Import fixes and changes from GROMACS repo

Limited to the gromacs/applied_forces directory, not the library

gromacs/gromacs-mdmodules/applied_forces/colvars/CMakeLists.txt

@@ -36,6 +36,7 @@
 if(NOT GMX_USE_COLVARS STREQUAL "INTERNAL")
     gmx_add_libgromacs_sources(
         colvarsMDModule_stub.cpp
+        colvarsoptions.cpp
         )
 else()
     gmx_add_libgromacs_sources(
@@ -46,8 +47,8 @@ else()
         colvarsforceprovider.cpp
         colvarproxygromacs.cpp
         )
+endif()
 
-    if (BUILD_TESTING)
-        add_subdirectory(tests)
-    endif()
+if (BUILD_TESTING)
+    add_subdirectory(tests)
 endif()

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.cpp

@@ -41,13 +41,21 @@
 
 #include "colvarproxygromacs.h"
 
+#include <cstddef>
+
 #include <sstream>
+#include <vector>
 
+#include "gromacs/math/vectypes.h"
+#include "gromacs/random/seed.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/path.h"
 
 #include "colvarproxy_gromacs_version.h"
 
+enum class PbcType : int;
+
 
 namespace gmx
 {
@@ -180,7 +188,7 @@ int ColvarProxyGromacs::backup_file(char const* filename)
     }
     else
     {
-        // General backup provedure
+        // General backup procedure
         make_backup(filename);
     }
     return COLVARS_OK;

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarproxygromacs.h

@@ -42,10 +42,15 @@
 #ifndef GMX_APPLIED_FORCES_COLVARPROXYGROMACS_H
 #define GMX_APPLIED_FORCES_COLVARPROXYGROMACS_H
 
+#include <map>
+#include <string>
+
 // NOLINTBEGIN
 // Disabling clang-tidy checks on Colvars library code that is not called directly by GROMACS,
 // or is not even used at all (e.g. code used by NAMD or VMD interfaces)
 #include "external/colvars/colvarproxy.h"
+
+#include "gromacs/utility/real.h"
 // NOLINTEND
 
 #include "gromacs/pbcutil/pbc.h"
@@ -54,6 +59,8 @@
 #include "gromacs/topology/atoms.h"
 #include "gromacs/utility/logger.h"
 
+enum class PbcType : int;
+
 
 namespace gmx
 {

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

@@ -42,22 +42,32 @@
 
 #include "colvarsMDModule.h"
 
+#include <functional>
 #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/iforceprovider.h"
 #include "gromacs/mdtypes/imdmodule.h"
 #include "gromacs/utility/keyvaluetreebuilder.h"
 
 #include "colvarsforceprovider.h"
 #include "colvarsoptions.h"
 #include "colvarssimulationsparameters.h"
 
+enum class PbcType : int;
+struct gmx_mtop_t;
+
 
 namespace gmx
 {
+class IMDOutputProvider;
+class IMdpOptionProvider;
+class KeyValueTreeObject;
+class MDLogger;
 
 namespace
 {

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsMDModule_stub.cpp

@@ -48,9 +48,11 @@
 #include "gromacs/fileio/checkpoint.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/imdmodule.h"
+#include "gromacs/mdtypes/imdpoptionprovider.h"
 #include "gromacs/utility/keyvaluetreebuilder.h"
 
 #include "colvarsMDModule.h"
+#include "colvarsoptions.h"
 
 
 namespace gmx
@@ -62,7 +64,7 @@ namespace
 /*! \internal
  * \brief Colvars module
  *
- * Stub Implementation
+ * Stub Implementation in case Colvars library is not compiled
  */
 class ColvarsMDModule final : public IMDModule
 {
@@ -71,15 +73,39 @@ class ColvarsMDModule final : public IMDModule
     explicit ColvarsMDModule() = default;
 
 
-    void subscribeToPreProcessingNotifications(MDModulesNotifiers* /*notifier*/) override {}
+    void subscribeToPreProcessingNotifications(MDModulesNotifiers* /*notifier*/) override
+    {
+        // Proper exit when Colvars is activated from the mdp but has not been compiled along with GROMACS.
+        // In this case, Colvars config file cannot be parsed & verified and the tpr created could be flawed.
+        if (colvarsOptionsStub_.isActive())
+        {
+            GMX_THROW(InternalError(
+                    "Colvars module is activated but GROMACS has not been compiled with Colvars, "
+                    "Colvars simulation is not possible.\n"
+                    "Please, reconfigure GROMACS with -DGMX_USE_COLVARS=internal.\n"));
+        }
+    }
 
     void subscribeToSimulationSetupNotifications(MDModulesNotifiers* /*notifier*/) override {}
 
-    IMdpOptionProvider* mdpOptionProvider() override { return nullptr; }
+    IMdpOptionProvider* mdpOptionProvider() override { return &colvarsOptionsStub_; }
 
     IMDOutputProvider* outputProvider() override { return nullptr; }
 
-    void initForceProviders(ForceProviders* /*forceProviders*/) override {}
+    void initForceProviders(ForceProviders* /*forceProviders*/) override
+    {
+        // Proper exit when Colvars is activated from the tpr but has not been compiled along with GROMACS.
+        if (colvarsOptionsStub_.isActive())
+        {
+            GMX_THROW(InternalError(
+                    "Colvars module is activated but GROMACS has not been compiled with Colvars, "
+                    "Colvars simulation is not possible.\n"
+                    "Please, reconfigure GROMACS with -DGMX_USE_COLVARS=internal.\n"));
+        }
+    }
+
+private:
+    ColvarsOptions colvarsOptionsStub_;
 };
 
 

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

@@ -41,22 +41,40 @@
 
 #include "colvarsforceprovider.h"
 
+#include <cstddef>
+#include <cstdint>
+
+#include <array>
 #include <string>
 
 #include "external/colvars/colvars_memstream.h"
 
+#include "gromacs/applied_forces/colvars/colvarproxygromacs.h"
+#include "gromacs/compat/pointers.h"
 #include "gromacs/domdec/localatomsetmanager.h"
 #include "gromacs/fileio/checkpoint.h"
 #include "gromacs/gmxlib/network.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/mdlib/broadcaststructs.h"
 #include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/mdtypes/commrec.h"
 #include "gromacs/mdtypes/enerdata.h"
 #include "gromacs/mdtypes/forceoutput.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/smalloc.h"
+
+enum class PbcType : int;
 
 
 namespace gmx
 {
+class MDLogger;
 
 /********************************************************************
  * ColvarsForceProviderState

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

@@ -43,15 +43,33 @@
 #define GMX_APPLIED_FORCES_COLVARSFORCEPROVIDER_H
 
 
+#include <cstdint>
+
+#include <map>
+#include <memory>
+#include <string>
+#include <vector>
+
 #include "gromacs/domdec/localatomset.h"
+#include "gromacs/math/vectypes.h"
 #include "gromacs/mdrunutility/mdmodulesnotifiers.h"
 #include "gromacs/mdtypes/iforceprovider.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/utility/real.h"
 
 #include "colvarproxygromacs.h"
 
+enum class PbcType : int;
+struct t_commrec;
+
 
 namespace gmx
 {
+class KeyValueTreeObject;
+class KeyValueTreeObjectBuilder;
+class LocalAtomSetManager;
+class MDLogger;
+struct MDModulesWriteCheckpointData;
 
 
 /*! \internal

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.cpp

@@ -34,25 +34,43 @@
 /*! \internal \file
  * \brief
  * Implements options for Colvars.
+ * Keep a minimal ColvarsOptions implementation in the case Colvars is not activated
+ * to ensure compatbility (with gmx tools for example).
  */
 #include "gmxpre.h"
 
 #include "colvarsoptions.h"
 
+#include "config.h"
+
+#include <cstddef>
+
+#include <filesystem>
 #include <fstream>
+#include <optional>
 
+#include "gromacs/math/arrayrefwithpadding.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/options/basicoptions.h"
+#include "gromacs/options/ioptionscontainerwithsections.h"
 #include "gromacs/options/optionsection.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/keyvaluetree.h"
 #include "gromacs/utility/keyvaluetreebuilder.h"
 #include "gromacs/utility/keyvaluetreetransform.h"
 #include "gromacs/utility/path.h"
 #include "gromacs/utility/strconvert.h"
 #include "gromacs/utility/textreader.h"
 
-#include "colvarspreprocessor.h"
+#if GMX_HAVE_COLVARS
+#    include "colvarspreprocessor.h"
+#endif
+
+enum class PbcType : int;
+struct gmx_mtop_t;
 
 
 namespace gmx
@@ -127,11 +145,23 @@ void ColvarsOptions::initMdpOptions(IOptionsContainerWithSections* options)
 }
 
 
+bool ColvarsOptions::isActive() const
+{
+    return active_;
+}
+
+
+#if GMX_HAVE_COLVARS
+
+
 void ColvarsOptions::writeInternalParametersToKvt(KeyValueTreeObjectBuilder treeBuilder)
 {
 
     // Copy the content of the colvars input file into a string for latter save in KVT
-    colvarsConfigString_ = TextReader::readFileToString(colvarsFileName_);
+    if (!colvarsFileName_.empty())
+    {
+        colvarsConfigString_ = TextReader::readFileToString(colvarsFileName_);
+    }
 
     // Write colvars input file as a string
     treeBuilder.addValue<std::string>(c_colvarsModuleName + "-" + c_configStringTag_, colvarsConfigString_);
@@ -270,8 +300,7 @@ void ColvarsOptions::processEdrFilename(const EdrOutputFilename& filename)
     // Provided name should not be empty
     GMX_RELEASE_ASSERT(!filename.edrOutputFilename_.empty(), "Empty name for the *.edr output file");
 
-    outputPrefix_ =
-            stripExtension(std::filesystem::path(filename.edrOutputFilename_).filename()).u8string();
+    outputPrefix_ = stripExtension(std::filesystem::path(filename.edrOutputFilename_)).string();
 }
 
 
@@ -287,11 +316,6 @@ void ColvarsOptions::processTemperature(const EnsembleTemperature& temp)
     }
 }
 
-bool ColvarsOptions::isActive() const
-{
-    return active_;
-}
-
 const std::string& ColvarsOptions::colvarsFileName() const
 {
     return colvarsFileName_;
@@ -344,4 +368,6 @@ void ColvarsOptions::setParameters(const std::string&   colvarsfile,
 }
 
 
+#endif // GMX_HAVE_COLVARS
+
 } // namespace gmx

gromacs/gromacs-mdmodules/applied_forces/colvars/colvarsoptions.h

@@ -50,9 +50,13 @@
 #include "gromacs/mdrunutility/mdmodulesnotifiers.h"
 #include "gromacs/mdtypes/imdpoptionprovider.h"
 #include "gromacs/topology/atoms.h"
+#include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/logger.h"
 #include "gromacs/utility/real.h"
 
+enum class PbcType : int;
+struct gmx_mtop_t;
+
 
 namespace gmx
 {
@@ -61,6 +65,9 @@ class KeyValueTreeObject;
 class KeyValueTreeBuilder;
 struct CoordinatesAndBoxPreprocessed;
 struct MdRunInputFilename;
+class IKeyValueTreeTransformRules;
+class IOptionsContainerWithSections;
+class KeyValueTreeObjectBuilder;
 
 
 //! Tag with name of the Colvars MDModule
@@ -185,8 +192,8 @@ class ColvarsOptions final : public IMdpOptionProvider
 
     //! \}
 
-    //! Colvars config filename, default colvars.dat
-    std::string colvarsFileName_ = "colvars.dat";
+    //! Colvars config filename
+    std::string colvarsFileName_;
 
 
     //! Colvars seed for Langevin integrator