Merge branch 'master'

README-versions.md

@@ -1,12 +1,21 @@
+[Versions included in GROMACS](#versions-included-in-GROMACS)
+
 [Versions included in LAMMPS](#versions-included-in-LAMMPS)
 
 [Versions included in NAMD](#versions-included-in-NAMD)
 
 [Versions included in VMD](#versions-included-in-VMD)
 
+### Versions included in GROMACS
+GROMACS version | Colvars version
+-------------- | ---------------
+2024 | [2023-12-05](https://github.com/Colvars/colvars/tree/gromacs-2024)
+
 ### Versions included in LAMMPS
 LAMMPS version | Colvars version
 -------------- | ---------------
+stable_29Aug2024 | [2024-06-04](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Aug2024)
+stable_2Aug2023 | [2023-05-01](https://github.com/Colvars/colvars/releases/tag/lammps-stable_2Aug2023)
 stable_23Jun2022 | [2022-05-24](https://github.com/Colvars/colvars/releases/tag/lammps-stable_23Jun2022)
 stable_29Sep2021 | [2021-09-13](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Sep2021)
 stable_29Oct2020 | [2020-09-17](https://github.com/Colvars/colvars/releases/tag/lammps-stable_29Oct2020)
@@ -27,6 +36,7 @@ stable_4Nov2016 | [2016-10-21](https://github.com/Colvars/colvars/releases/tag/l
 
 NAMD version | Colvars version
 -------------- | ---------------
+3.0 | [2024-06-04](https://github.com/Colvars/colvars/tree/namd-3.0)
 2.14 | [2020-07-07](https://github.com/Colvars/colvars/releases/tag/namd-2.14)
 2.13b2 | [2018-10-12](https://github.com/Colvars/colvars/releases/tag/namd-2.13b2)
 2.13b1 | [2018-09-07](https://github.com/Colvars/colvars/releases/tag/namd-2.13b1)
@@ -40,6 +50,7 @@ VMD version | Colvars version
 -------------- | ---------------
 1.9.4a58 | [2022-04-14](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a58)
 1.9.4a49 | [2020-10-22](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a49)
+1.9.4a12 | [2017-10-11](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.4a12)
 1.9.3 | [2016-10-26](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.3)
 1.9.2 | [2014-10-13](https://github.com/Colvars/colvars/releases/tag/vmd-1.9.2)
 

README.md

@@ -110,7 +110,7 @@ All of the above MD engine versions are automatically tested as part of GitHub A
 
 ## Legacy GROMACS-Colvars patched releases
 
-Versions GROMACS prior to 2024 are supported through the use of a customized `mdrun` command line; source code of these patched releases is available [here](https://github.com/Colvars/gromacs).  When posting a message to the [Gromacs forum](https://gromacs.bioexcel.eu/) regarding the use of these patched releases, please specify "GROMACS modification: **Yes**".
+Versions GROMACS prior to 2024 are no longer supported by the current version of Colvars: please use GROMACS 2024 or later.
 
 
 ## Which version of Colvars is recommended?

cmake/CMakeLists.txt

@@ -90,6 +90,25 @@ endif()
 
 include(buildColvarsLepton)
 
+
+option(COLVARS_MPI "Link against a MPI library" OFF)
+
+if(COLVARS_MPI)
+  find_package(MPI)
+  if(${MPI_FOUND})
+    include_directories(SYSTEM ${MPI_CXX_INCLUDE_PATH})
+    target_compile_options(colvars PRIVATE -DCOLVARS_MPI)
+    add_compile_options(-DCOLVARS_MPI)
+    target_link_libraries(colvars ${MPI_CXX_LIBRARIES})
+    set(COLVARS_MPI ON)
+  else()
+    if(NOT ${MPI_FOUND})
+      message(FATAL_ERROR "MPI not found.")
+    endif()
+  endif()
+endif()
+
+
 option(COLVARS_TCL "Link against the Tcl library" OFF)
 
 if(COLVARS_TCL)

doc/Makefile

@@ -1,6 +1,6 @@
 .PHONY: all pdf html doxygen webpage webpage-legacy images \
 	install clean clean-all \
-	update-code-refs update-cvscript-cmdline-doc updates
+	update-code-refs update-cvscript-cmdline-doc updates update-version-list
 
 ifeq ($(COLVARS_RELEASE),)
 # Unless defined otherwise, the release label is the name of the branch
@@ -90,7 +90,7 @@ clean-all: clean
 	@echo
 	@echo "Note: only removed files that this branch is set to build."
 
-version-list:
+update-version-list:
 	./print_engine_versions.sh > ../README-versions.md
 
 update-code-refs:

doc/cv_version.tex

@@ -1 +1 @@
-\newcommand{\cvversion}{2024-09-17}
+\newcommand{\cvversion}{2024-10-05}

doc/print_engine_versions.sh

@@ -1,6 +1,12 @@
 #!/bin/bash
 
-source ../devel-tools/version_functions.sh
+TOPDIR=$(git rev-parse --show-toplevel)
+if [ ! -d ${TOPDIR} ] ; then
+  echo "Error: cannot identify top project directory." >& 2
+  exit 1
+fi
+
+source ${TOPDIR}/devel-tools/version_functions.sh
 
 
 reformat_lammps_version() {
@@ -18,20 +24,32 @@ print_tag_versions() {
     local tag
     local colvars_version
     local lammps_version=""
-    for tag in $(git tag -l|grep ^${tag_prefix}); do
+
+    for tag in $(git tag -l | grep ^${tag_prefix}) ; do
         local package_version=${tag#${tag_prefix}}
         colvars_version=$(get_colvarmodule_version ${tag})
-        if [ ${package} = LAMMPS ] ; then
+        if [ ${package} == LAMMPS ] ; then
             lammps_version=$(reformat_lammps_version ${package_version#*_})" "
         fi
         echo "${lammps_version}${package_version} | [${colvars_version}](https://github.com/Colvars/colvars/releases/tag/${tag})"
     done
+
+    for branch in $(git branch -l --format='%(refname)' | sed -s 's/refs\/heads\///' | grep ^${tag_prefix}) ; do
+        local package_version=${branch#${tag_prefix}}
+        colvars_version=$(get_colvarmodule_version ${branch})
+        if [ ${package} == LAMMPS ] ; then
+            lammps_version=$(reformat_lammps_version ${package_version#*_})" "
+        fi
+        if [ ${package} == GROMACS ] ; then
+            if [ ${branch} == gromacs-2023 ] || [ ${branch} == gromacs-2022 ] ; then
+                # These branches do not reflect GROMACS standard releases
+                continue
+            fi
+        fi
+        echo "${lammps_version}${package_version} | [${colvars_version}](https://github.com/Colvars/colvars/tree/${branch})"
+    done
 }
 
-for package in LAMMPS NAMD VMD ; do
-    echo "[Versions included in ${package}](#versions-included-in-${package})"
-    echo
-done
 
 sort_versions(){
     sort -r
@@ -43,18 +61,24 @@ sort_lammps_versions(){
 }
 
 
-for package in LAMMPS NAMD VMD ; do
+for package in GROMACS LAMMPS NAMD VMD ; do
+    echo "[Versions included in ${package}](#versions-included-in-${package})"
+    echo
+done
+
+
+for package in GROMACS LAMMPS NAMD VMD ; do
     echo "### Versions included in ${package}"
-    if [ ${package} = NAMD ] ; then
+    if [ ${package} == NAMD ] ; then
         echo "(Note: the Colvars version included in NAMD 2.12 is the same as the one included in 2.12b1 with only bugfixes applied: therefore, NAMD 2.12 does not correspond to a specific version of the Colvars source tree)"
         echo
     fi
     echo "${package} version | Colvars version"
     echo "-------------- | ---------------"
     sort_command=sort_versions
-    if [ ${package} = LAMMPS ] ; then
+    if [ ${package} == LAMMPS ] ; then
         sort_command=sort_lammps_versions
     fi
-    print_tag_versions ${package} $(echo ${package}- | tr '[:upper:]' '[:lower:]') | ${sort_command}
+    print_tag_versions ${package} ${package,,}- | ${sort_command}
     echo
 done

gromacs/CMakeLists.txt.diff

@@ -1,13 +0,0 @@
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 70b0369bed..cccfe2aa1b 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -678,6 +678,8 @@ include(gmxManageLmfit)
-
- include(gmxManageMuparser)
-
-+include(gmxManageLepton)
-+
- include(gmxManageColvars)
-
- ##################################################

gromacs/cmake/gmxManageColvars.cmake

@@ -38,25 +38,25 @@ gmx_option_multichoice(GMX_USE_COLVARS
     INTERNAL NONE)
 mark_as_advanced(GMX_USE_COLVARS)
 
-function(gmx_set_colvars_torch)
-  find_package(Torch)
-  if (Torch_FOUND)
-    message(STATUS "Torch found, enabling for Colvars")
-    set_property(TARGET colvars_objlib PROPERTY CXX_STANDARD 17)
-    target_compile_definitions(colvars_objlib PRIVATE -DTORCH)
-    target_compile_options(colvars_objlib PRIVATE ${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS})
-    target_include_directories(colvars_objlib PRIVATE ${TORCH_INCLUDE_DIRS})
-    target_link_libraries(libgromacs PRIVATE "${TORCH_LIBRARIES}")
-  endif()
-endfunction()
-
-
 function(gmx_manage_colvars)
     if(GMX_USE_COLVARS STREQUAL "INTERNAL")
+
         # Create an object library for the colvars sources
         set(COLVARS_DIR "${CMAKE_SOURCE_DIR}/src/external/colvars")
         file(GLOB COLVARS_SOURCES ${COLVARS_DIR}/*.cpp)
         add_library(colvars_objlib OBJECT ${COLVARS_SOURCES})
+        if(GMX_LIB_MPI)
+            target_compile_definitions(colvars_objlib PRIVATE -DCOLVARS_MPI)
+        endif()
+        if(GMX_OPENMP)
+            target_link_libraries(colvars_objlib PRIVATE OpenMP::OpenMP_CXX)
+        endif()
+        if(GMX_TORCH)
+            target_compile_options(colvars_objlib PRIVATE ${CMAKE_CXX_FLAGS} ${TORCH_CXX_FLAGS})
+            target_include_directories(colvars_objlib PRIVATE ${TORCH_INCLUDE_DIRS})
+            target_compile_definitions(colvars_objlib PRIVATE -DCOLVARS_TORCH)
+        endif()
+
         # Set correctly the value of __cplusplus, which MSVC doesn't do by default
         target_compile_options(colvars_objlib PRIVATE $<$<CXX_COMPILER_ID:MSVC>:/Zc:__cplusplus>)
         # Ensure that colvars_objlib can be used in both STATIC and SHARED libraries.
@@ -66,10 +66,11 @@ function(gmx_manage_colvars)
         add_library(colvars INTERFACE)
         target_sources(colvars INTERFACE $<TARGET_OBJECTS:colvars_objlib>)
         target_include_directories(colvars SYSTEM INTERFACE $<BUILD_INTERFACE:${COLVARS_DIR}>)
-
-        if(GMX_OPENMP)
-            target_compile_options(colvars_objlib PRIVATE ${OpenMP_CXX_FLAGS})
-            target_link_libraries(colvars_objlib PRIVATE OpenMP::OpenMP_CXX)
+        if(GMX_LIB_MPI)
+            target_compile_definitions(colvars INTERFACE -DCOLVARS_MPI)
+        endif()
+        if(GMX_TORCH)
+            target_compile_definitions(colvars INTERFACE -DCOLVARS_TORCH)
         endif()
 
         set(GMX_HAVE_COLVARS 1 CACHE INTERNAL "Is colvars found?")
@@ -81,7 +82,5 @@ function(gmx_manage_colvars)
 
         set(GMX_HAVE_COLVARS 0 CACHE INTERNAL "Is colvars found?")
     endif()
-
-    gmx_set_colvars_torch()
     mark_as_advanced(GMX_HAVE_COLVARS)
 endfunction()

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule.cpp → gromacs/src/applied_forces/colvars/colvarsMDModule.cpp

@@ -49,6 +49,7 @@
 #include "gromacs/domdec/localatomsetmanager.h"
 #include "gromacs/fileio/checkpoint.h"
 #include "gromacs/mdrunutility/mdmodulesnotifiers.h"
+#include "gromacs/mdrunutility/multisim.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/iforceprovider.h"
 #include "gromacs/mdtypes/imdmodule.h"
@@ -97,7 +98,7 @@ class ColvarsMDModule final : public IMDModule
      *     KeyValueTreeObjectBuilder as parameter
      *   - Acess topology using gmx_mtop_t notification
      *   - Access MDLogger for notifications output
-     *   - Access warninp for for grompp warnings output
+     *   - Access warning for for grompp warnings output
      *   - Coordinates, PBC and box for setting up the proxy
      */
     void subscribeToPreProcessingNotifications(MDModulesNotifiers* notifier) override
@@ -192,6 +193,12 @@ class ColvarsMDModule final : public IMDModule
         };
         notifier->simulationSetupNotifier_.subscribe(setCommFunction);
 
+        // Retrieve the Multisim Record during simulations setup
+        const auto setMultisimFunction = [this](const gmx_multisim_t* ms) {
+            this->ColvarsSimulationsParameters_.setMultisim(ms);
+        };
+        notifier->simulationSetupNotifier_.subscribe(setMultisimFunction);
+
         // setting the simulation time step
         const auto setSimulationTimeStepFunction = [this](const SimulationTimeStep& simulationTimeStep) {
             this->ColvarsSimulationsParameters_.setSimulationTimeStep(simulationTimeStep.delta_t);
@@ -251,6 +258,7 @@ class ColvarsMDModule final : public IMDModule
                     colvarsOptions_.colvarsSeed(),
                     ColvarsSimulationsParameters_.localAtomSetManager(),
                     ColvarsSimulationsParameters_.comm(),
+                    ColvarsSimulationsParameters_.ms(),
                     ColvarsSimulationsParameters_.simulationTimeStep(),
                     colvarsOptions_.colvarsAtomCoords(),
                     colvarsOptions_.colvarsOutputPrefix(),

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.cpp → gromacs/src/applied_forces/colvars/colvarsforceprovider.cpp

@@ -57,6 +57,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/broadcaststructs.h"
 #include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/mdrunutility/multisim.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/enerdata.h"
 #include "gromacs/mdtypes/forceoutput.h"
@@ -65,6 +66,7 @@
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/keyvaluetree.h"
 #include "gromacs/utility/keyvaluetreebuilder.h"
 #include "gromacs/utility/smalloc.h"
@@ -173,6 +175,7 @@ ColvarsForceProvider::ColvarsForceProvider(const std::string& colvarsConfigStrin
                                            int                              seed,
                                            LocalAtomSetManager*             localAtomSetManager,
                                            const t_commrec*                 cr,
+                                           const gmx_multisim_t*            ms,
                                            double                           simulationTimeStep,
                                            const std::vector<RVec>&         colvarsCoords,
                                            const std::string&               outputPrefix,
@@ -236,6 +239,17 @@ ColvarsForceProvider::ColvarsForceProvider(const std::string& colvarsConfigStrin
     snew(fColvars, nColvarsAtoms);
     snew(xColvarsOldWhole, nColvarsAtoms);
 
+#if GMX_MPI
+    if (MAIN(cr))
+    {
+        if (isMultiSim(ms))
+        {
+            colvarproxy::set_replicas_mpi_communicator(ms->mainRanksComm_);
+        }
+    }
+#else
+    GMX_UNUSED_VALUE(ms);
+#endif
 
     // Check state status (did we read a cpt file?)
     if (MAIN(cr))

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsforceprovider.h → gromacs/src/applied_forces/colvars/colvarsforceprovider.h

@@ -61,6 +61,7 @@
 
 enum class PbcType : int;
 struct t_commrec;
+struct gmx_multisim_t;
 
 
 namespace gmx
@@ -182,6 +183,7 @@ class ColvarsForceProvider final : public ColvarProxyGromacs, public IForceProvi
      * \param[in] seed The colvars seed for random number generator
      * \param[in] localAtomSetManager Atom Manager to retrieve Colvars index atoms
      * \param[in] cr Communication Record
+     * \param[in] ms Multi-simulation record
      * \param[in] simulationTimeStep The simulation time step
      * \param[in] colvarsCoords The colvars atoms coordinates retrived from the TPR's KVT
      * \param[in] outputPrefix The prefix for output colvars files
@@ -196,6 +198,7 @@ class ColvarsForceProvider final : public ColvarProxyGromacs, public IForceProvi
                          int                                       seed,
                          LocalAtomSetManager*                      localAtomSetManager,
                          const t_commrec*                          cr,
+                         const gmx_multisim_t*                     ms,
                          double                                    simulationTimeStep,
                          const std::vector<RVec>&                  colvarsCoords,
                          const std::string&                        outputPrefix,

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarssimulationsparameters.cpp → gromacs/src/applied_forces/colvars/colvarssimulationsparameters.cpp

@@ -114,6 +114,16 @@ const t_commrec* ColvarsSimulationsParameters::comm() const
     return cr_;
 }
 
+void ColvarsSimulationsParameters::setMultisim(const gmx_multisim_t* ms)
+{
+    ms_ = ms;
+}
+
+const gmx_multisim_t* ColvarsSimulationsParameters::ms() const
+{
+    return ms_;
+}
+
 
 void ColvarsSimulationsParameters::setLogger(const MDLogger& logger)
 {