From fb1356c6029cdeb12404ba1d03aff349d72139bd Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Wed, 17 Sep 2025 07:48:38 -0400
Subject: [PATCH 01/12] refactor: Begin patching GlobalMaster.h

---
 namd/src/GlobalMaster.h.diff | 15 +++++++++++++++
 update-colvars-code.sh       |  7 +++++++
 2 files changed, 22 insertions(+)
 create mode 100644 namd/src/GlobalMaster.h.diff

diff --git a/namd/src/GlobalMaster.h.diff b/namd/src/GlobalMaster.h.diff
new file mode 100644
index 000000000..6271b7670
--- /dev/null
+++ b/namd/src/GlobalMaster.h.diff
@@ -0,0 +1,15 @@
+diff --git a/src/GlobalMaster.h b/src/GlobalMaster.h
+index bb27f2ee..b1d571b5 100644
+--- a/src/GlobalMaster.h
++++ b/src/GlobalMaster.h
+@@ -77,7 +77,9 @@ class GlobalMaster {
+   void check() const; // dies if there are problems with the rep invariants
+ 
+   void setLattice(const Lattice *lat) { lattice = lat; }
+-  
++
++  friend class colvarproxy_namd; // Temporary until refactoring is complete
++
+  protected:
+   GlobalMaster();
+ 
diff --git a/update-colvars-code.sh b/update-colvars-code.sh
index ddbf9af86..deb36f8ef 100755
--- a/update-colvars-code.sh
+++ b/update-colvars-code.sh
@@ -374,6 +374,13 @@ then
     tgt=$(basename ${src})
     condcopy "${src}" "${target}/src/${tgt}"
   done
+  for diff in *.diff ; do
+    if [ -s ${diff} ] ; then
+      set +e
+      patch -p1 -N -d "${target}" < "${diff}"
+      set -e
+    fi
+  done
 
   # Update abf_integrate
   for src in ${source}/colvartools/*h ${source}/colvartools/*cpp

From 73c6b8c60ff69edffbcebada4b466d83c5bc00d8 Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@nih.gov>
Date: Wed, 17 Sep 2025 07:48:42 -0400
Subject: [PATCH 02/12] refactor: Begin separating colvarproxy_namd class from
 GlobalMaster parent

---
 namd/src/GlobalMasterColvars.h |  26 +++++++
 namd/src/colvarproxy_namd.C    | 134 +++++++++++++++++----------------
 namd/src/colvarproxy_namd.h    |  16 +++-
 update-colvars-code.sh         |   5 +-
 4 files changed, 111 insertions(+), 70 deletions(-)
 create mode 100644 namd/src/GlobalMasterColvars.h

diff --git a/namd/src/GlobalMasterColvars.h b/namd/src/GlobalMasterColvars.h
new file mode 100644
index 000000000..471811257
--- /dev/null
+++ b/namd/src/GlobalMasterColvars.h
@@ -0,0 +1,26 @@
+#ifndef GLOBALMASTERCOLVARS_H
+#define GLOBALMASTERCOLVARS_H
+
+#include <memory>
+
+#include "colvarmodule.h"
+#include "colvarproxy.h"
+#include "colvarproxy_namd.h"
+
+
+class GlobalMasterColvars : public GlobalMaster {
+public:
+
+  GlobalMasterColvars() : proxy(new colvarproxy_namd(this)) {}
+
+  void calculate() override {
+    proxy->calculate();
+  }
+
+protected:
+
+  std::unique_ptr<colvarproxy_namd> cp;
+};
+
+
+#endif
diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index d84d87b9a..8fa2cfdf1 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -44,7 +44,8 @@
 #include "colvarscript.h"
 
 
-colvarproxy_namd::colvarproxy_namd()
+colvarproxy_namd::colvarproxy_namd(GlobalMaster *gm)
+  : globalmaster(gm)
 {
   engine_name_ = "NAMD";
 #if CMK_SMP && USE_CKLOOP
@@ -54,13 +55,13 @@ colvarproxy_namd::colvarproxy_namd()
   version_int = get_version_from_string(COLVARPROXY_VERSION);
 #if CMK_TRACE_ENABLED
   if ( 0 == CkMyPe() ) {
-    traceRegisterUserEvent("GM COLVAR item", GLOBAL_MASTER_CKLOOP_CALC_ITEM);
-    traceRegisterUserEvent("GM COLVAR bias", GLOBAL_MASTER_CKLOOP_CALC_BIASES );
-    traceRegisterUserEvent("GM COLVAR scripted bias", GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES );
+    globalmaster->traceRegisterUserEvent("GM COLVAR item", GLOBAL_MASTER_CKLOOP_CALC_ITEM);
+    globalmaster->traceRegisterUserEvent("GM COLVAR bias", GLOBAL_MASTER_CKLOOP_CALC_BIASES );
+    globalmaster->traceRegisterUserEvent("GM COLVAR scripted bias", GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES );
   }
 #endif
   first_timestep = true;
-  requestTotalForce(total_force_requested);
+  globalmaster->requestTotalForce(total_force_requested);
 
   boltzmann_ = 0.001987191;
 
@@ -220,7 +221,7 @@ int colvarproxy_namd::update_atoms_map(AtomIDList::const_iterator begin,
       // add it here anyway to avoid having to test for array boundaries at each step
       int const index = add_atom_slot(*a_i);
       atoms_map[*a_i] = index;
-      modifyRequestedAtoms().add(*a_i);
+      globalmaster->modifyRequestedAtoms().add(*a_i);
       update_atom_properties(index);
     }
   }
@@ -265,8 +266,8 @@ int colvarproxy_namd::setup()
   }
 
   size_t n_group_atoms = 0;
-  for (int ig = 0; ig < modifyRequestedGroups().size(); ig++) {
-    n_group_atoms += modifyRequestedGroups()[ig].size();
+  for (int ig = 0; ig < globalmaster->modifyRequestedGroups().size(); ig++) {
+    n_group_atoms += globalmaster->modifyRequestedGroups()[ig].size();
   }
 
   log("updating group data ("+cvm::to_str(atom_groups_ids.size())+
@@ -274,7 +275,7 @@ int colvarproxy_namd::setup()
       cvm::to_str(n_group_atoms)+" atoms in total).\n");
 
   // Note: groupMassBegin, groupMassEnd may be used here, but they won't work for charges
-  for (int ig = 0; ig < modifyRequestedGroups().size(); ig++) {
+  for (int ig = 0; ig < globalmaster->modifyRequestedGroups().size(); ig++) {
 
     // update mass and charge
     update_group_properties(ig);
@@ -287,7 +288,7 @@ int colvarproxy_namd::setup()
 #if NAMD_VERSION_NUMBER >= 34471681
   log("updating grid object data ("+cvm::to_str(volmaps_ids.size())+
       " grid objects in total).\n");
-  for (int imap = 0; imap < modifyGridObjForces().size(); imap++) {
+  for (int imap = 0; imap < globalmaster->modifyGridObjForces().size(); imap++) {
     volmaps_new_colvar_forces[imap] = 0.0;
   }
 #endif
@@ -321,19 +322,19 @@ int colvarproxy_namd::reset()
   int error_code = COLVARS_OK;
 
   // Unrequest all positions, total forces, etc from NAMD
-  modifyRequestedAtoms().clear();
-  modifyForcedAtoms().clear();
-  modifyAppliedForces().clear();
+  globalmaster->modifyRequestedAtoms().clear();
+  globalmaster->modifyForcedAtoms().clear();
+  globalmaster->modifyAppliedForces().clear();
 
-  modifyRequestedGroups().clear();
-  modifyGroupForces().clear();
+  globalmaster->modifyRequestedGroups().clear();
+  globalmaster->modifyGroupForces().clear();
 
 #if NAMD_VERSION_NUMBER >= 34471681
-  modifyRequestedGridObjects().clear();
-  modifyGridObjForces().clear();
+  globalmaster->modifyRequestedGridObjects().clear();
+  globalmaster->modifyGridObjForces().clear();
 #endif
 
-  requestTotalForce(false);
+  globalmaster->requestTotalForce(false);
 
   atoms_map.clear();
 
@@ -348,6 +349,8 @@ void colvarproxy_namd::calculate()
 {
   errno = 0;
 
+  auto const step = globalmaster->step;
+
   if (first_timestep) {
 
     // First run after the proxy is constructed
@@ -388,6 +391,8 @@ void colvarproxy_namd::calculate()
   previous_NAMD_step = step;
   if (accelMDOn) update_accelMD_info();
 
+  auto *lattice = globalmaster->lattice;
+
   {
     Vector const a = lattice->a();
     Vector const b = lattice->b();
@@ -420,17 +425,17 @@ void colvarproxy_namd::calculate()
   // must delete the forces applied at the previous step: we can do
   // that because they have already been used and copied to other
   // memory locations
-  modifyForcedAtoms().clear();
-  modifyAppliedForces().clear();
+  globalmaster->modifyForcedAtoms().clear();
+  globalmaster->modifyAppliedForces().clear();
 
   // If new atomic positions or forces have been requested by other
   // GlobalMaster objects, add these to the atom map as well
   size_t const n_all_atoms = Node::Object()->molecule->numAtoms;
   if ( (atoms_map.size() != n_all_atoms) ||
-       (int(atoms_ids.size()) < (getAtomIdEnd() - getAtomIdBegin())) ||
-       (int(atoms_ids.size()) < (getForceIdEnd() - getForceIdBegin())) ) {
-    update_atoms_map(getAtomIdBegin(), getAtomIdEnd());
-    update_atoms_map(getForceIdBegin(), getForceIdEnd());
+       (int(atoms_ids.size()) < (globalmaster->getAtomIdEnd() - globalmaster->getAtomIdBegin())) ||
+       (int(atoms_ids.size()) < (globalmaster->getForceIdEnd() - globalmaster->getForceIdBegin())) ) {
+    update_atoms_map(globalmaster->getAtomIdBegin(), globalmaster->getAtomIdEnd());
+    update_atoms_map(globalmaster->getForceIdBegin(), globalmaster->getForceIdEnd());
   }
 
   // prepare local arrays
@@ -456,9 +461,9 @@ void colvarproxy_namd::calculate()
       cvm::log("Updating positions arrays.\n");
     }
     size_t n_positions = 0;
-    AtomIDList::const_iterator a_i = getAtomIdBegin();
-    AtomIDList::const_iterator a_e = getAtomIdEnd();
-    PositionList::const_iterator p_i = getAtomPositionBegin();
+    AtomIDList::const_iterator a_i = globalmaster->getAtomIdBegin();
+    AtomIDList::const_iterator a_e = globalmaster->getAtomIdEnd();
+    PositionList::const_iterator p_i = globalmaster->getAtomPositionBegin();
 
     for ( ; a_i != a_e; ++a_i, ++p_i ) {
       atoms_positions[atoms_map[*a_i]] = cvm::rvector((*p_i).x, (*p_i).y, (*p_i).z);
@@ -481,9 +486,9 @@ void colvarproxy_namd::calculate()
         cvm::log("Updating total forces arrays.\n");
       }
       size_t n_total_forces = 0;
-      AtomIDList::const_iterator a_i = getForceIdBegin();
-      AtomIDList::const_iterator a_e = getForceIdEnd();
-      ForceList::const_iterator f_i = getTotalForce();
+      AtomIDList::const_iterator a_i = globalmaster->getForceIdBegin();
+      AtomIDList::const_iterator a_e = globalmaster->getForceIdEnd();
+      ForceList::const_iterator f_i = globalmaster->getTotalForce();
 
       for ( ; a_i != a_e; ++a_i, ++f_i ) {
         atoms_total_forces[atoms_map[*a_i]] = cvm::rvector((*f_i).x, (*f_i).y, (*f_i).z);
@@ -504,8 +509,8 @@ void colvarproxy_namd::calculate()
       if (cvm::debug()) {
         cvm::log("Updating group total forces arrays.\n");
       }
-      ForceList::const_iterator f_i = getGroupTotalForceBegin();
-      ForceList::const_iterator f_e = getGroupTotalForceEnd();
+      ForceList::const_iterator f_i = globalmaster->getGroupTotalForceBegin();
+      ForceList::const_iterator f_e = globalmaster->getGroupTotalForceEnd();
       size_t i = 0;
       if ( (! b_simulation_continuing) &&
            ((f_e - f_i) != ((int) atom_groups_ids.size())) ) {
@@ -529,8 +534,8 @@ void colvarproxy_namd::calculate()
     size_t ig;
     // note: getGroupMassBegin() could be used here, but masses and charges
     // have already been calculated from the last call to setup()
-    PositionList::const_iterator gp_i = getGroupPositionBegin();
-    for (ig = 0; gp_i != getGroupPositionEnd(); gp_i++, ig++) {
+    PositionList::const_iterator gp_i = globalmaster->getGroupPositionBegin();
+    for (ig = 0; gp_i != globalmaster->getGroupPositionEnd(); gp_i++, ig++) {
       atom_groups_coms[ig] = cvm::rvector(gp_i->x, gp_i->y, gp_i->z);
     }
   }
@@ -542,9 +547,12 @@ void colvarproxy_namd::calculate()
     }
     // Using a simple nested loop: there probably won't be so many maps that
     // this becomes performance-limiting
-    IntList::const_iterator goi_i = getGridObjIndexBegin();
-    BigRealList::const_iterator gov_i = getGridObjValueBegin();
-    for ( ; gov_i != getGridObjValueEnd(); goi_i++, gov_i++) {
+    IntList::const_iterator goi_i = globalmaster->getGridObjIndexBegin();
+    BigRealList::const_iterator gov_i = globalmaster->getGridObjValueBegin();
+    for ( ; gov_i != globalmaster->getGridObjValueEnd(); goi_i++, gov_i++) {
+      if (cvm::debug()) {
+        log("  ID = " + cvm::to_str(*goi_i) + ", value = " + cvm::to_str(*gov_i) + ".\n");
+      }
       for (size_t imap = 0; imap < volmaps_ids.size(); imap++) {
         if (volmaps_ids[imap] == *goi_i) {
           volmaps_values[imap] = *gov_i;
@@ -571,14 +579,14 @@ void colvarproxy_namd::calculate()
   // communicate all forces to the MD integrator
   for (size_t i = 0; i < atoms_ids.size(); i++) {
     cvm::rvector const &f = atoms_new_colvar_forces[i];
-    modifyForcedAtoms().add(atoms_ids[i]);
-    modifyAppliedForces().add(Vector(f.x, f.y, f.z));
+    globalmaster->modifyForcedAtoms().add(atoms_ids[i]);
+    globalmaster->modifyAppliedForces().add(Vector(f.x, f.y, f.z));
   }
 
   if (atom_groups_new_colvar_forces.size() > 0) {
-    modifyGroupForces().resize(requestedGroups().size());
-    ForceList::iterator gf_i = modifyGroupForces().begin();
-    for (int ig = 0; gf_i != modifyGroupForces().end(); gf_i++, ig++) {
+    globalmaster->modifyGroupForces().resize(globalmaster->requestedGroups().size());
+    ForceList::iterator gf_i = globalmaster->modifyGroupForces().begin();
+    for (int ig = 0; gf_i != globalmaster->modifyGroupForces().end(); gf_i++, ig++) {
       cvm::rvector const &f = atom_groups_new_colvar_forces[ig];
       *gf_i = Vector(f.x, f.y, f.z);
     }
@@ -586,11 +594,11 @@ void colvarproxy_namd::calculate()
 
 #if NAMD_VERSION_NUMBER >= 34471681
   if (volmaps_new_colvar_forces.size() > 0) {
-    modifyGridObjForces().resize(requestedGridObjs().size());
-    modifyGridObjForces().setall(0.0);
-    IntList::const_iterator goi_i = getGridObjIndexBegin();
-    BigRealList::iterator gof_i = modifyGridObjForces().begin();
-    for ( ; goi_i != getGridObjIndexEnd(); goi_i++, gof_i++) {
+    globalmaster->modifyGridObjForces().resize(globalmaster->requestedGridObjs().size());
+    globalmaster->modifyGridObjForces().setall(0.0);
+    IntList::const_iterator goi_i = globalmaster->getGridObjIndexBegin();
+    BigRealList::iterator gof_i = globalmaster->modifyGridObjForces().begin();
+    for ( ; goi_i != globalmaster->getGridObjIndexEnd(); goi_i++, gof_i++) {
       for (size_t imap = 0; imap < volmaps_ids.size(); imap++) {
         if (volmaps_ids[imap] == *goi_i) {
           *gof_i = volmaps_new_colvar_forces[imap];
@@ -674,7 +682,7 @@ void colvarproxy_namd::add_energy(cvm::real energy)
   #if !defined(NAMD_UNIFIED_REDUCTION)
   reduction->item(REDUCTION_MISC_ENERGY) += energy;
   #else
-  addReductionEnergy(REDUCTION_MISC_ENERGY, energy);
+  globalmaster->addReductionEnergy(REDUCTION_MISC_ENERGY, energy);
   #endif
   #endif
 }
@@ -685,7 +693,7 @@ void colvarproxy_namd::request_total_force(bool yesno)
     cvm::log("colvarproxy_namd::request_total_force()\n");
   }
   total_force_requested = yesno;
-  requestTotalForce(total_force_requested);
+  globalmaster->requestTotalForce(total_force_requested);
   if (cvm::debug()) {
     cvm::log("colvarproxy_namd::request_total_force() end\n");
   }
@@ -770,7 +778,7 @@ int colvarproxy_namd::init_atom(int atom_number)
 
   int const index = add_atom_slot(aid);
   atoms_map[aid] = index;
-  modifyRequestedAtoms().add(aid);
+  globalmaster->modifyRequestedAtoms().add(aid);
   update_atom_properties(index);
   return index;
 }
@@ -832,7 +840,7 @@ int colvarproxy_namd::init_atom(cvm::residue_id const &residue,
 
   int const index = add_atom_slot(aid);
   atoms_map[aid] = index;
-  modifyRequestedAtoms().add(aid);
+  globalmaster->modifyRequestedAtoms().add(aid);
   update_atom_properties(index);
   return index;
 }
@@ -868,7 +876,7 @@ cvm::rvector colvarproxy_namd::position_distance(cvm::atom_pos const &pos1,
   Position const p1(pos1.x, pos1.y, pos1.z);
   Position const p2(pos2.x, pos2.y, pos2.z);
   // return p2 - p1
-  Vector const d = this->lattice->delta(p2, p1);
+  Vector const d = globalmaster->lattice->delta(p2, p1);
   return cvm::rvector(d.x, d.y, d.z);
 }
 
@@ -1210,8 +1218,8 @@ int colvarproxy_namd::init_atom_group(std::vector<int> const &atoms_ids)
 
   // compare this new group to those already allocated inside GlobalMaster
   int ig;
-  for (ig = 0; ig < modifyRequestedGroups().size(); ig++) {
-    AtomIDList const &namd_group = modifyRequestedGroups()[ig];
+  for (ig = 0; ig < globalmaster->modifyRequestedGroups().size(); ig++) {
+    AtomIDList const &namd_group = globalmaster->modifyRequestedGroups()[ig];
     bool b_match = true;
 
     if (namd_group.size() != ((int) atoms_ids.size())) {
@@ -1238,10 +1246,10 @@ int colvarproxy_namd::init_atom_group(std::vector<int> const &atoms_ids)
 
   // add this group (note: the argument of add_atom_group_slot() is redundant for NAMD, and provided only for consistency)
   size_t const index = add_atom_group_slot(atom_groups_ids.size());
-  modifyRequestedGroups().resize(atom_groups_ids.size());
+  globalmaster->modifyRequestedGroups().resize(atom_groups_ids.size());
   // the following is done in calculate()
-  // modifyGroupForces().resize(atom_groups_ids.size());
-  AtomIDList &namd_group = modifyRequestedGroups()[index];
+  // globalmaster->modifyGroupForces().resize(atom_groups_ids.size());
+  AtomIDList &namd_group = globalmaster->modifyRequestedGroups()[index];
   namd_group.resize(atoms_ids.size());
   int const n_all_atoms = Node::Object()->molecule->numAtoms;
   for (size_t ia = 0; ia < atoms_ids.size(); ia++) {
@@ -1261,8 +1269,8 @@ int colvarproxy_namd::init_atom_group(std::vector<int> const &atoms_ids)
 
   if (cvm::debug()) {
     cvm::log("Group has index "+cvm::to_str(index)+"\n");
-    cvm::log("modifyRequestedGroups length = "+cvm::to_str(modifyRequestedGroups().size())+
-        ", modifyGroupForces length = "+cvm::to_str(modifyGroupForces().size())+"\n");
+    cvm::log("modifyRequestedGroups length = "+cvm::to_str(globalmaster->modifyRequestedGroups().size())+
+        ", modifyGroupForces length = "+cvm::to_str(globalmaster->modifyGroupForces().size())+"\n");
   }
 
   return index;
@@ -1278,7 +1286,7 @@ void colvarproxy_namd::clear_atom_group(int index)
 
 int colvarproxy_namd::update_group_properties(int index)
 {
-  AtomIDList const &namd_group = modifyRequestedGroups()[index];
+  AtomIDList const &namd_group = globalmaster->modifyRequestedGroups()[index];
   if (cvm::debug()) {
     cvm::log("Re-calculating total mass and charge for scalable group no. "+cvm::to_str(index+1)+" ("+
              cvm::to_str(namd_group.size())+" atoms).\n");
@@ -1336,7 +1344,7 @@ int colvarproxy_namd::init_volmap_by_id(int volmap_id)
   int index = -1;
   if (error_code == COLVARS_OK) {
     index = add_volmap_slot(volmap_id);
-    modifyRequestedGridObjects().add(volmap_id);
+    globalmaster->modifyRequestedGridObjects().add(volmap_id);
   }
 
   return (error_code == COLVARS_OK) ? index : -1;
@@ -1378,7 +1386,7 @@ int colvarproxy_namd::init_volmap_by_name(char const *volmap_name)
     }
 
     index = add_volmap_slot(volmap_id);
-    modifyRequestedGridObjects().add(volmap_id);
+    globalmaster->modifyRequestedGridObjects().add(volmap_id);
   }
 
   return (error_code == COLVARS_OK) ? index : -1;
@@ -1677,7 +1685,7 @@ int colvarproxy_namd::request_alch_energy_freq(int const freq) {
 
 /// Get value of alchemical lambda parameter from back-end
 int colvarproxy_namd::get_alch_lambda(cvm::real* lambda) {
-  *lambda = simparams->getCurrentLambda(step);
+  *lambda = simparams->getCurrentLambda(globalmaster->step);
   return COLVARS_OK;
 }
 
diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h
index 1de72d511..a36a0b396 100644
--- a/namd/src/colvarproxy_namd.h
+++ b/namd/src/colvarproxy_namd.h
@@ -15,6 +15,10 @@
 #define NAMD_VERSION_NUMBER 34471681
 #endif
 
+#include <memory>
+
+#include "colvarproxy_namd_version.h"
+
 #include "Vector.h"
 #include "ResizeArray.h"
 #include "NamdTypes.h"
@@ -32,12 +36,14 @@
 #define GLOBAL_MASTER_CKLOOP_CALC_BIASES 2001
 #define GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES 2002
 
-/// \brief Communication between colvars and NAMD (implementation of
-/// \link colvarproxy \endlink)
-class colvarproxy_namd : public colvarproxy, public GlobalMaster {
+
+/// Communication between colvars and NAMD (implementation of \link colvarproxy \endlink)
+class colvarproxy_namd : public colvarproxy {
 
 protected:
 
+  GlobalMaster *globalmaster;  // raw pointer as placeholder only
+
   /// \brief Array of atom indices (relative to the colvarproxy arrays),
   /// usedfor faster copy of atomic data
   std::vector<int> atoms_map;
@@ -71,7 +77,9 @@ class colvarproxy_namd : public colvarproxy, public GlobalMaster {
 
   void init_tcl_pointers() override;
 
-  colvarproxy_namd();
+  friend class cvm::atom;
+
+  colvarproxy_namd(GlobalMaster *gm);
   ~colvarproxy_namd();
 
   int setup() override;
diff --git a/update-colvars-code.sh b/update-colvars-code.sh
index deb36f8ef..ebe98c354 100755
--- a/update-colvars-code.sh
+++ b/update-colvars-code.sh
@@ -367,9 +367,8 @@ then
 
   # Update NAMD interface files
   for src in \
-      ${source}/namd/src/colvarproxy_namd.h \
-      ${source}/namd/src/colvarproxy_namd_version.h \
-      ${source}/namd/src/colvarproxy_namd.C
+      ${source}/namd/src/*.h \
+      ${source}/namd/src/*.C
   do \
     tgt=$(basename ${src})
     condcopy "${src}" "${target}/src/${tgt}"

From 6411c0d5e62fbeeb44e13e009dd396671ff280e5 Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Wed, 17 Sep 2025 07:48:42 -0400
Subject: [PATCH 03/12] refactor: Initial implementation of GlobalMasterColvars
 wrapper class

---
 namd/src/GlobalMasterColvars.C |  34 +++++++++
 namd/src/GlobalMasterColvars.h | 136 +++++++++++++++++++++++++++++++--
 namd/src/colvarproxy_namd.C    |   1 +
 3 files changed, 164 insertions(+), 7 deletions(-)
 create mode 100644 namd/src/GlobalMasterColvars.C

diff --git a/namd/src/GlobalMasterColvars.C b/namd/src/GlobalMasterColvars.C
new file mode 100644
index 000000000..18b5376f1
--- /dev/null
+++ b/namd/src/GlobalMasterColvars.C
@@ -0,0 +1,34 @@
+// -*- c++ -*-
+
+#include "Controller.h"
+#include "DataExchanger.h"
+#include "GlobalMaster.h"
+#include "GlobalMasterColvars.h"
+#include "colvarproxy_namd.h"
+#include "converse.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);
+}
diff --git a/namd/src/GlobalMasterColvars.h b/namd/src/GlobalMasterColvars.h
index 471811257..66fa60895 100644
--- a/namd/src/GlobalMasterColvars.h
+++ b/namd/src/GlobalMasterColvars.h
@@ -3,23 +3,145 @@
 
 #include <memory>
 
-#include "colvarmodule.h"
-#include "colvarproxy.h"
-#include "colvarproxy_namd.h"
+#include "GlobalMaster.h"
 
 
+class colvarproxy_namd;
+
 class GlobalMasterColvars : public GlobalMaster {
 public:
 
-  GlobalMasterColvars() : proxy(new colvarproxy_namd(this)) {}
+  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);
+  }
 
-  void calculate() override {
-    proxy->calculate();
+  inline Lattice const *get_lattice() const
+  {
+    return lattice;
   }
 
 protected:
 
-  std::unique_ptr<colvarproxy_namd> cp;
+  std::unique_ptr<colvarproxy_namd> proxy;
 };
 
 
diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index 8fa2cfdf1..50a62d17b 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -16,6 +16,7 @@
 #include "InfoStream.h"
 #include "Node.h"
 #include "Molecule.h"
+#include "GlobalMasterColvars.h"
 #include "GridForceGrid.h"
 #include "GridForceGrid.inl"
 #include "PDB.h"

From 305b0a7aae5e8c2834c85b9e3eaec06d14fc0fbc Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Wed, 17 Sep 2025 07:48:43 -0400
Subject: [PATCH 04/12] build: Patch NAMD Makefile files

---
 namd/Make.depends.patch | 59 +++++++++++++++++++++++++++++++++++++++++
 namd/Makefile.patch     | 19 +++++++------
 update-colvars-code.sh  |  5 +---
 3 files changed, 69 insertions(+), 14 deletions(-)
 create mode 100644 namd/Make.depends.patch

diff --git a/namd/Make.depends.patch b/namd/Make.depends.patch
new file mode 100644
index 000000000..0c02bf721
--- /dev/null
+++ b/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 \
diff --git a/namd/Makefile.patch b/namd/Makefile.patch
index 580c60b5b..89cdf7611 100644
--- a/namd/Makefile.patch
+++ b/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 \
+ 	$(DSTDIR)/GlobalMasterFreeEnergy.o \
diff --git a/update-colvars-code.sh b/update-colvars-code.sh
index ebe98c354..6bbbaf467 100755
--- a/update-colvars-code.sh
+++ b/update-colvars-code.sh
@@ -346,9 +346,6 @@ then
              "${target}/lepton/Make.depends"
     condcopy "${source}/namd/lepton/Makefile.namd" \
              "${target}/lepton/Makefile.namd"
-    if ! grep -q lepton/Makefile.namd "${target}/Makefile" ; then
-      patch -p1 -N -d ${target} < namd/Makefile.patch
-    fi
   fi
 
   # Copy library files to the "colvars" folder
@@ -373,7 +370,7 @@ then
     tgt=$(basename ${src})
     condcopy "${src}" "${target}/src/${tgt}"
   done
-  for diff in *.diff ; do
+  for diff in ${source}/namd/*.patch ${source}/namd/src/*.diff ; do
     if [ -s ${diff} ] ; then
       set +e
       patch -p1 -N -d "${target}" < "${diff}"

From 0052ed6785752332289f6b2a5b6de12911b98946 Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Wed, 17 Sep 2025 08:31:14 -0400
Subject: [PATCH 05/12] refactor: Use GlobalMasterColvars in colvarproxy_namd

---
 namd/src/GlobalMaster.h.diff |  15 -----
 namd/src/colvarproxy_namd.C  | 117 ++++++++++++++++-------------------
 namd/src/colvarproxy_namd.h  |   5 +-
 3 files changed, 55 insertions(+), 82 deletions(-)
 delete mode 100644 namd/src/GlobalMaster.h.diff

diff --git a/namd/src/GlobalMaster.h.diff b/namd/src/GlobalMaster.h.diff
deleted file mode 100644
index 6271b7670..000000000
--- a/namd/src/GlobalMaster.h.diff
+++ /dev/null
@@ -1,15 +0,0 @@
-diff --git a/src/GlobalMaster.h b/src/GlobalMaster.h
-index bb27f2ee..b1d571b5 100644
---- a/src/GlobalMaster.h
-+++ b/src/GlobalMaster.h
-@@ -77,7 +77,9 @@ class GlobalMaster {
-   void check() const; // dies if there are problems with the rep invariants
- 
-   void setLattice(const Lattice *lat) { lattice = lat; }
--  
-+
-+  friend class colvarproxy_namd; // Temporary until refactoring is complete
-+
-  protected:
-   GlobalMaster();
- 
diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index 50a62d17b..12d6f86a2 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -45,7 +45,7 @@
 #include "colvarscript.h"
 
 
-colvarproxy_namd::colvarproxy_namd(GlobalMaster *gm)
+colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
   : globalmaster(gm)
 {
   engine_name_ = "NAMD";
@@ -62,7 +62,7 @@ colvarproxy_namd::colvarproxy_namd(GlobalMaster *gm)
   }
 #endif
   first_timestep = true;
-  globalmaster->requestTotalForce(total_force_requested);
+  globalmaster->requestTotalForcePublic(total_force_requested);
 
   boltzmann_ = 0.001987191;
 
@@ -222,7 +222,7 @@ int colvarproxy_namd::update_atoms_map(AtomIDList::const_iterator begin,
       // add it here anyway to avoid having to test for array boundaries at each step
       int const index = add_atom_slot(*a_i);
       atoms_map[*a_i] = index;
-      globalmaster->modifyRequestedAtoms().add(*a_i);
+      globalmaster->modifyRequestedAtomsPublic().add(*a_i);
       update_atom_properties(index);
     }
   }
@@ -267,8 +267,8 @@ int colvarproxy_namd::setup()
   }
 
   size_t n_group_atoms = 0;
-  for (int ig = 0; ig < globalmaster->modifyRequestedGroups().size(); ig++) {
-    n_group_atoms += globalmaster->modifyRequestedGroups()[ig].size();
+  for (int ig = 0; ig < globalmaster->modifyRequestedGroupsPublic().size(); ig++) {
+    n_group_atoms += globalmaster->modifyRequestedGroupsPublic()[ig].size();
   }
 
   log("updating group data ("+cvm::to_str(atom_groups_ids.size())+
@@ -276,7 +276,7 @@ int colvarproxy_namd::setup()
       cvm::to_str(n_group_atoms)+" atoms in total).\n");
 
   // Note: groupMassBegin, groupMassEnd may be used here, but they won't work for charges
-  for (int ig = 0; ig < globalmaster->modifyRequestedGroups().size(); ig++) {
+  for (int ig = 0; ig < globalmaster->modifyRequestedGroupsPublic().size(); ig++) {
 
     // update mass and charge
     update_group_properties(ig);
@@ -289,7 +289,7 @@ int colvarproxy_namd::setup()
 #if NAMD_VERSION_NUMBER >= 34471681
   log("updating grid object data ("+cvm::to_str(volmaps_ids.size())+
       " grid objects in total).\n");
-  for (int imap = 0; imap < globalmaster->modifyGridObjForces().size(); imap++) {
+  for (int imap = 0; imap < globalmaster->modifyGridObjForcesPublic().size(); imap++) {
     volmaps_new_colvar_forces[imap] = 0.0;
   }
 #endif
@@ -322,20 +322,7 @@ int colvarproxy_namd::reset()
 
   int error_code = COLVARS_OK;
 
-  // Unrequest all positions, total forces, etc from NAMD
-  globalmaster->modifyRequestedAtoms().clear();
-  globalmaster->modifyForcedAtoms().clear();
-  globalmaster->modifyAppliedForces().clear();
-
-  globalmaster->modifyRequestedGroups().clear();
-  globalmaster->modifyGroupForces().clear();
-
-#if NAMD_VERSION_NUMBER >= 34471681
-  globalmaster->modifyRequestedGridObjects().clear();
-  globalmaster->modifyGridObjForces().clear();
-#endif
-
-  globalmaster->requestTotalForce(false);
+  globalmaster->reset();
 
   atoms_map.clear();
 
@@ -392,7 +379,7 @@ void colvarproxy_namd::calculate()
   previous_NAMD_step = step;
   if (accelMDOn) update_accelMD_info();
 
-  auto *lattice = globalmaster->lattice;
+  auto *lattice = globalmaster->get_lattice();
 
   {
     Vector const a = lattice->a();
@@ -426,17 +413,17 @@ void colvarproxy_namd::calculate()
   // must delete the forces applied at the previous step: we can do
   // that because they have already been used and copied to other
   // memory locations
-  globalmaster->modifyForcedAtoms().clear();
-  globalmaster->modifyAppliedForces().clear();
+  globalmaster->modifyForcedAtomsPublic().clear();
+  globalmaster->modifyAppliedForcesPublic().clear();
 
   // If new atomic positions or forces have been requested by other
   // GlobalMaster objects, add these to the atom map as well
   size_t const n_all_atoms = Node::Object()->molecule->numAtoms;
   if ( (atoms_map.size() != n_all_atoms) ||
-       (int(atoms_ids.size()) < (globalmaster->getAtomIdEnd() - globalmaster->getAtomIdBegin())) ||
-       (int(atoms_ids.size()) < (globalmaster->getForceIdEnd() - globalmaster->getForceIdBegin())) ) {
-    update_atoms_map(globalmaster->getAtomIdBegin(), globalmaster->getAtomIdEnd());
-    update_atoms_map(globalmaster->getForceIdBegin(), globalmaster->getForceIdEnd());
+       (int(atoms_ids.size()) < (globalmaster->getAtomIdEndPublic() - globalmaster->getAtomIdBeginPublic())) ||
+       (int(atoms_ids.size()) < (globalmaster->getForceIdEndPublic() - globalmaster->getForceIdBeginPublic())) ) {
+    update_atoms_map(globalmaster->getAtomIdBeginPublic(), globalmaster->getAtomIdEndPublic());
+    update_atoms_map(globalmaster->getForceIdBeginPublic(), globalmaster->getForceIdEndPublic());
   }
 
   // prepare local arrays
@@ -462,9 +449,9 @@ void colvarproxy_namd::calculate()
       cvm::log("Updating positions arrays.\n");
     }
     size_t n_positions = 0;
-    AtomIDList::const_iterator a_i = globalmaster->getAtomIdBegin();
-    AtomIDList::const_iterator a_e = globalmaster->getAtomIdEnd();
-    PositionList::const_iterator p_i = globalmaster->getAtomPositionBegin();
+    AtomIDList::const_iterator a_i = globalmaster->getAtomIdBeginPublic();
+    AtomIDList::const_iterator a_e = globalmaster->getAtomIdEndPublic();
+    PositionList::const_iterator p_i = globalmaster->getAtomPositionBeginPublic();
 
     for ( ; a_i != a_e; ++a_i, ++p_i ) {
       atoms_positions[atoms_map[*a_i]] = cvm::rvector((*p_i).x, (*p_i).y, (*p_i).z);
@@ -487,9 +474,9 @@ void colvarproxy_namd::calculate()
         cvm::log("Updating total forces arrays.\n");
       }
       size_t n_total_forces = 0;
-      AtomIDList::const_iterator a_i = globalmaster->getForceIdBegin();
-      AtomIDList::const_iterator a_e = globalmaster->getForceIdEnd();
-      ForceList::const_iterator f_i = globalmaster->getTotalForce();
+      AtomIDList::const_iterator a_i = globalmaster->getForceIdBeginPublic();
+      AtomIDList::const_iterator a_e = globalmaster->getForceIdEndPublic();
+      ForceList::const_iterator f_i = globalmaster->getTotalForcePublic();
 
       for ( ; a_i != a_e; ++a_i, ++f_i ) {
         atoms_total_forces[atoms_map[*a_i]] = cvm::rvector((*f_i).x, (*f_i).y, (*f_i).z);
@@ -510,8 +497,8 @@ void colvarproxy_namd::calculate()
       if (cvm::debug()) {
         cvm::log("Updating group total forces arrays.\n");
       }
-      ForceList::const_iterator f_i = globalmaster->getGroupTotalForceBegin();
-      ForceList::const_iterator f_e = globalmaster->getGroupTotalForceEnd();
+      ForceList::const_iterator f_i = globalmaster->getGroupTotalForceBeginPublic();
+      ForceList::const_iterator f_e = globalmaster->getGroupTotalForceEndPublic();
       size_t i = 0;
       if ( (! b_simulation_continuing) &&
            ((f_e - f_i) != ((int) atom_groups_ids.size())) ) {
@@ -535,8 +522,8 @@ void colvarproxy_namd::calculate()
     size_t ig;
     // note: getGroupMassBegin() could be used here, but masses and charges
     // have already been calculated from the last call to setup()
-    PositionList::const_iterator gp_i = globalmaster->getGroupPositionBegin();
-    for (ig = 0; gp_i != globalmaster->getGroupPositionEnd(); gp_i++, ig++) {
+    PositionList::const_iterator gp_i = globalmaster->getGroupPositionBeginPublic();
+    for (ig = 0; gp_i != globalmaster->getGroupPositionEndPublic(); gp_i++, ig++) {
       atom_groups_coms[ig] = cvm::rvector(gp_i->x, gp_i->y, gp_i->z);
     }
   }
@@ -548,9 +535,9 @@ void colvarproxy_namd::calculate()
     }
     // Using a simple nested loop: there probably won't be so many maps that
     // this becomes performance-limiting
-    IntList::const_iterator goi_i = globalmaster->getGridObjIndexBegin();
-    BigRealList::const_iterator gov_i = globalmaster->getGridObjValueBegin();
-    for ( ; gov_i != globalmaster->getGridObjValueEnd(); goi_i++, gov_i++) {
+    IntList::const_iterator goi_i = globalmaster->getGridObjIndexBeginPublic();
+    BigRealList::const_iterator gov_i = globalmaster->getGridObjValueBeginPublic();
+    for ( ; gov_i != globalmaster->getGridObjValueEndPublic(); goi_i++, gov_i++) {
       if (cvm::debug()) {
         log("  ID = " + cvm::to_str(*goi_i) + ", value = " + cvm::to_str(*gov_i) + ".\n");
       }
@@ -580,14 +567,14 @@ void colvarproxy_namd::calculate()
   // communicate all forces to the MD integrator
   for (size_t i = 0; i < atoms_ids.size(); i++) {
     cvm::rvector const &f = atoms_new_colvar_forces[i];
-    globalmaster->modifyForcedAtoms().add(atoms_ids[i]);
-    globalmaster->modifyAppliedForces().add(Vector(f.x, f.y, f.z));
+    globalmaster->modifyForcedAtomsPublic().add(atoms_ids[i]);
+    globalmaster->modifyAppliedForcesPublic().add(Vector(f.x, f.y, f.z));
   }
 
   if (atom_groups_new_colvar_forces.size() > 0) {
-    globalmaster->modifyGroupForces().resize(globalmaster->requestedGroups().size());
-    ForceList::iterator gf_i = globalmaster->modifyGroupForces().begin();
-    for (int ig = 0; gf_i != globalmaster->modifyGroupForces().end(); gf_i++, ig++) {
+    globalmaster->modifyGroupForcesPublic().resize(globalmaster->requestedGroups().size());
+    ForceList::iterator gf_i = globalmaster->modifyGroupForcesPublic().begin();
+    for (int ig = 0; gf_i != globalmaster->modifyGroupForcesPublic().end(); gf_i++, ig++) {
       cvm::rvector const &f = atom_groups_new_colvar_forces[ig];
       *gf_i = Vector(f.x, f.y, f.z);
     }
@@ -595,11 +582,11 @@ void colvarproxy_namd::calculate()
 
 #if NAMD_VERSION_NUMBER >= 34471681
   if (volmaps_new_colvar_forces.size() > 0) {
-    globalmaster->modifyGridObjForces().resize(globalmaster->requestedGridObjs().size());
-    globalmaster->modifyGridObjForces().setall(0.0);
-    IntList::const_iterator goi_i = globalmaster->getGridObjIndexBegin();
-    BigRealList::iterator gof_i = globalmaster->modifyGridObjForces().begin();
-    for ( ; goi_i != globalmaster->getGridObjIndexEnd(); goi_i++, gof_i++) {
+    globalmaster->modifyGridObjForcesPublic().resize(globalmaster->requestedGridObjs().size());
+    globalmaster->modifyGridObjForcesPublic().setall(0.0);
+    IntList::const_iterator goi_i = globalmaster->getGridObjIndexBeginPublic();
+    BigRealList::iterator gof_i = globalmaster->modifyGridObjForcesPublic().begin();
+    for ( ; goi_i != globalmaster->getGridObjIndexEndPublic(); goi_i++, gof_i++) {
       for (size_t imap = 0; imap < volmaps_ids.size(); imap++) {
         if (volmaps_ids[imap] == *goi_i) {
           *gof_i = volmaps_new_colvar_forces[imap];
@@ -683,7 +670,7 @@ void colvarproxy_namd::add_energy(cvm::real energy)
   #if !defined(NAMD_UNIFIED_REDUCTION)
   reduction->item(REDUCTION_MISC_ENERGY) += energy;
   #else
-  globalmaster->addReductionEnergy(REDUCTION_MISC_ENERGY, energy);
+  globalmaster->addReductionEnergyPublic(REDUCTION_MISC_ENERGY, energy);
   #endif
   #endif
 }
@@ -694,7 +681,7 @@ void colvarproxy_namd::request_total_force(bool yesno)
     cvm::log("colvarproxy_namd::request_total_force()\n");
   }
   total_force_requested = yesno;
-  globalmaster->requestTotalForce(total_force_requested);
+  globalmaster->requestTotalForcePublic(total_force_requested);
   if (cvm::debug()) {
     cvm::log("colvarproxy_namd::request_total_force() end\n");
   }
@@ -779,7 +766,7 @@ int colvarproxy_namd::init_atom(int atom_number)
 
   int const index = add_atom_slot(aid);
   atoms_map[aid] = index;
-  globalmaster->modifyRequestedAtoms().add(aid);
+  globalmaster->modifyRequestedAtomsPublic().add(aid);
   update_atom_properties(index);
   return index;
 }
@@ -841,7 +828,7 @@ int colvarproxy_namd::init_atom(cvm::residue_id const &residue,
 
   int const index = add_atom_slot(aid);
   atoms_map[aid] = index;
-  globalmaster->modifyRequestedAtoms().add(aid);
+  globalmaster->modifyRequestedAtomsPublic().add(aid);
   update_atom_properties(index);
   return index;
 }
@@ -877,7 +864,7 @@ cvm::rvector colvarproxy_namd::position_distance(cvm::atom_pos const &pos1,
   Position const p1(pos1.x, pos1.y, pos1.z);
   Position const p2(pos2.x, pos2.y, pos2.z);
   // return p2 - p1
-  Vector const d = globalmaster->lattice->delta(p2, p1);
+  Vector const d = globalmaster->get_lattice()->delta(p2, p1);
   return cvm::rvector(d.x, d.y, d.z);
 }
 
@@ -1219,8 +1206,8 @@ int colvarproxy_namd::init_atom_group(std::vector<int> const &atoms_ids)
 
   // compare this new group to those already allocated inside GlobalMaster
   int ig;
-  for (ig = 0; ig < globalmaster->modifyRequestedGroups().size(); ig++) {
-    AtomIDList const &namd_group = globalmaster->modifyRequestedGroups()[ig];
+  for (ig = 0; ig < globalmaster->modifyRequestedGroupsPublic().size(); ig++) {
+    AtomIDList const &namd_group = globalmaster->modifyRequestedGroupsPublic()[ig];
     bool b_match = true;
 
     if (namd_group.size() != ((int) atoms_ids.size())) {
@@ -1247,10 +1234,10 @@ int colvarproxy_namd::init_atom_group(std::vector<int> const &atoms_ids)
 
   // add this group (note: the argument of add_atom_group_slot() is redundant for NAMD, and provided only for consistency)
   size_t const index = add_atom_group_slot(atom_groups_ids.size());
-  globalmaster->modifyRequestedGroups().resize(atom_groups_ids.size());
+  globalmaster->modifyRequestedGroupsPublic().resize(atom_groups_ids.size());
   // the following is done in calculate()
   // globalmaster->modifyGroupForces().resize(atom_groups_ids.size());
-  AtomIDList &namd_group = globalmaster->modifyRequestedGroups()[index];
+  AtomIDList &namd_group = globalmaster->modifyRequestedGroupsPublic()[index];
   namd_group.resize(atoms_ids.size());
   int const n_all_atoms = Node::Object()->molecule->numAtoms;
   for (size_t ia = 0; ia < atoms_ids.size(); ia++) {
@@ -1270,8 +1257,8 @@ int colvarproxy_namd::init_atom_group(std::vector<int> const &atoms_ids)
 
   if (cvm::debug()) {
     cvm::log("Group has index "+cvm::to_str(index)+"\n");
-    cvm::log("modifyRequestedGroups length = "+cvm::to_str(globalmaster->modifyRequestedGroups().size())+
-        ", modifyGroupForces length = "+cvm::to_str(globalmaster->modifyGroupForces().size())+"\n");
+    cvm::log("modifyRequestedGroups length = "+cvm::to_str(globalmaster->modifyRequestedGroupsPublic().size())+
+        ", modifyGroupForces length = "+cvm::to_str(globalmaster->modifyGroupForcesPublic().size())+"\n");
   }
 
   return index;
@@ -1287,7 +1274,7 @@ void colvarproxy_namd::clear_atom_group(int index)
 
 int colvarproxy_namd::update_group_properties(int index)
 {
-  AtomIDList const &namd_group = globalmaster->modifyRequestedGroups()[index];
+  AtomIDList const &namd_group = globalmaster->modifyRequestedGroupsPublic()[index];
   if (cvm::debug()) {
     cvm::log("Re-calculating total mass and charge for scalable group no. "+cvm::to_str(index+1)+" ("+
              cvm::to_str(namd_group.size())+" atoms).\n");
@@ -1345,7 +1332,7 @@ int colvarproxy_namd::init_volmap_by_id(int volmap_id)
   int index = -1;
   if (error_code == COLVARS_OK) {
     index = add_volmap_slot(volmap_id);
-    globalmaster->modifyRequestedGridObjects().add(volmap_id);
+    globalmaster->modifyRequestedGridObjectsPublic().add(volmap_id);
   }
 
   return (error_code == COLVARS_OK) ? index : -1;
@@ -1387,7 +1374,7 @@ int colvarproxy_namd::init_volmap_by_name(char const *volmap_name)
     }
 
     index = add_volmap_slot(volmap_id);
-    globalmaster->modifyRequestedGridObjects().add(volmap_id);
+    globalmaster->modifyRequestedGridObjectsPublic().add(volmap_id);
   }
 
   return (error_code == COLVARS_OK) ? index : -1;
diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h
index a36a0b396..76b7969ca 100644
--- a/namd/src/colvarproxy_namd.h
+++ b/namd/src/colvarproxy_namd.h
@@ -42,7 +42,8 @@ class colvarproxy_namd : public colvarproxy {
 
 protected:
 
-  GlobalMaster *globalmaster;  // raw pointer as placeholder only
+  /// Pointer to the parent GlobalMaster object
+  GlobalMasterColvars *globalmaster = nullptr;
 
   /// \brief Array of atom indices (relative to the colvarproxy arrays),
   /// usedfor faster copy of atomic data
@@ -79,7 +80,7 @@ class colvarproxy_namd : public colvarproxy {
 
   friend class cvm::atom;
 
-  colvarproxy_namd(GlobalMaster *gm);
+  colvarproxy_namd(GlobalMasterColvars *gm);
   ~colvarproxy_namd();
 
   int setup() override;

From e16628d83e4f294720079544ce1042ee9cf275c4 Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Thu, 18 Sep 2025 11:23:17 -0400
Subject: [PATCH 06/12] fix: Add missing pointer for debug build, move macros
 to constexpr in more appropriate header

---
 namd/src/GlobalMasterColvars.h | 7 +++++++
 namd/src/colvarproxy_namd.C    | 6 +++---
 namd/src/colvarproxy_namd.h    | 4 ----
 3 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/namd/src/GlobalMasterColvars.h b/namd/src/GlobalMasterColvars.h
index 66fa60895..5ceaaf13c 100644
--- a/namd/src/GlobalMasterColvars.h
+++ b/namd/src/GlobalMasterColvars.h
@@ -145,4 +145,11 @@ class GlobalMasterColvars : public GlobalMaster {
 };
 
 
+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
diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index 12d6f86a2..84e5ca8da 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -1523,7 +1523,7 @@ int colvarproxy_namd::smp_loop(int n_items, std::function<int (int)> const &work
       worker(i);
     }
 #if CMK_TRACE_ENABLED
-    traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_ITEM, before, CmiWallTimer());
+    globalmaster->traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_ITEM, before, CmiWallTimer());
 #endif
   };
   const int numChunks = smp_num_threads() > n_items ?
@@ -1557,7 +1557,7 @@ void calc_cv_biases_smp(int first, int last, void *result, int paramNum, void *p
   }
   cvm::decrease_depth();
 #if CMK_TRACE_ENABLED
-  traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_BIASES,before,CmiWallTimer());
+  globalmaster->traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_BIASES,before,CmiWallTimer());
 #endif
 }
 
@@ -1587,7 +1587,7 @@ void calc_cv_scripted_forces(int paramNum, void *param)
   }
   cv->calc_scripted_forces();
 #if CMK_TRACE_ENABLED
-  traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES,before,CmiWallTimer());
+  globalmaster->traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES,before,CmiWallTimer());
 #endif
 }
 
diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h
index 76b7969ca..c7655a1f8 100644
--- a/namd/src/colvarproxy_namd.h
+++ b/namd/src/colvarproxy_namd.h
@@ -32,10 +32,6 @@
 #include "colvarproxy.h"
 #include "colvarvalue.h"
 
-#define GLOBAL_MASTER_CKLOOP_CALC_ITEM 2000
-#define GLOBAL_MASTER_CKLOOP_CALC_BIASES 2001
-#define GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES 2002
-
 
 /// Communication between colvars and NAMD (implementation of \link colvarproxy \endlink)
 class colvarproxy_namd : public colvarproxy {

From 26dceddc6c021324be27931f9277c32d52571afd Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Thu, 13 Nov 2025 11:20:14 -0500
Subject: [PATCH 07/12] cleanup: Use forward declaration and tidy up NAMD
 header includes

---
 namd/src/GlobalMasterColvars.C |  3 ---
 namd/src/colvarproxy_namd.C    | 41 +++++++++++++++++++++-------------
 namd/src/colvarproxy_namd.h    | 30 +++++++++----------------
 3 files changed, 35 insertions(+), 39 deletions(-)

diff --git a/namd/src/GlobalMasterColvars.C b/namd/src/GlobalMasterColvars.C
index 18b5376f1..1789867c1 100644
--- a/namd/src/GlobalMasterColvars.C
+++ b/namd/src/GlobalMasterColvars.C
@@ -1,11 +1,8 @@
 // -*- c++ -*-
 
-#include "Controller.h"
-#include "DataExchanger.h"
 #include "GlobalMaster.h"
 #include "GlobalMasterColvars.h"
 #include "colvarproxy_namd.h"
-#include "converse.h"
 
 
 GlobalMasterColvars::GlobalMasterColvars() : proxy(new colvarproxy_namd(this)) {}
diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index 84e5ca8da..3bc843963 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -9,32 +9,34 @@
 
 #include <errno.h>
 
-#include "common.h"
-#include "fstream_namd.h"
+#include "ConfigList.h"
+#include "Controller.h"
+#include "DataExchanger.h"
 #include "Debug.h"
-#include "BackEnd.h"
-#include "InfoStream.h"
-#include "Node.h"
-#include "Molecule.h"
+#include "GlobalMaster.h"
 #include "GlobalMasterColvars.h"
 #include "GridForceGrid.h"
 #include "GridForceGrid.inl"
+#include "InfoStream.h"
+#include "Lattice.h"
+#include "Molecule.h"
+#include "NamdState.h"
+#include "NamdTypes.h"
+#include "Node.h"
 #include "PDB.h"
-#include "PDBData.h"
+#include "Random.h"
 #include "ReductionMgr.h"
+#include "ResizeArray.h"
 #include "ScriptTcl.h"
-#include "NamdState.h"
-#include "Controller.h"
-#include "PatchData.h"
+#include "SimParameters.h"
+#include "Vector.h"
+#include "common.h"
+#include "fstream_namd.h"
 
 #ifdef NAMD_TCL
 #include <tcl.h>
 #endif
 
-// For replica exchange
-#include "converse.h"
-#include "DataExchanger.h"
-
 #include "colvarmodule.h"
 #include "colvar.h"
 #include "colvarbias.h"
@@ -42,7 +44,6 @@
 #include "colvarproxy.h"
 #include "colvarproxy_namd.h"
 #include "colvarproxy_namd_version.h"
-#include "colvarscript.h"
 
 
 colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
@@ -85,7 +86,7 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
   set_integration_timestep(simparams->dt);
   set_time_step_factor(simparams->globalMasterFrequency);
 
-  random = Random(simparams->randomSeed);
+  random.reset(new Random(simparams->randomSeed));
 
   // both fields are taken from data structures already available
   updated_masses_ = updated_charges_ = true;
@@ -617,11 +618,19 @@ void colvarproxy_namd::calculate()
   }
 }
 
+
+cvm::real colvarproxy_namd::rand_gaussian() { return random->gaussian(); }
+
+
 void colvarproxy_namd::update_accelMD_info() {
   // This aMD factor is from previous step!
   amd_weight_factor = std::exp(controller->accelMDdV / (target_temperature() * boltzmann()));
 }
 
+cvm::real colvarproxy_namd::get_accelMD_factor() const { return amd_weight_factor; }
+
+bool colvarproxy_namd::accelMD_enabled() const { return accelMDOn; }
+
 
 // Callback functions
 
diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h
index c7655a1f8..340b370e9 100644
--- a/namd/src/colvarproxy_namd.h
+++ b/namd/src/colvarproxy_namd.h
@@ -19,20 +19,17 @@
 
 #include "colvarproxy_namd_version.h"
 
-#include "Vector.h"
-#include "ResizeArray.h"
-#include "NamdTypes.h"
-#include "SimParameters.h"
-#include "Lattice.h"
-#include "GlobalMaster.h"
-#include "Random.h"
-#include "ConfigList.h"
-
 #include "colvarmodule.h"
 #include "colvarproxy.h"
 #include "colvarvalue.h"
 
 
+class Controller;
+class GlobalMasterColvars;
+class Random;
+class SimParameters;
+
+
 /// Communication between colvars and NAMD (implementation of \link colvarproxy \endlink)
 class colvarproxy_namd : public colvarproxy {
 
@@ -52,7 +49,7 @@ class colvarproxy_namd : public colvarproxy {
   Controller const *controller;
 
   /// NAMD-style PRNG object
-  Random random;
+  std::unique_ptr<Random> random;
 
   bool first_timestep;
   cvm::step_number previous_NAMD_step;
@@ -113,18 +110,11 @@ class colvarproxy_namd : public colvarproxy {
                                    std::vector<const colvarvalue *> const &cvcs,
                                    std::vector<cvm::matrix2d<cvm::real> > &gradient) override;
 
-  cvm::real rand_gaussian() override
-  {
-    return random.gaussian();
-  }
+  cvm::real rand_gaussian() override;
 
-  cvm::real get_accelMD_factor() const override {
-    return amd_weight_factor;
-  }
+  cvm::real get_accelMD_factor() const override;
 
-  bool accelMD_enabled() const override {
-    return accelMDOn;
-  }
+  bool accelMD_enabled() const override;
 
 #if CMK_SMP && USE_CKLOOP
   colvarproxy::smp_mode_t get_smp_mode() const override;

From 871037f052b51af02053c441163c22b9a092eb6d Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Thu, 13 Nov 2025 11:20:15 -0500
Subject: [PATCH 08/12] cleanup: Delete unused friend declaration

---
 namd/src/colvarproxy_namd.h | 2 --
 1 file changed, 2 deletions(-)

diff --git a/namd/src/colvarproxy_namd.h b/namd/src/colvarproxy_namd.h
index 340b370e9..4e36e0fcf 100644
--- a/namd/src/colvarproxy_namd.h
+++ b/namd/src/colvarproxy_namd.h
@@ -71,8 +71,6 @@ class colvarproxy_namd : public colvarproxy {
 
   void init_tcl_pointers() override;
 
-  friend class cvm::atom;
-
   colvarproxy_namd(GlobalMasterColvars *gm);
   ~colvarproxy_namd();
 

From b6cfc84ab13ea4cf01cb1a6ca990170a65b94cfc Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Thu, 13 Nov 2025 11:20:17 -0500
Subject: [PATCH 09/12] cleanup: Add .clang-format for NAMD folder

---
 namd/src/.clang-format | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 namd/src/.clang-format

diff --git a/namd/src/.clang-format b/namd/src/.clang-format
new file mode 100644
index 000000000..66e78c8b5
--- /dev/null
+++ b/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
+...

From 7cc73f9855d06826d2e4681508ec7642911f193e Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Thu, 13 Nov 2025 11:20:18 -0500
Subject: [PATCH 10/12] fix: Remove wrong pointer from Charm++ trace functions

---
 namd/src/colvarproxy_namd.C | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/namd/src/colvarproxy_namd.C b/namd/src/colvarproxy_namd.C
index 3bc843963..d4612686f 100644
--- a/namd/src/colvarproxy_namd.C
+++ b/namd/src/colvarproxy_namd.C
@@ -57,9 +57,9 @@ colvarproxy_namd::colvarproxy_namd(GlobalMasterColvars *gm)
   version_int = get_version_from_string(COLVARPROXY_VERSION);
 #if CMK_TRACE_ENABLED
   if ( 0 == CkMyPe() ) {
-    globalmaster->traceRegisterUserEvent("GM COLVAR item", GLOBAL_MASTER_CKLOOP_CALC_ITEM);
-    globalmaster->traceRegisterUserEvent("GM COLVAR bias", GLOBAL_MASTER_CKLOOP_CALC_BIASES );
-    globalmaster->traceRegisterUserEvent("GM COLVAR scripted bias", GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES );
+    traceRegisterUserEvent("GM COLVAR item", GLOBAL_MASTER_CKLOOP_CALC_ITEM);
+    traceRegisterUserEvent("GM COLVAR bias", GLOBAL_MASTER_CKLOOP_CALC_BIASES );
+    traceRegisterUserEvent("GM COLVAR scripted bias", GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES );
   }
 #endif
   first_timestep = true;
@@ -1532,7 +1532,7 @@ int colvarproxy_namd::smp_loop(int n_items, std::function<int (int)> const &work
       worker(i);
     }
 #if CMK_TRACE_ENABLED
-    globalmaster->traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_ITEM, before, CmiWallTimer());
+    traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_ITEM, before, CmiWallTimer());
 #endif
   };
   const int numChunks = smp_num_threads() > n_items ?
@@ -1566,7 +1566,7 @@ void calc_cv_biases_smp(int first, int last, void *result, int paramNum, void *p
   }
   cvm::decrease_depth();
 #if CMK_TRACE_ENABLED
-  globalmaster->traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_BIASES,before,CmiWallTimer());
+  traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_BIASES,before,CmiWallTimer());
 #endif
 }
 
@@ -1596,7 +1596,7 @@ void calc_cv_scripted_forces(int paramNum, void *param)
   }
   cv->calc_scripted_forces();
 #if CMK_TRACE_ENABLED
-  globalmaster->traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES,before,CmiWallTimer());
+  traceUserBracketEvent(GLOBAL_MASTER_CKLOOP_CALC_SCRIPTED_BIASES,before,CmiWallTimer());
 #endif
 }
 

From 88669191380f5dbb0070d7d5b24f9b97e4f001a1 Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Thu, 13 Nov 2025 11:20:20 -0500
Subject: [PATCH 11/12] fix: Update NAMD patch files

---
 namd/config.patch | 59 -----------------------------------------------
 1 file changed, 59 deletions(-)

diff --git a/namd/config.patch b/namd/config.patch
index 76618f2e5..e69de29bb 100644
--- a/namd/config.patch
+++ b/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

From 4d45617de50a7ec1c12e65ebd6d8a23e52025bc4 Mon Sep 17 00:00:00 2001
From: Giacomo Fiorin <giacomo.fiorin@gmail.com>
Date: Fri, 14 Nov 2025 12:41:24 -0500
Subject: [PATCH 12/12] Use .patch extension for patch files to other codes,
 clean up updater script

---
 ...epton.diff => CMakeLists.txt.Lepton.patch} |  0
 ...akeLists.txt.diff => CMakeLists.txt.patch} |  0
 ...make.diff => gmxManageColvars.cmake.patch} |  0
 ...COLVARS.cmake.diff => COLVARS.cmake.patch} |  0
 update-colvars-code.sh                        | 52 ++++++++-----------
 ...l_commands.C.diff => tcl_commands.C.patch} |  0
 6 files changed, 23 insertions(+), 29 deletions(-)
 rename gromacs/{CMakeLists.txt.Lepton.diff => CMakeLists.txt.Lepton.patch} (100%)
 rename gromacs/{CMakeLists.txt.diff => CMakeLists.txt.patch} (100%)
 rename gromacs/{gmxManageColvars.cmake.diff => gmxManageColvars.cmake.patch} (100%)
 rename lammps/{COLVARS.cmake.diff => COLVARS.cmake.patch} (100%)
 rename vmd/src/{tcl_commands.C.diff => tcl_commands.C.patch} (100%)

diff --git a/gromacs/CMakeLists.txt.Lepton.diff b/gromacs/CMakeLists.txt.Lepton.patch
similarity index 100%
rename from gromacs/CMakeLists.txt.Lepton.diff
rename to gromacs/CMakeLists.txt.Lepton.patch
diff --git a/gromacs/CMakeLists.txt.diff b/gromacs/CMakeLists.txt.patch
similarity index 100%
rename from gromacs/CMakeLists.txt.diff
rename to gromacs/CMakeLists.txt.patch
diff --git a/gromacs/gmxManageColvars.cmake.diff b/gromacs/gmxManageColvars.cmake.patch
similarity index 100%
rename from gromacs/gmxManageColvars.cmake.diff
rename to gromacs/gmxManageColvars.cmake.patch
diff --git a/lammps/COLVARS.cmake.diff b/lammps/COLVARS.cmake.patch
similarity index 100%
rename from lammps/COLVARS.cmake.diff
rename to lammps/COLVARS.cmake.patch
diff --git a/update-colvars-code.sh b/update-colvars-code.sh
index 6bbbaf467..a333e26e4 100755
--- a/update-colvars-code.sh
+++ b/update-colvars-code.sh
@@ -45,12 +45,16 @@ then
   shift
 fi
 
+# Assume forward patching
+PATCH_OPTS="-p1 --forward -s"
+
 # Undocumented flag
 reverse=0
 if [ $1 = "-R" ]
 then
   echo "Reverse: updating git tree from downstream tree"
   reverse=1
+  PATCH_OPTS="-p1 --reverse -s"
   shift
 fi
 
@@ -211,11 +215,9 @@ condcopy() {
   then
     a=$2
     b=$1
-    PATCH_OPT="-R"
   else
     a=$1
     b=$2
-    PATCH_OPT=""
   fi
 
   updated_file=0
@@ -261,6 +263,7 @@ checkfile() {
 }
 
 
+
 # Update LAMMPS tree
 if [ ${code} = "LAMMPS" ]
 then
@@ -284,11 +287,9 @@ then
     condcopy "${src}" "${target}/src/COLVARS/${tgt}"
   done
 
-  if [ -f ${source}/lammps/COLVARS.cmake.diff ] ; then
+  if [ -f ${source}/lammps/COLVARS.cmake.patch ] ; then
     # Do not exit if the patch fails - already applied in development branch
-    set +e
-    patch -p1 -N -d ${target} < ${source}/lammps/COLVARS.cmake.diff
-    set -e
+    patch ${PATCH_OPTS} -d ${target} < ${source}/lammps/COLVARS.cmake.patch || true
   fi
 
   downloaded_pdf=0
@@ -370,11 +371,9 @@ then
     tgt=$(basename ${src})
     condcopy "${src}" "${target}/src/${tgt}"
   done
-  for diff in ${source}/namd/*.patch ${source}/namd/src/*.diff ; do
-    if [ -s ${diff} ] ; then
-      set +e
-      patch -p1 -N -d "${target}" < "${diff}"
-      set -e
+  for patch in ${source}/namd/*.patch ${source}/namd/src/*.patch ; do
+    if [ -s ${patch} ] ; then
+      patch ${PATCH_OPTS} -d "${target}" < "${patch}" || true
     fi
   done
 
@@ -441,11 +440,9 @@ then
     condcopy "${src}" "${target}/src/${tgt}.C"
   done
 
-  if [ -f ${source}/vmd/src/tcl_commands.C.diff ] ; then
+  if [ -f ${source}/vmd/src/tcl_commands.C.patch ] ; then
     # Do not exit if the patch fails - already applied in development branch
-    set +e
-    patch -p1 -N -d ${target} < ${source}/vmd/src/tcl_commands.C.diff
-    set -e
+    patch ${PATCH_OPTS} -d ${target} < ${source}/vmd/src/tcl_commands.C.patch || true
   fi
 
   # Update replacement text for the Colvars manual
@@ -498,7 +495,6 @@ if [ ${code} = "GROMACS" ]
 then
 
   target_folder=${target}/src/external/colvars
-  patch_opts="-p1 --forward -s"
 
   mkdir -p ${target_folder}
 
@@ -511,21 +507,21 @@ then
   echo ""
 
   # Patch CMake build recipes when applicable
-  if [ -s ${source}/gromacs/gmxManageColvars.cmake.diff ] ; then
-    patch ${patch_opts} -d ${target} < ${source}/gromacs/gmxManageColvars.cmake.diff || true
+  if [ -s ${source}/gromacs/gmxManageColvars.cmake.patch ] ; then
+    patch ${PATCH_OPTS} -d ${target} < ${source}/gromacs/gmxManageColvars.cmake.patch || true
   fi
-  if [ -s ${source}/gromacs/CMakeLists.txt.diff ] ; then
-    patch ${patch_opts} -d ${target} < ${source}/gromacs/CMakeLists.txt.diff || true
+  if [ -s ${source}/gromacs/CMakeLists.txt.patch ] ; then
+    patch ${PATCH_OPTS} -d ${target} < ${source}/gromacs/CMakeLists.txt.patch || true
   fi
-  if [ -s ${source}/gromacs/CMakeLists.txt.diff ] ; then
-    patch ${patch_opts} -d ${target} < ${source}/gromacs/CMakeLists.txt.diff || true
+  if [ -s ${source}/gromacs/CMakeLists.txt.patch ] ; then
+    patch ${PATCH_OPTS} -d ${target} < ${source}/gromacs/CMakeLists.txt.patch || true
   fi
 
   if [ "x${UPDATE_LEPTON}" == "xyes" ] ; then
     echo -n "(note: adding/updating Lepton)"
     copy_lepton ${target}/src/external/ || exit 1
-    if [ -s ${source}/gromacs/CMakeLists.txt.Lepton.diff ] ; then
-      patch ${patch_opts} -d ${target} < ${source}/gromacs/CMakeLists.txt.Lepton.diff || true
+    if [ -s ${source}/gromacs/CMakeLists.txt.Lepton.patch ] ; then
+      patch ${PATCH_OPTS} -d ${target} < ${source}/gromacs/CMakeLists.txt.Lepton.patch || true
     fi
     condcopy ${source}/gromacs/cmake/gmxManageLepton.cmake "${target}/cmake/gmxManageLepton.cmake"
   fi
@@ -535,12 +531,10 @@ then
   # Copy MDModules files to the "src/gromacs/src/applied_forces/colvars" folder
   target_folder=${target}/src/gromacs/applied_forces/colvars
 
-  for patch_file in ${source}/gromacs/src/applied_forces/colvars/*.diff ; do
+  for patch_file in ${source}/gromacs/src/applied_forces/colvars/*.patch ; do
     if [ -s ${patch_file} ] ; then
       # Do not exit if the patch fails - already applied
-      set +e
-      patch -p1 -N -d ${target} < ${patch_file}
-      set -e
+      patch ${PATCH_OPTS} -d ${target} < ${patch_file} || true
     fi
   done
 
@@ -570,7 +564,7 @@ then
 
   # Apply patch for Gromacs files
   if [ -s ${source}/gromacs/gromacs-mdmodules.patch ] ; then
-    patch ${patch_opts} -d ${target} < ${source}/gromacs/gromacs-mdmodules.patch || true
+    patch ${PATCH_OPTS} -d ${target} < ${source}/gromacs/gromacs-mdmodules.patch || true
   fi
   ret_val=$?
   if [ $ret_val -ne 0 ]
diff --git a/vmd/src/tcl_commands.C.diff b/vmd/src/tcl_commands.C.patch
similarity index 100%
rename from vmd/src/tcl_commands.C.diff
rename to vmd/src/tcl_commands.C.patch