Add Colvars module version 2023-10-23

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 +1,57 @@
+#
+# 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")
+        file(GLOB COLVARS_SOURCES ${PROJECT_SOURCE_DIR}/src/external/colvars/*.cpp)
+        add_library(colvars OBJECT ${COLVARS_SOURCES})
+        # Set correctly the value of __cplusplus, which MSVC doesn't do by default
+        target_compile_options(colvars PRIVATE $<$<CXX_COMPILER_ID:MSVC>:/Zc:__cplusplus>)
+        set(HAVE_COLVARS 1 CACHE INTERNAL "Is Colvars available?")
+    else()
+        set(HAVE_COLVARS 0 CACHE INTERNAL "Is Colvars available?")
+    endif()
+endfunction()
+
+function(gmx_include_colvars_headers)
+    if(GMX_USE_COLVARS STREQUAL "INTERNAL")
+        target_include_directories(libgromacs PRIVATE ${PROJECT_SOURCE_DIR}/src/external/colvars)
+    endif()
+endfunction()

cmake/gmxManageLepton.cmake

@@ -0,0 +1,22 @@
+# This file is part of the Collective Variables module (Colvars).
+# The original version of Colvars and its updates are located at:
+# https://github.com/Colvars/colvars
+# Please update all Colvars source files before making any changes.
+# If you wish to distribute your changes, please submit them to the
+# Colvars repository at GitHub.
+
+function(gmx_manage_lepton)
+
+  # Add Lepton library, which is developed and distributed as part of OpenMM:
+  # https://github.com/openmm/openmm
+
+  file(GLOB LEPTON_SOURCES ${PROJECT_SOURCE_DIR}/src/external/lepton/src/*.cpp)
+  add_library(lepton OBJECT ${LEPTON_SOURCES})
+
+  target_include_directories(lepton PRIVATE ${PROJECT_SOURCE_DIR}/src/external/lepton/include)
+  target_compile_options(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
+
+  # Set flags so that Colvars can leverage Lepton functionality
+  target_include_directories(colvars PRIVATE ${PROJECT_SOURCE_DIR}/src/external/lepton/include)
+  target_compile_options(colvars PRIVATE -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES)
+endfunction()

cmake/gmxVersionInfo.cmake

@@ -259,7 +259,7 @@ set(REGRESSIONTEST_MD5SUM "15b29966b53accf5306c9a3d7e009963" 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-2023-10-23" 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)