V2.10 patches/gromacs2025

patches/gromacs-2025.0.config

@@ -0,0 +1,38 @@
+
+
+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
+A basic PLUMED interface is already present in GROMACS
+
+This patch previes extra features to be implemented in the official PLUMED integration in the next GROMACS version
+
+Patching must be done in the gromacs root directory  _before_ the cmake command is invoked.
+
+The GROMACS integration has some improvements with the compatibility wiht the multi-threading implementation
+but it is still preferable to configure gromacs as
+
+cmake -DGMX_THREAD_MPI=OFF and add -DGMX_MPI=ON if you want to use MPI.
+
+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
+}
+
+PLUMED_PATCH_NO_INCLUDE=true
+
+PLUMED_PATCH_EXTRA_FILES="src/external/plumed/PlumedInclude.h src/external/plumed/PlumedKernel.cpp src/gromacs/applied_forces/plumed/PlumedOutside.cpp src/gromacs/applied_forces/plumed/PlumedOutside.h"

patches/gromacs-2025.0.diff/cmake/gmxManagePlumed.cmake

@@ -0,0 +1,82 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright 2024- The GROMACS Authors
+# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+#
+# 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
+# https://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 https://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out https://www.gromacs.org.
+
+
+
+
+
+
+
+# Builds the interface to plumed and add the linkage to libPlumed
+
+gmx_option_multichoice(GMX_USE_PLUMED
+    "Build the PLUMED wrapper with GROMACS"
+    ON
+    ON)
+mark_as_advanced(GMX_USE_PLUMED)
+
+function(gmx_manage_plumed)
+    # Create a link target, leave it empty if the plumed option is not active
+    add_library(plumedgmx INTERFACE)
+    set (GMX_PLUMED_ACTIVE OFF CACHE INTERNAL "Cache entry for PLUMED activation")
+    if(WIN32)
+        if(GMX_USE_PLUMED STREQUAL "ON")
+                message(FATAL_ERROR "PLUMED is not supported on Windows. Reconfigure with -DGMX_USE_PLUMED=OFF.")
+        endif()
+    elseif(NOT GMX_USE_PLUMED STREQUAL "OFF")
+        include(CMakePushCheckState)
+        cmake_push_check_state(RESET)
+        set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_DL_LIBS})
+        include(CheckFunctionExists)
+        check_function_exists(dlopen HAVE_DLOPEN)
+        cmake_pop_check_state()
+        if(HAVE_DLOPEN)
+            # Plumed.h  compiled in c++ mode creates a fully inlined interface
+            # So we just need to activate the directory in applied_forces
+            set(PLUMED_DIR "${CMAKE_SOURCE_DIR}/src/external/plumed")
+            target_link_libraries( plumedgmx INTERFACE ${CMAKE_DL_LIBS} )
+            # The plumedgmx already exists, now we set it up:
+            target_include_directories(plumedgmx SYSTEM INTERFACE $<BUILD_INTERFACE:${PLUMED_DIR}>)
+            set (GMX_PLUMED_ACTIVE ON CACHE INTERNAL "Cache entry for PLUMED activation")
+        else()
+            if(GMX_USE_PLUMED STREQUAL "ON")
+                message(FATAL_ERROR "PLUMED needs dlopen or anything equivalent. Reconfigure with -DGMX_USE_PLUMED=OFF.")
+            else() # "AUTO"
+                message(STATUS "PLUMED needs dlopen or anything equivalent. Disabling support.")
+            endif()
+
+        endif()
+
+    endif()
+
+endfunction()

patches/gromacs-2025.0.diff/cmake/gmxManagePlumed.cmake.preplumed

@@ -0,0 +1,82 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright 2024- The GROMACS Authors
+# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+#
+# 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
+# https://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 https://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out https://www.gromacs.org.
+
+
+
+
+
+
+
+# Builds the interface to plumed and add the linkage to libPlumed
+
+gmx_option_multichoice(GMX_USE_PLUMED
+    "Build the PLUMED wrapper with GROMACS"
+    AUTO
+    AUTO ON OFF)
+mark_as_advanced(GMX_USE_PLUMED)
+
+function(gmx_manage_plumed)
+    # Create a link target, leave it empty if the plumed option is not active
+    add_library(plumedgmx INTERFACE)
+    set (GMX_PLUMED_ACTIVE OFF CACHE INTERNAL "Cache entry for PLUMED activation")
+    if(WIN32)
+        if(GMX_USE_PLUMED STREQUAL "ON")
+                message(FATAL_ERROR "PLUMED is not supported on Windows. Reconfigure with -DGMX_USE_PLUMED=OFF.")
+        endif()
+    elseif(NOT GMX_USE_PLUMED STREQUAL "OFF")
+        include(CMakePushCheckState)
+        cmake_push_check_state(RESET)
+        set(CMAKE_REQUIRED_LIBRARIES ${CMAKE_DL_LIBS})
+        include(CheckFunctionExists)
+        check_function_exists(dlopen HAVE_DLOPEN)
+        cmake_pop_check_state()
+        if(HAVE_DLOPEN)
+            # Plumed.h  compiled in c++ mode creates a fully inlined interface
+            # So we just need to activate the directory in applied_forces
+            set(PLUMED_DIR "${CMAKE_SOURCE_DIR}/src/external/plumed")
+            target_link_libraries( plumedgmx INTERFACE ${CMAKE_DL_LIBS} )
+            # The plumedgmx already exists, now we set it up:
+            target_include_directories(plumedgmx SYSTEM INTERFACE $<BUILD_INTERFACE:${PLUMED_DIR}>)
+            set (GMX_PLUMED_ACTIVE ON CACHE INTERNAL "Cache entry for PLUMED activation")
+        else()
+            if(GMX_USE_PLUMED STREQUAL "ON")
+                message(FATAL_ERROR "PLUMED needs dlopen or anything equivalent. Reconfigure with -DGMX_USE_PLUMED=OFF.")
+            else() # "AUTO"
+                message(STATUS "PLUMED needs dlopen or anything equivalent. Disabling support.")
+            endif()
+
+        endif()
+
+    endif()
+
+endfunction()

patches/gromacs-2025.0.diff/src/external/plumed/PlumedInclude.h

@@ -0,0 +1,14 @@
+#define __PLUMED_WRAPPER_FORTRAN 0 // NOLINT(bugprone-reserved-identifier)
+
+#define __PLUMED_WRAPPER_LINK_RUNTIME 1 // NOLINT(bugprone-reserved-identifier)
+#define __PLUMED_WRAPPER_EXTERN 1       // NOLINT(bugprone-reserved-identifier)
+
+#define __PLUMED_WRAPPER_CXX 1            // NOLINT(bugprone-reserved-identifier)
+#define __PLUMED_WRAPPER_LIBCXX11 1       // NOLINT(bugprone-reserved-identifier)
+#define __PLUMED_WRAPPER_LIBCXX17 1       // NOLINT(bugprone-reserved-identifier)
+#ifndef __PLUMED_WRAPPER_IMPLEMENTATION  // NOLINT(bugprone-reserved-identifier)
+#  define __PLUMED_WRAPPER_IMPLEMENTATION 0 // NOLINT(bugprone-reserved-identifier)
+#endif
+#define __PLUMED_HAS_DLOPEN               // NOLINT(bugprone-reserved-identifier)
+
+#include "external/plumed/Plumed.h"

patches/gromacs-2025.0.diff/src/external/plumed/PlumedKernel.cpp

@@ -0,0 +1,3 @@
+#define __PLUMED_WRAPPER_IMPLEMENTATION 1 // NOLINT(bugprone-reserved-identifier)
+
+#include "PlumedInclude.h"

patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/CMakeLists.txt

@@ -0,0 +1,55 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright 2024- The GROMACS Authors
+# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+#
+# 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
+# https://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 https://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out https://www.gromacs.org.
+
+# If Plumed is not activated then compile just the stub implementation plumedMDModule_stub.cpp
+# In other case compile regular plumedMDModule.cpp and tests
+if(GMX_PLUMED_ACTIVE)
+    set(PLUMED_SOURCES 
+    ../../../external/plumed/PlumedKernel.cpp
+    PlumedOutside.cpp
+    plumedforceprovider.cpp
+    plumedOptions.cpp
+    plumedMDModule.cpp
+    )
+    gmx_add_libgromacs_sources(
+        ${PLUMED_SOURCES}
+    )
+
+    if (BUILD_TESTING)
+        add_subdirectory(tests)
+    endif()
+else()
+gmx_add_libgromacs_sources(
+        plumedMDModule_stub.cpp
+    )    
+endif()

patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/CMakeLists.txt.preplumed

@@ -0,0 +1,52 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright 2024- The GROMACS Authors
+# and the project initiators Erik Lindahl, Berk Hess and David van der Spoel.
+# Consult the AUTHORS/COPYING files and https://www.gromacs.org for details.
+#
+# 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
+# https://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 https://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out https://www.gromacs.org.
+
+# If Plumed is not activated then compile just the stub implementation plumedMDModule_stub.cpp
+# In other case compile regular plumedMDModule.cpp and tests
+if(GMX_PLUMED_ACTIVE)
+    set(PLUMED_SOURCES plumedforceprovider.cpp
+    plumedOptions.cpp
+    plumedMDModule.cpp
+    )
+    gmx_add_libgromacs_sources(
+        ${PLUMED_SOURCES}
+    )
+
+    if (BUILD_TESTING)
+        add_subdirectory(tests)
+    endif()
+else()
+gmx_add_libgromacs_sources(
+        plumedMDModule_stub.cpp
+    )    
+endif()

patches/gromacs-2025.0.diff/src/gromacs/applied_forces/plumed/PlumedOutside.cpp

@@ -0,0 +1,32 @@
+#include "PlumedOutside.h"
+
+/*PLUMED*/
+namespace PLMD
+{
+PlumedOutside::PlumedOutside() {}
+PlumedOutside::~PlumedOutside() {}
+void PlumedOutside::setPlumed(Plumed* plumed)
+{
+    plumed_ = plumed;
+    active_ = true;
+}
+
+bool PlumedOutside::plumedHREX()
+{
+    return false;
+    // not yet integrated
+    // return plumedHREX_;
+}
+
+bool PlumedOutside::active()
+{
+    return active_;
+}
+
+PlumedOutside& plumedOutside()
+{
+    static PlumedOutside outside;
+    return outside;
+} /* */
+} // namespace PLMD
+/*ENDPLUMED*/