Merge branch 'Colvars:master' into harmonicDynamics

Author: fhh2626

doc/cv_version.tex

@@ -1 +1 @@
-\newcommand{\cvversion}{2025-10-13}
+\newcommand{\cvversion}{2025-11-14}

doc/doxygen/Doxyfile

@@ -753,7 +753,7 @@ WARN_LOGFILE           =
 # spaces.
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = "../../src" "../../namd/src" "../../vmd/src" "../../lammps/src/COLVARS" "../../gromacs/src"
+INPUT                  = "../../src" "../../namd/src" "../../vmd/src" "../../lammps/src/COLVARS" "../../gromacs/src" "../../src/cuda"
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1955,7 +1955,7 @@ INCLUDE_FILE_PATTERNS  =
 # recursively expanded use the := operator instead of the = operator.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-PREDEFINED             =
+PREDEFINED             = COLVARS_CUDA COLVARS_NVTX_PROFILING
 
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then this
 # tag can be used to specify a list of macro names that should be expanded. The

gromacs/CMakeLists.txt.Lepton.diff renamed to gromacs/CMakeLists.txt.Lepton.patch

@@ -1,3 +1,3 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2025-05-12"
+#define COLVARPROXY_VERSION "2025-11-14"
 #endif

gromacs/CMakeLists.txt.diff renamed to gromacs/CMakeLists.txt.patch

@@ -1,3 +1,3 @@
 #ifndef COLVARPROXY_VERSION
-#define COLVARPROXY_VERSION "2025-05-12"
+#define COLVARPROXY_VERSION "2025-11-14"
 #endif

gromacs/gmxManageColvars.cmake.diff renamed to gromacs/gmxManageColvars.cmake.patch

@@ -0,0 +1,59 @@
+diff --git a/Make.depends b/Make.depends
+index 994b3914..1d54373f 100644
+--- a/Make.depends
++++ b/Make.depends
+@@ -6398,6 +6398,45 @@ obj/GlobalMasterTMD.o: \
+ 	src/fitrms.h \
+ 	src/Debug.h
+ 	$(CXX) $(CXXFLAGS) $(COPTO)obj/GlobalMasterTMD.o $(COPTC) src/GlobalMasterTMD.C
++obj/GlobalMasterColvars.o: \
++	obj/.exists \
++	src/GlobalMasterColvars.C \
++	src/Controller.h \
++	src/common.h \
++	src/Vector.h \
++	src/Tensor.h \
++	src/Lattice.h \
++	src/NamdTypes.h \
++	src/CudaRecord.h \
++	src/HipDefines.h \
++	src/ResizeArray.h \
++	src/ResizeArrayRaw.h \
++	src/fstream_namd.h \
++	src/DataExchanger.h \
++	src/main.h \
++	inc/DataExchanger.decl.h \
++	src/Pointer.h \
++	src/GlobalMaster.h \
++	src/GlobalMasterColvars.h \
++	src/colvarproxy_namd.h \
++	src/colvarproxy_namd_version.h \
++	src/SimParameters.h \
++	src/imd.h \
++	src/MGridforceParams.h \
++	src/GroupRestraintsParam.h \
++	src/Random.h \
++	src/ConfigList.h \
++	colvars/src/colvarmodule.h \
++	colvars/src/colvarproxy.h \
++	colvars/src/colvarmodule.h \
++	colvars/src/colvartypes.h \
++	colvars/src/colvarproxy_io.h \
++	colvars/src/colvarproxy_replicas.h \
++	colvars/src/colvarproxy_system.h \
++	colvars/src/colvarproxy_tcl.h \
++	colvars/src/colvarproxy_volmaps.h \
++	colvars/src/colvarvalue.h
++	$(CXX) $(CXXFLAGS) $(COPTO)obj/GlobalMasterColvars.o $(COPTC) src/GlobalMasterColvars.C
+ obj/Matrix4Symmetry.o: \
+ 	obj/.exists \
+ 	src/Matrix4Symmetry.C \
+@@ -6637,6 +6676,8 @@ obj/colvarproxy_namd.o: \
+ 	src/MStream.h \
+ 	plugins/include/molfile_plugin.h \
+ 	plugins/include/vmdplugin.h \
++	src/GlobalMasterColvars.h \
++	src/GlobalMaster.h \
+ 	src/GridForceGrid.inl \
+ 	src/PDB.h \
+ 	src/parm.h \

gromacs/src/colvarproxy_gromacs_version.h

@@ -1,13 +1,12 @@
 diff --git a/Makefile b/Makefile
-index fb23fcac..541fe8ca 100644
+index 960f7718..85126dff 100644
 --- a/Makefile
 +++ b/Makefile
-@@ -446,7 +446,7 @@ CXXMICFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(CXXMICOPTS)
- CXXTHREADFLAGS = $(CXXBASEFLAGS) $(CXXTHREADOPTS)
- CXXSIMPARAMFLAGS = $(CXXBASEFLAGS) $(CXXSIMPARAMOPTS)
- CXXNOALIASFLAGS = $(CXXBASEFLAGS) $(CXXNOALIASOPTS)
--COLVARSCXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(COPTI)$(LEPTONINCDIR) -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES
-+COLVARSCXXFLAGS = $(CXXBASEFLAGS) $(CXXOPTS) $(COPTI)$(LEPTONINCDIR) -DLEPTON -DLEPTON_USE_STATIC_LIBRARIES $(EXTRACOLVARSFLAGS)
- GXXFLAGS = $(CXXBASEFLAGS) -DNO_STRSTREAM_H
- CFLAGS = $(COPTI)$(SRCDIR) $(TCL) $(COPTS) $(RELEASE) $(EXTRADEFINES) $(TRACEOBJDEF)
- PLUGINGCCFLAGS = $(COPTI)$(PLUGINSRCDIR) $(COPTI)$(PLUGININCDIR) $(COPTD)STATIC_PLUGIN
+@@ -231,6 +231,7 @@ OBJS = \
+ 	$(DSTDIR)/GlobalMasterTcl.o \
+ 	$(DSTDIR)/GlobalMasterSMD.o \
+ 	$(DSTDIR)/GlobalMasterTMD.o \
++	$(DSTDIR)/GlobalMasterColvars.o \
+ 	$(DSTDIR)/Matrix4Symmetry.o \
+ 	$(DSTDIR)/GlobalMasterSymmetry.o \
+ 	$(DSTDIR)/GlobalMasterFreeEnergy.o \