Separate NAMD GlobalMaster and colvarproxy_namd classes

namd/Make.depends.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 \

namd/Makefile.patch

@@ -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 \

namd/config.patch

@@ -1,59 +0,0 @@
-diff --git a/config b/config
-index ddf9f860..4148d87c 100755
---- a/config
-+++ b/config
-@@ -57,6 +57,8 @@ function error_syntax {
-   echo '  --cuda-dlink arch=<arch>,code=<code> (for cuFFT, may be repeated)'
-   echo '  --with-cuda-profiling (enables CUDA profiling with NVTX)'
-   echo '  --with-rocm-profiling (enables ROCm profiling with ROCtracer API)'
-+  echo '  --with-colvars-torch (enables torchann in Colvars)'
-+  echo '  --torch-prefix <directory containing libTorch>'
-   echo ''
-   if [ -n "${PRINT_ARCH_LIST+set}" ]; then
-     ARCH_PAT=''
-@@ -152,6 +154,7 @@ function error_exists {
-   use_mkl=0
-   use_cuda=0
-   use_hip=0
-+  use_colvars_torch=0
-   use_cuda_prof=0
-   use_rocm_prof=0
-   use_memopt=0
-@@ -257,6 +260,19 @@ function error_exists {
-         ARCH_SUFFIX_ARG=$ARCH_SUFFIX_ARG-$1
-       ;;
-
-+      --with-colvars-torch)
-+        use_colvars_torch=1
-+      ;;
-+
-+      --torch-prefix)
-+        shift
-+        if [ ! -d "$1" ]; then
-+          echo "ERROR: No such directory $1"
-+          error_syntax
-+        fi
-+        TORCH_PREFIX=$1
-+      ;;
-+
-       --with-debug)
-         use_debug=1
-       ;;
-@@ -1015,7 +1031,16 @@ function error_exists {
-   if [ -n "$CC_OPTS" ]; then
-     echo "COPTS = $CC_OPTS" >> Make.config
-   fi
--
-+  if (( "$use_colvars_torch" )); then
-+    echo "TORCHDIR = $TORCH_PREFIX" >> Make.config
-+    echo 'TORCHINCFLAGS = $(COPTI)$(TORCHDIR)/include $(COPTI)$(TORCHDIR)/include/torch/csrc/api/include' >> Make.config
-+    echo 'EXTRACOLVARSFLAGS = -std=c++17 -DCOLVARS_TORCH $(TORCHINCFLAGS)' >> Make.config
-+    if [[ $use_cuda && -f "${TORCH_PREFIX}/lib/libtorch_cuda.so" ]]; then 
-+      echo 'EXTRALINKLIBS = -Wl,-rpath,$(TORCHDIR)/lib -L$(TORCHDIR)/lib -ltorch -ltorch_cpu -lc10 -ltorch_cuda -lc10_cuda' >> Make.config
-+    else
-+      echo 'EXTRALINKLIBS = -Wl,-rpath,$(TORCHDIR)/lib -L$(TORCHDIR)/lib -ltorch -ltorch_cpu -lc10' >> Make.config
-+    fi
-+  fi
-
-   if (( $use_debug )); then
-     echo 'CXXOPTS = -g' >> Make.config

namd/src/.clang-format

@@ -0,0 +1,14 @@
+---
+Language: Cpp
+ColumnLimit: 100
+UseTab: Never
+TabWidth: 2
+IndentWidth: 2
+ObjCBlockIndentWidth: 2
+PenaltyBreakAssignment: 2
+AccessModifierOffset: -2
+BreakBeforeBraces: WebKit
+EmptyLineAfterAccessModifier: Leave
+NamespaceIndentation: None
+MaxEmptyLinesToKeep: 2
+...

namd/src/GlobalMasterColvars.C

@@ -0,0 +1,31 @@
+// -*- c++ -*-
+
+#include "GlobalMaster.h"
+#include "GlobalMasterColvars.h"
+#include "colvarproxy_namd.h"
+
+
+GlobalMasterColvars::GlobalMasterColvars() : proxy(new colvarproxy_namd(this)) {}
+
+GlobalMasterColvars::~GlobalMasterColvars() { reset(); }
+
+void GlobalMasterColvars::calculate() { proxy->calculate(); }
+
+
+void GlobalMasterColvars::reset()
+{
+  // Unrequest all positions, total forces, etc from NAMD
+  modifyRequestedAtoms().clear();
+  modifyForcedAtoms().clear();
+  modifyAppliedForces().clear();
+
+  modifyRequestedGroups().clear();
+  modifyGroupForces().clear();
+
+#if NAMD_VERSION_NUMBER >= 34471681
+  modifyRequestedGridObjects().clear();
+  modifyGridObjForces().clear();
+#endif
+
+  requestTotalForce(false);
+}

namd/src/GlobalMasterColvars.h

@@ -0,0 +1,155 @@
+#ifndef GLOBALMASTERCOLVARS_H
+#define GLOBALMASTERCOLVARS_H
+
+#include <memory>
+
+#include "GlobalMaster.h"
+
+
+class colvarproxy_namd;
+
+class GlobalMasterColvars : public GlobalMaster {
+public:
+
+  GlobalMasterColvars();
+
+  ~GlobalMasterColvars();
+
+  void reset();
+
+  void calculate() override;
+
+  inline void requestTotalForcePublic(bool yesno = true)
+  {
+    requestTotalForce(yesno);
+  }
+
+  inline AtomIDList &modifyRequestedAtomsPublic()
+  {
+    return modifyRequestedAtoms();
+  }
+
+  inline AtomIDList &modifyForcedAtomsPublic()
+  {
+    return modifyForcedAtoms();
+  }
+
+  inline ForceList &modifyAppliedForcesPublic()
+  {
+    return modifyAppliedForces();
+  }
+
+  inline ResizeArray<AtomIDList> &modifyRequestedGroupsPublic()
+  {
+    return modifyRequestedGroups();
+  }
+
+  inline ForceList &modifyGroupForcesPublic()
+  {
+    return modifyGroupForces();
+  }
+
+  inline IntList &modifyRequestedGridObjectsPublic()
+  {
+    return modifyRequestedGridObjects();
+  }
+
+  inline BigRealList &modifyGridObjForcesPublic()
+  {
+    return modifyGridObjForces();
+  }
+
+  inline AtomIDList::const_iterator getAtomIdBeginPublic()
+  {
+    return getAtomIdBegin();
+  }
+
+  inline AtomIDList::const_iterator getAtomIdEndPublic()
+  {
+    return getAtomIdEnd();
+  }
+
+  inline PositionList::const_iterator getAtomPositionBeginPublic()
+  {
+    return getAtomPositionBegin();
+  }
+
+  inline PositionList::const_iterator getGroupPositionBeginPublic()
+  {
+    return getGroupPositionBegin();
+  }
+
+  inline PositionList::const_iterator getGroupPositionEndPublic()
+  {
+    return getGroupPositionEnd();
+  }
+
+  inline ForceList::const_iterator getGroupTotalForceBeginPublic()
+  {
+    return getGroupTotalForceBegin();
+  }
+
+  inline ForceList::const_iterator getGroupTotalForceEndPublic()
+  {
+    return getGroupTotalForceEnd();
+  }
+
+  inline IntList::const_iterator getGridObjIndexBeginPublic()
+  {
+    return getGridObjIndexBegin();
+  }
+
+  inline IntList::const_iterator getGridObjIndexEndPublic()
+  {
+    return getGridObjIndexEnd();
+  }
+
+  inline BigRealList::const_iterator getGridObjValueBeginPublic()
+  {
+    return getGridObjValueBegin();
+  }
+
+  inline BigRealList::const_iterator getGridObjValueEndPublic()
+  {
+    return getGridObjValueEnd();
+  }
+
+  inline AtomIDList::const_iterator getForceIdBeginPublic()
+  {
+    return getForceIdBegin();
+  }
+
+  inline AtomIDList::const_iterator getForceIdEndPublic()
+  {
+    return getForceIdEnd();
+  }
+
+  inline ForceList::const_iterator getTotalForcePublic()
+  {
+    return getTotalForce();
+  }
+
+  inline void addReductionEnergyPublic(int reductionTag, BigReal energy)
+  {
+    addReductionEnergy(reductionTag, energy);
+  }
+
+  inline Lattice const *get_lattice() const
+  {
+    return lattice;
+  }
+
+protected:
+
+  std::unique_ptr<colvarproxy_namd> proxy;
+};
+
+
+namespace {
+  // Constants used for profiling CkLoop calls
+  constexpr int32_t GLOBAL_MASTER_CKLOOP_CALC_ITEM = 2000;
+  constexpr int32_t GLOBAL_MASTER_CKLOOP_CALC_BIASES = 2001;
+  constexpr int32_t GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES = 2002;
+}
+
+#endif