination of the simulation from IMD client" },
- { "-imdpull", FALSE, etBOOL, {&bIMDpull},
- "HIDDENAllow pulling in the simulation from IMD client" },
- { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
- "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
- { "-confout", FALSE, etBOOL, {&bConfout},
- "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
- { "-stepout", FALSE, etINT, {&nstepout},
- "HIDDENFrequency of writing the remaining wall clock time for the run" },
- { "-resetstep", FALSE, etINT, {&resetstep},
- "HIDDENReset cycle counters after these many time steps" },
- { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
- "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
- };
- unsigned long Flags;
- ivec ddxyz;
- int dd_node_order;
- gmx_bool bDoAppendFiles, bStartFromCpt;
- FILE *fplog;
- int rc;
- char **multidir = NULL;
-
- cr = init_commrec();
-
- unsigned long PCA_Flags = PCA_CAN_SET_DEFFNM;
- // With -multi or -multidir, the file names are going to get processed
- // further (or the working directory changed), so we can't check for their
- // existence during parsing. It isn't useful to do any completion based on
- // file system contents, either.
- if (is_multisim_option_set(argc, argv))
- {
- PCA_Flags |= PCA_DISABLE_INPUT_FILE_CHECKING;
- }
-
- /* Comment this in to do fexist calls only on master
- * works not with rerun or tables at the moment
- * also comment out the version of init_forcerec in md.c
- * with NULL instead of opt2fn
- */
- /*
- if (!MASTER(cr))
- {
- PCA_Flags |= PCA_NOT_READ_NODE;
- }
- */
-
- if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
- {
- return 0;
- }
-
-
- /* we set these early because they might be used in init_multisystem()
- Note that there is the potential for npme>nnodes until the number of
- threads is set later on, if there's thread parallelization. That shouldn't
- lead to problems. */
- dd_node_order = nenum(ddno_opt);
- cr->npmenodes = npme;
-
- hw_opt.thread_affinity = nenum(thread_aff_opt);
-
- /* now check the -multi and -multidir option */
- if (opt2bSet("-multidir", NFILE, fnm))
- {
- if (nmultisim > 0)
- {
- gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
- }
- nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
- }
-
-
- if (repl_ex_nst != 0 && nmultisim < 2)
- {
- gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
- }
-
- if (repl_ex_nex < 0)
- {
- gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
- }
-
- if (nmultisim >= 1)
- {
-#ifndef GMX_THREAD_MPI
- gmx_bool bParFn = (multidir == NULL);
- init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
-#else
- gmx_fatal(FARGS, "mdrun -multi or -multidir are not supported with the thread-MPI library. "
- "Please compile GROMACS with a proper external MPI library.");
-#endif
- }
-
- handleRestart(cr, bTryToAppendFiles, NFILE, fnm,
- &bDoAppendFiles, &bStartFromCpt);
-
- Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
- Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
- Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
- Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
- Flags = Flags | (bConfout ? MD_CONFOUT : 0);
- Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
- Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
- Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
- Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
- Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
- Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
- Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
- Flags = Flags | (opt2parg_bSet("-ntomp", asize(pa), pa) ? MD_NTOMPSET : 0);
- Flags = Flags | (bIMDwait ? MD_IMDWAIT : 0);
- Flags = Flags | (bIMDterm ? MD_IMDTERM : 0);
- Flags = Flags | (bIMDpull ? MD_IMDPULL : 0);
-
- /* We postpone opening the log file if we are appending, so we can
- first truncate the old log file and append to the correct position
- there instead. */
- if (MASTER(cr) && !bDoAppendFiles)
- {
- gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
- Flags & MD_APPENDFILES, &fplog);
- }
- else
- {
- fplog = NULL;
- }
-
- ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
- ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
- ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
-
- rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
- nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
- dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
- nbpu_opt[0], nstlist,
- nsteps, nstepout, resetstep,
- nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
- pforce, cpt_period, max_hours, imdport, Flags);
-
- /* Log file has to be closed in mdrunner if we are appending to it
- (fplog not set here) */
- if (MASTER(cr) && !bDoAppendFiles)
- {
- gmx_log_close(fplog);
- }
-
- return rc;
-}
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.cpp b/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.cpp
deleted file mode 100644
index e799bc66964a891d20d901b8fd0e543a9cfc03a3..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.cpp
+++ /dev/null
@@ -1,1542 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#include "gmxpre.h"
-
-#include "repl_ex.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/random/random.h"
-#include "gromacs/utility/smalloc.h"
-
-/* PLUMED */
-#include "../../../Plumed.h"
-extern int plumedswitch;
-extern plumed plumedmain;
-/* END PLUMED */
-
-/* PLUMED HREX */
-extern int plumed_hrex;
-/* END PLUMED HREX */
-
-#define PROBABILITYCUTOFF 100
-/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
-
-enum {
- ereTEMP, ereLAMBDA, ereENDSINGLE, ereTL, ereNR
-};
-const char *erename[ereNR] = { "temperature", "lambda", "end_single_marker", "temperature and lambda"};
-/* end_single_marker merely notes the end of single variable replica exchange. All types higher than
- it are multiple replica exchange methods */
-/* Eventually, should add 'pressure', 'temperature and pressure', 'lambda_and_pressure', 'temperature_lambda_pressure'?;
- Let's wait until we feel better about the pressure control methods giving exact ensembles. Right now, we assume constant pressure */
-
-typedef struct gmx_repl_ex
-{
- int repl;
- int nrepl;
- real temp;
- int type;
- real **q;
- gmx_bool bNPT;
- real *pres;
- int *ind;
- int *allswaps;
- int nst;
- int nex;
- int seed;
- int nattempt[2];
- real *prob_sum;
- int **nmoves;
- int *nexchange;
- gmx_rng_t rng;
-
- /* these are helper arrays for replica exchange; allocated here so they
- don't have to be allocated each time */
- int *destinations;
- int **cyclic;
- int **order;
- int *tmpswap;
- gmx_bool *incycle;
- gmx_bool *bEx;
-
- /* helper arrays to hold the quantities that are exchanged */
- real *prob;
- real *Epot;
- real *beta;
- real *Vol;
- real **de;
-
-} t_gmx_repl_ex;
-
-static gmx_bool repl_quantity(const gmx_multisim_t *ms,
- struct gmx_repl_ex *re, int ere, real q)
-{
- real *qall;
- gmx_bool bDiff;
- int s;
-
- snew(qall, ms->nsim);
- qall[re->repl] = q;
- gmx_sum_sim(ms->nsim, qall, ms);
-
- /* PLUMED */
- //bDiff = FALSE;
- //for (s = 1; s < ms->nsim; s++)
- //{
- // if (qall[s] != qall[0])
- // {
- bDiff = TRUE;
- // }
- //}
- /* END PLUMED */
-
- if (bDiff)
- {
- /* Set the replica exchange type and quantities */
- re->type = ere;
-
- snew(re->q[ere], re->nrepl);
- for (s = 0; s < ms->nsim; s++)
- {
- re->q[ere][s] = qall[s];
- }
- }
- sfree(qall);
- return bDiff;
-}
-
-gmx_repl_ex_t init_replica_exchange(FILE *fplog,
- const gmx_multisim_t *ms,
- const t_state *state,
- const t_inputrec *ir,
- int nst, int nex, int init_seed)
-{
- real pres;
- int i, j, k;
- struct gmx_repl_ex *re;
- gmx_bool bTemp;
- gmx_bool bLambda = FALSE;
-
- fprintf(fplog, "\nInitializing Replica Exchange\n");
-
- if (ms == NULL || ms->nsim == 1)
- {
- gmx_fatal(FARGS, "Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
- }
- if (!EI_DYNAMICS(ir->eI))
- {
- gmx_fatal(FARGS, "Replica exchange is only supported by dynamical simulations");
- /* Note that PAR(cr) is defined by cr->nnodes > 1, which is
- * distinct from MULTISIM(cr). A multi-simulation only runs
- * with real MPI parallelism, but this does not imply PAR(cr)
- * is true!
- *
- * Since we are using a dynamical integrator, the only
- * decomposition is DD, so PAR(cr) and DOMAINDECOMP(cr) are
- * synonymous. The only way for cr->nnodes > 1 to be true is
- * if we are using DD. */
- }
-
- snew(re, 1);
-
- re->repl = ms->sim;
- re->nrepl = ms->nsim;
- snew(re->q, ereENDSINGLE);
-
- fprintf(fplog, "Repl There are %d replicas:\n", re->nrepl);
-
- check_multi_int(fplog, ms, state->natoms, "the number of atoms", FALSE);
- check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
- check_multi_int64(fplog, ms, ir->init_step+ir->nsteps, "init_step+nsteps", FALSE);
- check_multi_int64(fplog, ms, (ir->init_step+nst-1)/nst,
- "first exchange step: init_step/-replex", FALSE);
- check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
- check_multi_int(fplog, ms, ir->opts.ngtc,
- "the number of temperature coupling groups", FALSE);
- check_multi_int(fplog, ms, ir->epc, "the pressure coupling", FALSE);
- check_multi_int(fplog, ms, ir->efep, "free energy", FALSE);
- check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
-
- re->temp = ir->opts.ref_t[0];
- for (i = 1; (i < ir->opts.ngtc); i++)
- {
- if (ir->opts.ref_t[i] != re->temp)
- {
- fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
- fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
- }
- }
-
- re->type = -1;
- bTemp = repl_quantity(ms, re, ereTEMP, re->temp);
- if (ir->efep != efepNO)
- {
- bLambda = repl_quantity(ms, re, ereLAMBDA, (real)ir->fepvals->init_fep_state);
- }
- if (re->type == -1) /* nothing was assigned */
- {
- gmx_fatal(FARGS, "The properties of the %d systems are all the same, there is nothing to exchange", re->nrepl);
- }
- if (bLambda && bTemp)
- {
- re->type = ereTL;
- }
-
- if (bTemp)
- {
- please_cite(fplog, "Sugita1999a");
- if (ir->epc != epcNO)
- {
- re->bNPT = TRUE;
- fprintf(fplog, "Repl Using Constant Pressure REMD.\n");
- please_cite(fplog, "Okabe2001a");
- }
- if (ir->etc == etcBERENDSEN)
- {
- gmx_fatal(FARGS, "REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
- ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
- }
- }
- if (bLambda)
- {
- if (ir->fepvals->delta_lambda != 0) /* check this? */
- {
- gmx_fatal(FARGS, "delta_lambda is not zero");
- }
- }
- if (re->bNPT)
- {
- snew(re->pres, re->nrepl);
- if (ir->epct == epctSURFACETENSION)
- {
- pres = ir->ref_p[ZZ][ZZ];
- }
- else
- {
- pres = 0;
- j = 0;
- for (i = 0; i < DIM; i++)
- {
- if (ir->compress[i][i] != 0)
- {
- pres += ir->ref_p[i][i];
- j++;
- }
- }
- pres /= j;
- }
- re->pres[re->repl] = pres;
- gmx_sum_sim(re->nrepl, re->pres, ms);
- }
-
- /* Make an index for increasing replica order */
- /* only makes sense if one or the other is varying, not both!
- if both are varying, we trust the order the person gave. */
- snew(re->ind, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- re->ind[i] = i;
- }
-
- /* PLUMED */
- // plumed2: check if we want alternative patterns (i.e. for bias-exchange metaD)
- // in those cases replicas can share the same temperature.
- /*
- if (re->type < ereENDSINGLE)
- {
-
- for (i = 0; i < re->nrepl; i++)
- {
- for (j = i+1; j < re->nrepl; j++)
- {
- if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
- {*/
- /* Unordered replicas are supposed to work, but there
- * is still an issues somewhere.
- * Note that at this point still re->ind[i]=i.
- */
- /*
- gmx_fatal(FARGS, "Replicas with indices %d < %d have %ss %g > %g, please order your replicas on increasing %s",
- i, j,
- erename[re->type],
- re->q[re->type][i], re->q[re->type][j],
- erename[re->type]);
-
- k = re->ind[i];
- re->ind[i] = re->ind[j];
- re->ind[j] = k;
- }
- else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
- {
- gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
- }
- }
- }
- }
- */
- /* END PLUMED */
-
- /* keep track of all the swaps, starting with the initial placement. */
- snew(re->allswaps, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- re->allswaps[i] = re->ind[i];
- }
-
- switch (re->type)
- {
- case ereTEMP:
- fprintf(fplog, "\nReplica exchange in temperature\n");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %5.1f", re->q[re->type][re->ind[i]]);
- }
- fprintf(fplog, "\n");
- break;
- case ereLAMBDA:
- fprintf(fplog, "\nReplica exchange in lambda\n");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %3d", (int)re->q[re->type][re->ind[i]]);
- }
- fprintf(fplog, "\n");
- break;
- case ereTL:
- fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %5.1f", re->q[ereTEMP][re->ind[i]]);
- }
- fprintf(fplog, "\n");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %5d", (int)re->q[ereLAMBDA][re->ind[i]]);
- }
- fprintf(fplog, "\n");
- break;
- default:
- gmx_incons("Unknown replica exchange quantity");
- }
- if (re->bNPT)
- {
- fprintf(fplog, "\nRepl p");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %5.2f", re->pres[re->ind[i]]);
- }
-
- for (i = 0; i < re->nrepl; i++)
- {
- if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
- {
- fprintf(fplog, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
- fprintf(stderr, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
- }
- }
- }
- re->nst = nst;
- if (init_seed == -1)
- {
- if (MASTERSIM(ms))
- {
- re->seed = (int)gmx_rng_make_seed();
- }
- else
- {
- re->seed = 0;
- }
- gmx_sumi_sim(1, &(re->seed), ms);
- }
- else
- {
- re->seed = init_seed;
- }
- fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
- fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
- re->rng = gmx_rng_init(re->seed);
-
- re->nattempt[0] = 0;
- re->nattempt[1] = 0;
-
- snew(re->prob_sum, re->nrepl);
- snew(re->nexchange, re->nrepl);
- snew(re->nmoves, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- snew(re->nmoves[i], re->nrepl);
- }
- fprintf(fplog, "Replica exchange information below: x=exchange, pr=probability\n");
-
- /* generate space for the helper functions so we don't have to snew each time */
-
- snew(re->destinations, re->nrepl);
- snew(re->incycle, re->nrepl);
- snew(re->tmpswap, re->nrepl);
- snew(re->cyclic, re->nrepl);
- snew(re->order, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- snew(re->cyclic[i], re->nrepl+1);
- snew(re->order[i], re->nrepl);
- }
- /* allocate space for the functions storing the data for the replicas */
- /* not all of these arrays needed in all cases, but they don't take
- up much space, since the max size is nrepl**2 */
- snew(re->prob, re->nrepl);
- snew(re->bEx, re->nrepl);
- snew(re->beta, re->nrepl);
- snew(re->Vol, re->nrepl);
- snew(re->Epot, re->nrepl);
- snew(re->de, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- snew(re->de[i], re->nrepl);
- }
- re->nex = nex;
- return re;
-}
-
-static void exchange_reals(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, real *v, int n)
-{
- real *buf;
- int i;
-
- if (v)
- {
- snew(buf, n);
-#ifdef GMX_MPI
- /*
- MPI_Sendrecv(v, n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
- buf,n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
- ms->mpi_comm_masters,MPI_STATUS_IGNORE);
- */
- {
- MPI_Request mpi_req;
-
- MPI_Isend(v, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, &mpi_req);
- MPI_Recv(buf, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, MPI_STATUS_IGNORE);
- MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
- }
-#endif
- for (i = 0; i < n; i++)
- {
- v[i] = buf[i];
- }
- sfree(buf);
- }
-}
-
-
-static void exchange_ints(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, int *v, int n)
-{
- int *buf;
- int i;
-
- if (v)
- {
- snew(buf, n);
-#ifdef GMX_MPI
- /*
- MPI_Sendrecv(v, n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
- buf,n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
- ms->mpi_comm_masters,MPI_STATUS_IGNORE);
- */
- {
- MPI_Request mpi_req;
-
- MPI_Isend(v, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, &mpi_req);
- MPI_Recv(buf, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, MPI_STATUS_IGNORE);
- MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
- }
-#endif
- for (i = 0; i < n; i++)
- {
- v[i] = buf[i];
- }
- sfree(buf);
- }
-}
-
-static void exchange_doubles(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, double *v, int n)
-{
- double *buf;
- int i;
-
- if (v)
- {
- snew(buf, n);
-#ifdef GMX_MPI
- /*
- MPI_Sendrecv(v, n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
- buf,n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
- ms->mpi_comm_masters,MPI_STATUS_IGNORE);
- */
- {
- MPI_Request mpi_req;
-
- MPI_Isend(v, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, &mpi_req);
- MPI_Recv(buf, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, MPI_STATUS_IGNORE);
- MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
- }
-#endif
- for (i = 0; i < n; i++)
- {
- v[i] = buf[i];
- }
- sfree(buf);
- }
-}
-
-static void exchange_rvecs(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, rvec *v, int n)
-{
- rvec *buf;
- int i;
-
- if (v)
- {
- snew(buf, n);
-#ifdef GMX_MPI
- /*
- MPI_Sendrecv(v[0], n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
- buf[0],n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
- ms->mpi_comm_masters,MPI_STATUS_IGNORE);
- */
- {
- MPI_Request mpi_req;
-
- MPI_Isend(v[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, &mpi_req);
- MPI_Recv(buf[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, MPI_STATUS_IGNORE);
- MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
- }
-#endif
- for (i = 0; i < n; i++)
- {
- copy_rvec(buf[i], v[i]);
- }
- sfree(buf);
- }
-}
-
-void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
-{
- /* When t_state changes, this code should be updated. */
- int ngtc, nnhpres;
- ngtc = state->ngtc * state->nhchainlength;
- nnhpres = state->nnhpres* state->nhchainlength;
- exchange_rvecs(ms, b, state->box, DIM);
- exchange_rvecs(ms, b, state->box_rel, DIM);
- exchange_rvecs(ms, b, state->boxv, DIM);
- exchange_reals(ms, b, &(state->veta), 1);
- exchange_reals(ms, b, &(state->vol0), 1);
- exchange_rvecs(ms, b, state->svir_prev, DIM);
- exchange_rvecs(ms, b, state->fvir_prev, DIM);
- exchange_rvecs(ms, b, state->pres_prev, DIM);
- exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
- exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
- exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
- exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
- exchange_doubles(ms, b, state->therm_integral, state->ngtc);
- exchange_rvecs(ms, b, state->x, state->natoms);
- exchange_rvecs(ms, b, state->v, state->natoms);
- exchange_rvecs(ms, b, state->sd_X, state->natoms);
-}
-
-static void copy_rvecs(rvec *s, rvec *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- copy_rvec(s[i], d[i]);
- }
- }
-}
-
-static void copy_doubles(const double *s, double *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
- }
-}
-
-static void copy_reals(const real *s, real *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
- }
-}
-
-static void copy_ints(const int *s, int *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
- }
-}
-
-#define scopy_rvecs(v, n) copy_rvecs(state->v, state_local->v, n);
-#define scopy_doubles(v, n) copy_doubles(state->v, state_local->v, n);
-#define scopy_reals(v, n) copy_reals(state->v, state_local->v, n);
-#define scopy_ints(v, n) copy_ints(state->v, state_local->v, n);
-
-void copy_state_nonatomdata(t_state *state, t_state *state_local)
-{
- /* When t_state changes, this code should be updated. */
- int ngtc, nnhpres;
- ngtc = state->ngtc * state->nhchainlength;
- nnhpres = state->nnhpres* state->nhchainlength;
- scopy_rvecs(box, DIM);
- scopy_rvecs(box_rel, DIM);
- scopy_rvecs(boxv, DIM);
- state_local->veta = state->veta;
- state_local->vol0 = state->vol0;
- scopy_rvecs(svir_prev, DIM);
- scopy_rvecs(fvir_prev, DIM);
- scopy_rvecs(pres_prev, DIM);
- scopy_doubles(nosehoover_xi, ngtc);
- scopy_doubles(nosehoover_vxi, ngtc);
- scopy_doubles(nhpres_xi, nnhpres);
- scopy_doubles(nhpres_vxi, nnhpres);
- scopy_doubles(therm_integral, state->ngtc);
- scopy_rvecs(x, state->natoms);
- scopy_rvecs(v, state->natoms);
- scopy_rvecs(sd_X, state->natoms);
- copy_ints(&(state->fep_state), &(state_local->fep_state), 1);
- scopy_reals(lambda, efptNR);
-}
-
-static void scale_velocities(t_state *state, real fac)
-{
- int i;
-
- if (state->v)
- {
- for (i = 0; i < state->natoms; i++)
- {
- svmul(fac, state->v[i], state->v[i]);
- }
- }
-}
-
-static void print_transition_matrix(FILE *fplog, int n, int **nmoves, int *nattempt)
-{
- int i, j, ntot;
- float Tprint;
-
- ntot = nattempt[0] + nattempt[1];
- fprintf(fplog, "\n");
- fprintf(fplog, "Repl");
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, " "); /* put the title closer to the center */
- }
- fprintf(fplog, "Empirical Transition Matrix\n");
-
- fprintf(fplog, "Repl");
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, "%8d", (i+1));
- }
- fprintf(fplog, "\n");
-
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, "Repl");
- for (j = 0; j < n; j++)
- {
- Tprint = 0.0;
- if (nmoves[i][j] > 0)
- {
- Tprint = nmoves[i][j]/(2.0*ntot);
- }
- fprintf(fplog, "%8.4f", Tprint);
- }
- fprintf(fplog, "%3d\n", i);
- }
-}
-
-static void print_ind(FILE *fplog, const char *leg, int n, int *ind, gmx_bool *bEx)
-{
- int i;
-
- fprintf(fplog, "Repl %2s %2d", leg, ind[0]);
- for (i = 1; i < n; i++)
- {
- fprintf(fplog, " %c %2d", (bEx != 0 && bEx[i]) ? 'x' : ' ', ind[i]);
- }
- fprintf(fplog, "\n");
-}
-
-static void print_allswitchind(FILE *fplog, int n, int *pind, int *allswaps, int *tmpswap)
-{
- int i;
-
- for (i = 0; i < n; i++)
- {
- tmpswap[i] = allswaps[i];
- }
- for (i = 0; i < n; i++)
- {
- allswaps[i] = tmpswap[pind[i]];
- }
-
- fprintf(fplog, "\nAccepted Exchanges: ");
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, "%d ", pind[i]);
- }
- fprintf(fplog, "\n");
-
- /* the "Order After Exchange" is the state label corresponding to the configuration that
- started in state listed in order, i.e.
-
- 3 0 1 2
-
- means that the:
- configuration starting in simulation 3 is now in simulation 0,
- configuration starting in simulation 0 is now in simulation 1,
- configuration starting in simulation 1 is now in simulation 2,
- configuration starting in simulation 2 is now in simulation 3
- */
- fprintf(fplog, "Order After Exchange: ");
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, "%d ", allswaps[i]);
- }
- fprintf(fplog, "\n\n");
-}
-
-static void print_prob(FILE *fplog, const char *leg, int n, real *prob)
-{
- int i;
- char buf[8];
-
- fprintf(fplog, "Repl %2s ", leg);
- for (i = 1; i < n; i++)
- {
- if (prob[i] >= 0)
- {
- sprintf(buf, "%4.2f", prob[i]);
- fprintf(fplog, " %3s", buf[0] == '1' ? "1.0" : buf+1);
- }
- else
- {
- fprintf(fplog, " ");
- }
- }
- fprintf(fplog, "\n");
-}
-
-static void print_count(FILE *fplog, const char *leg, int n, int *count)
-{
- int i;
-
- fprintf(fplog, "Repl %2s ", leg);
- for (i = 1; i < n; i++)
- {
- fprintf(fplog, " %4d", count[i]);
- }
- fprintf(fplog, "\n");
-}
-
-static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int a, int b, int ap, int bp)
-{
-
- real ediff, dpV, delta = 0;
- real *Epot = re->Epot;
- real *Vol = re->Vol;
- real **de = re->de;
- real *beta = re->beta;
-
- /* Two cases; we are permuted and not. In all cases, setting ap = a and bp = b will reduce
- to the non permuted case */
-
- switch (re->type)
- {
- case ereTEMP:
- /*
- * Okabe et. al. Chem. Phys. Lett. 335 (2001) 435-439
- */
- ediff = Epot[b] - Epot[a];
- delta = -(beta[bp] - beta[ap])*ediff;
- break;
- case ereLAMBDA:
- /* two cases: when we are permuted, and not. */
- /* non-permuted:
- ediff = E_new - E_old
- = [H_b(x_a) + H_a(x_b)] - [H_b(x_b) + H_a(x_a)]
- = [H_b(x_a) - H_a(x_a)] + [H_a(x_b) - H_b(x_b)]
- = de[b][a] + de[a][b] */
-
- /* permuted:
- ediff = E_new - E_old
- = [H_bp(x_a) + H_ap(x_b)] - [H_bp(x_b) + H_ap(x_a)]
- = [H_bp(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_bp(x_b)]
- = [H_bp(x_a) - H_a(x_a) + H_a(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_b(x_b) + H_b(x_b) - H_bp(x_b)]
- = [H_bp(x_a) - H_a(x_a)] - [H_ap(x_a) - H_a(x_a)] + [H_ap(x_b) - H_b(x_b)] - H_bp(x_b) - H_b(x_b)]
- = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]) */
- /* but, in the current code implementation, we flip configurations, not indices . . .
- So let's examine that.
- = [H_b(x_ap) - H_a(x_a)] - [H_a(x_ap) - H_a(x_a)] + [H_a(x_bp) - H_b(x_b)] - H_b(x_bp) - H_b(x_b)]
- = [H_b(x_ap) - H_a(x_ap)] + [H_a(x_bp) - H_b(x_pb)]
- = (de[b][ap] - de[a][ap]) + (de[a][bp] - de[b][bp]
- So, if we exchange b<=> bp and a<=> ap, we return to the same result.
- So the simple solution is to flip the
- position of perturbed and original indices in the tests.
- */
-
- ediff = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]);
- delta = ediff*beta[a]; /* assume all same temperature in this case */
- break;
- case ereTL:
- /* not permuted: */
- /* delta = reduced E_new - reduced E_old
- = [beta_b H_b(x_a) + beta_a H_a(x_b)] - [beta_b H_b(x_b) + beta_a H_a(x_a)]
- = [beta_b H_b(x_a) - beta_a H_a(x_a)] + [beta_a H_a(x_b) - beta_b H_b(x_b)]
- = [beta_b dH_b(x_a) + beta_b H_a(x_a) - beta_a H_a(x_a)] +
- [beta_a dH_a(x_b) + beta_a H_b(x_b) - beta_b H_b(x_b)]
- = [beta_b dH_b(x_a) + [beta_a dH_a(x_b) +
- beta_b (H_a(x_a) - H_b(x_b)]) - beta_a (H_a(x_a) - H_b(x_b))
- = beta_b dH_b(x_a) + beta_a dH_a(x_b) - (beta_b - beta_a)(H_b(x_b) - H_a(x_a) */
- /* delta = beta[b]*de[b][a] + beta[a]*de[a][b] - (beta[b] - beta[a])*(Epot[b] - Epot[a]; */
- /* permuted (big breath!) */
- /* delta = reduced E_new - reduced E_old
- = [beta_bp H_bp(x_a) + beta_ap H_ap(x_b)] - [beta_bp H_bp(x_b) + beta_ap H_ap(x_a)]
- = [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
- = [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
- - beta_pb H_a(x_a) + beta_ap H_a(x_a) + beta_pb H_a(x_a) - beta_ap H_a(x_a)
- - beta_ap H_b(x_b) + beta_bp H_b(x_b) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
- = [(beta_bp H_bp(x_a) - beta_bp H_a(x_a)) - (beta_ap H_ap(x_a) - beta_ap H_a(x_a))] +
- [(beta_ap H_ap(x_b) - beta_ap H_b(x_b)) - (beta_bp H_bp(x_b) - beta_bp H_b(x_b))]
- + beta_pb H_a(x_a) - beta_ap H_a(x_a) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
- = [beta_bp (H_bp(x_a) - H_a(x_a)) - beta_ap (H_ap(x_a) - H_a(x_a))] +
- [beta_ap (H_ap(x_b) - H_b(x_b)) - beta_bp (H_bp(x_b) - H_b(x_b))]
- + beta_pb (H_a(x_a) - H_b(x_b)) - beta_ap (H_a(x_a) - H_b(x_b))
- = ([beta_bp de[bp][a] - beta_ap de[ap][a]) + beta_ap de[ap][b] - beta_bp de[bp][b])
- + (beta_pb-beta_ap)(H_a(x_a) - H_b(x_b)) */
- delta = beta[bp]*(de[bp][a] - de[bp][b]) + beta[ap]*(de[ap][b] - de[ap][a]) - (beta[bp]-beta[ap])*(Epot[b]-Epot[a]);
- break;
- default:
- gmx_incons("Unknown replica exchange quantity");
- }
- if (bPrint)
- {
- fprintf(fplog, "Repl %d <-> %d dE_term = %10.3e (kT)\n", a, b, delta);
- }
-
-/* this is necessary because with plumed HREX the energy contribution is
- already taken into account */
- if(plumed_hrex) delta=0.0;
-
- if (re->bNPT)
- {
- /* revist the calculation for 5.0. Might be some improvements. */
- dpV = (beta[ap]*re->pres[ap]-beta[bp]*re->pres[bp])*(Vol[b]-Vol[a])/PRESFAC;
- if (bPrint)
- {
- fprintf(fplog, " dpV = %10.3e d = %10.3e\n", dpV, delta + dpV);
- }
- delta += dpV;
- }
- return delta;
-}
-
-static void
-test_for_replica_exchange(FILE *fplog,
- const gmx_multisim_t *ms,
- struct gmx_repl_ex *re,
- gmx_enerdata_t *enerd,
- real vol,
- gmx_int64_t step,
- real time)
-{
- int m, i, j, a, b, ap, bp, i0, i1, tmp;
- real delta = 0;
- gmx_bool bPrint, bMultiEx;
- gmx_bool *bEx = re->bEx;
- real *prob = re->prob;
- int *pind = re->destinations; /* permuted index */
- gmx_bool bEpot = FALSE;
- gmx_bool bDLambda = FALSE;
- gmx_bool bVol = FALSE;
-
- bMultiEx = (re->nex > 1); /* multiple exchanges at each state */
- fprintf(fplog, "Replica exchange at step %" GMX_PRId64 " time %.5f\n", step, time);
-
- if (re->bNPT)
- {
- for (i = 0; i < re->nrepl; i++)
- {
- re->Vol[i] = 0;
- }
- bVol = TRUE;
- re->Vol[re->repl] = vol;
- }
- if ((re->type == ereTEMP || re->type == ereTL))
- {
- for (i = 0; i < re->nrepl; i++)
- {
- re->Epot[i] = 0;
- }
- bEpot = TRUE;
- re->Epot[re->repl] = enerd->term[F_EPOT];
- /* temperatures of different states*/
- for (i = 0; i < re->nrepl; i++)
- {
- re->beta[i] = 1.0/(re->q[ereTEMP][i]*BOLTZ);
- }
- }
- else
- {
- for (i = 0; i < re->nrepl; i++)
- {
- re->beta[i] = 1.0/(re->temp*BOLTZ); /* we have a single temperature */
- }
- }
- if (re->type == ereLAMBDA || re->type == ereTL)
- {
- bDLambda = TRUE;
- /* lambda differences. */
- /* de[i][j] is the energy of the jth simulation in the ith Hamiltonian
- minus the energy of the jth simulation in the jth Hamiltonian */
- for (i = 0; i < re->nrepl; i++)
- {
- for (j = 0; j < re->nrepl; j++)
- {
- re->de[i][j] = 0;
- }
- }
- for (i = 0; i < re->nrepl; i++)
- {
- re->de[i][re->repl] = (enerd->enerpart_lambda[(int)re->q[ereLAMBDA][i]+1]-enerd->enerpart_lambda[0]);
- }
- }
-
- /* now actually do the communication */
- if (bVol)
- {
- gmx_sum_sim(re->nrepl, re->Vol, ms);
- }
- if (bEpot)
- {
- gmx_sum_sim(re->nrepl, re->Epot, ms);
- }
- if (bDLambda)
- {
- for (i = 0; i < re->nrepl; i++)
- {
- gmx_sum_sim(re->nrepl, re->de[i], ms);
- }
- }
-
- /* make a duplicate set of indices for shuffling */
- for (i = 0; i < re->nrepl; i++)
- {
- pind[i] = re->ind[i];
- }
-
- /* PLUMED */
- int plumed_test_exchange_pattern=0;
- /* END PLUMED */
-
- if(plumed_test_exchange_pattern && plumed_hrex) gmx_fatal(FARGS,"hrex not compatible with ad hoc exchange patterns");
-
- if (bMultiEx)
- {
- /* multiple random switch exchange */
- int nself = 0;
- for (i = 0; i < re->nex + nself; i++)
- {
- double rnd[2];
-
- gmx_rng_cycle_2uniform(step, i*2, re->seed, RND_SEED_REPLEX, rnd);
- /* randomly select a pair */
- /* in theory, could reduce this by identifying only which switches had a nonneglibible
- probability of occurring (log p > -100) and only operate on those switches */
- /* find out which state it is from, and what label that state currently has. Likely
- more work that useful. */
- i0 = (int)(re->nrepl*rnd[0]);
- i1 = (int)(re->nrepl*rnd[1]);
- if (i0 == i1)
- {
- nself++;
- continue; /* self-exchange, back up and do it again */
- }
-
- a = re->ind[i0]; /* what are the indices of these states? */
- b = re->ind[i1];
- ap = pind[i0];
- bp = pind[i1];
-
- bPrint = FALSE; /* too noisy */
- /* calculate the energy difference */
- /* if the code changes to flip the STATES, rather than the configurations,
- use the commented version of the code */
- /* delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); */
- delta = calc_delta(fplog, bPrint, re, ap, bp, a, b);
-
- /* we actually only use the first space in the prob and bEx array,
- since there are actually many switches between pairs. */
-
- if (delta <= 0)
- {
- /* accepted */
- prob[0] = 1;
- bEx[0] = TRUE;
- }
- else
- {
- if (delta > PROBABILITYCUTOFF)
- {
- prob[0] = 0;
- }
- else
- {
- prob[0] = exp(-delta);
- }
- /* roll a number to determine if accepted */
- gmx_rng_cycle_2uniform(step, i*2+1, re->seed, RND_SEED_REPLEX, rnd);
- bEx[0] = rnd[0] < prob[0];
- }
- re->prob_sum[0] += prob[0];
-
- if (bEx[0])
- {
- /* swap the states */
- tmp = pind[i0];
- pind[i0] = pind[i1];
- pind[i1] = tmp;
- }
- }
- re->nattempt[0]++; /* keep track of total permutation trials here */
- print_allswitchind(fplog, re->nrepl, pind, re->allswaps, re->tmpswap);
- }
- else
- {
- /* standard nearest neighbor replica exchange */
-
- m = (step / re->nst) % 2;
- /* PLUMED */
- if(plumedswitch){
- int partner=re->repl;
- plumed_cmd(plumedmain,"getExchangesFlag",&plumed_test_exchange_pattern);
- if(plumed_test_exchange_pattern>0){
- int *list;
- snew(list,re->nrepl);
- plumed_cmd(plumedmain,"setNumberOfReplicas",&(re->nrepl));
- plumed_cmd(plumedmain,"getExchangesList",list);
- for(i=0; i<re->nrepl; i++) re->ind[i]=list[i];
- sfree(list);
- }
-
- for(i=1; i<re->nrepl; i++) {
- if (i % 2 != m) continue;
- a = re->ind[i-1];
- b = re->ind[i];
- if(re->repl==a) partner=b;
- if(re->repl==b) partner=a;
- }
- plumed_cmd(plumedmain,"GREX setPartner",&partner);
- plumed_cmd(plumedmain,"GREX calculate",NULL);
- plumed_cmd(plumedmain,"GREX shareAllDeltaBias",NULL);
- }
- /* END PLUMED */
- for (i = 1; i < re->nrepl; i++)
- {
- a = re->ind[i-1];
- b = re->ind[i];
-
- bPrint = (re->repl == a || re->repl == b);
- if (i % 2 == m)
- {
- delta = calc_delta(fplog, bPrint, re, a, b, a, b);
-
- /* PLUMED */
- if(plumedswitch){
- real adb,bdb,dplumed;
- char buf[300];
- sprintf(buf,"GREX getDeltaBias %d",a); plumed_cmd(plumedmain,buf,&adb);
- sprintf(buf,"GREX getDeltaBias %d",b); plumed_cmd(plumedmain,buf,&bdb);
- dplumed=adb*re->beta[a]+bdb*re->beta[b];
- delta+=dplumed;
- if (bPrint)
- fprintf(fplog,"dplumed = %10.3e dE_Term = %10.3e (kT)\n",dplumed,delta);
- }
- /* END PLUMED */
- if (delta <= 0)
- {
- /* accepted */
- prob[i] = 1;
- bEx[i] = TRUE;
- }
- else
- {
- double rnd[2];
-
- if (delta > PROBABILITYCUTOFF)
- {
- prob[i] = 0;
- }
- else
- {
- prob[i] = exp(-delta);
- }
- /* roll a number to determine if accepted */
- gmx_rng_cycle_2uniform(step, i, re->seed, RND_SEED_REPLEX, rnd);
- bEx[i] = rnd[0] < prob[i];
- }
- re->prob_sum[i] += prob[i];
-
- if (bEx[i])
- {
- /* PLUMED */
- if(!plumed_test_exchange_pattern) {
- /* standard neighbour swapping */
- /* swap these two */
- tmp = pind[i-1];
- pind[i-1] = pind[i];
- pind[i] = tmp;
- re->nexchange[i]++; /* statistics for back compatibility */
- } else {
- /* alternative swapping patterns */
- tmp = pind[a];
- pind[a] = pind[b];
- pind[b] = tmp;
- re->nexchange[i]++; /* statistics for back compatibility */
- }
- /* END PLUMED */
- }
- }
- else
- {
- prob[i] = -1;
- bEx[i] = FALSE;
- }
- }
- /* print some statistics */
- print_ind(fplog, "ex", re->nrepl, re->ind, bEx);
- print_prob(fplog, "pr", re->nrepl, prob);
- fprintf(fplog, "\n");
- re->nattempt[m]++;
- }
-
- /* PLUMED */
- if(plumed_test_exchange_pattern>0) {
- for (i = 0; i < re->nrepl; i++)
- {
- re->ind[i] = i;
- }
- }
- /* END PLUMED */
-
- /* record which moves were made and accepted */
- for (i = 0; i < re->nrepl; i++)
- {
- re->nmoves[re->ind[i]][pind[i]] += 1;
- re->nmoves[pind[i]][re->ind[i]] += 1;
- }
- fflush(fplog); /* make sure we can see what the last exchange was */
-}
-
-static void write_debug_x(t_state *state)
-{
- int i;
-
- if (debug)
- {
- for (i = 0; i < state->natoms; i += 10)
- {
- fprintf(debug, "dx %5d %10.5f %10.5f %10.5f\n", i, state->x[i][XX], state->x[i][YY], state->x[i][ZZ]);
- }
- }
-}
-
-static void
-cyclic_decomposition(const int *destinations,
- int **cyclic,
- gmx_bool *incycle,
- const int nrepl,
- int *nswap)
-{
-
- int i, j, c, p;
- int maxlen = 1;
- for (i = 0; i < nrepl; i++)
- {
- incycle[i] = FALSE;
- }
- for (i = 0; i < nrepl; i++) /* one cycle for each replica */
- {
- if (incycle[i])
- {
- cyclic[i][0] = -1;
- continue;
- }
- cyclic[i][0] = i;
- incycle[i] = TRUE;
- c = 1;
- p = i;
- for (j = 0; j < nrepl; j++) /* potentially all cycles are part, but we will break first */
- {
- p = destinations[p]; /* start permuting */
- if (p == i)
- {
- cyclic[i][c] = -1;
- if (c > maxlen)
- {
- maxlen = c;
- }
- break; /* we've reached the original element, the cycle is complete, and we marked the end. */
- }
- else
- {
- cyclic[i][c] = p; /* each permutation gives a new member of the cycle */
- incycle[p] = TRUE;
- c++;
- }
- }
- }
- *nswap = maxlen - 1;
-
- if (debug)
- {
- for (i = 0; i < nrepl; i++)
- {
- fprintf(debug, "Cycle %d:", i);
- for (j = 0; j < nrepl; j++)
- {
- if (cyclic[i][j] < 0)
- {
- break;
- }
- fprintf(debug, "%2d", cyclic[i][j]);
- }
- fprintf(debug, "\n");
- }
- fflush(debug);
- }
-}
-
-static void
-compute_exchange_order(FILE *fplog,
- int **cyclic,
- int **order,
- const int nrepl,
- const int maxswap)
-{
- int i, j;
-
- for (j = 0; j < maxswap; j++)
- {
- for (i = 0; i < nrepl; i++)
- {
- if (cyclic[i][j+1] >= 0)
- {
- order[cyclic[i][j+1]][j] = cyclic[i][j];
- order[cyclic[i][j]][j] = cyclic[i][j+1];
- }
- }
- for (i = 0; i < nrepl; i++)
- {
- if (order[i][j] < 0)
- {
- order[i][j] = i; /* if it's not exchanging, it should stay this round*/
- }
- }
- }
-
- if (debug)
- {
- fprintf(fplog, "Replica Exchange Order\n");
- for (i = 0; i < nrepl; i++)
- {
- fprintf(fplog, "Replica %d:", i);
- for (j = 0; j < maxswap; j++)
- {
- if (order[i][j] < 0)
- {
- break;
- }
- fprintf(debug, "%2d", order[i][j]);
- }
- fprintf(fplog, "\n");
- }
- fflush(fplog);
- }
-}
-
-static void
-prepare_to_do_exchange(FILE *fplog,
- struct gmx_repl_ex *re,
- const int replica_id,
- int *maxswap,
- gmx_bool *bThisReplicaExchanged)
-{
- int i, j;
- /* Hold the cyclic decomposition of the (multiple) replica
- * exchange. */
- gmx_bool bAnyReplicaExchanged = FALSE;
- *bThisReplicaExchanged = FALSE;
-
- for (i = 0; i < re->nrepl; i++)
- {
- if (re->destinations[i] != re->ind[i])
- {
- /* only mark as exchanged if the index has been shuffled */
- bAnyReplicaExchanged = TRUE;
- break;
- }
- }
- if (bAnyReplicaExchanged)
- {
- /* reinitialize the placeholder arrays */
- for (i = 0; i < re->nrepl; i++)
- {
- for (j = 0; j < re->nrepl; j++)
- {
- re->cyclic[i][j] = -1;
- re->order[i][j] = -1;
- }
- }
-
- /* Identify the cyclic decomposition of the permutation (very
- * fast if neighbor replica exchange). */
- cyclic_decomposition(re->destinations, re->cyclic, re->incycle, re->nrepl, maxswap);
-
- /* Now translate the decomposition into a replica exchange
- * order at each step. */
- compute_exchange_order(fplog, re->cyclic, re->order, re->nrepl, *maxswap);
-
- /* Did this replica do any exchange at any point? */
- for (j = 0; j < *maxswap; j++)
- {
- if (replica_id != re->order[replica_id][j])
- {
- *bThisReplicaExchanged = TRUE;
- break;
- }
- }
- }
-}
-
-gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *re,
- t_state *state, gmx_enerdata_t *enerd,
- t_state *state_local, gmx_int64_t step, real time)
-{
- int j;
- int replica_id = 0;
- int exchange_partner;
- int maxswap = 0;
- /* Number of rounds of exchanges needed to deal with any multiple
- * exchanges. */
- /* Where each replica ends up after the exchange attempt(s). */
- /* The order in which multiple exchanges will occur. */
- gmx_bool bThisReplicaExchanged = FALSE;
-
- /* PLUMED */
- if(plumedswitch)plumed_cmd(plumedmain,"GREX prepare",NULL);
- /* END PLUMED */
-
- if (MASTER(cr))
- {
- replica_id = re->repl;
- test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
- prepare_to_do_exchange(fplog, re, replica_id, &maxswap, &bThisReplicaExchanged);
- }
- /* Do intra-simulation broadcast so all processors belonging to
- * each simulation know whether they need to participate in
- * collecting the state. Otherwise, they might as well get on with
- * the next thing to do. */
- if (DOMAINDECOMP(cr))
- {
-#ifdef GMX_MPI
- MPI_Bcast(&bThisReplicaExchanged, sizeof(gmx_bool), MPI_BYTE, MASTERRANK(cr),
- cr->mpi_comm_mygroup);
-#endif
- }
-
- if (bThisReplicaExchanged)
- {
- /* Exchange the states */
- /* Collect the global state on the master node */
- if (DOMAINDECOMP(cr))
- {
- dd_collect_state(cr->dd, state_local, state);
- }
- else
- {
- copy_state_nonatomdata(state_local, state);
- }
-
- if (MASTER(cr))
- {
- /* There will be only one swap cycle with standard replica
- * exchange, but there may be multiple swap cycles if we
- * allow multiple swaps. */
-
- for (j = 0; j < maxswap; j++)
- {
- exchange_partner = re->order[replica_id][j];
-
- if (exchange_partner != replica_id)
- {
- /* Exchange the global states between the master nodes */
- if (debug)
- {
- fprintf(debug, "Exchanging %d with %d\n", replica_id, exchange_partner);
- }
- exchange_state(cr->ms, exchange_partner, state);
- }
- }
- /* For temperature-type replica exchange, we need to scale
- * the velocities. */
- if (re->type == ereTEMP || re->type == ereTL)
- {
- scale_velocities(state, sqrt(re->q[ereTEMP][replica_id]/re->q[ereTEMP][re->destinations[replica_id]]));
- }
-
- }
-
- /* With domain decomposition the global state is distributed later */
- if (!DOMAINDECOMP(cr))
- {
- /* Copy the global state to the local state data structure */
- copy_state_nonatomdata(state, state_local);
- }
- }
-
- return bThisReplicaExchanged;
-}
-
-void print_replica_exchange_statistics(FILE *fplog, struct gmx_repl_ex *re)
-{
- int i;
-
- fprintf(fplog, "\nReplica exchange statistics\n");
-
- if (re->nex == 0)
- {
- fprintf(fplog, "Repl %d attempts, %d odd, %d even\n",
- re->nattempt[0]+re->nattempt[1], re->nattempt[1], re->nattempt[0]);
-
- fprintf(fplog, "Repl average probabilities:\n");
- for (i = 1; i < re->nrepl; i++)
- {
- if (re->nattempt[i%2] == 0)
- {
- re->prob[i] = 0;
- }
- else
- {
- re->prob[i] = re->prob_sum[i]/re->nattempt[i%2];
- }
- }
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
- print_prob(fplog, "", re->nrepl, re->prob);
-
- fprintf(fplog, "Repl number of exchanges:\n");
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
- print_count(fplog, "", re->nrepl, re->nexchange);
-
- fprintf(fplog, "Repl average number of exchanges:\n");
- for (i = 1; i < re->nrepl; i++)
- {
- if (re->nattempt[i%2] == 0)
- {
- re->prob[i] = 0;
- }
- else
- {
- re->prob[i] = ((real)re->nexchange[i])/re->nattempt[i%2];
- }
- }
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
- print_prob(fplog, "", re->nrepl, re->prob);
-
- fprintf(fplog, "\n");
- }
- /* print the transition matrix */
- print_transition_matrix(fplog, re->nrepl, re->nmoves, re->nattempt);
-}
-
-
-int replica_exchange_get_repl(const gmx_repl_ex_t re){
- return re->repl;
-};
-
-int replica_exchange_get_nrepl(const gmx_repl_ex_t re){
- return re->nrepl;
-};
-
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.cpp.preplumed b/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.cpp.preplumed
deleted file mode 100644
index 4b0e81063a0d383606a9bb2bcb00080d8ac89990..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.cpp.preplumed
+++ /dev/null
@@ -1,1440 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#include "gmxpre.h"
-
-#include "repl_ex.h"
-
-#include "config.h"
-
-#include <math.h>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/units.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/random/random.h"
-#include "gromacs/utility/smalloc.h"
-
-#define PROBABILITYCUTOFF 100
-/* we don't bother evaluating if events are more rare than exp(-100) = 3.7x10^-44 */
-
-enum {
- ereTEMP, ereLAMBDA, ereENDSINGLE, ereTL, ereNR
-};
-const char *erename[ereNR] = { "temperature", "lambda", "end_single_marker", "temperature and lambda"};
-/* end_single_marker merely notes the end of single variable replica exchange. All types higher than
- it are multiple replica exchange methods */
-/* Eventually, should add 'pressure', 'temperature and pressure', 'lambda_and_pressure', 'temperature_lambda_pressure'?;
- Let's wait until we feel better about the pressure control methods giving exact ensembles. Right now, we assume constant pressure */
-
-typedef struct gmx_repl_ex
-{
- int repl;
- int nrepl;
- real temp;
- int type;
- real **q;
- gmx_bool bNPT;
- real *pres;
- int *ind;
- int *allswaps;
- int nst;
- int nex;
- int seed;
- int nattempt[2];
- real *prob_sum;
- int **nmoves;
- int *nexchange;
- gmx_rng_t rng;
-
- /* these are helper arrays for replica exchange; allocated here so they
- don't have to be allocated each time */
- int *destinations;
- int **cyclic;
- int **order;
- int *tmpswap;
- gmx_bool *incycle;
- gmx_bool *bEx;
-
- /* helper arrays to hold the quantities that are exchanged */
- real *prob;
- real *Epot;
- real *beta;
- real *Vol;
- real **de;
-
-} t_gmx_repl_ex;
-
-static gmx_bool repl_quantity(const gmx_multisim_t *ms,
- struct gmx_repl_ex *re, int ere, real q)
-{
- real *qall;
- gmx_bool bDiff;
- int s;
-
- snew(qall, ms->nsim);
- qall[re->repl] = q;
- gmx_sum_sim(ms->nsim, qall, ms);
-
- bDiff = FALSE;
- for (s = 1; s < ms->nsim; s++)
- {
- if (qall[s] != qall[0])
- {
- bDiff = TRUE;
- }
- }
-
- if (bDiff)
- {
- /* Set the replica exchange type and quantities */
- re->type = ere;
-
- snew(re->q[ere], re->nrepl);
- for (s = 0; s < ms->nsim; s++)
- {
- re->q[ere][s] = qall[s];
- }
- }
- sfree(qall);
- return bDiff;
-}
-
-gmx_repl_ex_t init_replica_exchange(FILE *fplog,
- const gmx_multisim_t *ms,
- const t_state *state,
- const t_inputrec *ir,
- int nst, int nex, int init_seed)
-{
- real pres;
- int i, j, k;
- struct gmx_repl_ex *re;
- gmx_bool bTemp;
- gmx_bool bLambda = FALSE;
-
- fprintf(fplog, "\nInitializing Replica Exchange\n");
-
- if (ms == NULL || ms->nsim == 1)
- {
- gmx_fatal(FARGS, "Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
- }
- if (!EI_DYNAMICS(ir->eI))
- {
- gmx_fatal(FARGS, "Replica exchange is only supported by dynamical simulations");
- /* Note that PAR(cr) is defined by cr->nnodes > 1, which is
- * distinct from MULTISIM(cr). A multi-simulation only runs
- * with real MPI parallelism, but this does not imply PAR(cr)
- * is true!
- *
- * Since we are using a dynamical integrator, the only
- * decomposition is DD, so PAR(cr) and DOMAINDECOMP(cr) are
- * synonymous. The only way for cr->nnodes > 1 to be true is
- * if we are using DD. */
- }
-
- snew(re, 1);
-
- re->repl = ms->sim;
- re->nrepl = ms->nsim;
- snew(re->q, ereENDSINGLE);
-
- fprintf(fplog, "Repl There are %d replicas:\n", re->nrepl);
-
- check_multi_int(fplog, ms, state->natoms, "the number of atoms", FALSE);
- check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
- check_multi_int64(fplog, ms, ir->init_step+ir->nsteps, "init_step+nsteps", FALSE);
- check_multi_int64(fplog, ms, (ir->init_step+nst-1)/nst,
- "first exchange step: init_step/-replex", FALSE);
- check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
- check_multi_int(fplog, ms, ir->opts.ngtc,
- "the number of temperature coupling groups", FALSE);
- check_multi_int(fplog, ms, ir->epc, "the pressure coupling", FALSE);
- check_multi_int(fplog, ms, ir->efep, "free energy", FALSE);
- check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
-
- re->temp = ir->opts.ref_t[0];
- for (i = 1; (i < ir->opts.ngtc); i++)
- {
- if (ir->opts.ref_t[i] != re->temp)
- {
- fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
- fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
- }
- }
-
- re->type = -1;
- bTemp = repl_quantity(ms, re, ereTEMP, re->temp);
- if (ir->efep != efepNO)
- {
- bLambda = repl_quantity(ms, re, ereLAMBDA, (real)ir->fepvals->init_fep_state);
- }
- if (re->type == -1) /* nothing was assigned */
- {
- gmx_fatal(FARGS, "The properties of the %d systems are all the same, there is nothing to exchange", re->nrepl);
- }
- if (bLambda && bTemp)
- {
- re->type = ereTL;
- }
-
- if (bTemp)
- {
- please_cite(fplog, "Sugita1999a");
- if (ir->epc != epcNO)
- {
- re->bNPT = TRUE;
- fprintf(fplog, "Repl Using Constant Pressure REMD.\n");
- please_cite(fplog, "Okabe2001a");
- }
- if (ir->etc == etcBERENDSEN)
- {
- gmx_fatal(FARGS, "REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
- ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
- }
- }
- if (bLambda)
- {
- if (ir->fepvals->delta_lambda != 0) /* check this? */
- {
- gmx_fatal(FARGS, "delta_lambda is not zero");
- }
- }
- if (re->bNPT)
- {
- snew(re->pres, re->nrepl);
- if (ir->epct == epctSURFACETENSION)
- {
- pres = ir->ref_p[ZZ][ZZ];
- }
- else
- {
- pres = 0;
- j = 0;
- for (i = 0; i < DIM; i++)
- {
- if (ir->compress[i][i] != 0)
- {
- pres += ir->ref_p[i][i];
- j++;
- }
- }
- pres /= j;
- }
- re->pres[re->repl] = pres;
- gmx_sum_sim(re->nrepl, re->pres, ms);
- }
-
- /* Make an index for increasing replica order */
- /* only makes sense if one or the other is varying, not both!
- if both are varying, we trust the order the person gave. */
- snew(re->ind, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- re->ind[i] = i;
- }
-
- if (re->type < ereENDSINGLE)
- {
-
- for (i = 0; i < re->nrepl; i++)
- {
- for (j = i+1; j < re->nrepl; j++)
- {
- if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
- {
- /* Unordered replicas are supposed to work, but there
- * is still an issues somewhere.
- * Note that at this point still re->ind[i]=i.
- */
- gmx_fatal(FARGS, "Replicas with indices %d < %d have %ss %g > %g, please order your replicas on increasing %s",
- i, j,
- erename[re->type],
- re->q[re->type][i], re->q[re->type][j],
- erename[re->type]);
-
- k = re->ind[i];
- re->ind[i] = re->ind[j];
- re->ind[j] = k;
- }
- else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
- {
- gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
- }
- }
- }
- }
-
- /* keep track of all the swaps, starting with the initial placement. */
- snew(re->allswaps, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- re->allswaps[i] = re->ind[i];
- }
-
- switch (re->type)
- {
- case ereTEMP:
- fprintf(fplog, "\nReplica exchange in temperature\n");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %5.1f", re->q[re->type][re->ind[i]]);
- }
- fprintf(fplog, "\n");
- break;
- case ereLAMBDA:
- fprintf(fplog, "\nReplica exchange in lambda\n");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %3d", (int)re->q[re->type][re->ind[i]]);
- }
- fprintf(fplog, "\n");
- break;
- case ereTL:
- fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %5.1f", re->q[ereTEMP][re->ind[i]]);
- }
- fprintf(fplog, "\n");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %5d", (int)re->q[ereLAMBDA][re->ind[i]]);
- }
- fprintf(fplog, "\n");
- break;
- default:
- gmx_incons("Unknown replica exchange quantity");
- }
- if (re->bNPT)
- {
- fprintf(fplog, "\nRepl p");
- for (i = 0; i < re->nrepl; i++)
- {
- fprintf(fplog, " %5.2f", re->pres[re->ind[i]]);
- }
-
- for (i = 0; i < re->nrepl; i++)
- {
- if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
- {
- fprintf(fplog, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
- fprintf(stderr, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
- }
- }
- }
- re->nst = nst;
- if (init_seed == -1)
- {
- if (MASTERSIM(ms))
- {
- re->seed = (int)gmx_rng_make_seed();
- }
- else
- {
- re->seed = 0;
- }
- gmx_sumi_sim(1, &(re->seed), ms);
- }
- else
- {
- re->seed = init_seed;
- }
- fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
- fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
- re->rng = gmx_rng_init(re->seed);
-
- re->nattempt[0] = 0;
- re->nattempt[1] = 0;
-
- snew(re->prob_sum, re->nrepl);
- snew(re->nexchange, re->nrepl);
- snew(re->nmoves, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- snew(re->nmoves[i], re->nrepl);
- }
- fprintf(fplog, "Replica exchange information below: x=exchange, pr=probability\n");
-
- /* generate space for the helper functions so we don't have to snew each time */
-
- snew(re->destinations, re->nrepl);
- snew(re->incycle, re->nrepl);
- snew(re->tmpswap, re->nrepl);
- snew(re->cyclic, re->nrepl);
- snew(re->order, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- snew(re->cyclic[i], re->nrepl+1);
- snew(re->order[i], re->nrepl);
- }
- /* allocate space for the functions storing the data for the replicas */
- /* not all of these arrays needed in all cases, but they don't take
- up much space, since the max size is nrepl**2 */
- snew(re->prob, re->nrepl);
- snew(re->bEx, re->nrepl);
- snew(re->beta, re->nrepl);
- snew(re->Vol, re->nrepl);
- snew(re->Epot, re->nrepl);
- snew(re->de, re->nrepl);
- for (i = 0; i < re->nrepl; i++)
- {
- snew(re->de[i], re->nrepl);
- }
- re->nex = nex;
- return re;
-}
-
-static void exchange_reals(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, real *v, int n)
-{
- real *buf;
- int i;
-
- if (v)
- {
- snew(buf, n);
-#ifdef GMX_MPI
- /*
- MPI_Sendrecv(v, n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
- buf,n*sizeof(real),MPI_BYTE,MSRANK(ms,b),0,
- ms->mpi_comm_masters,MPI_STATUS_IGNORE);
- */
- {
- MPI_Request mpi_req;
-
- MPI_Isend(v, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, &mpi_req);
- MPI_Recv(buf, n*sizeof(real), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, MPI_STATUS_IGNORE);
- MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
- }
-#endif
- for (i = 0; i < n; i++)
- {
- v[i] = buf[i];
- }
- sfree(buf);
- }
-}
-
-
-static void exchange_ints(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, int *v, int n)
-{
- int *buf;
- int i;
-
- if (v)
- {
- snew(buf, n);
-#ifdef GMX_MPI
- /*
- MPI_Sendrecv(v, n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
- buf,n*sizeof(int),MPI_BYTE,MSRANK(ms,b),0,
- ms->mpi_comm_masters,MPI_STATUS_IGNORE);
- */
- {
- MPI_Request mpi_req;
-
- MPI_Isend(v, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, &mpi_req);
- MPI_Recv(buf, n*sizeof(int), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, MPI_STATUS_IGNORE);
- MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
- }
-#endif
- for (i = 0; i < n; i++)
- {
- v[i] = buf[i];
- }
- sfree(buf);
- }
-}
-
-static void exchange_doubles(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, double *v, int n)
-{
- double *buf;
- int i;
-
- if (v)
- {
- snew(buf, n);
-#ifdef GMX_MPI
- /*
- MPI_Sendrecv(v, n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
- buf,n*sizeof(double),MPI_BYTE,MSRANK(ms,b),0,
- ms->mpi_comm_masters,MPI_STATUS_IGNORE);
- */
- {
- MPI_Request mpi_req;
-
- MPI_Isend(v, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, &mpi_req);
- MPI_Recv(buf, n*sizeof(double), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, MPI_STATUS_IGNORE);
- MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
- }
-#endif
- for (i = 0; i < n; i++)
- {
- v[i] = buf[i];
- }
- sfree(buf);
- }
-}
-
-static void exchange_rvecs(const gmx_multisim_t gmx_unused *ms, int gmx_unused b, rvec *v, int n)
-{
- rvec *buf;
- int i;
-
- if (v)
- {
- snew(buf, n);
-#ifdef GMX_MPI
- /*
- MPI_Sendrecv(v[0], n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
- buf[0],n*sizeof(rvec),MPI_BYTE,MSRANK(ms,b),0,
- ms->mpi_comm_masters,MPI_STATUS_IGNORE);
- */
- {
- MPI_Request mpi_req;
-
- MPI_Isend(v[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, &mpi_req);
- MPI_Recv(buf[0], n*sizeof(rvec), MPI_BYTE, MSRANK(ms, b), 0,
- ms->mpi_comm_masters, MPI_STATUS_IGNORE);
- MPI_Wait(&mpi_req, MPI_STATUS_IGNORE);
- }
-#endif
- for (i = 0; i < n; i++)
- {
- copy_rvec(buf[i], v[i]);
- }
- sfree(buf);
- }
-}
-
-static void exchange_state(const gmx_multisim_t *ms, int b, t_state *state)
-{
- /* When t_state changes, this code should be updated. */
- int ngtc, nnhpres;
- ngtc = state->ngtc * state->nhchainlength;
- nnhpres = state->nnhpres* state->nhchainlength;
- exchange_rvecs(ms, b, state->box, DIM);
- exchange_rvecs(ms, b, state->box_rel, DIM);
- exchange_rvecs(ms, b, state->boxv, DIM);
- exchange_reals(ms, b, &(state->veta), 1);
- exchange_reals(ms, b, &(state->vol0), 1);
- exchange_rvecs(ms, b, state->svir_prev, DIM);
- exchange_rvecs(ms, b, state->fvir_prev, DIM);
- exchange_rvecs(ms, b, state->pres_prev, DIM);
- exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
- exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
- exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
- exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
- exchange_doubles(ms, b, state->therm_integral, state->ngtc);
- exchange_rvecs(ms, b, state->x, state->natoms);
- exchange_rvecs(ms, b, state->v, state->natoms);
- exchange_rvecs(ms, b, state->sd_X, state->natoms);
-}
-
-static void copy_rvecs(rvec *s, rvec *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- copy_rvec(s[i], d[i]);
- }
- }
-}
-
-static void copy_doubles(const double *s, double *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
- }
-}
-
-static void copy_reals(const real *s, real *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
- }
-}
-
-static void copy_ints(const int *s, int *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
- }
-}
-
-#define scopy_rvecs(v, n) copy_rvecs(state->v, state_local->v, n);
-#define scopy_doubles(v, n) copy_doubles(state->v, state_local->v, n);
-#define scopy_reals(v, n) copy_reals(state->v, state_local->v, n);
-#define scopy_ints(v, n) copy_ints(state->v, state_local->v, n);
-
-static void copy_state_nonatomdata(t_state *state, t_state *state_local)
-{
- /* When t_state changes, this code should be updated. */
- int ngtc, nnhpres;
- ngtc = state->ngtc * state->nhchainlength;
- nnhpres = state->nnhpres* state->nhchainlength;
- scopy_rvecs(box, DIM);
- scopy_rvecs(box_rel, DIM);
- scopy_rvecs(boxv, DIM);
- state_local->veta = state->veta;
- state_local->vol0 = state->vol0;
- scopy_rvecs(svir_prev, DIM);
- scopy_rvecs(fvir_prev, DIM);
- scopy_rvecs(pres_prev, DIM);
- scopy_doubles(nosehoover_xi, ngtc);
- scopy_doubles(nosehoover_vxi, ngtc);
- scopy_doubles(nhpres_xi, nnhpres);
- scopy_doubles(nhpres_vxi, nnhpres);
- scopy_doubles(therm_integral, state->ngtc);
- scopy_rvecs(x, state->natoms);
- scopy_rvecs(v, state->natoms);
- scopy_rvecs(sd_X, state->natoms);
- copy_ints(&(state->fep_state), &(state_local->fep_state), 1);
- scopy_reals(lambda, efptNR);
-}
-
-static void scale_velocities(t_state *state, real fac)
-{
- int i;
-
- if (state->v)
- {
- for (i = 0; i < state->natoms; i++)
- {
- svmul(fac, state->v[i], state->v[i]);
- }
- }
-}
-
-static void print_transition_matrix(FILE *fplog, int n, int **nmoves, int *nattempt)
-{
- int i, j, ntot;
- float Tprint;
-
- ntot = nattempt[0] + nattempt[1];
- fprintf(fplog, "\n");
- fprintf(fplog, "Repl");
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, " "); /* put the title closer to the center */
- }
- fprintf(fplog, "Empirical Transition Matrix\n");
-
- fprintf(fplog, "Repl");
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, "%8d", (i+1));
- }
- fprintf(fplog, "\n");
-
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, "Repl");
- for (j = 0; j < n; j++)
- {
- Tprint = 0.0;
- if (nmoves[i][j] > 0)
- {
- Tprint = nmoves[i][j]/(2.0*ntot);
- }
- fprintf(fplog, "%8.4f", Tprint);
- }
- fprintf(fplog, "%3d\n", i);
- }
-}
-
-static void print_ind(FILE *fplog, const char *leg, int n, int *ind, gmx_bool *bEx)
-{
- int i;
-
- fprintf(fplog, "Repl %2s %2d", leg, ind[0]);
- for (i = 1; i < n; i++)
- {
- fprintf(fplog, " %c %2d", (bEx != 0 && bEx[i]) ? 'x' : ' ', ind[i]);
- }
- fprintf(fplog, "\n");
-}
-
-static void print_allswitchind(FILE *fplog, int n, int *pind, int *allswaps, int *tmpswap)
-{
- int i;
-
- for (i = 0; i < n; i++)
- {
- tmpswap[i] = allswaps[i];
- }
- for (i = 0; i < n; i++)
- {
- allswaps[i] = tmpswap[pind[i]];
- }
-
- fprintf(fplog, "\nAccepted Exchanges: ");
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, "%d ", pind[i]);
- }
- fprintf(fplog, "\n");
-
- /* the "Order After Exchange" is the state label corresponding to the configuration that
- started in state listed in order, i.e.
-
- 3 0 1 2
-
- means that the:
- configuration starting in simulation 3 is now in simulation 0,
- configuration starting in simulation 0 is now in simulation 1,
- configuration starting in simulation 1 is now in simulation 2,
- configuration starting in simulation 2 is now in simulation 3
- */
- fprintf(fplog, "Order After Exchange: ");
- for (i = 0; i < n; i++)
- {
- fprintf(fplog, "%d ", allswaps[i]);
- }
- fprintf(fplog, "\n\n");
-}
-
-static void print_prob(FILE *fplog, const char *leg, int n, real *prob)
-{
- int i;
- char buf[8];
-
- fprintf(fplog, "Repl %2s ", leg);
- for (i = 1; i < n; i++)
- {
- if (prob[i] >= 0)
- {
- sprintf(buf, "%4.2f", prob[i]);
- fprintf(fplog, " %3s", buf[0] == '1' ? "1.0" : buf+1);
- }
- else
- {
- fprintf(fplog, " ");
- }
- }
- fprintf(fplog, "\n");
-}
-
-static void print_count(FILE *fplog, const char *leg, int n, int *count)
-{
- int i;
-
- fprintf(fplog, "Repl %2s ", leg);
- for (i = 1; i < n; i++)
- {
- fprintf(fplog, " %4d", count[i]);
- }
- fprintf(fplog, "\n");
-}
-
-static real calc_delta(FILE *fplog, gmx_bool bPrint, struct gmx_repl_ex *re, int a, int b, int ap, int bp)
-{
-
- real ediff, dpV, delta = 0;
- real *Epot = re->Epot;
- real *Vol = re->Vol;
- real **de = re->de;
- real *beta = re->beta;
-
- /* Two cases; we are permuted and not. In all cases, setting ap = a and bp = b will reduce
- to the non permuted case */
-
- switch (re->type)
- {
- case ereTEMP:
- /*
- * Okabe et. al. Chem. Phys. Lett. 335 (2001) 435-439
- */
- ediff = Epot[b] - Epot[a];
- delta = -(beta[bp] - beta[ap])*ediff;
- break;
- case ereLAMBDA:
- /* two cases: when we are permuted, and not. */
- /* non-permuted:
- ediff = E_new - E_old
- = [H_b(x_a) + H_a(x_b)] - [H_b(x_b) + H_a(x_a)]
- = [H_b(x_a) - H_a(x_a)] + [H_a(x_b) - H_b(x_b)]
- = de[b][a] + de[a][b] */
-
- /* permuted:
- ediff = E_new - E_old
- = [H_bp(x_a) + H_ap(x_b)] - [H_bp(x_b) + H_ap(x_a)]
- = [H_bp(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_bp(x_b)]
- = [H_bp(x_a) - H_a(x_a) + H_a(x_a) - H_ap(x_a)] + [H_ap(x_b) - H_b(x_b) + H_b(x_b) - H_bp(x_b)]
- = [H_bp(x_a) - H_a(x_a)] - [H_ap(x_a) - H_a(x_a)] + [H_ap(x_b) - H_b(x_b)] - H_bp(x_b) - H_b(x_b)]
- = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]) */
- /* but, in the current code implementation, we flip configurations, not indices . . .
- So let's examine that.
- = [H_b(x_ap) - H_a(x_a)] - [H_a(x_ap) - H_a(x_a)] + [H_a(x_bp) - H_b(x_b)] - H_b(x_bp) - H_b(x_b)]
- = [H_b(x_ap) - H_a(x_ap)] + [H_a(x_bp) - H_b(x_pb)]
- = (de[b][ap] - de[a][ap]) + (de[a][bp] - de[b][bp]
- So, if we exchange b<=> bp and a<=> ap, we return to the same result.
- So the simple solution is to flip the
- position of perturbed and original indices in the tests.
- */
-
- ediff = (de[bp][a] - de[ap][a]) + (de[ap][b] - de[bp][b]);
- delta = ediff*beta[a]; /* assume all same temperature in this case */
- break;
- case ereTL:
- /* not permuted: */
- /* delta = reduced E_new - reduced E_old
- = [beta_b H_b(x_a) + beta_a H_a(x_b)] - [beta_b H_b(x_b) + beta_a H_a(x_a)]
- = [beta_b H_b(x_a) - beta_a H_a(x_a)] + [beta_a H_a(x_b) - beta_b H_b(x_b)]
- = [beta_b dH_b(x_a) + beta_b H_a(x_a) - beta_a H_a(x_a)] +
- [beta_a dH_a(x_b) + beta_a H_b(x_b) - beta_b H_b(x_b)]
- = [beta_b dH_b(x_a) + [beta_a dH_a(x_b) +
- beta_b (H_a(x_a) - H_b(x_b)]) - beta_a (H_a(x_a) - H_b(x_b))
- = beta_b dH_b(x_a) + beta_a dH_a(x_b) - (beta_b - beta_a)(H_b(x_b) - H_a(x_a) */
- /* delta = beta[b]*de[b][a] + beta[a]*de[a][b] - (beta[b] - beta[a])*(Epot[b] - Epot[a]; */
- /* permuted (big breath!) */
- /* delta = reduced E_new - reduced E_old
- = [beta_bp H_bp(x_a) + beta_ap H_ap(x_b)] - [beta_bp H_bp(x_b) + beta_ap H_ap(x_a)]
- = [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
- = [beta_bp H_bp(x_a) - beta_ap H_ap(x_a)] + [beta_ap H_ap(x_b) - beta_bp H_bp(x_b)]
- - beta_pb H_a(x_a) + beta_ap H_a(x_a) + beta_pb H_a(x_a) - beta_ap H_a(x_a)
- - beta_ap H_b(x_b) + beta_bp H_b(x_b) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
- = [(beta_bp H_bp(x_a) - beta_bp H_a(x_a)) - (beta_ap H_ap(x_a) - beta_ap H_a(x_a))] +
- [(beta_ap H_ap(x_b) - beta_ap H_b(x_b)) - (beta_bp H_bp(x_b) - beta_bp H_b(x_b))]
- + beta_pb H_a(x_a) - beta_ap H_a(x_a) + beta_ap H_b(x_b) - beta_bp H_b(x_b)
- = [beta_bp (H_bp(x_a) - H_a(x_a)) - beta_ap (H_ap(x_a) - H_a(x_a))] +
- [beta_ap (H_ap(x_b) - H_b(x_b)) - beta_bp (H_bp(x_b) - H_b(x_b))]
- + beta_pb (H_a(x_a) - H_b(x_b)) - beta_ap (H_a(x_a) - H_b(x_b))
- = ([beta_bp de[bp][a] - beta_ap de[ap][a]) + beta_ap de[ap][b] - beta_bp de[bp][b])
- + (beta_pb-beta_ap)(H_a(x_a) - H_b(x_b)) */
- delta = beta[bp]*(de[bp][a] - de[bp][b]) + beta[ap]*(de[ap][b] - de[ap][a]) - (beta[bp]-beta[ap])*(Epot[b]-Epot[a]);
- break;
- default:
- gmx_incons("Unknown replica exchange quantity");
- }
- if (bPrint)
- {
- fprintf(fplog, "Repl %d <-> %d dE_term = %10.3e (kT)\n", a, b, delta);
- }
- if (re->bNPT)
- {
- /* revist the calculation for 5.0. Might be some improvements. */
- dpV = (beta[ap]*re->pres[ap]-beta[bp]*re->pres[bp])*(Vol[b]-Vol[a])/PRESFAC;
- if (bPrint)
- {
- fprintf(fplog, " dpV = %10.3e d = %10.3e\n", dpV, delta + dpV);
- }
- delta += dpV;
- }
- return delta;
-}
-
-static void
-test_for_replica_exchange(FILE *fplog,
- const gmx_multisim_t *ms,
- struct gmx_repl_ex *re,
- gmx_enerdata_t *enerd,
- real vol,
- gmx_int64_t step,
- real time)
-{
- int m, i, j, a, b, ap, bp, i0, i1, tmp;
- real delta = 0;
- gmx_bool bPrint, bMultiEx;
- gmx_bool *bEx = re->bEx;
- real *prob = re->prob;
- int *pind = re->destinations; /* permuted index */
- gmx_bool bEpot = FALSE;
- gmx_bool bDLambda = FALSE;
- gmx_bool bVol = FALSE;
-
- bMultiEx = (re->nex > 1); /* multiple exchanges at each state */
- fprintf(fplog, "Replica exchange at step %" GMX_PRId64 " time %.5f\n", step, time);
-
- if (re->bNPT)
- {
- for (i = 0; i < re->nrepl; i++)
- {
- re->Vol[i] = 0;
- }
- bVol = TRUE;
- re->Vol[re->repl] = vol;
- }
- if ((re->type == ereTEMP || re->type == ereTL))
- {
- for (i = 0; i < re->nrepl; i++)
- {
- re->Epot[i] = 0;
- }
- bEpot = TRUE;
- re->Epot[re->repl] = enerd->term[F_EPOT];
- /* temperatures of different states*/
- for (i = 0; i < re->nrepl; i++)
- {
- re->beta[i] = 1.0/(re->q[ereTEMP][i]*BOLTZ);
- }
- }
- else
- {
- for (i = 0; i < re->nrepl; i++)
- {
- re->beta[i] = 1.0/(re->temp*BOLTZ); /* we have a single temperature */
- }
- }
- if (re->type == ereLAMBDA || re->type == ereTL)
- {
- bDLambda = TRUE;
- /* lambda differences. */
- /* de[i][j] is the energy of the jth simulation in the ith Hamiltonian
- minus the energy of the jth simulation in the jth Hamiltonian */
- for (i = 0; i < re->nrepl; i++)
- {
- for (j = 0; j < re->nrepl; j++)
- {
- re->de[i][j] = 0;
- }
- }
- for (i = 0; i < re->nrepl; i++)
- {
- re->de[i][re->repl] = (enerd->enerpart_lambda[(int)re->q[ereLAMBDA][i]+1]-enerd->enerpart_lambda[0]);
- }
- }
-
- /* now actually do the communication */
- if (bVol)
- {
- gmx_sum_sim(re->nrepl, re->Vol, ms);
- }
- if (bEpot)
- {
- gmx_sum_sim(re->nrepl, re->Epot, ms);
- }
- if (bDLambda)
- {
- for (i = 0; i < re->nrepl; i++)
- {
- gmx_sum_sim(re->nrepl, re->de[i], ms);
- }
- }
-
- /* make a duplicate set of indices for shuffling */
- for (i = 0; i < re->nrepl; i++)
- {
- pind[i] = re->ind[i];
- }
-
- if (bMultiEx)
- {
- /* multiple random switch exchange */
- int nself = 0;
- for (i = 0; i < re->nex + nself; i++)
- {
- double rnd[2];
-
- gmx_rng_cycle_2uniform(step, i*2, re->seed, RND_SEED_REPLEX, rnd);
- /* randomly select a pair */
- /* in theory, could reduce this by identifying only which switches had a nonneglibible
- probability of occurring (log p > -100) and only operate on those switches */
- /* find out which state it is from, and what label that state currently has. Likely
- more work that useful. */
- i0 = (int)(re->nrepl*rnd[0]);
- i1 = (int)(re->nrepl*rnd[1]);
- if (i0 == i1)
- {
- nself++;
- continue; /* self-exchange, back up and do it again */
- }
-
- a = re->ind[i0]; /* what are the indices of these states? */
- b = re->ind[i1];
- ap = pind[i0];
- bp = pind[i1];
-
- bPrint = FALSE; /* too noisy */
- /* calculate the energy difference */
- /* if the code changes to flip the STATES, rather than the configurations,
- use the commented version of the code */
- /* delta = calc_delta(fplog,bPrint,re,a,b,ap,bp); */
- delta = calc_delta(fplog, bPrint, re, ap, bp, a, b);
-
- /* we actually only use the first space in the prob and bEx array,
- since there are actually many switches between pairs. */
-
- if (delta <= 0)
- {
- /* accepted */
- prob[0] = 1;
- bEx[0] = TRUE;
- }
- else
- {
- if (delta > PROBABILITYCUTOFF)
- {
- prob[0] = 0;
- }
- else
- {
- prob[0] = exp(-delta);
- }
- /* roll a number to determine if accepted */
- gmx_rng_cycle_2uniform(step, i*2+1, re->seed, RND_SEED_REPLEX, rnd);
- bEx[0] = rnd[0] < prob[0];
- }
- re->prob_sum[0] += prob[0];
-
- if (bEx[0])
- {
- /* swap the states */
- tmp = pind[i0];
- pind[i0] = pind[i1];
- pind[i1] = tmp;
- }
- }
- re->nattempt[0]++; /* keep track of total permutation trials here */
- print_allswitchind(fplog, re->nrepl, pind, re->allswaps, re->tmpswap);
- }
- else
- {
- /* standard nearest neighbor replica exchange */
-
- m = (step / re->nst) % 2;
- for (i = 1; i < re->nrepl; i++)
- {
- a = re->ind[i-1];
- b = re->ind[i];
-
- bPrint = (re->repl == a || re->repl == b);
- if (i % 2 == m)
- {
- delta = calc_delta(fplog, bPrint, re, a, b, a, b);
- if (delta <= 0)
- {
- /* accepted */
- prob[i] = 1;
- bEx[i] = TRUE;
- }
- else
- {
- double rnd[2];
-
- if (delta > PROBABILITYCUTOFF)
- {
- prob[i] = 0;
- }
- else
- {
- prob[i] = exp(-delta);
- }
- /* roll a number to determine if accepted */
- gmx_rng_cycle_2uniform(step, i, re->seed, RND_SEED_REPLEX, rnd);
- bEx[i] = rnd[0] < prob[i];
- }
- re->prob_sum[i] += prob[i];
-
- if (bEx[i])
- {
- /* swap these two */
- tmp = pind[i-1];
- pind[i-1] = pind[i];
- pind[i] = tmp;
- re->nexchange[i]++; /* statistics for back compatibility */
- }
- }
- else
- {
- prob[i] = -1;
- bEx[i] = FALSE;
- }
- }
- /* print some statistics */
- print_ind(fplog, "ex", re->nrepl, re->ind, bEx);
- print_prob(fplog, "pr", re->nrepl, prob);
- fprintf(fplog, "\n");
- re->nattempt[m]++;
- }
-
- /* record which moves were made and accepted */
- for (i = 0; i < re->nrepl; i++)
- {
- re->nmoves[re->ind[i]][pind[i]] += 1;
- re->nmoves[pind[i]][re->ind[i]] += 1;
- }
- fflush(fplog); /* make sure we can see what the last exchange was */
-}
-
-static void write_debug_x(t_state *state)
-{
- int i;
-
- if (debug)
- {
- for (i = 0; i < state->natoms; i += 10)
- {
- fprintf(debug, "dx %5d %10.5f %10.5f %10.5f\n", i, state->x[i][XX], state->x[i][YY], state->x[i][ZZ]);
- }
- }
-}
-
-static void
-cyclic_decomposition(const int *destinations,
- int **cyclic,
- gmx_bool *incycle,
- const int nrepl,
- int *nswap)
-{
-
- int i, j, c, p;
- int maxlen = 1;
- for (i = 0; i < nrepl; i++)
- {
- incycle[i] = FALSE;
- }
- for (i = 0; i < nrepl; i++) /* one cycle for each replica */
- {
- if (incycle[i])
- {
- cyclic[i][0] = -1;
- continue;
- }
- cyclic[i][0] = i;
- incycle[i] = TRUE;
- c = 1;
- p = i;
- for (j = 0; j < nrepl; j++) /* potentially all cycles are part, but we will break first */
- {
- p = destinations[p]; /* start permuting */
- if (p == i)
- {
- cyclic[i][c] = -1;
- if (c > maxlen)
- {
- maxlen = c;
- }
- break; /* we've reached the original element, the cycle is complete, and we marked the end. */
- }
- else
- {
- cyclic[i][c] = p; /* each permutation gives a new member of the cycle */
- incycle[p] = TRUE;
- c++;
- }
- }
- }
- *nswap = maxlen - 1;
-
- if (debug)
- {
- for (i = 0; i < nrepl; i++)
- {
- fprintf(debug, "Cycle %d:", i);
- for (j = 0; j < nrepl; j++)
- {
- if (cyclic[i][j] < 0)
- {
- break;
- }
- fprintf(debug, "%2d", cyclic[i][j]);
- }
- fprintf(debug, "\n");
- }
- fflush(debug);
- }
-}
-
-static void
-compute_exchange_order(FILE *fplog,
- int **cyclic,
- int **order,
- const int nrepl,
- const int maxswap)
-{
- int i, j;
-
- for (j = 0; j < maxswap; j++)
- {
- for (i = 0; i < nrepl; i++)
- {
- if (cyclic[i][j+1] >= 0)
- {
- order[cyclic[i][j+1]][j] = cyclic[i][j];
- order[cyclic[i][j]][j] = cyclic[i][j+1];
- }
- }
- for (i = 0; i < nrepl; i++)
- {
- if (order[i][j] < 0)
- {
- order[i][j] = i; /* if it's not exchanging, it should stay this round*/
- }
- }
- }
-
- if (debug)
- {
- fprintf(fplog, "Replica Exchange Order\n");
- for (i = 0; i < nrepl; i++)
- {
- fprintf(fplog, "Replica %d:", i);
- for (j = 0; j < maxswap; j++)
- {
- if (order[i][j] < 0)
- {
- break;
- }
- fprintf(debug, "%2d", order[i][j]);
- }
- fprintf(fplog, "\n");
- }
- fflush(fplog);
- }
-}
-
-static void
-prepare_to_do_exchange(FILE *fplog,
- struct gmx_repl_ex *re,
- const int replica_id,
- int *maxswap,
- gmx_bool *bThisReplicaExchanged)
-{
- int i, j;
- /* Hold the cyclic decomposition of the (multiple) replica
- * exchange. */
- gmx_bool bAnyReplicaExchanged = FALSE;
- *bThisReplicaExchanged = FALSE;
-
- for (i = 0; i < re->nrepl; i++)
- {
- if (re->destinations[i] != re->ind[i])
- {
- /* only mark as exchanged if the index has been shuffled */
- bAnyReplicaExchanged = TRUE;
- break;
- }
- }
- if (bAnyReplicaExchanged)
- {
- /* reinitialize the placeholder arrays */
- for (i = 0; i < re->nrepl; i++)
- {
- for (j = 0; j < re->nrepl; j++)
- {
- re->cyclic[i][j] = -1;
- re->order[i][j] = -1;
- }
- }
-
- /* Identify the cyclic decomposition of the permutation (very
- * fast if neighbor replica exchange). */
- cyclic_decomposition(re->destinations, re->cyclic, re->incycle, re->nrepl, maxswap);
-
- /* Now translate the decomposition into a replica exchange
- * order at each step. */
- compute_exchange_order(fplog, re->cyclic, re->order, re->nrepl, *maxswap);
-
- /* Did this replica do any exchange at any point? */
- for (j = 0; j < *maxswap; j++)
- {
- if (replica_id != re->order[replica_id][j])
- {
- *bThisReplicaExchanged = TRUE;
- break;
- }
- }
- }
-}
-
-gmx_bool replica_exchange(FILE *fplog, const t_commrec *cr, struct gmx_repl_ex *re,
- t_state *state, gmx_enerdata_t *enerd,
- t_state *state_local, gmx_int64_t step, real time)
-{
- int j;
- int replica_id = 0;
- int exchange_partner;
- int maxswap = 0;
- /* Number of rounds of exchanges needed to deal with any multiple
- * exchanges. */
- /* Where each replica ends up after the exchange attempt(s). */
- /* The order in which multiple exchanges will occur. */
- gmx_bool bThisReplicaExchanged = FALSE;
-
- if (MASTER(cr))
- {
- replica_id = re->repl;
- test_for_replica_exchange(fplog, cr->ms, re, enerd, det(state_local->box), step, time);
- prepare_to_do_exchange(fplog, re, replica_id, &maxswap, &bThisReplicaExchanged);
- }
- /* Do intra-simulation broadcast so all processors belonging to
- * each simulation know whether they need to participate in
- * collecting the state. Otherwise, they might as well get on with
- * the next thing to do. */
- if (DOMAINDECOMP(cr))
- {
-#ifdef GMX_MPI
- MPI_Bcast(&bThisReplicaExchanged, sizeof(gmx_bool), MPI_BYTE, MASTERRANK(cr),
- cr->mpi_comm_mygroup);
-#endif
- }
-
- if (bThisReplicaExchanged)
- {
- /* Exchange the states */
- /* Collect the global state on the master node */
- if (DOMAINDECOMP(cr))
- {
- dd_collect_state(cr->dd, state_local, state);
- }
- else
- {
- copy_state_nonatomdata(state_local, state);
- }
-
- if (MASTER(cr))
- {
- /* There will be only one swap cycle with standard replica
- * exchange, but there may be multiple swap cycles if we
- * allow multiple swaps. */
-
- for (j = 0; j < maxswap; j++)
- {
- exchange_partner = re->order[replica_id][j];
-
- if (exchange_partner != replica_id)
- {
- /* Exchange the global states between the master nodes */
- if (debug)
- {
- fprintf(debug, "Exchanging %d with %d\n", replica_id, exchange_partner);
- }
- exchange_state(cr->ms, exchange_partner, state);
- }
- }
- /* For temperature-type replica exchange, we need to scale
- * the velocities. */
- if (re->type == ereTEMP || re->type == ereTL)
- {
- scale_velocities(state, sqrt(re->q[ereTEMP][replica_id]/re->q[ereTEMP][re->destinations[replica_id]]));
- }
-
- }
-
- /* With domain decomposition the global state is distributed later */
- if (!DOMAINDECOMP(cr))
- {
- /* Copy the global state to the local state data structure */
- copy_state_nonatomdata(state, state_local);
- }
- }
-
- return bThisReplicaExchanged;
-}
-
-void print_replica_exchange_statistics(FILE *fplog, struct gmx_repl_ex *re)
-{
- int i;
-
- fprintf(fplog, "\nReplica exchange statistics\n");
-
- if (re->nex == 0)
- {
- fprintf(fplog, "Repl %d attempts, %d odd, %d even\n",
- re->nattempt[0]+re->nattempt[1], re->nattempt[1], re->nattempt[0]);
-
- fprintf(fplog, "Repl average probabilities:\n");
- for (i = 1; i < re->nrepl; i++)
- {
- if (re->nattempt[i%2] == 0)
- {
- re->prob[i] = 0;
- }
- else
- {
- re->prob[i] = re->prob_sum[i]/re->nattempt[i%2];
- }
- }
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
- print_prob(fplog, "", re->nrepl, re->prob);
-
- fprintf(fplog, "Repl number of exchanges:\n");
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
- print_count(fplog, "", re->nrepl, re->nexchange);
-
- fprintf(fplog, "Repl average number of exchanges:\n");
- for (i = 1; i < re->nrepl; i++)
- {
- if (re->nattempt[i%2] == 0)
- {
- re->prob[i] = 0;
- }
- else
- {
- re->prob[i] = ((real)re->nexchange[i])/re->nattempt[i%2];
- }
- }
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
- print_prob(fplog, "", re->nrepl, re->prob);
-
- fprintf(fplog, "\n");
- }
- /* print the transition matrix */
- print_transition_matrix(fplog, re->nrepl, re->nmoves, re->nattempt);
-}
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.h b/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.h
deleted file mode 100644
index 29d7bfa4954834b9b02dcaed60e0e4f496e3ff67..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.h
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef _repl_ex_h
-#define _repl_ex_h
-
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* Abstract type for replica exchange */
-typedef struct gmx_repl_ex *gmx_repl_ex_t;
-
-extern gmx_repl_ex_t init_replica_exchange(FILE *fplog,
- const gmx_multisim_t *ms,
- const t_state *state,
- const t_inputrec *ir,
- int nst, int nmultiex, int init_seed);
-/* Should only be called on the master nodes */
-
-extern gmx_bool replica_exchange(FILE *fplog,
- const t_commrec *cr,
- gmx_repl_ex_t re,
- t_state *state, gmx_enerdata_t *enerd,
- t_state *state_local,
- gmx_int64_t step, real time);
-/* Attempts replica exchange, should be called on all nodes.
- * Returns TRUE if this state has been exchanged.
- * When running each replica in parallel,
- * this routine collects the state on the master node before exchange.
- * With domain decomposition, the global state after exchange is stored
- * in state and still needs to be redistributed over the nodes.
- */
-
-extern void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
-/* Should only be called on the master nodes */
-
-extern int replica_exchange_get_repl(const gmx_repl_ex_t re);
-extern int replica_exchange_get_nrepl(const gmx_repl_ex_t re);
-extern void pd_collect_state(const t_commrec *cr, t_state *state);
-extern void exchange_state(const gmx_multisim_t *ms, int b, t_state *state);
-extern void copy_state_nonatomdata(t_state *state, t_state *state_local);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _repl_ex_h */
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.h.preplumed b/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.h.preplumed
deleted file mode 100644
index ffedd2305f626acdec1086a2aaa0169a029548f8..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/repl_ex.h.preplumed
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#ifndef _repl_ex_h
-#define _repl_ex_h
-
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-/* Abstract type for replica exchange */
-typedef struct gmx_repl_ex *gmx_repl_ex_t;
-
-extern gmx_repl_ex_t init_replica_exchange(FILE *fplog,
- const gmx_multisim_t *ms,
- const t_state *state,
- const t_inputrec *ir,
- int nst, int nmultiex, int init_seed);
-/* Should only be called on the master nodes */
-
-extern gmx_bool replica_exchange(FILE *fplog,
- const t_commrec *cr,
- gmx_repl_ex_t re,
- t_state *state, gmx_enerdata_t *enerd,
- t_state *state_local,
- gmx_int64_t step, real time);
-/* Attempts replica exchange, should be called on all nodes.
- * Returns TRUE if this state has been exchanged.
- * When running each replica in parallel,
- * this routine collects the state on the master node before exchange.
- * With domain decomposition, the global state after exchange is stored
- * in state and still needs to be redistributed over the nodes.
- */
-
-extern void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
-/* Should only be called on the master nodes */
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _repl_ex_h */
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/runner.cpp b/patches/gromacs-5.1.4.diff/src/programs/mdrun/runner.cpp
deleted file mode 100644
index 6e1adee9cf5fc7dacc09308331d9484261210de3..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/runner.cpp
+++ /dev/null
@@ -1,1363 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <assert.h>
-#include <signal.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include <algorithm>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/ewald/pme.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/gmx_thread_affinity.h"
-#include "gromacs/legacyheaders/inputrec.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/sighandler.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/calc_verletbuf.h"
-#include "gromacs/mdlib/nbnxn_search.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/swap/swapcoords.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/smalloc.h"
-
-#include "deform.h"
-#include "membed.h"
-#include "repl_ex.h"
-#include "resource-division.h"
-
-/* PLUMED */
-#include "../../../Plumed.h"
-extern int plumedswitch;
-extern plumed plumedmain;
-/* END PLUMED */
-
-#ifdef GMX_FAHCORE
-#include "corewrap.h"
-#endif
-
-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_int64_t deform_init_init_step_tpx;
-matrix deform_init_box_tpx;
-tMPI_Thread_mutex_t deform_init_box_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-
-
-#ifdef GMX_THREAD_MPI
-/* The minimum number of atoms per tMPI thread. With fewer atoms than this,
- * the number of threads will get lowered.
- */
-#define MIN_ATOMS_PER_MPI_THREAD 90
-#define MIN_ATOMS_PER_GPU 900
-
-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;
- int nstlist_cmdline;
- gmx_int64_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;
- int imdport;
- unsigned long Flags;
-};
-
-
-/* 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 = reinitialize_commrec_for_this_thread(mc.cr);
-
- if (MASTER(cr))
- {
- fplog = mc.fplog;
- }
-
- 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.nstlist_cmdline,
- 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.imdport, 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, int nstlist_cmdline,
- gmx_int64_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,
- 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 */
- /* hw_opt contains pointers, which should all be NULL at this stage */
- 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->nstlist_cmdline = nstlist_cmdline;
- 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->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;
- }
-
- crn = reinitialize_commrec_for_this_thread(cr);
- return crn;
-}
-
-#endif /* GMX_THREAD_MPI */
-
-
-/* We determine the extra cost of the non-bonded kernels compared to
- * a reference nstlist value of 10 (which is the default in grompp).
- */
-static const int nbnxnReferenceNstlist = 10;
-/* The values to try when switching */
-const int nstlist_try[] = { 20, 25, 40 };
-#define NNSTL sizeof(nstlist_try)/sizeof(nstlist_try[0])
-/* Increase nstlist until the non-bonded cost increases more than listfac_ok,
- * but never more than listfac_max.
- * A standard (protein+)water system at 300K with PME ewald_rtol=1e-5
- * needs 1.28 at rcoulomb=0.9 and 1.24 at rcoulomb=1.0 to get to nstlist=40.
- * Note that both CPU and GPU factors are conservative. Performance should
- * not go down due to this tuning, except with a relatively slow GPU.
- * On the other hand, at medium/high parallelization or with fast GPUs
- * nstlist will not be increased enough to reach optimal performance.
- */
-/* CPU: pair-search is about a factor 1.5 slower than the non-bonded kernel */
-static const float nbnxn_cpu_listfac_ok = 1.05;
-static const float nbnxn_cpu_listfac_max = 1.09;
-/* GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel */
-static const float nbnxn_gpu_listfac_ok = 1.20;
-static const float nbnxn_gpu_listfac_max = 1.30;
-
-/* Try to increase nstlist when using the Verlet cut-off scheme */
-static void increase_nstlist(FILE *fp, t_commrec *cr,
- t_inputrec *ir, int nstlist_cmdline,
- const gmx_mtop_t *mtop, matrix box,
- gmx_bool bGPU)
-{
- float listfac_ok, listfac_max;
- int nstlist_orig, nstlist_prev;
- verletbuf_list_setup_t ls;
- real rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
- real rlist_new, rlist_prev;
- size_t nstlist_ind = 0;
- t_state state_tmp;
- gmx_bool bBox, bDD, bCont;
- const char *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
- const char *nve_err = "Can not increase nstlist because an NVE ensemble is used";
- const char *vbd_err = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
- const char *box_err = "Can not increase nstlist because the box is too small";
- const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
- char buf[STRLEN];
- const float oneThird = 1.0f / 3.0f;
-
- if (nstlist_cmdline <= 0)
- {
- if (ir->nstlist == 1)
- {
- /* The user probably set nstlist=1 for a reason,
- * don't mess with the settings.
- */
- return;
- }
-
- if (fp != NULL && bGPU && ir->nstlist < nstlist_try[0])
- {
- fprintf(fp, nstl_gpu, ir->nstlist);
- }
- nstlist_ind = 0;
- while (nstlist_ind < NNSTL && ir->nstlist >= nstlist_try[nstlist_ind])
- {
- nstlist_ind++;
- }
- if (nstlist_ind == NNSTL)
- {
- /* There are no larger nstlist value to try */
- return;
- }
- }
-
- if (EI_MD(ir->eI) && ir->etc == etcNO)
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "%s\n", nve_err);
- }
- if (fp != NULL)
- {
- fprintf(fp, "%s\n", nve_err);
- }
-
- return;
- }
-
- if (ir->verletbuf_tol == 0 && bGPU)
- {
- 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_tol < 0)
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "%s\n", vbd_err);
- }
- if (fp != NULL)
- {
- fprintf(fp, "%s\n", vbd_err);
- }
-
- return;
- }
-
- if (bGPU)
- {
- listfac_ok = nbnxn_gpu_listfac_ok;
- listfac_max = nbnxn_gpu_listfac_max;
- }
- else
- {
- listfac_ok = nbnxn_cpu_listfac_ok;
- listfac_max = nbnxn_cpu_listfac_max;
- }
-
- nstlist_orig = ir->nstlist;
- if (nstlist_cmdline > 0)
- {
- if (fp)
- {
- sprintf(buf, "Getting nstlist=%d from command line option",
- nstlist_cmdline);
- }
- ir->nstlist = nstlist_cmdline;
- }
-
- verletbuf_get_list_setup(TRUE, bGPU, &ls);
-
- /* Allow rlist to make the list a given factor larger than the list
- * would be with the reference value for nstlist (10).
- */
- nstlist_prev = ir->nstlist;
- ir->nstlist = nbnxnReferenceNstlist;
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL,
- &rlistWithReferenceNstlist);
- ir->nstlist = nstlist_prev;
-
- /* Determine the pair list size increase due to zero interactions */
- rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
- mtop->natoms/det(box));
- rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_ok, oneThird) - rlist_inc;
- rlist_max = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_max, oneThird) - rlist_inc;
- if (debug)
- {
- fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
- rlist_inc, rlist_ok, rlist_max);
- }
-
- nstlist_prev = nstlist_orig;
- rlist_prev = ir->rlist;
- do
- {
- if (nstlist_cmdline <= 0)
- {
- ir->nstlist = nstlist_try[nstlist_ind];
- }
-
- /* Set the pair-list buffer size in ir */
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &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);
- }
-
- if (debug)
- {
- fprintf(debug, "nstlist %d rlist %.3f bBox %d bDD %d\n",
- ir->nstlist, rlist_new, bBox, bDD);
- }
-
- bCont = FALSE;
-
- if (nstlist_cmdline <= 0)
- {
- if (bBox && bDD && rlist_new <= rlist_max)
- {
- /* Increase nstlist */
- nstlist_prev = ir->nstlist;
- rlist_prev = rlist_new;
- bCont = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
- }
- else
- {
- /* Stick with the previous nstlist */
- ir->nstlist = nstlist_prev;
- rlist_new = rlist_prev;
- bBox = TRUE;
- bDD = TRUE;
- }
- }
-
- nstlist_ind++;
- }
- 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,
- t_commrec *cr,
- t_inputrec *ir,
- int nstlist_cmdline,
- const gmx_mtop_t *mtop,
- matrix box,
- gmx_bool bUseGPU)
-{
- /* For NVE simulations, we will retain the initial list buffer */
- if (EI_DYNAMICS(ir->eI) &&
- ir->verletbuf_tol > 0 &&
- !(EI_MD(ir->eI) && ir->etc == etcNO))
- {
- /* Update the Verlet buffer size for the current run setup */
- verletbuf_list_setup_t ls;
- real rlist_new;
-
- /* Here we assume SIMD-enabled kernels are being used. 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(TRUE, bUseGPU, &ls);
-
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &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;
- }
- }
-
- if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
- {
- gmx_fatal(FARGS, "Can not set nstlist without %s",
- !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
- }
-
- if (EI_DYNAMICS(ir->eI))
- {
- /* Set or try nstlist values */
- increase_nstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, bUseGPU);
- }
-}
-
-/* Override the value in inputrec with value passed on the command line (if any) */
-static void override_nsteps_cmdline(FILE *fplog,
- gmx_int64_t nsteps_cmdline,
- t_inputrec *ir,
- const t_commrec *cr)
-{
- assert(ir);
- assert(cr);
-
- /* override with anything else than the default -2 */
- if (nsteps_cmdline > -2)
- {
- char sbuf_steps[STEPSTRSIZE];
- char sbuf_msg[STRLEN];
-
- ir->nsteps = nsteps_cmdline;
- if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
- {
- sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
- gmx_step_str(nsteps_cmdline, sbuf_steps),
- fabs(nsteps_cmdline*ir->delta_t));
- }
- else
- {
- sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
- gmx_step_str(nsteps_cmdline, sbuf_steps));
- }
-
- md_print_warn(cr, fplog, "%s\n", sbuf_msg);
- }
- else if (nsteps_cmdline < -2)
- {
- gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %d",
- nsteps_cmdline);
- }
- /* Do nothing if nsteps_cmdline == -2 */
-}
-
-int mdrunner(gmx_hw_opt_t *hw_opt,
- 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, int nstlist_cmdline,
- gmx_int64_t nsteps_cmdline, int nstepout, int resetstep,
- int gmx_unused nmultisim, int repl_ex_nst, int repl_ex_nex,
- int repl_ex_seed, real pforce, real cpt_period, real max_hours,
- int imdport, unsigned long Flags)
-{
- gmx_bool bForceUseGPU, bTryUseGPU, bRerunMD;
- t_inputrec *inputrec;
- t_state *state = NULL;
- matrix box;
- gmx_ddbox_t ddbox = {0};
- int npme_major, npme_minor;
- t_nrnb *nrnb;
- gmx_mtop_t *mtop = NULL;
- t_mdatoms *mdatoms = NULL;
- t_forcerec *fr = NULL;
- t_fcdata *fcd = NULL;
- real ewaldcoeff_q = 0;
- real ewaldcoeff_lj = 0;
- struct gmx_pme_t **pmedata = NULL;
- gmx_vsite_t *vsite = NULL;
- gmx_constr_t constr;
- int nChargePerturbed = -1, nTypePerturbed = 0, status;
- gmx_wallcycle_t wcycle;
- gmx_bool bReadEkin;
- gmx_walltime_accounting_t walltime_accounting = NULL;
- int rc;
- gmx_int64_t reset_counters;
- gmx_edsam_t ed = NULL;
- int nthreads_pme = 1;
- int nthreads_pp = 1;
- gmx_membed_t membed = NULL;
- gmx_hw_info_t *hwinfo = NULL;
- /* The master rank decides early on bUseGPU and broadcasts this later */
- gmx_bool bUseGPU = 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;
- }
-
- bRerunMD = (Flags & MD_RERUN);
- bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
- bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
-
- /* Detect hardware, gather information. This is an operation that is
- * global for this process (MPI rank). */
- hwinfo = gmx_detect_hardware(fplog, cr, bTryUseGPU);
-
- gmx_print_detected_hardware(fplog, cr, hwinfo);
-
- if (fplog != NULL)
- {
- /* Print references after all software/hardware printing */
- please_cite(fplog, "Abraham2015");
- please_cite(fplog, "Pall2015");
- please_cite(fplog, "Pronk2013");
- please_cite(fplog, "Hess2008b");
- please_cite(fplog, "Spoel2005a");
- please_cite(fplog, "Lindahl2001a");
- please_cite(fplog, "Berendsen95a");
- }
-
- snew(state, 1);
- if (SIMMASTER(cr))
- {
- /* Read (nearly) all data required for the simulation */
- read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, NULL, mtop);
-
- if (inputrec->cutoff_scheme == ecutsVERLET)
- {
- /* Here the master rank decides if all ranks will use GPUs */
- bUseGPU = (hwinfo->gpu_info.n_dev_compatible > 0 ||
- getenv("GMX_EMULATE_GPU") != NULL);
-
- /* TODO add GPU kernels for this and replace this check by:
- * (bUseGPU && (ir->vdwtype == evdwPME &&
- * ir->ljpme_combination_rule == eljpmeLB))
- * update the message text and the content of nbnxn_acceleration_supported.
- */
- if (bUseGPU &&
- !nbnxn_gpu_acceleration_supported(fplog, cr, inputrec, bRerunMD))
- {
- /* Fallback message printed by nbnxn_acceleration_supported */
- if (bForceUseGPU)
- {
- gmx_fatal(FARGS, "GPU acceleration requested, but not supported with the given input settings");
- }
- bUseGPU = FALSE;
- }
-
- prepare_verlet_scheme(fplog, cr,
- inputrec, nstlist_cmdline, mtop, state->box,
- bUseGPU);
- }
- else
- {
- if (nstlist_cmdline > 0)
- {
- gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
- }
-
- if (hwinfo->gpu_info.n_dev_compatible > 0)
- {
- 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");
- }
-
- if (bForceUseGPU)
- {
- gmx_fatal(FARGS, "GPU requested, but can't be used without cutoff-scheme=Verlet");
- }
-
-#ifdef GMX_TARGET_BGQ
- md_print_warn(cr, fplog,
- "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
- " BlueGene/Q. You will observe better performance from using the\n"
- " Verlet cut-off scheme.\n");
-#endif
- }
-
- if (inputrec->eI == eiSD2)
- {
- md_print_warn(cr, fplog, "The stochastic dynamics integrator %s is deprecated, since\n"
- "it is slower than integrator %s and is slightly less accurate\n"
- "with constraints. Use the %s integrator.",
- ei_names[inputrec->eI], ei_names[eiSD1], ei_names[eiSD1]);
- }
- }
-
- /* Check and update the hardware options for internal consistency */
- check_and_update_hw_opt_1(hw_opt, cr);
-
- /* Early check for externally set process affinity. */
- gmx_check_thread_affinity_set(fplog, cr,
- hw_opt, hwinfo->nthreads_hw_avail, FALSE);
-
-#ifdef GMX_THREAD_MPI
- if (SIMMASTER(cr))
- {
- 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 ranks");
- }
-
- /* Since the master knows the cut-off scheme, update hw_opt for this.
- * This is done later for normal MPI and also once more with tMPI
- * for all tMPI ranks.
- */
- check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);
-
- /* NOW the threads will be started: */
- hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
- hw_opt,
- inputrec, mtop,
- cr, fplog, bUseGPU);
-
- if (hw_opt->nthreads_tmpi > 1)
- {
- t_commrec *cr_old = cr;
- /* now start the threads. */
- cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
- oenv, bVerbose, bCompact, nstglobalcomm,
- ddxyz, dd_node_order, rdd, rconstr,
- dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
- nbpu_opt, nstlist_cmdline,
- nsteps_cmdline, nstepout, resetstep, nmultisim,
- repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
- cpt_period, max_hours,
- 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(cr, inputrec, mtop);
-
- /* The master rank decided on the use of GPUs,
- * broadcast this information to all ranks.
- */
- gmx_bcast_sim(sizeof(bUseGPU), &bUseGPU, cr);
- }
-
- if (fplog != NULL)
- {
- pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
- fprintf(fplog, "\n");
- }
-
- /* now make sure the state is initialized and propagated */
- set_state_entries(state, inputrec);
-
- /* 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 MPI-threads (option -ntmpi) is not set or is 1"
-#else
- "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec"
-#endif
-#endif
- , output_env_get_program_display_name(oenv)
- );
- }
-
- if (bRerunMD &&
- (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, TRUE, cr, fplog) && DOMAINDECOMP(cr))
- {
- gmx_fatal(FARGS, "All-vs-all loops do not work with domain decomposition, use a single MPI rank");
- }
-
- if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
- {
- if (cr->npmenodes > 0)
- {
- gmx_fatal_collective(FARGS, cr, NULL,
- "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
- }
-
- cr->npmenodes = 0;
- }
-
- if (bUseGPU && cr->npmenodes < 0)
- {
- /* With GPUs we don't automatically use PME-only ranks. PME ranks can
- * improve performance with many threads per GPU, since our OpenMP
- * scaling is bad, but it's difficult to automate the setup.
- */
- cr->npmenodes = 0;
- }
-
-#ifdef GMX_FAHCORE
- if (MASTER(cr))
- {
- 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, fcd, state, repl_ex_nst > 0);
-
- init_orires(fplog, mtop, state->x, inputrec, cr, &(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.
- */
- tMPI_Thread_mutex_lock(&deform_init_box_mutex);
- deform_init_init_step_tpx = inputrec->init_step;
- copy_mat(box, deform_init_box_tpx);
- tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
- }
-
- 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, ddxyz,
- inputrec, state, &bReadEkin,
- (Flags & MD_APPENDFILES),
- (Flags & MD_APPENDFILESSET));
-
- if (bReadEkin)
- {
- Flags |= MD_READ_EKIN;
- }
- }
- }
-
- if (MASTER(cr) && (Flags & MD_APPENDFILES))
- {
- gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
- 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) && !(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 (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
- if (MULTISIM(cr))
- {
- md_print_info(cr, fplog,
- "This is simulation %d out of %d running as a composite GROMACS\n"
- "multi-simulation job. Setup for this simulation:\n\n",
- cr->ms->sim, cr->ms->nsim);
- }
- 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
-
- /* Check and update hw_opt for the cut-off scheme */
- check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);
-
- /* Check and update hw_opt for the number of MPI ranks */
- check_and_update_hw_opt_3(hw_opt);
-
- 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);
-
-#ifndef NDEBUG
- if (integrator[inputrec->eI].func != do_tpi &&
- inputrec->cutoff_scheme == ecutsVERLET)
- {
- gmx_feenableexcept();
- }
-#endif
-
- if (bUseGPU)
- {
- /* Select GPU id's to use */
- gmx_select_gpu_ids(fplog, cr, &hwinfo->gpu_info, bForceUseGPU,
- &hw_opt->gpu_opt);
- }
- else
- {
- /* Ignore (potentially) manually selected GPUs */
- hw_opt->gpu_opt.n_dev_use = 0;
- }
-
- /* check consistency across ranks of things like SIMD
- * support and number of GPUs selected */
- gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt, bUseGPU);
-
- /* Now that we know the setup is consistent, check for efficiency */
- check_resource_division_efficiency(hwinfo, hw_opt, Flags & MD_NTOMPSET,
- cr, fplog);
-
- if (DOMAINDECOMP(cr))
- {
- /* When we share GPUs over ranks, we need to know this for the DLB */
- dd_setup_dlb_resource_sharing(cr, hwinfo, hw_opt);
- }
-
- /* 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)
- {
- bcast_state(cr, state);
-
- /* Initiate forcerecord */
- fr = mk_forcerec();
- fr->hwinfo = hwinfo;
- fr->gpu_opt = &hw_opt->gpu_opt;
- init_forcerec(fplog, oenv, fr, fcd, inputrec, mtop, cr, box,
- opt2fn("-table", nfile, fnm),
- opt2fn("-tabletf", nfile, fnm),
- opt2fn("-tablep", nfile, fnm),
- getFilenm("-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);
- */
-
- /* Initialize QM-MM */
- if (fr->bQMMM)
- {
- init_QMMMrec(cr, 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);
-
- /* 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(vsite, mtop, state->x);
- }
- }
-
- if (EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype))
- {
- ewaldcoeff_q = fr->ewaldcoeff_q;
- ewaldcoeff_lj = fr->ewaldcoeff_lj;
- pmedata = &fr->pmedata;
- }
- else
- {
- pmedata = NULL;
- }
- }
- else
- {
- /* This is a PME only node */
-
- /* We don't need the state */
- done_state(state);
-
- ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
- ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
- 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, hwinfo);
- }
-
- /* Initiate PME if necessary,
- * either on all nodes or on dedicated PME nodes only. */
- if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
- {
- if (mdatoms)
- {
- nChargePerturbed = mdatoms->nChargePerturbed;
- if (EVDW_PME(inputrec->vdwtype))
- {
- nTypePerturbed = mdatoms->nTypePerturbed;
- }
- }
- if (cr->npmenodes > 0)
- {
- /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
- gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
- gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
- }
-
- if (cr->duty & DUTY_PME)
- {
- status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
- mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
- (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)
- {
- /* Assumes uniform use of the number of OpenMP threads */
- walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
-
- if (inputrec->bPull)
- {
- /* Initialize pull code */
- inputrec->pull_work =
- init_pull(fplog, inputrec->pull, 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);
- }
-
- if (inputrec->eSwapCoords != eswapNO)
- {
- /* Initialize ion swapping code */
- init_swapcoords(fplog, bVerbose, inputrec, opt2fn_master("-swap", nfile, fnm, cr),
- mtop, state->x, state->box, &state->swapstate, cr, oenv, Flags);
- }
-
- constr = init_constraints(fplog, mtop, inputrec, ed, state, cr);
-
- if (DOMAINDECOMP(cr))
- {
- GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
- dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
- Flags & MD_DDBONDCHECK, fr->cginfo_mb);
-
- set_dd_parameters(fplog, cr->dd, dlb_scale, inputrec, &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,
- imdport,
- Flags,
- walltime_accounting);
-
- if (inputrec->bPull)
- {
- finish_pull(inputrec->pull_work);
- }
-
- if (inputrec->bRot)
- {
- finish_rot(inputrec->rot);
- }
-
- }
- else
- {
- GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
- /* do PME only */
- walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
- gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff_q, ewaldcoeff_lj, inputrec);
- }
-
- wallcycle_stop(wcycle, ewcRUN);
-
- /* Finish up, write some stuff
- * if rerunMD, don't write last frame again
- */
- finish_run(fplog, cr,
- inputrec, nrnb, wcycle, walltime_accounting,
- fr ? fr->nbv : NULL,
- EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
-
-
- /* Free GPU memory and context */
- free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);
-
- if (opt2bSet("-membed", nfile, fnm))
- {
- sfree(membed);
- }
-
- gmx_hardware_info_free(hwinfo);
-
- /* Does what it says */
- print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
- walltime_accounting_destroy(walltime_accounting);
-
- /* PLUMED */
- if(plumedswitch){
- plumed_finalize(plumedmain);
- }
- /* END PLUMED */
-
- /* 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();
-
- done_ed(&ed);
-
-#ifdef GMX_THREAD_MPI
- /* we need to join all threads. The sub-threads join when they
- exit this function, but the master thread needs to be told to
- wait for that. */
- if (PAR(cr) && MASTER(cr))
- {
- tMPI_Finalize();
- }
-#endif
-
- return rc;
-}
diff --git a/patches/gromacs-5.1.4.diff/src/programs/mdrun/runner.cpp.preplumed b/patches/gromacs-5.1.4.diff/src/programs/mdrun/runner.cpp.preplumed
deleted file mode 100644
index 7489b07dcbee6c6f730415ef166ed857afaffe4b..0000000000000000000000000000000000000000
--- a/patches/gromacs-5.1.4.diff/src/programs/mdrun/runner.cpp.preplumed
+++ /dev/null
@@ -1,1351 +0,0 @@
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include <assert.h>
-#include <signal.h>
-#include <stdlib.h>
-#include <string.h>
-
-#include <algorithm>
-
-#include "gromacs/domdec/domdec.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/ewald/pme.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/gmx_thread_affinity.h"
-#include "gromacs/legacyheaders/inputrec.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/sighandler.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/mdlib/calc_verletbuf.h"
-#include "gromacs/mdlib/nbnxn_search.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/swap/swapcoords.h"
-#include "gromacs/timing/wallcycle.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/gmxmpi.h"
-#include "gromacs/utility/smalloc.h"
-
-#include "deform.h"
-#include "membed.h"
-#include "repl_ex.h"
-#include "resource-division.h"
-
-#ifdef GMX_FAHCORE
-#include "corewrap.h"
-#endif
-
-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_int64_t deform_init_init_step_tpx;
-matrix deform_init_box_tpx;
-tMPI_Thread_mutex_t deform_init_box_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-
-
-#ifdef GMX_THREAD_MPI
-/* The minimum number of atoms per tMPI thread. With fewer atoms than this,
- * the number of threads will get lowered.
- */
-#define MIN_ATOMS_PER_MPI_THREAD 90
-#define MIN_ATOMS_PER_GPU 900
-
-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;
- int nstlist_cmdline;
- gmx_int64_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;
- int imdport;
- unsigned long Flags;
-};
-
-
-/* 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 = reinitialize_commrec_for_this_thread(mc.cr);
-
- if (MASTER(cr))
- {
- fplog = mc.fplog;
- }
-
- 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.nstlist_cmdline,
- 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.imdport, 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, int nstlist_cmdline,
- gmx_int64_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,
- 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 */
- /* hw_opt contains pointers, which should all be NULL at this stage */
- 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->nstlist_cmdline = nstlist_cmdline;
- 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->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;
- }
-
- crn = reinitialize_commrec_for_this_thread(cr);
- return crn;
-}
-
-#endif /* GMX_THREAD_MPI */
-
-
-/* We determine the extra cost of the non-bonded kernels compared to
- * a reference nstlist value of 10 (which is the default in grompp).
- */
-static const int nbnxnReferenceNstlist = 10;
-/* The values to try when switching */
-const int nstlist_try[] = { 20, 25, 40 };
-#define NNSTL sizeof(nstlist_try)/sizeof(nstlist_try[0])
-/* Increase nstlist until the non-bonded cost increases more than listfac_ok,
- * but never more than listfac_max.
- * A standard (protein+)water system at 300K with PME ewald_rtol=1e-5
- * needs 1.28 at rcoulomb=0.9 and 1.24 at rcoulomb=1.0 to get to nstlist=40.
- * Note that both CPU and GPU factors are conservative. Performance should
- * not go down due to this tuning, except with a relatively slow GPU.
- * On the other hand, at medium/high parallelization or with fast GPUs
- * nstlist will not be increased enough to reach optimal performance.
- */
-/* CPU: pair-search is about a factor 1.5 slower than the non-bonded kernel */
-static const float nbnxn_cpu_listfac_ok = 1.05;
-static const float nbnxn_cpu_listfac_max = 1.09;
-/* GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel */
-static const float nbnxn_gpu_listfac_ok = 1.20;
-static const float nbnxn_gpu_listfac_max = 1.30;
-
-/* Try to increase nstlist when using the Verlet cut-off scheme */
-static void increase_nstlist(FILE *fp, t_commrec *cr,
- t_inputrec *ir, int nstlist_cmdline,
- const gmx_mtop_t *mtop, matrix box,
- gmx_bool bGPU)
-{
- float listfac_ok, listfac_max;
- int nstlist_orig, nstlist_prev;
- verletbuf_list_setup_t ls;
- real rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
- real rlist_new, rlist_prev;
- size_t nstlist_ind = 0;
- t_state state_tmp;
- gmx_bool bBox, bDD, bCont;
- const char *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
- const char *nve_err = "Can not increase nstlist because an NVE ensemble is used";
- const char *vbd_err = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
- const char *box_err = "Can not increase nstlist because the box is too small";
- const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
- char buf[STRLEN];
- const float oneThird = 1.0f / 3.0f;
-
- if (nstlist_cmdline <= 0)
- {
- if (ir->nstlist == 1)
- {
- /* The user probably set nstlist=1 for a reason,
- * don't mess with the settings.
- */
- return;
- }
-
- if (fp != NULL && bGPU && ir->nstlist < nstlist_try[0])
- {
- fprintf(fp, nstl_gpu, ir->nstlist);
- }
- nstlist_ind = 0;
- while (nstlist_ind < NNSTL && ir->nstlist >= nstlist_try[nstlist_ind])
- {
- nstlist_ind++;
- }
- if (nstlist_ind == NNSTL)
- {
- /* There are no larger nstlist value to try */
- return;
- }
- }
-
- if (EI_MD(ir->eI) && ir->etc == etcNO)
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "%s\n", nve_err);
- }
- if (fp != NULL)
- {
- fprintf(fp, "%s\n", nve_err);
- }
-
- return;
- }
-
- if (ir->verletbuf_tol == 0 && bGPU)
- {
- 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_tol < 0)
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "%s\n", vbd_err);
- }
- if (fp != NULL)
- {
- fprintf(fp, "%s\n", vbd_err);
- }
-
- return;
- }
-
- if (bGPU)
- {
- listfac_ok = nbnxn_gpu_listfac_ok;
- listfac_max = nbnxn_gpu_listfac_max;
- }
- else
- {
- listfac_ok = nbnxn_cpu_listfac_ok;
- listfac_max = nbnxn_cpu_listfac_max;
- }
-
- nstlist_orig = ir->nstlist;
- if (nstlist_cmdline > 0)
- {
- if (fp)
- {
- sprintf(buf, "Getting nstlist=%d from command line option",
- nstlist_cmdline);
- }
- ir->nstlist = nstlist_cmdline;
- }
-
- verletbuf_get_list_setup(TRUE, bGPU, &ls);
-
- /* Allow rlist to make the list a given factor larger than the list
- * would be with the reference value for nstlist (10).
- */
- nstlist_prev = ir->nstlist;
- ir->nstlist = nbnxnReferenceNstlist;
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL,
- &rlistWithReferenceNstlist);
- ir->nstlist = nstlist_prev;
-
- /* Determine the pair list size increase due to zero interactions */
- rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
- mtop->natoms/det(box));
- rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_ok, oneThird) - rlist_inc;
- rlist_max = (rlistWithReferenceNstlist + rlist_inc)*pow(listfac_max, oneThird) - rlist_inc;
- if (debug)
- {
- fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
- rlist_inc, rlist_ok, rlist_max);
- }
-
- nstlist_prev = nstlist_orig;
- rlist_prev = ir->rlist;
- do
- {
- if (nstlist_cmdline <= 0)
- {
- ir->nstlist = nstlist_try[nstlist_ind];
- }
-
- /* Set the pair-list buffer size in ir */
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &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);
- }
-
- if (debug)
- {
- fprintf(debug, "nstlist %d rlist %.3f bBox %d bDD %d\n",
- ir->nstlist, rlist_new, bBox, bDD);
- }
-
- bCont = FALSE;
-
- if (nstlist_cmdline <= 0)
- {
- if (bBox && bDD && rlist_new <= rlist_max)
- {
- /* Increase nstlist */
- nstlist_prev = ir->nstlist;
- rlist_prev = rlist_new;
- bCont = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
- }
- else
- {
- /* Stick with the previous nstlist */
- ir->nstlist = nstlist_prev;
- rlist_new = rlist_prev;
- bBox = TRUE;
- bDD = TRUE;
- }
- }
-
- nstlist_ind++;
- }
- 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,
- t_commrec *cr,
- t_inputrec *ir,
- int nstlist_cmdline,
- const gmx_mtop_t *mtop,
- matrix box,
- gmx_bool bUseGPU)
-{
- /* For NVE simulations, we will retain the initial list buffer */
- if (EI_DYNAMICS(ir->eI) &&
- ir->verletbuf_tol > 0 &&
- !(EI_MD(ir->eI) && ir->etc == etcNO))
- {
- /* Update the Verlet buffer size for the current run setup */
- verletbuf_list_setup_t ls;
- real rlist_new;
-
- /* Here we assume SIMD-enabled kernels are being used. 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(TRUE, bUseGPU, &ls);
-
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &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;
- }
- }
-
- if (nstlist_cmdline > 0 && (!EI_DYNAMICS(ir->eI) || ir->verletbuf_tol <= 0))
- {
- gmx_fatal(FARGS, "Can not set nstlist without %s",
- !EI_DYNAMICS(ir->eI) ? "dynamics" : "verlet-buffer-tolerance");
- }
-
- if (EI_DYNAMICS(ir->eI))
- {
- /* Set or try nstlist values */
- increase_nstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, bUseGPU);
- }
-}
-
-/* Override the value in inputrec with value passed on the command line (if any) */
-static void override_nsteps_cmdline(FILE *fplog,
- gmx_int64_t nsteps_cmdline,
- t_inputrec *ir,
- const t_commrec *cr)
-{
- assert(ir);
- assert(cr);
-
- /* override with anything else than the default -2 */
- if (nsteps_cmdline > -2)
- {
- char sbuf_steps[STEPSTRSIZE];
- char sbuf_msg[STRLEN];
-
- ir->nsteps = nsteps_cmdline;
- if (EI_DYNAMICS(ir->eI) && nsteps_cmdline != -1)
- {
- sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps, %.3g ps",
- gmx_step_str(nsteps_cmdline, sbuf_steps),
- fabs(nsteps_cmdline*ir->delta_t));
- }
- else
- {
- sprintf(sbuf_msg, "Overriding nsteps with value passed on the command line: %s steps",
- gmx_step_str(nsteps_cmdline, sbuf_steps));
- }
-
- md_print_warn(cr, fplog, "%s\n", sbuf_msg);
- }
- else if (nsteps_cmdline < -2)
- {
- gmx_fatal(FARGS, "Invalid nsteps value passed on the command line: %d",
- nsteps_cmdline);
- }
- /* Do nothing if nsteps_cmdline == -2 */
-}
-
-int mdrunner(gmx_hw_opt_t *hw_opt,
- 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, int nstlist_cmdline,
- gmx_int64_t nsteps_cmdline, int nstepout, int resetstep,
- int gmx_unused nmultisim, int repl_ex_nst, int repl_ex_nex,
- int repl_ex_seed, real pforce, real cpt_period, real max_hours,
- int imdport, unsigned long Flags)
-{
- gmx_bool bForceUseGPU, bTryUseGPU, bRerunMD;
- t_inputrec *inputrec;
- t_state *state = NULL;
- matrix box;
- gmx_ddbox_t ddbox = {0};
- int npme_major, npme_minor;
- t_nrnb *nrnb;
- gmx_mtop_t *mtop = NULL;
- t_mdatoms *mdatoms = NULL;
- t_forcerec *fr = NULL;
- t_fcdata *fcd = NULL;
- real ewaldcoeff_q = 0;
- real ewaldcoeff_lj = 0;
- struct gmx_pme_t **pmedata = NULL;
- gmx_vsite_t *vsite = NULL;
- gmx_constr_t constr;
- int nChargePerturbed = -1, nTypePerturbed = 0, status;
- gmx_wallcycle_t wcycle;
- gmx_bool bReadEkin;
- gmx_walltime_accounting_t walltime_accounting = NULL;
- int rc;
- gmx_int64_t reset_counters;
- gmx_edsam_t ed = NULL;
- int nthreads_pme = 1;
- int nthreads_pp = 1;
- gmx_membed_t membed = NULL;
- gmx_hw_info_t *hwinfo = NULL;
- /* The master rank decides early on bUseGPU and broadcasts this later */
- gmx_bool bUseGPU = 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;
- }
-
- bRerunMD = (Flags & MD_RERUN);
- bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
- bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
-
- /* Detect hardware, gather information. This is an operation that is
- * global for this process (MPI rank). */
- hwinfo = gmx_detect_hardware(fplog, cr, bTryUseGPU);
-
- gmx_print_detected_hardware(fplog, cr, hwinfo);
-
- if (fplog != NULL)
- {
- /* Print references after all software/hardware printing */
- please_cite(fplog, "Abraham2015");
- please_cite(fplog, "Pall2015");
- please_cite(fplog, "Pronk2013");
- please_cite(fplog, "Hess2008b");
- please_cite(fplog, "Spoel2005a");
- please_cite(fplog, "Lindahl2001a");
- please_cite(fplog, "Berendsen95a");
- }
-
- snew(state, 1);
- if (SIMMASTER(cr))
- {
- /* Read (nearly) all data required for the simulation */
- read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, NULL, mtop);
-
- if (inputrec->cutoff_scheme == ecutsVERLET)
- {
- /* Here the master rank decides if all ranks will use GPUs */
- bUseGPU = (hwinfo->gpu_info.n_dev_compatible > 0 ||
- getenv("GMX_EMULATE_GPU") != NULL);
-
- /* TODO add GPU kernels for this and replace this check by:
- * (bUseGPU && (ir->vdwtype == evdwPME &&
- * ir->ljpme_combination_rule == eljpmeLB))
- * update the message text and the content of nbnxn_acceleration_supported.
- */
- if (bUseGPU &&
- !nbnxn_gpu_acceleration_supported(fplog, cr, inputrec, bRerunMD))
- {
- /* Fallback message printed by nbnxn_acceleration_supported */
- if (bForceUseGPU)
- {
- gmx_fatal(FARGS, "GPU acceleration requested, but not supported with the given input settings");
- }
- bUseGPU = FALSE;
- }
-
- prepare_verlet_scheme(fplog, cr,
- inputrec, nstlist_cmdline, mtop, state->box,
- bUseGPU);
- }
- else
- {
- if (nstlist_cmdline > 0)
- {
- gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
- }
-
- if (hwinfo->gpu_info.n_dev_compatible > 0)
- {
- 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");
- }
-
- if (bForceUseGPU)
- {
- gmx_fatal(FARGS, "GPU requested, but can't be used without cutoff-scheme=Verlet");
- }
-
-#ifdef GMX_TARGET_BGQ
- md_print_warn(cr, fplog,
- "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
- " BlueGene/Q. You will observe better performance from using the\n"
- " Verlet cut-off scheme.\n");
-#endif
- }
-
- if (inputrec->eI == eiSD2)
- {
- md_print_warn(cr, fplog, "The stochastic dynamics integrator %s is deprecated, since\n"
- "it is slower than integrator %s and is slightly less accurate\n"
- "with constraints. Use the %s integrator.",
- ei_names[inputrec->eI], ei_names[eiSD1], ei_names[eiSD1]);
- }
- }
-
- /* Check and update the hardware options for internal consistency */
- check_and_update_hw_opt_1(hw_opt, cr);
-
- /* Early check for externally set process affinity. */
- gmx_check_thread_affinity_set(fplog, cr,
- hw_opt, hwinfo->nthreads_hw_avail, FALSE);
-
-#ifdef GMX_THREAD_MPI
- if (SIMMASTER(cr))
- {
- 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 ranks");
- }
-
- /* Since the master knows the cut-off scheme, update hw_opt for this.
- * This is done later for normal MPI and also once more with tMPI
- * for all tMPI ranks.
- */
- check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);
-
- /* NOW the threads will be started: */
- hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
- hw_opt,
- inputrec, mtop,
- cr, fplog, bUseGPU);
-
- if (hw_opt->nthreads_tmpi > 1)
- {
- t_commrec *cr_old = cr;
- /* now start the threads. */
- cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
- oenv, bVerbose, bCompact, nstglobalcomm,
- ddxyz, dd_node_order, rdd, rconstr,
- dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
- nbpu_opt, nstlist_cmdline,
- nsteps_cmdline, nstepout, resetstep, nmultisim,
- repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
- cpt_period, max_hours,
- 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(cr, inputrec, mtop);
-
- /* The master rank decided on the use of GPUs,
- * broadcast this information to all ranks.
- */
- gmx_bcast_sim(sizeof(bUseGPU), &bUseGPU, cr);
- }
-
- if (fplog != NULL)
- {
- pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
- fprintf(fplog, "\n");
- }
-
- /* now make sure the state is initialized and propagated */
- set_state_entries(state, inputrec);
-
- /* 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 MPI-threads (option -ntmpi) is not set or is 1"
-#else
- "but %s was not started through mpirun/mpiexec or only one rank was requested through mpirun/mpiexec"
-#endif
-#endif
- , output_env_get_program_display_name(oenv)
- );
- }
-
- if (bRerunMD &&
- (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, TRUE, cr, fplog) && DOMAINDECOMP(cr))
- {
- gmx_fatal(FARGS, "All-vs-all loops do not work with domain decomposition, use a single MPI rank");
- }
-
- if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
- {
- if (cr->npmenodes > 0)
- {
- gmx_fatal_collective(FARGS, cr, NULL,
- "PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
- }
-
- cr->npmenodes = 0;
- }
-
- if (bUseGPU && cr->npmenodes < 0)
- {
- /* With GPUs we don't automatically use PME-only ranks. PME ranks can
- * improve performance with many threads per GPU, since our OpenMP
- * scaling is bad, but it's difficult to automate the setup.
- */
- cr->npmenodes = 0;
- }
-
-#ifdef GMX_FAHCORE
- if (MASTER(cr))
- {
- 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, fcd, state, repl_ex_nst > 0);
-
- init_orires(fplog, mtop, state->x, inputrec, cr, &(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.
- */
- tMPI_Thread_mutex_lock(&deform_init_box_mutex);
- deform_init_init_step_tpx = inputrec->init_step;
- copy_mat(box, deform_init_box_tpx);
- tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
- }
-
- 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, ddxyz,
- inputrec, state, &bReadEkin,
- (Flags & MD_APPENDFILES),
- (Flags & MD_APPENDFILESSET));
-
- if (bReadEkin)
- {
- Flags |= MD_READ_EKIN;
- }
- }
- }
-
- if (MASTER(cr) && (Flags & MD_APPENDFILES))
- {
- gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
- 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) && !(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 (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
- if (MULTISIM(cr))
- {
- md_print_info(cr, fplog,
- "This is simulation %d out of %d running as a composite GROMACS\n"
- "multi-simulation job. Setup for this simulation:\n\n",
- cr->ms->sim, cr->ms->nsim);
- }
- 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
-
- /* Check and update hw_opt for the cut-off scheme */
- check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);
-
- /* Check and update hw_opt for the number of MPI ranks */
- check_and_update_hw_opt_3(hw_opt);
-
- 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);
-
-#ifndef NDEBUG
- if (integrator[inputrec->eI].func != do_tpi &&
- inputrec->cutoff_scheme == ecutsVERLET)
- {
- gmx_feenableexcept();
- }
-#endif
-
- if (bUseGPU)
- {
- /* Select GPU id's to use */
- gmx_select_gpu_ids(fplog, cr, &hwinfo->gpu_info, bForceUseGPU,
- &hw_opt->gpu_opt);
- }
- else
- {
- /* Ignore (potentially) manually selected GPUs */
- hw_opt->gpu_opt.n_dev_use = 0;
- }
-
- /* check consistency across ranks of things like SIMD
- * support and number of GPUs selected */
- gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt, bUseGPU);
-
- /* Now that we know the setup is consistent, check for efficiency */
- check_resource_division_efficiency(hwinfo, hw_opt, Flags & MD_NTOMPSET,
- cr, fplog);
-
- if (DOMAINDECOMP(cr))
- {
- /* When we share GPUs over ranks, we need to know this for the DLB */
- dd_setup_dlb_resource_sharing(cr, hwinfo, hw_opt);
- }
-
- /* 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)
- {
- bcast_state(cr, state);
-
- /* Initiate forcerecord */
- fr = mk_forcerec();
- fr->hwinfo = hwinfo;
- fr->gpu_opt = &hw_opt->gpu_opt;
- init_forcerec(fplog, oenv, fr, fcd, inputrec, mtop, cr, box,
- opt2fn("-table", nfile, fnm),
- opt2fn("-tabletf", nfile, fnm),
- opt2fn("-tablep", nfile, fnm),
- getFilenm("-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);
- */
-
- /* Initialize QM-MM */
- if (fr->bQMMM)
- {
- init_QMMMrec(cr, 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);
-
- /* 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(vsite, mtop, state->x);
- }
- }
-
- if (EEL_PME(fr->eeltype) || EVDW_PME(fr->vdwtype))
- {
- ewaldcoeff_q = fr->ewaldcoeff_q;
- ewaldcoeff_lj = fr->ewaldcoeff_lj;
- pmedata = &fr->pmedata;
- }
- else
- {
- pmedata = NULL;
- }
- }
- else
- {
- /* This is a PME only node */
-
- /* We don't need the state */
- done_state(state);
-
- ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
- ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
- 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, hwinfo);
- }
-
- /* Initiate PME if necessary,
- * either on all nodes or on dedicated PME nodes only. */
- if (EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype))
- {
- if (mdatoms)
- {
- nChargePerturbed = mdatoms->nChargePerturbed;
- if (EVDW_PME(inputrec->vdwtype))
- {
- nTypePerturbed = mdatoms->nTypePerturbed;
- }
- }
- if (cr->npmenodes > 0)
- {
- /* The PME only nodes need to know nChargePerturbed(FEP on Q) and nTypePerturbed(FEP on LJ)*/
- gmx_bcast_sim(sizeof(nChargePerturbed), &nChargePerturbed, cr);
- gmx_bcast_sim(sizeof(nTypePerturbed), &nTypePerturbed, cr);
- }
-
- if (cr->duty & DUTY_PME)
- {
- status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
- mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
- (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)
- {
- /* Assumes uniform use of the number of OpenMP threads */
- walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntDefault));
-
- if (inputrec->bPull)
- {
- /* Initialize pull code */
- inputrec->pull_work =
- init_pull(fplog, inputrec->pull, 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);
- }
-
- if (inputrec->eSwapCoords != eswapNO)
- {
- /* Initialize ion swapping code */
- init_swapcoords(fplog, bVerbose, inputrec, opt2fn_master("-swap", nfile, fnm, cr),
- mtop, state->x, state->box, &state->swapstate, cr, oenv, Flags);
- }
-
- constr = init_constraints(fplog, mtop, inputrec, ed, state, cr);
-
- if (DOMAINDECOMP(cr))
- {
- GMX_RELEASE_ASSERT(fr, "fr was NULL while cr->duty was DUTY_PP");
- dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
- Flags & MD_DDBONDCHECK, fr->cginfo_mb);
-
- set_dd_parameters(fplog, cr->dd, dlb_scale, inputrec, &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,
- imdport,
- Flags,
- walltime_accounting);
-
- if (inputrec->bPull)
- {
- finish_pull(inputrec->pull_work);
- }
-
- if (inputrec->bRot)
- {
- finish_rot(inputrec->rot);
- }
-
- }
- else
- {
- GMX_RELEASE_ASSERT(pmedata, "pmedata was NULL while cr->duty was not DUTY_PP");
- /* do PME only */
- walltime_accounting = walltime_accounting_init(gmx_omp_nthreads_get(emntPME));
- gmx_pmeonly(*pmedata, cr, nrnb, wcycle, walltime_accounting, ewaldcoeff_q, ewaldcoeff_lj, inputrec);
- }
-
- wallcycle_stop(wcycle, ewcRUN);
-
- /* Finish up, write some stuff
- * if rerunMD, don't write last frame again
- */
- finish_run(fplog, cr,
- inputrec, nrnb, wcycle, walltime_accounting,
- fr ? fr->nbv : NULL,
- EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
-
-
- /* Free GPU memory and context */
- free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);
-
- if (opt2bSet("-membed", nfile, fnm))
- {
- sfree(membed);
- }
-
- gmx_hardware_info_free(hwinfo);
-
- /* Does what it says */
- print_date_and_time(fplog, cr->nodeid, "Finished mdrun", gmx_gettime());
- walltime_accounting_destroy(walltime_accounting);
-
- /* 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();
-
- done_ed(&ed);
-
-#ifdef GMX_THREAD_MPI
- /* we need to join all threads. The sub-threads join when they
- exit this function, but the master thread needs to be told to
- wait for that. */
- if (PAR(cr) && MASTER(cr))
- {
- tMPI_Finalize();
- }
-#endif
-
- return rc;
-}