Add Colvars module version 2024-03-12

CMakeLists.txt

@@ -638,6 +638,10 @@ include(gmxManageLmfit)
 
 include(gmxManageMuparser)
 
+include(gmxManageColvars)
+
+include(gmxManageLepton)
+
 ##################################################
 # Process SIMD instruction settings
 ##################################################

api/legacy/include/gromacs/mdtypes/inputrec.h

@@ -51,6 +51,8 @@ struct gmx_enfrot;
 struct gmx_enfrotgrp;
 struct pull_params_t;
 
+class colvarproxy_gromacs;
+
 namespace gmx
 {
 class Awh;
@@ -587,6 +589,10 @@ struct t_inputrec // NOLINT (clang-analyzer-optin.performance.Padding)
 
     //! KVT for storing simulation parameters that are not part of the mdp file.
     std::unique_ptr<gmx::KeyValueTreeObject> internalParameters;
+
+    /* COLVARS */
+    bool                bColvars = false;       /* Do we do colvars calculations ? */
+    colvarproxy_gromacs     *colvars_proxy = nullptr; /* The object for the colvars calculations */
 };
 
 int tcouple_min_integration_steps(TemperatureCoupling etc);

cmake/gmxManageColvars.cmake

@@ -0,0 +1,67 @@
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright 2023- 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.
+
+# Build Colvars library as bundled in a GROMACS worktree; not supporting external linkage yet
+gmx_option_multichoice(GMX_USE_COLVARS
+    "Build the collective variables (Colvars) library interfaced with GROMACS"
+    INTERNAL
+    INTERNAL NONE)
+mark_as_advanced(GMX_USE_COLVARS)
+
+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})
+        # 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.
+        set_target_properties(colvars_objlib PROPERTIES POSITION_INDEPENDENT_CODE ON)
+
+        # Create an INTERFACE library for colvars with the object library as a dependency
+        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)
+        endif()
+
+    else()
+        # Create a dummy link target so the calling code doesn't need to know
+        # whether colvars support is being compiled.
+        add_library(colvars INTERFACE)
+    endif()
+endfunction()

cmake/gmxManageLepton.cmake

@@ -0,0 +1,36 @@
+# Add Lepton library, which is developed and distributed as part of OpenMM:
+# https://github.com/openmm/openmm
+
+gmx_option_multichoice(GMX_USE_LEPTON
+    "Build the Lepton library interfaced with GROMACS"
+    INTERNAL
+    INTERNAL NONE)
+mark_as_advanced(GMX_USE_LEPTON)
+
+function(gmx_manage_lepton)
+  if(GMX_USE_LEPTON STREQUAL "INTERNAL")
+
+    set(LEPTON_DIR "${CMAKE_SOURCE_DIR}/src/external/lepton")
+
+    file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/*.cpp)
+    add_library(lepton_objlib OBJECT ${LEPTON_SOURCES})
+    target_include_directories(lepton_objlib PRIVATE ${LEPTON_DIR}/include)
+    # TODO support building as shared library
+    target_compile_options(lepton_objlib PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
+    set_target_properties(lepton_objlib PROPERTIES POSITION_INDEPENDENT_CODE ON)
+
+    add_library(lepton INTERFACE)
+    target_sources(lepton INTERFACE $<TARGET_OBJECTS:lepton_objlib>)
+    target_include_directories(lepton SYSTEM INTERFACE $<BUILD_INTERFACE:${LEPTON_DIR}>)
+
+    # Set flags so that Colvars can leverage Lepton functionality
+    # TODO handle the case when Lepton is built without Colvars?
+    target_include_directories(colvars_objlib PRIVATE ${LEPTON_DIR}/include)
+    target_compile_options(colvars_objlib PRIVATE -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES)
+
+  else()
+
+    # Dummy target
+    add_library(lepton INTERFACE)
+  endif()
+endfunction()

cmake/gmxVersionInfo.cmake

@@ -259,7 +259,7 @@ set(REGRESSIONTEST_MD5SUM "e88c8ba9592d01d5cfe95f5d3b9836f9" CACHE INTERNAL "MD5
 # If you are distributing a patch to GROMACS, then this change would
 # be great as part of your patch. Otherwise for personal use, you can
 # also just set a CMake cache variable.
-set(GMX_VERSION_STRING_OF_FORK "" CACHE INTERNAL
+set(GMX_VERSION_STRING_OF_FORK "Colvars-2024-03-12" CACHE INTERNAL
     "Version string for forks of GROMACS to set to describe themselves")
 mark_as_advanced(GMX_VERSION_STRING_OF_FORK)
 if (GMX_VERSION_STRING_OF_FORK)