gromacs 2019.1 patch --NOT WORKING--

this is not really working yet, but hopefully we are not far

patches/gromacs-2019.1.config

+
+
+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
+
+For more information on gromacs you should visit http://www.gromacs.org
+
+EOF
+}
+
+plumed_before_patch(){
+  plumed_patch_info
+}
+

patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and 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)
+
+if (GMX_CLANG_CUDA)
+    include(gmxClangCudaUtils)
+endif()
+
+set_property(GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
+set_property(GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
+set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+set_property(GLOBAL PROPERTY GMX_AVX_512_SOURCE)
+
+add_library(libgromacs_external OBJECT "")
+if(CMAKE_COMPILER_IS_GNUCXX)
+    # Keep quiet about e.g. linearalgebra module
+    target_compile_options(libgromacs_external PRIVATE ${CXXFLAGS_NO_STRINGOP_TRUNCATION})
+endif()
+
+add_library(libgromacs_generated OBJECT "")
+if (BUILD_SHARED_LIBS)
+    set_target_properties(libgromacs_external PROPERTIES POSITION_INDEPENDENT_CODE true)
+    set_target_properties(libgromacs_generated PROPERTIES POSITION_INDEPENDENT_CODE true)
+endif()
+
+function (_gmx_add_files_to_property PROPERTY)
+    foreach (_file ${ARGN})
+        if (IS_ABSOLUTE "${_file}")
+            set_property(GLOBAL APPEND PROPERTY ${PROPERTY} ${_file})
+        else()
+            set_property(GLOBAL APPEND PROPERTY ${PROPERTY}
+                         ${CMAKE_CURRENT_LIST_DIR}/${_file})
+        endif()
+    endforeach()
+endfunction ()
+
+function (gmx_add_libgromacs_sources)
+    _gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
+endfunction ()
+
+# TODO Reconsider this, as the CUDA driver API is probably a simpler
+# approach, at least for the build system. See Redmine #2530
+function (gmx_compile_cpp_as_cuda)
+    _gmx_add_files_to_property(GMX_LIBGROMACS_GPU_IMPL_SOURCES ${ARGN})
+endfunction ()
+
+function (gmx_install_headers)
+    if (NOT GMX_BUILD_MDRUN_ONLY)
+        file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
+        install(FILES       ${ARGN}
+                DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${_dest}"
+                COMPONENT   development)
+    endif()
+    _gmx_add_files_to_property(GMX_INSTALLED_HEADERS ${ARGN})
+endfunction ()
+
+function (gmx_write_installed_header_list)
+    get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+    string(REPLACE ";" "\n" _list "${_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()
+
+add_subdirectory(gmxlib)
+add_subdirectory(mdlib)
+add_subdirectory(applied-forces)
+add_subdirectory(listed-forces)
+add_subdirectory(commandline)
+add_subdirectory(domdec)
+add_subdirectory(ewald)
+add_subdirectory(fft)
+add_subdirectory(gpu_utils)
+add_subdirectory(hardware)
+add_subdirectory(linearalgebra)
+add_subdirectory(math)
+add_subdirectory(mdrun)
+add_subdirectory(mdrunutility)
+add_subdirectory(mdtypes)
+add_subdirectory(onlinehelp)
+add_subdirectory(options)
+add_subdirectory(pbcutil)
+add_subdirectory(random)
+add_subdirectory(restraint)
+add_subdirectory(tables)
+add_subdirectory(taskassignment)
+add_subdirectory(timing)
+add_subdirectory(topology)
+add_subdirectory(trajectory)
+add_subdirectory(utility)
+add_subdirectory(fileio)
+add_subdirectory(swap)
+add_subdirectory(essentialdynamics)
+add_subdirectory(pulling)
+add_subdirectory(awh)
+add_subdirectory(simd)
+add_subdirectory(imd)
+add_subdirectory(compat)
+add_subdirectory(mimic)
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    add_subdirectory(gmxana)
+    add_subdirectory(gmxpreprocess)
+    add_subdirectory(correlationfunctions)
+    add_subdirectory(statistics)
+    add_subdirectory(analysisdata)
+    add_subdirectory(selection)
+    add_subdirectory(trajectoryanalysis)
+    add_subdirectory(energyanalysis)
+    add_subdirectory(tools)
+endif()
+
+get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
+list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_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)
+target_sources(libgromacs_external PRIVATE ${THREAD_MPI_SOURCES})
+
+configure_file(version.h.cmakein version.h)
+gmx_install_headers(
+    analysisdata.h
+    commandline.h
+    options.h
+    random.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.cpp)
+gmx_configure_version_file(
+    utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
+    REMOTE_HASH
+    EXTRA_VARS
+        GMX_SOURCE_DOI
+    )
+list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE}
+     $<TARGET_OBJECTS:libgromacs_external>
+     $<TARGET_OBJECTS:libgromacs_generated>)
+
+# Mark some shared GPU implementation files to compile with CUDA if needed
+if (GMX_USE_CUDA)
+    get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
+    set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
+endif()
+
+# set up CUDA compilation with clang
+if (GMX_CLANG_CUDA)
+    foreach (_file ${LIBGROMACS_SOURCES})
+        get_filename_component(_ext ${_file} EXT)
+        get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
+        if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
+            gmx_compile_cuda_file_with_clang(${_file})
+        endif()
+    endforeach()
+endif()
+
+if (GMX_USE_CUDA)
+    # Work around FindCUDA that prevents using target_link_libraries()
+    # with keywords otherwise...
+    set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
+    if (NOT GMX_CLANG_CUDA)
+        cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
+    else()
+        add_library(libgromacs ${LIBGROMACS_SOURCES})
+    endif()
+    target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
+else()
+    add_library(libgromacs ${LIBGROMACS_SOURCES})
+endif()
+
+if (GMX_USE_OPENCL)
+    option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
+    mark_as_advanced(GMX_EXTERNAL_CLFFT)
+
+    # Default to using clFFT found on the system
+    # switch to quiet at the second run.
+    if (DEFINED clFFT_LIBRARY)
+        set (clFFT_FIND_QUIETLY TRUE)
+    endif()
+    find_package(clFFT)
+    if (NOT clFFT_FOUND)
+        if (GMX_EXTERNAL_CLFFT)
+            message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
+        endif()
+
+        if(MSVC)
+            message(FATAL_ERROR
+"An OpenCL build was requested with Visual Studio compiler, but GROMACS
+requires clFFT, which was not found on your system. GROMACS does bundle
+clFFT to help with building for OpenCL, but that clFFT has not yet been
+ported to the more recent versions of that compiler that GROMACS itself
+requires. Thus for now, OpenCL is not available with MSVC and the internal
+build of clFFT in GROMACS 2019. Either change compiler, try installing
+a clFFT package, or use the latest GROMACS 2018 point release.")
+        endif()
+
+        # Fall back on the internal version
+        set (_clFFT_dir ../external/clFFT/src)
+        add_subdirectory(${_clFFT_dir} clFFT-build)
+        target_sources(libgromacs PRIVATE
+            $<TARGET_OBJECTS:clFFT>
+        )
+        target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
+        # Use the magic variable for how to link any library needed for
+        # dlopen, etc.  which is -ldl where needed, and empty otherwise
+        # (e.g. Windows, BSD, Mac).
+        target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
+    else()
+        target_link_libraries(libgromacs PRIVATE clFFT)
+    endif()
+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). Same issue exists for nonbonded kernels
+# so we supress them for all generated files.
+include(CheckCXXCompilerFlag)
+check_cxx_compiler_flag("-Wno-unused -Wno-unused-parameter" HAS_NO_UNUSED)
+check_cxx_compiler_flag(-Wno-missing-declarations HAS_NO_MISSING_DECL)
+check_cxx_compiler_flag(-Wno-missing-prototypes HAS_NO_MISSING_PROTO)
+check_cxx_compiler_flag(/wd4101 HAS_NO_MSVC_UNUSED)
+if (NOT MSVC)
+    check_cxx_compiler_flag(-wd1419 HAS_DECL_IN_SOURCE)
+endif()
+if (HAS_NO_UNUSED)
+    target_compile_options(libgromacs_generated PRIVATE "-Wno-unused;-Wno-unused-parameter")
+endif()
+if (HAS_NO_MISSING_DECL)
+    target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-declarations")
+endif()
+# TODO The group scheme kernels don't use proper function prototype
+# declarations, and clang warns about such use, which we suppress
+# rather than fix. We would prefer to use no suppressions. However
+# other compilers do not support such a warning suppression for C++
+# source files, and issue warnings about that. Remove the use of
+# -Wno-missing-prototypes here and above when the group scheme is
+# removed.
+if (HAS_NO_MISSING_PROTO AND "${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+    target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-prototypes")
+endif()
+if (HAS_NO_MSVC_UNUSED)
+    target_compile_options(libgromacs_generated PRIVATE "/wd4101")
+endif()
+if (HAS_DECL_IN_SOURCE)
+    target_compile_options(libgromacs_generated PRIVATE "-wd1419")
+endif()
+
+if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
+    # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
+    # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
+    # with the SIMD_AVX_512_CXX_FLAGS flags.
+    set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
+endif()
+
+gmx_setup_tng_for_libgromacs()
+
+target_link_libraries(libgromacs
+                      PRIVATE
+                      ${EXTRAE_LIBRARIES}
+                      ${GMX_EXTRA_LIBRARIES}
+                      ${GMX_COMMON_LIBRARIES}
+                      ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
+                      ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
+                      ${OpenCL_LIBRARIES}
+                      ${GMX_STDLIB_LIBRARIES}
+                      PUBLIC
+                      ${GMX_PUBLIC_LIBRARIES}
+                      ${PLUMED_LOAD}
+                      )
+set_target_properties(libgromacs PROPERTIES
+                      OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
+                      SOVERSION ${LIBRARY_SOVERSION_MAJOR}
+                      VERSION ${LIBRARY_VERSION}
+                      COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+gmx_manage_lmfit()
+target_link_libraries(libgromacs PRIVATE lmfit)
+
+if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^6\.0")
+   target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
+endif()
+if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+   target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
+     #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
+     #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
+     /wd6001  #unitialized memory
+     /wd6011  #derefencing NULL
+     /wd6053  #prior call not zero-terminate
+     /wd6054  #might not be zero-terminated
+     /wd6385  #reading invalid data
+     /wd6386  #buffer overrun
+     /wd6387  #could be '0'
+     /wd28199 #uninitialized memory
+     # For compile time constant (e.g. templates) the following warnings have flase postives
+     /wd6239  #(<non-zero> && <expr>)
+     /wd6240  #(<expr> && <non-zero>)
+     /wd6294  #Ill-defined for-loop
+     /wd6326  #comparison of constant with other constant
+     /wd28020 #expression involving paramter is not true
+     # Misc
+     /wd6330  #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
+     /wd6993  #OpenMP ignored
+     #TODO
+     /wd6031  #return value ignored (important - mostly warnigns about sscanf)
+     /wd6244  #hides declaration (known issue - we ingore similar warnings for other compilers)
+     /wd6246  #hides declaration
+     >
+   )
+endif()
+
+if (GMX_CLANG_TIDY)
+   set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
+       "${CLANG_TIDY_EXE};-warnings-as-errors=*")
+endif()
+
+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 ${CMAKE_INSTALL_LIBDIR}
+            RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+            ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+            COMPONENT libraries)
+endif()
+
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    include(InstallLibInfo.cmake)
+endif()
+
+# Technically, the user could want to do this for an OpenCL build
+# using the CUDA runtime, but currently there's no reason to want to
+# do that.
+if (INSTALL_CUDART_LIB) #can be set manual by user
+    if (GMX_USE_CUDA)
+        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
+                    ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
+    endif()
+endif()
+
+if(GMX_USE_OPENCL)
+    # Install the utility headers
+    file(GLOB OPENCL_INSTALLED_FILES
+        gpu_utils/vectype_ops.clh
+        gpu_utils/device_utils.clh
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
+        COMPONENT libraries)
+    file(GLOB OPENCL_INSTALLED_FILES
+        pbcutil/ishift.h
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
+        COMPONENT libraries)
+
+    # Install the NB source and headers
+    file(GLOB OPENCL_INSTALLED_FILES
+        mdlib/nbnxn_consts.h
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/mdlib
+        COMPONENT libraries)
+    file(GLOB OPENCL_INSTALLED_FILES
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernel.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernel_pruneonly.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernels.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernels_fastgen.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernels_fastgen_add_twincut.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernel_utils.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_consts.h
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/mdlib/nbnxn_ocl
+        COMPONENT libraries)
+
+    # Install the PME source and headers
+    file(GLOB OPENCL_INSTALLED_FILES
+        ewald/pme-spread.clh
+        ewald/pme-solve.clh
+        ewald/pme-gather.clh
+        ewald/pme-gpu-utils.clh
+        ewald/pme-program.cl
+        ewald/pme-gpu-types.h
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald
+        COMPONENT libraries)
+endif()

patches/gromacs-2019.1.diff/src/gromacs/CMakeLists.txt.preplumed

+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and 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)
+
+if (GMX_CLANG_CUDA)
+    include(gmxClangCudaUtils)
+endif()
+
+set_property(GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
+set_property(GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
+set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+set_property(GLOBAL PROPERTY GMX_AVX_512_SOURCE)
+
+add_library(libgromacs_external OBJECT "")
+if(CMAKE_COMPILER_IS_GNUCXX)
+    # Keep quiet about e.g. linearalgebra module
+    target_compile_options(libgromacs_external PRIVATE ${CXXFLAGS_NO_STRINGOP_TRUNCATION})
+endif()
+
+add_library(libgromacs_generated OBJECT "")
+if (BUILD_SHARED_LIBS)
+    set_target_properties(libgromacs_external PROPERTIES POSITION_INDEPENDENT_CODE true)
+    set_target_properties(libgromacs_generated PROPERTIES POSITION_INDEPENDENT_CODE true)
+endif()
+
+function (_gmx_add_files_to_property PROPERTY)
+    foreach (_file ${ARGN})
+        if (IS_ABSOLUTE "${_file}")
+            set_property(GLOBAL APPEND PROPERTY ${PROPERTY} ${_file})
+        else()
+            set_property(GLOBAL APPEND PROPERTY ${PROPERTY}
+                         ${CMAKE_CURRENT_LIST_DIR}/${_file})
+        endif()
+    endforeach()
+endfunction ()
+
+function (gmx_add_libgromacs_sources)
+    _gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
+endfunction ()
+
+# TODO Reconsider this, as the CUDA driver API is probably a simpler
+# approach, at least for the build system. See Redmine #2530
+function (gmx_compile_cpp_as_cuda)
+    _gmx_add_files_to_property(GMX_LIBGROMACS_GPU_IMPL_SOURCES ${ARGN})
+endfunction ()
+
+function (gmx_install_headers)
+    if (NOT GMX_BUILD_MDRUN_ONLY)
+        file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
+        install(FILES       ${ARGN}
+                DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${_dest}"
+                COMPONENT   development)
+    endif()
+    _gmx_add_files_to_property(GMX_INSTALLED_HEADERS ${ARGN})
+endfunction ()
+
+function (gmx_write_installed_header_list)
+    get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
+    string(REPLACE ";" "\n" _list "${_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()
+
+add_subdirectory(gmxlib)
+add_subdirectory(mdlib)
+add_subdirectory(applied-forces)
+add_subdirectory(listed-forces)
+add_subdirectory(commandline)
+add_subdirectory(domdec)
+add_subdirectory(ewald)
+add_subdirectory(fft)
+add_subdirectory(gpu_utils)
+add_subdirectory(hardware)
+add_subdirectory(linearalgebra)
+add_subdirectory(math)
+add_subdirectory(mdrun)
+add_subdirectory(mdrunutility)
+add_subdirectory(mdtypes)
+add_subdirectory(onlinehelp)
+add_subdirectory(options)
+add_subdirectory(pbcutil)
+add_subdirectory(random)
+add_subdirectory(restraint)
+add_subdirectory(tables)
+add_subdirectory(taskassignment)
+add_subdirectory(timing)
+add_subdirectory(topology)
+add_subdirectory(trajectory)
+add_subdirectory(utility)
+add_subdirectory(fileio)
+add_subdirectory(swap)
+add_subdirectory(essentialdynamics)
+add_subdirectory(pulling)
+add_subdirectory(awh)
+add_subdirectory(simd)
+add_subdirectory(imd)
+add_subdirectory(compat)
+add_subdirectory(mimic)
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    add_subdirectory(gmxana)
+    add_subdirectory(gmxpreprocess)
+    add_subdirectory(correlationfunctions)
+    add_subdirectory(statistics)
+    add_subdirectory(analysisdata)
+    add_subdirectory(selection)
+    add_subdirectory(trajectoryanalysis)
+    add_subdirectory(energyanalysis)
+    add_subdirectory(tools)
+endif()
+
+get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
+list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_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)
+target_sources(libgromacs_external PRIVATE ${THREAD_MPI_SOURCES})
+
+configure_file(version.h.cmakein version.h)
+gmx_install_headers(
+    analysisdata.h
+    commandline.h
+    options.h
+    random.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.cpp)
+gmx_configure_version_file(
+    utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
+    REMOTE_HASH
+    EXTRA_VARS
+        GMX_SOURCE_DOI
+    )
+list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE}
+     $<TARGET_OBJECTS:libgromacs_external>
+     $<TARGET_OBJECTS:libgromacs_generated>)
+
+# Mark some shared GPU implementation files to compile with CUDA if needed
+if (GMX_USE_CUDA)
+    get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
+    set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
+endif()
+
+# set up CUDA compilation with clang
+if (GMX_CLANG_CUDA)
+    foreach (_file ${LIBGROMACS_SOURCES})
+        get_filename_component(_ext ${_file} EXT)
+        get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
+        if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
+            gmx_compile_cuda_file_with_clang(${_file})
+        endif()
+    endforeach()
+endif()
+
+if (GMX_USE_CUDA)
+    # Work around FindCUDA that prevents using target_link_libraries()
+    # with keywords otherwise...
+    set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
+    if (NOT GMX_CLANG_CUDA)
+        cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
+    else()
+        add_library(libgromacs ${LIBGROMACS_SOURCES})
+    endif()
+    target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
+else()
+    add_library(libgromacs ${LIBGROMACS_SOURCES})
+endif()
+
+if (GMX_USE_OPENCL)
+    option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
+    mark_as_advanced(GMX_EXTERNAL_CLFFT)
+
+    # Default to using clFFT found on the system
+    # switch to quiet at the second run.
+    if (DEFINED clFFT_LIBRARY)
+        set (clFFT_FIND_QUIETLY TRUE)
+    endif()
+    find_package(clFFT)
+    if (NOT clFFT_FOUND)
+        if (GMX_EXTERNAL_CLFFT)
+            message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
+        endif()
+
+        if(MSVC)
+            message(FATAL_ERROR
+"An OpenCL build was requested with Visual Studio compiler, but GROMACS
+requires clFFT, which was not found on your system. GROMACS does bundle
+clFFT to help with building for OpenCL, but that clFFT has not yet been
+ported to the more recent versions of that compiler that GROMACS itself
+requires. Thus for now, OpenCL is not available with MSVC and the internal
+build of clFFT in GROMACS 2019. Either change compiler, try installing
+a clFFT package, or use the latest GROMACS 2018 point release.")
+        endif()
+
+        # Fall back on the internal version
+        set (_clFFT_dir ../external/clFFT/src)
+        add_subdirectory(${_clFFT_dir} clFFT-build)
+        target_sources(libgromacs PRIVATE
+            $<TARGET_OBJECTS:clFFT>
+        )
+        target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
+        # Use the magic variable for how to link any library needed for
+        # dlopen, etc.  which is -ldl where needed, and empty otherwise
+        # (e.g. Windows, BSD, Mac).
+        target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
+    else()
+        target_link_libraries(libgromacs PRIVATE clFFT)
+    endif()
+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). Same issue exists for nonbonded kernels
+# so we supress them for all generated files.
+include(CheckCXXCompilerFlag)
+check_cxx_compiler_flag("-Wno-unused -Wno-unused-parameter" HAS_NO_UNUSED)
+check_cxx_compiler_flag(-Wno-missing-declarations HAS_NO_MISSING_DECL)
+check_cxx_compiler_flag(-Wno-missing-prototypes HAS_NO_MISSING_PROTO)
+check_cxx_compiler_flag(/wd4101 HAS_NO_MSVC_UNUSED)
+if (NOT MSVC)
+    check_cxx_compiler_flag(-wd1419 HAS_DECL_IN_SOURCE)
+endif()
+if (HAS_NO_UNUSED)
+    target_compile_options(libgromacs_generated PRIVATE "-Wno-unused;-Wno-unused-parameter")
+endif()
+if (HAS_NO_MISSING_DECL)
+    target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-declarations")
+endif()
+# TODO The group scheme kernels don't use proper function prototype
+# declarations, and clang warns about such use, which we suppress
+# rather than fix. We would prefer to use no suppressions. However
+# other compilers do not support such a warning suppression for C++
+# source files, and issue warnings about that. Remove the use of
+# -Wno-missing-prototypes here and above when the group scheme is
+# removed.
+if (HAS_NO_MISSING_PROTO AND "${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+    target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-prototypes")
+endif()
+if (HAS_NO_MSVC_UNUSED)
+    target_compile_options(libgromacs_generated PRIVATE "/wd4101")
+endif()
+if (HAS_DECL_IN_SOURCE)
+    target_compile_options(libgromacs_generated PRIVATE "-wd1419")
+endif()
+
+if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
+    # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
+    # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
+    # with the SIMD_AVX_512_CXX_FLAGS flags.
+    set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
+endif()
+
+gmx_setup_tng_for_libgromacs()
+
+target_link_libraries(libgromacs
+                      PRIVATE
+                      ${EXTRAE_LIBRARIES}
+                      ${GMX_EXTRA_LIBRARIES}
+                      ${GMX_COMMON_LIBRARIES}
+                      ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
+                      ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
+                      ${OpenCL_LIBRARIES}
+                      ${GMX_STDLIB_LIBRARIES}
+                      PUBLIC
+                      ${GMX_PUBLIC_LIBRARIES}
+                      )
+set_target_properties(libgromacs PROPERTIES
+                      OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
+                      SOVERSION ${LIBRARY_SOVERSION_MAJOR}
+                      VERSION ${LIBRARY_VERSION}
+                      COMPILE_FLAGS "${OpenMP_C_FLAGS}")
+
+gmx_manage_lmfit()
+target_link_libraries(libgromacs PRIVATE lmfit)
+
+if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^6\.0")
+   target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
+endif()
+if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+   target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
+     #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
+     #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
+     /wd6001  #unitialized memory
+     /wd6011  #derefencing NULL
+     /wd6053  #prior call not zero-terminate
+     /wd6054  #might not be zero-terminated
+     /wd6385  #reading invalid data
+     /wd6386  #buffer overrun
+     /wd6387  #could be '0'
+     /wd28199 #uninitialized memory
+     # For compile time constant (e.g. templates) the following warnings have flase postives
+     /wd6239  #(<non-zero> && <expr>)
+     /wd6240  #(<expr> && <non-zero>)
+     /wd6294  #Ill-defined for-loop
+     /wd6326  #comparison of constant with other constant
+     /wd28020 #expression involving paramter is not true
+     # Misc
+     /wd6330  #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
+     /wd6993  #OpenMP ignored
+     #TODO
+     /wd6031  #return value ignored (important - mostly warnigns about sscanf)
+     /wd6244  #hides declaration (known issue - we ingore similar warnings for other compilers)
+     /wd6246  #hides declaration
+     >
+   )
+endif()
+
+if (GMX_CLANG_TIDY)
+   set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
+       "${CLANG_TIDY_EXE};-warnings-as-errors=*")
+endif()
+
+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 ${CMAKE_INSTALL_LIBDIR}
+            RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+            ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+            COMPONENT libraries)
+endif()
+
+if (NOT GMX_BUILD_MDRUN_ONLY)
+    include(InstallLibInfo.cmake)
+endif()
+
+# Technically, the user could want to do this for an OpenCL build
+# using the CUDA runtime, but currently there's no reason to want to
+# do that.
+if (INSTALL_CUDART_LIB) #can be set manual by user
+    if (GMX_USE_CUDA)
+        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
+                    ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
+            endif()
+        endforeach()
+    else()
+        message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
+    endif()
+endif()
+
+if(GMX_USE_OPENCL)
+    # Install the utility headers
+    file(GLOB OPENCL_INSTALLED_FILES
+        gpu_utils/vectype_ops.clh
+        gpu_utils/device_utils.clh
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
+        COMPONENT libraries)
+    file(GLOB OPENCL_INSTALLED_FILES
+        pbcutil/ishift.h
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
+        COMPONENT libraries)
+
+    # Install the NB source and headers
+    file(GLOB OPENCL_INSTALLED_FILES
+        mdlib/nbnxn_consts.h
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/mdlib
+        COMPONENT libraries)
+    file(GLOB OPENCL_INSTALLED_FILES
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernel.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernel_pruneonly.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernels.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernels_fastgen.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernels_fastgen_add_twincut.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_kernel_utils.clh
+        mdlib/nbnxn_ocl/nbnxn_ocl_consts.h
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/mdlib/nbnxn_ocl
+        COMPONENT libraries)
+
+    # Install the PME source and headers
+    file(GLOB OPENCL_INSTALLED_FILES
+        ewald/pme-spread.clh
+        ewald/pme-solve.clh
+        ewald/pme-gather.clh
+        ewald/pme-gpu-utils.clh
+        ewald/pme-program.cl
+        ewald/pme-gpu-types.h
+        )
+    install(FILES ${OPENCL_INSTALLED_FILES}
+        DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald
+        COMPONENT libraries)
+endif()

patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp

+/*
+ * 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) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file declares helper functionality for legacy option handling for 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 "legacymdrunoptions.h"
+
+#include "config.h"
+
+#include <cstring>
+
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/mdrun/multisim.h"
+#include "gromacs/mdrunutility/handlerestart.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/utility/arraysize.h"
+#include "gromacs/utility/fatalerror.h"
+
+/* PLUMED */
+#include "../../../Plumed.h"
+extern int    plumedswitch;
+extern plumed plumedmain; 
+extern void(*plumedcmd)(plumed,const char*,const void*);
+/* END PLUMED */
+
+namespace gmx
+{
+
+/*! \brief Return whether the command-line parameter 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], "-multidir") == 0)
+        {
+            return true;
+        }
+    }
+    return false;
+}
+
+int LegacyMdrunOptions::updateFromCommandLine(int argc, char **argv, ArrayRef<const char *> desc)
+{
+    unsigned long     PCA_Flags = PCA_CAN_SET_DEFFNM;
+    // With -multidir, the working directory still needs to be
+    // changed, so we can't check for the existence of files 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;
+    }
+
+    if (!parse_common_args(&argc, argv, PCA_Flags,
+                           static_cast<int>(filenames.size()), filenames.data(), asize(pa), pa,
+                           static_cast<int>(desc.size()), desc.data(), 0, nullptr, &oenv))
+    {
+        return 0;
+    }
+
+    // Handle the options that permits the user to either declare
+    // which compatible GPUs are availble for use, or to select a GPU
+    // task assignment. Either could be in an environment variable (so
+    // that there is a way to customize it, when using MPI in
+    // heterogeneous contexts).
+    {
+        // TODO Argument parsing can't handle std::string. We should
+        // fix that by changing the parsing, once more of the roles of
+        // handling, validating and implementing defaults for user
+        // command-line options have been seperated.
+        hw_opt.gpuIdsAvailable       = gpuIdsAvailable;
+        hw_opt.userGpuTaskAssignment = userGpuTaskAssignment;
+
+        const char *env = getenv("GMX_GPU_ID");
+        if (env != nullptr)
+        {
+            if (!hw_opt.gpuIdsAvailable.empty())
+            {
+                gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
+            }
+            hw_opt.gpuIdsAvailable = env;
+        }
+
+        env = getenv("GMX_GPUTASKS");
+        if (env != nullptr)
+        {
+            if (!hw_opt.userGpuTaskAssignment.empty())
+            {
+                gmx_fatal(FARGS, "GMX_GPUTASKS and -gputasks can not be used at the same time");
+            }
+            hw_opt.userGpuTaskAssignment = env;
+        }
+
+        if (!hw_opt.gpuIdsAvailable.empty() && !hw_opt.userGpuTaskAssignment.empty())
+        {
+            gmx_fatal(FARGS, "-gpu_id and -gputasks cannot be used at the same time");
+        }
+    }
+
+    hw_opt.thread_affinity = nenum(thread_aff_opt_choices);
+
+    // now check for a multi-simulation
+    ArrayRef<const std::string> multidir = opt2fnsIfOptionSet("-multidir",
+                                                              static_cast<int>(filenames.size()),
+                                                              filenames.data());
+
+    if (replExParams.exchangeInterval != 0 && multidir.size() < 2)
+    {
+        gmx_fatal(FARGS, "Need at least two replicas for replica exchange (use option -multidir)");
+    }
+
+    if (replExParams.numExchanges < 0)
+    {
+        gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
+    }
+
+    ms = init_multisystem(MPI_COMM_WORLD, multidir);
+
+    /* Prepare the intra-simulation communication */
+    // TODO consolidate this with init_commrec, after changing the
+    // relative ordering of init_commrec and init_multisystem
+#if GMX_MPI
+    if (ms != nullptr)
+    {
+        cr->nnodes = cr->nnodes / ms->nsim;
+        MPI_Comm_split(MPI_COMM_WORLD, ms->sim, cr->sim_nodeid, &cr->mpi_comm_mysim);
+        cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
+        MPI_Comm_rank(cr->mpi_comm_mysim, &cr->sim_nodeid);
+        MPI_Comm_rank(cr->mpi_comm_mygroup, &cr->nodeid);
+    }
+#endif
+
+    if (!opt2bSet("-cpi",
+                  static_cast<int>(filenames.size()), filenames.data()))
+    {
+        // If we are not starting from a checkpoint we never allow files to be appended
+        // to, since that has caused a ton of strange behaviour and bugs in the past.
+        if (opt2parg_bSet("-append", asize(pa), pa))
+        {
+            // If the user explicitly used the -append option, explain that it is not possible.
+            gmx_fatal(FARGS, "GROMACS can only append to files when restarting from a checkpoint.");
+        }
+        else
+        {
+            // If the user did not say anything explicit, just disable appending.
+            bTryToAppendFiles = FALSE;
+        }
+    }
+
+    ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
+
+    continuationOptions.appendFilesOptionSet = opt2parg_bSet("-append", asize(pa), pa);
+
+    handleRestart(cr, ms, bTryToAppendFiles,
+                  static_cast<int>(filenames.size()),
+                  filenames.data(),
+                  &continuationOptions.appendFiles,
+                  &continuationOptions.startedFromCheckpoint);
+
+    mdrunOptions.rerun            = opt2bSet("-rerun",
+                                             static_cast<int>(filenames.size()),
+                                             filenames.data());
+    mdrunOptions.ntompOptionIsSet = opt2parg_bSet("-ntomp", asize(pa), pa);
+
+    domdecOptions.rankOrder    = static_cast<DdRankOrder>(nenum(ddrank_opt_choices));
+    domdecOptions.dlbOption    = static_cast<DlbOption>(nenum(dddlb_opt_choices));
+    domdecOptions.numCells[XX] = roundToInt(realddxyz[XX]);
+    domdecOptions.numCells[YY] = roundToInt(realddxyz[YY]);
+    domdecOptions.numCells[ZZ] = roundToInt(realddxyz[ZZ]);
+
+    /* PLUMED */
+    plumedswitch=0;
+    if (opt2bSet("-plumed", static_cast<int>(filenames.size()), filenames.data())) 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,static_cast<int>(filenames.size()), filenames.data()));
+      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(replExParams.exchangeInterval==0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) replica exchange");
+      if(replExParams.numExchanges!=0) gmx_fatal(FARGS,"-hrex (or PLUMED_HREX) not compatible with -nex");
+    }
+    /* END PLUMED HREX */
+
+    /* END PLUMED */
+
+    return 1;
+}
+
+LegacyMdrunOptions::~LegacyMdrunOptions()
+{
+    if (GMX_LIB_MPI)
+    {
+        done_commrec(cr);
+    }
+    done_multisim(ms);
+}
+
+} // namespace gmx

patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.cpp.preplumed

+/*
+ * 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) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ *
+ * \brief This file declares helper functionality for legacy option handling for 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 "legacymdrunoptions.h"
+
+#include "config.h"
+
+#include <cstring>
+
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/math/functions.h"
+#include "gromacs/mdrun/multisim.h"
+#include "gromacs/mdrunutility/handlerestart.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/utility/arraysize.h"
+#include "gromacs/utility/fatalerror.h"
+
+namespace gmx
+{
+
+/*! \brief Return whether the command-line parameter 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], "-multidir") == 0)
+        {
+            return true;
+        }
+    }
+    return false;
+}
+
+int LegacyMdrunOptions::updateFromCommandLine(int argc, char **argv, ArrayRef<const char *> desc)
+{
+    unsigned long     PCA_Flags = PCA_CAN_SET_DEFFNM;
+    // With -multidir, the working directory still needs to be
+    // changed, so we can't check for the existence of files 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;
+    }
+
+    if (!parse_common_args(&argc, argv, PCA_Flags,
+                           static_cast<int>(filenames.size()), filenames.data(), asize(pa), pa,
+                           static_cast<int>(desc.size()), desc.data(), 0, nullptr, &oenv))
+    {
+        return 0;
+    }
+
+    // Handle the options that permits the user to either declare
+    // which compatible GPUs are availble for use, or to select a GPU
+    // task assignment. Either could be in an environment variable (so
+    // that there is a way to customize it, when using MPI in
+    // heterogeneous contexts).
+    {
+        // TODO Argument parsing can't handle std::string. We should
+        // fix that by changing the parsing, once more of the roles of
+        // handling, validating and implementing defaults for user
+        // command-line options have been seperated.
+        hw_opt.gpuIdsAvailable       = gpuIdsAvailable;
+        hw_opt.userGpuTaskAssignment = userGpuTaskAssignment;
+
+        const char *env = getenv("GMX_GPU_ID");
+        if (env != nullptr)
+        {
+            if (!hw_opt.gpuIdsAvailable.empty())
+            {
+                gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
+            }
+            hw_opt.gpuIdsAvailable = env;
+        }
+
+        env = getenv("GMX_GPUTASKS");
+        if (env != nullptr)
+        {
+            if (!hw_opt.userGpuTaskAssignment.empty())
+            {
+                gmx_fatal(FARGS, "GMX_GPUTASKS and -gputasks can not be used at the same time");
+            }
+            hw_opt.userGpuTaskAssignment = env;
+        }
+
+        if (!hw_opt.gpuIdsAvailable.empty() && !hw_opt.userGpuTaskAssignment.empty())
+        {
+            gmx_fatal(FARGS, "-gpu_id and -gputasks cannot be used at the same time");
+        }
+    }
+
+    hw_opt.thread_affinity = nenum(thread_aff_opt_choices);
+
+    // now check for a multi-simulation
+    ArrayRef<const std::string> multidir = opt2fnsIfOptionSet("-multidir",
+                                                              static_cast<int>(filenames.size()),
+                                                              filenames.data());
+
+    if (replExParams.exchangeInterval != 0 && multidir.size() < 2)
+    {
+        gmx_fatal(FARGS, "Need at least two replicas for replica exchange (use option -multidir)");
+    }
+
+    if (replExParams.numExchanges < 0)
+    {
+        gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
+    }
+
+    ms = init_multisystem(MPI_COMM_WORLD, multidir);
+
+    /* Prepare the intra-simulation communication */
+    // TODO consolidate this with init_commrec, after changing the
+    // relative ordering of init_commrec and init_multisystem
+#if GMX_MPI
+    if (ms != nullptr)
+    {
+        cr->nnodes = cr->nnodes / ms->nsim;
+        MPI_Comm_split(MPI_COMM_WORLD, ms->sim, cr->sim_nodeid, &cr->mpi_comm_mysim);
+        cr->mpi_comm_mygroup = cr->mpi_comm_mysim;
+        MPI_Comm_rank(cr->mpi_comm_mysim, &cr->sim_nodeid);
+        MPI_Comm_rank(cr->mpi_comm_mygroup, &cr->nodeid);
+    }
+#endif
+
+    if (!opt2bSet("-cpi",
+                  static_cast<int>(filenames.size()), filenames.data()))
+    {
+        // If we are not starting from a checkpoint we never allow files to be appended
+        // to, since that has caused a ton of strange behaviour and bugs in the past.
+        if (opt2parg_bSet("-append", asize(pa), pa))
+        {
+            // If the user explicitly used the -append option, explain that it is not possible.
+            gmx_fatal(FARGS, "GROMACS can only append to files when restarting from a checkpoint.");
+        }
+        else
+        {
+            // If the user did not say anything explicit, just disable appending.
+            bTryToAppendFiles = FALSE;
+        }
+    }
+
+    ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
+
+    continuationOptions.appendFilesOptionSet = opt2parg_bSet("-append", asize(pa), pa);
+
+    handleRestart(cr, ms, bTryToAppendFiles,
+                  static_cast<int>(filenames.size()),
+                  filenames.data(),
+                  &continuationOptions.appendFiles,
+                  &continuationOptions.startedFromCheckpoint);
+
+    mdrunOptions.rerun            = opt2bSet("-rerun",
+                                             static_cast<int>(filenames.size()),
+                                             filenames.data());
+    mdrunOptions.ntompOptionIsSet = opt2parg_bSet("-ntomp", asize(pa), pa);
+
+    domdecOptions.rankOrder    = static_cast<DdRankOrder>(nenum(ddrank_opt_choices));
+    domdecOptions.dlbOption    = static_cast<DlbOption>(nenum(dddlb_opt_choices));
+    domdecOptions.numCells[XX] = roundToInt(realddxyz[XX]);
+    domdecOptions.numCells[YY] = roundToInt(realddxyz[YY]);
+    domdecOptions.numCells[ZZ] = roundToInt(realddxyz[ZZ]);
+
+    return 1;
+}
+
+LegacyMdrunOptions::~LegacyMdrunOptions()
+{
+    if (GMX_LIB_MPI)
+    {
+        done_commrec(cr);
+    }
+    done_multisim(ms);
+}
+
+} // namespace gmx

patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h

+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief This file declares helper functionality for legacy option handling for 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
+ * \inlibraryapi
+ */
+#ifndef GMX_MDRUN_LEGACYMDRUNOPTIONS_H
+#define GMX_MDRUN_LEGACYMDRUNOPTIONS_H
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/hardware/hw_info.h"
+#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdrun/logging.h"
+
+#include "replicaexchange.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 */
+
+struct gmx_multisim_t;
+
+namespace gmx
+{
+
+/*! \libinternal
+ * \brief This class provides the same command-line option
+ * functionality to both CLI and API sessions.
+ *
+ * This class should not exist, but is necessary now to introduce
+ * support for the CLI and API without duplicating code. It should be
+ * eliminated following the TODOs below.
+ *
+ * \todo Modules in mdrun should acquire proper option handling so
+ * that all of these declarations and defaults are local to the
+ * modules.
+ *
+ * \todo Contextual aspects, such as working directory, MPI
+ * environment, and environment variable handling are more properly
+ * the role of SimulationContext, and should be moved there */
+class LegacyMdrunOptions
+{
+    public:
+        //! Ongoing collection of mdrun options
+        MdrunOptions                     mdrunOptions;
+        //! Options for the domain decomposition.
+        DomdecOptions                    domdecOptions;
+        //! Parallelism-related user options.
+        gmx_hw_opt_t                     hw_opt;
+        //! Command-line override for the duration of a neighbor list with the Verlet scheme.
+        int                              nstlist_cmdline = 0;
+        //! Parameters for replica-exchange simulations.
+        ReplicaExchangeParameters        replExParams;
+
+        //! Filename options to fill from command-line argument values.
+        std::vector<t_filenm> filenames =
+        {{{ efTPR, nullptr,     nullptr,     ffREAD },
+          { efTRN, "-o",        nullptr,     ffWRITE },
+          { efCOMPRESSED, "-x", nullptr,     ffOPTWR },
+          { efCPT, "-cpi",      nullptr,     ffOPTRD | ffALLOW_MISSING },
+          { efCPT, "-cpo",      nullptr,     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, "-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 },
+          { efRND, "-multidir", nullptr,     ffOPTRDMULT},
+          { efXVG, "-awh",      "awhinit",   ffOPTRD },
+          { 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 }}};
+
+        //! Print a warning if any force is larger than this (in kJ/mol nm).
+        real                             pforce = -1;
+
+        /*! \brief Output context for writing text files
+         *
+         * \todo Clarify initialization, ownership, and lifetime. */
+        gmx_output_env_t                *oenv = nullptr;
+
+        //! Handle to file used for logging.
+        LogFilePtr logFileGuard = nullptr;
+
+        /*! \brief Command line options, defaults, docs and storage for them to fill. */
+        /*! \{ */
+        rvec              realddxyz                                               = {0, 0, 0};
+        const char       *ddrank_opt_choices[static_cast<int>(DdRankOrder::nr)+1] =
+        { nullptr, "interleave", "pp_pme", "cartesian", nullptr };
+        const char       *dddlb_opt_choices[static_cast<int>(DlbOption::nr)+1] =
+        { nullptr, "auto", "no", "yes", nullptr };
+        const char       *thread_aff_opt_choices[threadaffNR+1] =
+        { nullptr, "auto", "on", "off", nullptr };
+        const char       *nbpu_opt_choices[5] =
+        { nullptr, "auto", "cpu", "gpu", nullptr };
+        const char       *pme_opt_choices[5] =
+        { nullptr, "auto", "cpu", "gpu", nullptr };
+        const char       *pme_fft_opt_choices[5] =
+        { nullptr, "auto", "cpu", "gpu", nullptr };
+        const char       *bonded_opt_choices[5] =
+        { nullptr, "auto", "cpu", "gpu", nullptr };
+        gmx_bool          bTryToAppendFiles     = TRUE;
+        const char       *gpuIdsAvailable       = "";
+        const char       *userGpuTaskAssignment = "";
+
+        ImdOptions       &imdOptions = mdrunOptions.imdOptions;
+
+        t_pargs           pa[49] = {
+
+            { "-dd",      FALSE, etRVEC, {&realddxyz},
+              "Domain decomposition grid, 0 is optimize" },
+            { "-ddorder", FALSE, etENUM, {ddrank_opt_choices},
+              "DD rank order" },
+            { "-npme",    FALSE, etINT, {&domdecOptions.numPmeRanks},
+              "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 ranks 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_choices},
+              "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, {&gpuIdsAvailable},
+              "List of unique GPU device IDs available to use" },
+            { "-gputasks",  FALSE, etSTR, {&userGpuTaskAssignment},
+              "List of GPU device IDs, mapping each PP task on each node to a device" },
+            { "-ddcheck", FALSE, etBOOL, {&domdecOptions.checkBondedInteractions},
+              "Check for all bonded interactions with DD" },
+            { "-ddbondcomm", FALSE, etBOOL, {&domdecOptions.useBondedCommunication},
+              "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
+            { "-rdd",     FALSE, etREAL, {&domdecOptions.minimumCommunicationRange},
+              "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
+            { "-rcon",    FALSE, etREAL, {&domdecOptions.constraintCommunicationRange},
+              "Maximum distance for P-LINCS (nm), 0 is estimate" },
+            { "-dlb",     FALSE, etENUM, {dddlb_opt_choices},
+              "Dynamic load balancing (with DD)" },
+            { "-dds",     FALSE, etREAL, {&domdecOptions.dlbScaling},
+              "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, {&domdecOptions.cellSizeX},
+              "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, {&domdecOptions.cellSizeY},
+              "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, {&domdecOptions.cellSizeZ},
+              "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, {&mdrunOptions.globalCommunicationInterval},
+              "Global communication frequency" },
+            { "-nb",      FALSE, etENUM, {nbpu_opt_choices},
+              "Calculate non-bonded interactions on" },
+            { "-nstlist", FALSE, etINT, {&nstlist_cmdline},
+              "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
+            { "-tunepme", FALSE, etBOOL, {&mdrunOptions.tunePme},
+              "Optimize PME load between PP/PME ranks or GPU/CPU (only with the Verlet cut-off scheme)" },
+            { "-pme",     FALSE, etENUM, {pme_opt_choices},
+              "Perform PME calculations on" },
+            { "-pmefft", FALSE, etENUM, {pme_fft_opt_choices},
+              "Perform PME FFT calculations on" },
+            { "-bonded",     FALSE, etENUM, {bonded_opt_choices},
+              "Perform bonded calculations on" },
+            { "-v",       FALSE, etBOOL, {&mdrunOptions.verbose},
+              "Be loud and noisy" },
+            { "-pforce",  FALSE, etREAL, {&pforce},
+              "Print all forces larger than this (kJ/mol nm)" },
+            { "-reprod",  FALSE, etBOOL, {&mdrunOptions.reproducible},
+              "Try to avoid optimizations that affect binary reproducibility" },
+            { "-cpt",     FALSE, etREAL, {&mdrunOptions.checkpointOptions.period},
+              "Checkpoint interval (minutes)" },
+            { "-cpnum",   FALSE, etBOOL, {&mdrunOptions.checkpointOptions.keepAndNumberCheckpointFiles},
+              "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, {&mdrunOptions.numStepsCommandline},
+              "Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
+            { "-maxh",   FALSE, etREAL, {&mdrunOptions.maximumHoursToRun},
+              "Terminate after 0.99 times this time (hours)" },
+            { "-replex",  FALSE, etINT, {&replExParams.exchangeInterval},
+              "Attempt replica exchange periodically with this period (steps)" },
+            { "-nex",  FALSE, etINT, {&replExParams.numExchanges},
+              "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, {&replExParams.randomSeed},
+              "Seed for replica exchange, -1 is generate a seed" },
+            { "-hrex",  FALSE, etBOOL, {&plumed_hrex}, /* PLUMED HREX */
+              "Enable hamiltonian replica exchange" },
+            { "-imdport",    FALSE, etINT, {&imdOptions.port},
+              "HIDDENIMD listening port" },
+            { "-imdwait",  FALSE, etBOOL, {&imdOptions.wait},
+              "HIDDENPause the simulation while no IMD client is connected" },
+            { "-imdterm",  FALSE, etBOOL, {&imdOptions.terminatable},
+              "HIDDENAllow termination of the simulation from IMD client" },
+            { "-imdpull",  FALSE, etBOOL, {&imdOptions.pull},
+              "HIDDENAllow pulling in the simulation from IMD client" },
+            { "-rerunvsite", FALSE, etBOOL, {&mdrunOptions.rerunConstructVsites},
+              "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
+            { "-confout", FALSE, etBOOL, {&mdrunOptions.writeConfout},
+              "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
+            { "-stepout", FALSE, etINT, {&mdrunOptions.verboseStepPrintInterval},
+              "HIDDENFrequency of writing the remaining wall clock time for the run" },
+            { "-resetstep", FALSE, etINT, {&mdrunOptions.timingOptions.resetStep},
+              "HIDDENReset cycle counters after these many time steps" },
+            { "-resethway", FALSE, etBOOL, {&mdrunOptions.timingOptions.resetHalfway},
+              "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
+        };
+        /*! \} */
+
+        //! Handle to communication object.
+        t_commrec        *cr = nullptr;
+        //! Multi-simulation object.
+        gmx_multisim_t   *ms = nullptr;
+
+        //! Parses the command-line input and prepares to start mdrun.
+        int updateFromCommandLine(int argc, char **argv, ArrayRef<const char *> desc);
+
+        ~LegacyMdrunOptions();
+};
+
+} // end namespace gmx
+
+#endif

patches/gromacs-2019.1.diff/src/gromacs/mdrun/legacymdrunoptions.h.preplumed

+/*
+ * 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) 2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief This file declares helper functionality for legacy option handling for 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
+ * \inlibraryapi
+ */
+#ifndef GMX_MDRUN_LEGACYMDRUNOPTIONS_H
+#define GMX_MDRUN_LEGACYMDRUNOPTIONS_H
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/hardware/hw_info.h"
+#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdrun/logging.h"
+
+#include "replicaexchange.h"
+
+struct gmx_multisim_t;
+
+namespace gmx
+{
+
+/*! \libinternal
+ * \brief This class provides the same command-line option
+ * functionality to both CLI and API sessions.
+ *
+ * This class should not exist, but is necessary now to introduce
+ * support for the CLI and API without duplicating code. It should be
+ * eliminated following the TODOs below.
+ *
+ * \todo Modules in mdrun should acquire proper option handling so
+ * that all of these declarations and defaults are local to the
+ * modules.
+ *
+ * \todo Contextual aspects, such as working directory, MPI
+ * environment, and environment variable handling are more properly
+ * the role of SimulationContext, and should be moved there */
+class LegacyMdrunOptions
+{
+    public:
+        //! Ongoing collection of mdrun options
+        MdrunOptions                     mdrunOptions;
+        //! Options for the domain decomposition.
+        DomdecOptions                    domdecOptions;
+        //! Parallelism-related user options.
+        gmx_hw_opt_t                     hw_opt;
+        //! Command-line override for the duration of a neighbor list with the Verlet scheme.
+        int                              nstlist_cmdline = 0;
+        //! Parameters for replica-exchange simulations.
+        ReplicaExchangeParameters        replExParams;
+
+        //! Filename options to fill from command-line argument values.
+        std::vector<t_filenm> filenames =
+        {{{ efTPR, nullptr,     nullptr,     ffREAD },
+          { efTRN, "-o",        nullptr,     ffWRITE },
+          { efCOMPRESSED, "-x", nullptr,     ffOPTWR },
+          { efCPT, "-cpi",      nullptr,     ffOPTRD | ffALLOW_MISSING },
+          { efCPT, "-cpo",      nullptr,     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, "-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 },
+          { efRND, "-multidir", nullptr,     ffOPTRDMULT},
+          { efXVG, "-awh",      "awhinit",   ffOPTRD },
+          { efDAT, "-membed",   "membed",    ffOPTRD },
+          { efTOP, "-mp",       "membed",    ffOPTRD },
+          { efNDX, "-mn",       "membed",    ffOPTRD },
+          { efXVG, "-if",       "imdforces", ffOPTWR },
+          { efXVG, "-swap",     "swapions",  ffOPTWR }}};
+
+        //! Print a warning if any force is larger than this (in kJ/mol nm).
+        real                             pforce = -1;
+
+        /*! \brief Output context for writing text files
+         *
+         * \todo Clarify initialization, ownership, and lifetime. */
+        gmx_output_env_t                *oenv = nullptr;
+
+        //! Handle to file used for logging.
+        LogFilePtr logFileGuard = nullptr;
+
+        /*! \brief Command line options, defaults, docs and storage for them to fill. */
+        /*! \{ */
+        rvec              realddxyz                                               = {0, 0, 0};
+        const char       *ddrank_opt_choices[static_cast<int>(DdRankOrder::nr)+1] =
+        { nullptr, "interleave", "pp_pme", "cartesian", nullptr };
+        const char       *dddlb_opt_choices[static_cast<int>(DlbOption::nr)+1] =
+        { nullptr, "auto", "no", "yes", nullptr };
+        const char       *thread_aff_opt_choices[threadaffNR+1] =
+        { nullptr, "auto", "on", "off", nullptr };
+        const char       *nbpu_opt_choices[5] =
+        { nullptr, "auto", "cpu", "gpu", nullptr };
+        const char       *pme_opt_choices[5] =
+        { nullptr, "auto", "cpu", "gpu", nullptr };
+        const char       *pme_fft_opt_choices[5] =
+        { nullptr, "auto", "cpu", "gpu", nullptr };
+        const char       *bonded_opt_choices[5] =
+        { nullptr, "auto", "cpu", "gpu", nullptr };
+        gmx_bool          bTryToAppendFiles     = TRUE;
+        const char       *gpuIdsAvailable       = "";
+        const char       *userGpuTaskAssignment = "";
+
+        ImdOptions       &imdOptions = mdrunOptions.imdOptions;
+
+        t_pargs           pa[48] = {
+
+            { "-dd",      FALSE, etRVEC, {&realddxyz},
+              "Domain decomposition grid, 0 is optimize" },
+            { "-ddorder", FALSE, etENUM, {ddrank_opt_choices},
+              "DD rank order" },
+            { "-npme",    FALSE, etINT, {&domdecOptions.numPmeRanks},
+              "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 ranks 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_choices},
+              "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, {&gpuIdsAvailable},
+              "List of unique GPU device IDs available to use" },
+            { "-gputasks",  FALSE, etSTR, {&userGpuTaskAssignment},
+              "List of GPU device IDs, mapping each PP task on each node to a device" },
+            { "-ddcheck", FALSE, etBOOL, {&domdecOptions.checkBondedInteractions},
+              "Check for all bonded interactions with DD" },
+            { "-ddbondcomm", FALSE, etBOOL, {&domdecOptions.useBondedCommunication},
+              "HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
+            { "-rdd",     FALSE, etREAL, {&domdecOptions.minimumCommunicationRange},
+              "The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
+            { "-rcon",    FALSE, etREAL, {&domdecOptions.constraintCommunicationRange},
+              "Maximum distance for P-LINCS (nm), 0 is estimate" },
+            { "-dlb",     FALSE, etENUM, {dddlb_opt_choices},
+              "Dynamic load balancing (with DD)" },
+            { "-dds",     FALSE, etREAL, {&domdecOptions.dlbScaling},
+              "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, {&domdecOptions.cellSizeX},
+              "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, {&domdecOptions.cellSizeY},
+              "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, {&domdecOptions.cellSizeZ},
+              "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, {&mdrunOptions.globalCommunicationInterval},
+              "Global communication frequency" },
+            { "-nb",      FALSE, etENUM, {nbpu_opt_choices},
+              "Calculate non-bonded interactions on" },
+            { "-nstlist", FALSE, etINT, {&nstlist_cmdline},
+              "Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
+            { "-tunepme", FALSE, etBOOL, {&mdrunOptions.tunePme},
+              "Optimize PME load between PP/PME ranks or GPU/CPU (only with the Verlet cut-off scheme)" },
+            { "-pme",     FALSE, etENUM, {pme_opt_choices},
+              "Perform PME calculations on" },
+            { "-pmefft", FALSE, etENUM, {pme_fft_opt_choices},
+              "Perform PME FFT calculations on" },
+            { "-bonded",     FALSE, etENUM, {bonded_opt_choices},
+              "Perform bonded calculations on" },
+            { "-v",       FALSE, etBOOL, {&mdrunOptions.verbose},
+              "Be loud and noisy" },
+            { "-pforce",  FALSE, etREAL, {&pforce},
+              "Print all forces larger than this (kJ/mol nm)" },
+            { "-reprod",  FALSE, etBOOL, {&mdrunOptions.reproducible},
+              "Try to avoid optimizations that affect binary reproducibility" },
+            { "-cpt",     FALSE, etREAL, {&mdrunOptions.checkpointOptions.period},
+              "Checkpoint interval (minutes)" },
+            { "-cpnum",   FALSE, etBOOL, {&mdrunOptions.checkpointOptions.keepAndNumberCheckpointFiles},
+              "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, {&mdrunOptions.numStepsCommandline},
+              "Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
+            { "-maxh",   FALSE, etREAL, {&mdrunOptions.maximumHoursToRun},
+              "Terminate after 0.99 times this time (hours)" },
+            { "-replex",  FALSE, etINT, {&replExParams.exchangeInterval},
+              "Attempt replica exchange periodically with this period (steps)" },
+            { "-nex",  FALSE, etINT, {&replExParams.numExchanges},
+              "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, {&replExParams.randomSeed},
+              "Seed for replica exchange, -1 is generate a seed" },
+            { "-imdport",    FALSE, etINT, {&imdOptions.port},
+              "HIDDENIMD listening port" },
+            { "-imdwait",  FALSE, etBOOL, {&imdOptions.wait},
+              "HIDDENPause the simulation while no IMD client is connected" },
+            { "-imdterm",  FALSE, etBOOL, {&imdOptions.terminatable},
+              "HIDDENAllow termination of the simulation from IMD client" },
+            { "-imdpull",  FALSE, etBOOL, {&imdOptions.pull},
+              "HIDDENAllow pulling in the simulation from IMD client" },
+            { "-rerunvsite", FALSE, etBOOL, {&mdrunOptions.rerunConstructVsites},
+              "HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
+            { "-confout", FALSE, etBOOL, {&mdrunOptions.writeConfout},
+              "HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
+            { "-stepout", FALSE, etINT, {&mdrunOptions.verboseStepPrintInterval},
+              "HIDDENFrequency of writing the remaining wall clock time for the run" },
+            { "-resetstep", FALSE, etINT, {&mdrunOptions.timingOptions.resetStep},
+              "HIDDENReset cycle counters after these many time steps" },
+            { "-resethway", FALSE, etBOOL, {&mdrunOptions.timingOptions.resetHalfway},
+              "HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
+        };
+        /*! \} */
+
+        //! Handle to communication object.
+        t_commrec        *cr = nullptr;
+        //! Multi-simulation object.
+        gmx_multisim_t   *ms = nullptr;
+
+        //! Parses the command-line input and prepares to start mdrun.
+        int updateFromCommandLine(int argc, char **argv, ArrayRef<const char *> desc);
+
+        ~LegacyMdrunOptions();
+};
+
+} // end namespace gmx
+
+#endif

patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.h

+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2011,2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief Declares the routines for replica exchange.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_mdrun
+ */
+#ifndef GMX_MDRUN_REPLICAEXCHANGE_H
+#define GMX_MDRUN_REPLICAEXCHANGE_H
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_enerdata_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+class t_state;
+
+/*! \libinternal
+ * \brief The parameters for the replica exchange algorithm. */
+struct ReplicaExchangeParameters
+{
+    //! Interval in steps at which to attempt exchanges, 0 means no replica exchange.
+    int exchangeInterval = 0;
+    //! The number of exchanges to attempt at an exchange step.
+    int numExchanges = 0;
+    //! The random seed, -1 means generate a seed.
+    int randomSeed = -1;
+};
+
+//! Abstract type for replica exchange
+typedef struct gmx_repl_ex *gmx_repl_ex_t;
+
+/*! \brief Setup function.
+ *
+ * Should only be called on the master ranks */
+gmx_repl_ex_t
+init_replica_exchange(FILE                            *fplog,
+                      const gmx_multisim_t            *ms,
+                      int                              numAtomsInSystem,
+                      const t_inputrec                *ir,
+                      const ReplicaExchangeParameters &replExParams);
+
+/*! \brief Attempts replica exchange.
+ *
+ * Should be called on all ranks.  When running each replica in
+ * parallel, this routine collects the state on the master rank before
+ * exchange.  With domain decomposition, the global state after
+ * exchange is stored in state and still needs to be redistributed
+ * over the ranks.
+ *
+ * \returns TRUE if the state has been exchanged.
+ */
+gmx_bool replica_exchange(FILE *fplog,
+                          const t_commrec *cr,
+                          const gmx_multisim_t *ms,
+                          gmx_repl_ex_t re,
+                          t_state *state, const gmx_enerdata_t *enerd,
+                          t_state *state_local,
+                          int64_t step, real time);
+
+/*! \brief Prints replica exchange statistics to the log file.
+ *
+ * Should only be called on the master ranks */
+void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
+
+/* PLUMED HREX */
+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_serial(const t_state *src, t_state *dest);
+/* END PLUMED HREX */
+
+#endif

patches/gromacs-2019.1.diff/src/gromacs/mdrun/replicaexchange.h.preplumed

+/*
+ * 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) 2011,2012,2013,2014,2015,2017,2018, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and 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
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+/*! \libinternal \file
+ *
+ * \brief Declares the routines for replica exchange.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \ingroup module_mdrun
+ */
+#ifndef GMX_MDRUN_REPLICAEXCHANGE_H
+#define GMX_MDRUN_REPLICAEXCHANGE_H
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct gmx_enerdata_t;
+struct gmx_multisim_t;
+struct t_commrec;
+struct t_inputrec;
+class t_state;
+
+/*! \libinternal
+ * \brief The parameters for the replica exchange algorithm. */
+struct ReplicaExchangeParameters
+{
+    //! Interval in steps at which to attempt exchanges, 0 means no replica exchange.
+    int exchangeInterval = 0;
+    //! The number of exchanges to attempt at an exchange step.
+    int numExchanges = 0;
+    //! The random seed, -1 means generate a seed.
+    int randomSeed = -1;
+};
+
+//! Abstract type for replica exchange
+typedef struct gmx_repl_ex *gmx_repl_ex_t;
+
+/*! \brief Setup function.
+ *
+ * Should only be called on the master ranks */
+gmx_repl_ex_t
+init_replica_exchange(FILE                            *fplog,
+                      const gmx_multisim_t            *ms,
+                      int                              numAtomsInSystem,
+                      const t_inputrec                *ir,
+                      const ReplicaExchangeParameters &replExParams);
+
+/*! \brief Attempts replica exchange.
+ *
+ * Should be called on all ranks.  When running each replica in
+ * parallel, this routine collects the state on the master rank before
+ * exchange.  With domain decomposition, the global state after
+ * exchange is stored in state and still needs to be redistributed
+ * over the ranks.
+ *
+ * \returns TRUE if the state has been exchanged.
+ */
+gmx_bool replica_exchange(FILE *fplog,
+                          const t_commrec *cr,
+                          const gmx_multisim_t *ms,
+                          gmx_repl_ex_t re,
+                          t_state *state, const gmx_enerdata_t *enerd,
+                          t_state *state_local,
+                          int64_t step, real time);
+
+/*! \brief Prints replica exchange statistics to the log file.
+ *
+ * Should only be called on the master ranks */
+void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
+
+#endif