Fix reinitialization issues when using total forces in NAMD

.github/workflows/backend-template.yml

@@ -135,10 +135,7 @@ jobs:
           sudo apt install -y apptainer-suid
 
       - name: Get container images for build dependencies
-        shell: bash
-        working-directory: devel-tools
-        run: |
-          apptainer pull ${{ inputs.container_name }}.sif oras://ghcr.io/colvars/devel-containers:${{ inputs.container_name }}
+        run: devel-tools/get_container ${{ inputs.container_name }}
 
       - name: Update and build ${{ inputs.backend_name }}
         shell: bash

.github/workflows/test-library.yml

@@ -92,10 +92,7 @@ jobs:
           sudo apt install -y apptainer-suid
 
       - name: Get container image
-        shell: bash
-        working-directory: devel-tools
-        run: |
-          apptainer pull texlive.sif oras://ghcr.io/colvars/devel-containers:texlive
+        run: devel-tools/get_container texlive
 
       - name: Checkout website repository
         uses: actions/checkout@v4
@@ -191,10 +188,7 @@ jobs:
           sudo apt install -y apptainer-suid
 
       - name: Get container images for build dependencies
-        shell: bash
-        working-directory: devel-tools
-        run: |
-          apptainer pull CentOS9-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel
+        run: devel-tools/get_container CentOS9-devel
 
       - name: Run build with Clang static analyser
         env:
@@ -252,10 +246,7 @@ jobs:
           sudo apt install -y apptainer-suid
 
       - name: Get container images for build dependencies
-        shell: bash
-        working-directory: devel-tools
-        run: |
-          apptainer pull CentOS9-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel
+        run: devel-tools/get_container CentOS9-devel
 
       - name: Build with Clang and address sanitizer
         env:
@@ -307,11 +298,8 @@ jobs:
           sudo apt update
           sudo apt install -y apptainer-suid
 
-      - name: Get container images for build environment
-        shell: bash
-        working-directory: devel-tools
-        run: |
-          apptainer pull CentOS9-devel.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel
+      - name: Get container images for build dependencies
+        run: devel-tools/get_container CentOS9-devel
 
       - name: GCC 11, C++11 (CentOS 9)
         env:
@@ -447,10 +435,7 @@ jobs:
           sudo apt install -y apptainer-suid
 
       - name: Get container images for build dependencies
-        shell: bash
-        working-directory: devel-tools
-        run: |
-          apptainer pull CentOS9-oneAPI.sif oras://ghcr.io/colvars/devel-containers:CentOS9-oneAPI
+        run: devel-tools/get_container CentOS9-oneAPI
 
       - name: Intel oneAPI 2024.2, C++11
         shell: bash
@@ -573,10 +558,7 @@ jobs:
           sudo apt install -y apptainer-suid
 
       - name: Get container images for build dependencies
-        shell: bash
-        working-directory: devel-tools
-        run: |
-          apptainer pull CentOS9-devel-arm64.sif oras://ghcr.io/colvars/devel-containers:CentOS9-devel-arm64
+        run: devel-tools/get_container CentOS9-devel-arm64
 
       - name: GCC 11, C++20 (CentOS 9)
         env:

devel-tools/get_container

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+DOWNLOAD_DIR=$(dirname $0)
+
+label=$1
+if [ -n "${label}" ] ; then
+    if [ ! -f "${DOWNLOAD_DIR}/${label}.sif" ] ; then
+        echo "Downloading container image \"${label}\"..."
+        for try in {1..3}; do
+            apptainer pull "${DOWNLOAD_DIR}/${label}.sif" oras://ghcr.io/colvars/devel-containers:"${label}" && break
+            retcode=$?
+            if [ ${retcode} != 0 ] ; then
+                echo "(download failed, retrying...)"
+                sleep 15s
+            fi
+        done
+    fi
+fi
+
+exit ${retcode}

gromacs/src/applied_forces/colvars/colvarproxygromacs.cpp.patch

@@ -0,0 +1,14 @@
+diff --git a/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp b/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
+index 76b350c611..37e5b53647 100644
+--- a/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
++++ b/src/gromacs/applied_forces/colvars/colvarproxygromacs.cpp
+@@ -79,9 +79,6 @@ ColvarProxyGromacs::ColvarProxyGromacs(const std::string& colvarsConfigString,
+     // Retrieve masses and charges from input file
+     updated_masses_ = updated_charges_ = true;
+
+-    // User-scripted forces are not available in GROMACS
+-    have_scripts = false;
+-
+     angstrom_value_ = 0.1;
+
+     // From Gnu units

lammps/src/COLVARS/colvarproxy_lammps.h

@@ -85,7 +85,18 @@ class colvarproxy_lammps : public colvarproxy {
   cvm::real rand_gaussian() override;
 
   int init_atom(int atom_number) override;
+  int init_atom(cvm::residue_id const &residue, std::string const &atom_name,
+                std::string const &segment_id) override
+  {
+    return colvarproxy::init_atom(residue, atom_name, segment_id);
+  }
+
   int check_atom_id(int atom_number) override;
+  int check_atom_id(cvm::residue_id const &residue, std::string const &atom_name,
+                    std::string const &segment_id) override
+  {
+    return colvarproxy::check_atom_id(residue, atom_name, segment_id);
+  }
 
   inline std::vector<int> *modify_atom_types() { return &atoms_types; }
 };

lammps/src/COLVARS/fix_colvars.cpp

@@ -27,7 +27,6 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_colvars.h"
-#include "inthash.h"
 
 #include "atom.h"
 #include "citeme.h"
@@ -61,7 +60,6 @@ struct LAMMPS_NS::commdata {
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
-using namespace IntHash_NS;
 
 // initialize static class members
 int FixColvars::instances = 0;
@@ -122,7 +120,6 @@ FixColvars::FixColvars(LAMMPS *lmp, int narg, char **arg) :
   comm_buf = nullptr;
   taglist = nullptr;
   force_buf = nullptr;
-  idmap = nullptr;
 
   script_args[0] = reinterpret_cast<unsigned char *>(utils::strdup("fix_modify"));
 
@@ -227,11 +224,6 @@ FixColvars::~FixColvars()
 
   if (proxy) delete proxy;
 
-  if (idmap) {
-    inthash_destroy(idmap);
-    delete idmap;
-  }
-
   if (root2root != MPI_COMM_NULL)
     MPI_Comm_free(&root2root);
 
@@ -349,16 +341,11 @@ void FixColvars::init_taglist()
 
     std::vector<int> const &tl = *(proxy->get_atom_ids());
 
-    if (idmap) {
-      delete idmap;
-      idmap = nullptr;
-    }
-
-    idmap = new inthash_t;
-    inthash_init(idmap, num_coords);
+    idmap.clear();
+    idmap.reserve(num_coords);
     for (int i = 0; i < num_coords; ++i) {
       taglist[i] = tl[i];
-      inthash_insert(idmap, tl[i], i);
+      idmap[tl[i]] = i;
     }
   }
 
@@ -497,7 +484,6 @@ void FixColvars::setup(int vflag)
 
     std::vector<int>           &tp = *(proxy->modify_atom_types());
     std::vector<cvm::atom_pos> &cd = *(proxy->modify_atom_positions());
-    std::vector<cvm::rvector>  &of = *(proxy->modify_atom_total_forces());
     std::vector<cvm::real>     &m  = *(proxy->modify_atom_masses());
     std::vector<cvm::real>     &q  = *(proxy->modify_atom_charges());
 
@@ -508,8 +494,6 @@ void FixColvars::setup(int vflag)
       const tagint k = atom->map(taglist[i]);
       if ((k >= 0) && (k < nlocal)) {
 
-        of[i].x = of[i].y = of[i].z = 0.0;
-
         if (unwrap_flag) {
           const int ix = (image[k] & IMGMASK) - IMGMAX;
           const int iy = (image[k] >> IMGBITS & IMGMASK) - IMGMAX;
@@ -545,10 +529,9 @@ void FixColvars::setup(int vflag)
       ndata /= size_one;
 
       for (int k=0; k<ndata; ++k) {
-
-        const int j = inthash_lookup(idmap, comm_buf[k].tag);
-
-        if (j != HASH_FAIL) {
+        auto search = idmap.find(comm_buf[k].tag);
+        if (search != idmap.end()) {
+          const int j = search->second;
 
           tp[j] = comm_buf[k].type;
 
@@ -558,11 +541,14 @@ void FixColvars::setup(int vflag)
 
           m[j] = comm_buf[k].m;
           q[j] = comm_buf[k].q;
-
-          of[j].x = of[j].y = of[j].z = 0.0;
         }
       }
     }
+
+    if (proxy->total_forces_enabled()) {
+      proxy->set_total_forces_invalid();
+    }
+
   } else { // me != 0
 
     // copy coordinate data into communication buffer
@@ -701,8 +687,10 @@ void FixColvars::post_force(int /*vflag*/)
       ndata /= size_one;
 
       for (int k=0; k<ndata; ++k) {
-        const int j = inthash_lookup(idmap, comm_buf[k].tag);
-        if (j != HASH_FAIL) {
+        auto search = idmap.find(comm_buf[k].tag);
+        if (search != idmap.end()) {
+          const int j = search->second;
+
           cd[j].x = comm_buf[k].x;
           cd[j].y = comm_buf[k].y;
           cd[j].z = comm_buf[k].z;
@@ -826,8 +814,10 @@ void FixColvars::end_of_step()
         const tagint k = atom->map(taglist[i]);
         if ((k >= 0) && (k < nlocal)) {
 
-          const int j = inthash_lookup(idmap, tag[k]);
-          if (j != HASH_FAIL) {
+          auto search = idmap.find(tag[k]);
+          if (search != idmap.end()) {
+            const int j = search->second;
+
             of[j].x = f[k][0];
             of[j].y = f[k][1];
             of[j].z = f[k][2];
@@ -845,15 +835,21 @@ void FixColvars::end_of_step()
         ndata /= size_one;
 
         for (int k=0; k<ndata; ++k) {
-          const int j = inthash_lookup(idmap, comm_buf[k].tag);
-          if (j != HASH_FAIL) {
+          auto search = idmap.find(comm_buf[k].tag);
+          if (search != idmap.end()) {
+            const int j = search->second;
+
             of[j].x = comm_buf[k].x;
             of[j].y = comm_buf[k].y;
             of[j].z = comm_buf[k].z;
           }
         }
       }
 
+      if (proxy->total_forces_enabled()) {
+        proxy->set_total_forces_valid();
+      }
+
     } else { // me != 0
       /* copy total force data into communication buffer */
       nme = 0;
@@ -871,6 +867,7 @@ void FixColvars::end_of_step()
       MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, MPI_STATUS_IGNORE);
       MPI_Rsend(comm_buf, nme*size_one, MPI_BYTE, 0, 0, world);
     }
+
   }
 }
 

lammps/src/COLVARS/fix_colvars.h

@@ -35,11 +35,9 @@ FixStyle(colvars,FixColvars);
 #define LMP_FIX_COLVARS_H
 
 #include "fix.h"
+#include <unordered_map>
 
 // Forward declarations
-namespace IntHash_NS {
-struct inthash_t;
-}
 class colvarproxy_lammps;
 
 namespace LAMMPS_NS {
@@ -87,7 +85,7 @@ class FixColvars : public Fix {
   /// Arguments passed from fix_modify to the Colvars script interface
   unsigned char *script_args[100];
 
-  IntHash_NS::inthash_t *idmap;    // hash for mapping atom indices to consistent order.
+  std::unordered_map<int, int> idmap; // for mapping atom indices to consistent order.
 
   int nlevels_respa;       // flag to determine respa levels.
   int store_forces;        // flag to determine whether to store total forces

namd/src/GlobalMasterColvars.h

@@ -39,6 +39,11 @@ class GlobalMasterColvars : public GlobalMaster {
     return modifyAppliedForces();
   }
 
+  inline ResizeArray<AtomIDList> const &getRequestedGroups() const
+  {
+    return reqGroups;
+  }
+
   inline ResizeArray<AtomIDList> &modifyRequestedGroupsPublic()
   {
     return modifyRequestedGroups();
@@ -49,6 +54,11 @@ class GlobalMasterColvars : public GlobalMaster {
     return modifyGroupForces();
   }
 
+  inline IntList const &getRequestedGridObjects() const
+  {
+    return reqGridObjs;
+  }
+
   inline IntList &modifyRequestedGridObjectsPublic()
   {
     return modifyRequestedGridObjects();