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Commit 8b05608c authored by carlocamilloni's avatar carlocamilloni
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remove GMX 5.1.4

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CHANGES/v2.5.md
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......@@ -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`.
......
patches/gromacs-5.1.4.config deleted 100644 → 0
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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
}
patches/gromacs-5.1.4.diff/src/gromacs/CMakeLists.txt deleted 100644 → 0
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#
# 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()
patches/gromacs-5.1.4.diff/src/gromacs/CMakeLists.txt.preplumed deleted 100644 → 0
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#
# 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()
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/*
* 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 */
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/*
* 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 */
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