V2.10 patches/gromacs2025

patches/gromacs-2025.0.config

@@ -0,0 +1,39 @@
+
+
+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
+
+#this will be added later
+#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/gromacs/applied_forces/plumed/plumedMDModule.cpp

@@ -0,0 +1,160 @@
+/*
+ * 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.
+ */
+/*! \internal \file
+ * \brief
+ * Implements Plumed MDModule class
+ *
+ * \author Daniele Rapetti <[email protected]>
+ * \ingroup module_applied_forces
+ */
+#include "gmxpre.h"
+
+#include "plumedMDModule.h"
+
+#include <memory>
+#include <string>
+
+#include "gromacs/domdec/localatomsetmanager.h"
+#include "gromacs/fileio/checkpoint.h"
+#include "gromacs/mdrunutility/mdmodulesnotifiers.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/imdmodule.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+
+#include "plumedOptions.h"
+#include "plumedforceprovider.h"
+
+class gmx_multisim_t;
+
+namespace gmx
+{
+
+namespace
+{
+
+/*! \internal
+ * \brief Plumed module
+ *
+ * Class that implements the plumed MDModule
+ */
+class PlumedMDModule final : public IMDModule
+{
+public:
+    //! \brief Construct the plumed module.
+    explicit PlumedMDModule() = default;
+    // Now callbacks for several kinds of MdModuleNotification are created
+    // and subscribed, and will be dispatched correctly at run time
+    // based on the type of the parameter required by the lambda.
+
+    /*! \brief Requests to be notified during pre-processing.
+     *
+     * Plumed does not act during the preprocessing phase of a simulation, so the input are ignored
+     */
+    void subscribeToPreProcessingNotifications(MDModulesNotifiers* /*notifier*/) override {}
+
+    /*! \brief Subscribe to MDModules notifications for information needed just before the simulation.
+     */
+    void subscribeToSimulationSetupNotifications(MDModulesNotifiers* notifier) override
+    {
+        // TODO: add a check for threadmpi (see #5104, https://gitlab.com/gromacs/gromacs/-/merge_requests/4367#note_2102475958, the manual and the force provider for the details)
+
+        // Access the plumed filename this is used to activate the plumed module
+        notifier->simulationSetupNotifier_.subscribe(
+                [this](const PlumedInputFilename& plumedFilename)
+                { this->options_.setPlumedFile(plumedFilename.plumedFilename_); });
+        // Retrieve the Multisim options
+        notifier->simulationSetupNotifier_.subscribe(
+                [this](const gmx_multisim_t* ms)
+                { this->options_.setMultisim(ms); });
+        // Access the temperature if it is constant during the simulation
+        notifier->simulationSetupNotifier_.subscribe(
+                [this](const EnsembleTemperature& ensembleT)
+                { this->options_.setEnsembleTemperature(ensembleT); });
+        // Access of the topology
+        notifier->simulationSetupNotifier_.subscribe([this](const gmx_mtop_t& mtop)
+                                                     { this->options_.setTopology(mtop); });
+        // Retrieve the Communication Record during simulations setup
+        notifier->simulationSetupNotifier_.subscribe([this](const t_commrec& cr)
+                                                     { this->options_.setComm(cr); });
+        // setting the simulation time step
+        notifier->simulationSetupNotifier_.subscribe(
+                [this](const SimulationTimeStep& simulationTimeStep)
+                { this->options_.setSimulationTimeStep(simulationTimeStep.delta_t); });
+        // Retrieve the starting behavior
+        notifier->simulationSetupNotifier_.subscribe(
+                [this](const StartingBehavior& startingBehavior)
+                { this->options_.setStartingBehavior(startingBehavior); });
+        //  writing checkpoint data
+        notifier->checkpointingNotifier_.subscribe(
+                [this](MDModulesWriteCheckpointData /*checkpointData*/)
+                {
+                    if (options_.active())
+                    {
+                        plumedForceProvider_->writeCheckpointData();
+                    }
+                });
+    }
+
+    //! From IMDModule
+    IMdpOptionProvider* mdpOptionProvider() override { return nullptr; }
+    //! From IMDModule
+    IMDOutputProvider* outputProvider() override
+    { // Plumed provide its own output
+        return nullptr;
+    }
+    //! From IMDModule - Adds this module to the force providers if active
+    void initForceProviders(ForceProviders* forceProviders) override
+    {
+        if (options_.active())
+        {
+            plumedForceProvider_ = std::make_unique<PlumedForceProvider>(options_.options());
+            forceProviders->addForceProvider(plumedForceProvider_.get(), "Plumed");
+        }
+    }
+
+
+private:
+    //! Parameters that become available at simulation setup time.
+    PlumedOptionProvider options_{};
+    //! Object that evaluates the forces
+    std::unique_ptr<PlumedForceProvider> plumedForceProvider_{};
+};
+
+} // namespace
+
+std::unique_ptr<IMDModule> PlumedModuleInfo::create()
+{
+    return std::make_unique<PlumedMDModule>();
+}
+} // namespace gmx