Merge branch 'maintenance' of github.com:lammps/lammps into maintenance

fortran/lammps.f90

@@ -3224,6 +3224,7 @@ CONTAINS
     TYPE(c_ptr) :: c_id, c_caller
     TYPE(c_funptr) :: c_callback
     INTEGER :: i, this_fix
+    TYPE(fix_external_data), DIMENSION(:), ALLOCATABLE :: tmp_ext_data
 
     c_id = f2c_string(id)
     IF (ALLOCATED(ext_data)) THEN
@@ -3235,9 +3236,13 @@ CONTAINS
         END IF
       END DO
       IF (this_fix > SIZE(ext_data)) THEN
-        ! reallocates ext_data; this requires us to re-bind "caller" on the C
+        ! reallocate ext_data in a pre-fortran 2008 compatible way.
+        ALLOCATE(tmp_ext_data(this_fix))
+        tmp_ext_data(1:this_fix-1) = ext_data(1:this_fix-1)
+        tmp_ext_data(this_fix) = fix_external_data()
+        CALL move_alloc(tmp_ext_data, ext_data)
+        ! this requires us to re-bind "caller" on the C
         ! side to the new data structure, which likely moved to a new address
-        ext_data = [ext_data, fix_external_data()] ! extends ext_data by 1
         CALL rebind_external_callback_data()
       END IF
     ELSE

src/GRANULAR/fix_pour.cpp

@@ -701,6 +701,8 @@ void FixPour::pre_exchange()
       atom->nangles += (bigint) onemols[imol]->nangles * ninserted_mols;
       atom->ndihedrals += (bigint) onemols[imol]->ndihedrals * ninserted_mols;
       atom->nimpropers += (bigint) onemols[imol]->nimpropers * ninserted_mols;
+      // body particle molecule template must contain only one atom
+      atom->nbodies += (bigint) onemols[imol]->bodyflag * ninserted_mols;
     }
     if (maxtag_all >= MAXTAGINT) error->all(FLERR, "New atom IDs exceed maximum allowed ID");
   }

src/KOKKOS/pair_mliap_kokkos.cpp

@@ -83,14 +83,26 @@ void PairMLIAPKokkos<DeviceType>::compute(int eflag, int vflag)
     error->all(FLERR, "Incompatible model and descriptor element count");
 
   ev_init(eflag, vflag, 0);
-  if (eflag_atom && (int)k_eatom.h_view.extent(0) < maxeatom) {
-    memoryKK->destroy_kokkos(k_eatom,eatom);
-    memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
+  if (eflag_atom) {
+    if ((int)k_eatom.h_view.extent(0) < maxeatom) {
+      memoryKK->destroy_kokkos(k_eatom,eatom);
+      memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
+    } else {
+      Kokkos::deep_copy(k_eatom.template view<DeviceType>(),0);
+      k_eatom.modify<DeviceType>();
+      k_eatom.sync_host();
+    }
   }
 
-  if (vflag_atom && (int)k_vatom.h_view.extent(0) < maxeatom) {
-    memoryKK->destroy_kokkos(k_vatom,vatom);
-    memoryKK->create_kokkos(k_vatom,vatom,maxeatom,6,"pair:eatom");
+  if (vflag_atom) {
+    if ((int)k_vatom.h_view.extent(0) < maxeatom) {
+      memoryKK->destroy_kokkos(k_vatom,vatom);
+      memoryKK->create_kokkos(k_vatom,vatom,maxeatom,6,"pair:eatom");
+    } else {
+      Kokkos::deep_copy(k_vatom.template view<DeviceType>(),0);
+      k_vatom.modify<DeviceType>();
+      k_vatom.sync_host();
+    }
   }
 
   data->generate_neighdata(list, eflag, vflag);

src/fix_deposit.cpp

@@ -614,6 +614,8 @@ void FixDeposit::pre_exchange()
       atom->nangles += onemols[imol]->nangles;
       atom->ndihedrals += onemols[imol]->ndihedrals;
       atom->nimpropers += onemols[imol]->nimpropers;
+      // body particle molecule template must contain only one atom
+      atom->nbodies += (bigint) onemols[imol]->bodyflag;
     }
     maxtag_all += natom;
     if (maxtag_all >= MAXTAGINT)

src/molecule.cpp

@@ -1461,30 +1461,44 @@ void Molecule::nspecial_read(int flag, char *line)
 {
   if (flag == 0) maxspecial = 0;
 
+  for (int i = 0; i < natoms; ++i) count[i] = 0;
   for (int i = 0; i < natoms; i++) {
     readline(line);
 
-    int c1, c2, c3;
+    int c0, c1, c2, c3;
 
     try {
       ValueTokenizer values(utils::trim_comment(line));
       if (values.count() != 4)
         error->all(FLERR, "Invalid line in Special Bond Counts section of molecule file: {}", line);
-      values.next_int();
-      c1 = values.next_tagint();
-      c2 = values.next_tagint();
-      c3 = values.next_tagint();
+      c0 = values.next_int();
+      c1 = values.next_int();
+      c2 = values.next_int();
+      c3 = values.next_int();
     } catch (TokenizerException &e) {
       error->all(FLERR, "Invalid line in Special Bond Counts section of molecule file: {}\n{}",
                  e.what(), line);
     }
 
     if (flag) {
+      int iatom = c0 - 1;
+      if (iatom < 0 || iatom >= natoms)
+        error->all(FLERR, "Invalid atom index in Special Bond Counts section of molecule file");
+      count[iatom]++;
       nspecial[i][0] = c1;
       nspecial[i][1] = c1 + c2;
       nspecial[i][2] = c1 + c2 + c3;
-    } else
+    } else {
       maxspecial = MAX(maxspecial, c1 + c2 + c3);
+    }
+  }
+
+  // check
+  if (flag) {
+    for (int i = 0; i < natoms; i++) {
+      if (count[i] == 0)
+        error->all(FLERR, "Atom {} missing in Special Bond Counts section of molecule file", i + 1);
+    }
   }
 }
 
@@ -1494,6 +1508,7 @@ void Molecule::nspecial_read(int flag, char *line)
 
 void Molecule::special_read(char *line)
 {
+  for (int i = 0; i < natoms; ++i) count[i] = 0;
   try {
     for (int i = 0; i < natoms; i++) {
       readline(line);
@@ -1504,18 +1519,27 @@ void Molecule::special_read(char *line)
       if (nwords != nspecial[i][2] + 1)
         error->all(FLERR, "Molecule file special list does not match special count");
 
-      values.next_int();    // ignore
+      int iatom = values.next_int() - 1;
+      if (iatom < 0 || iatom >= natoms)
+        error->all(FLERR, "Invalid atom index {} in Special Bonds section of molecule file", iatom);
 
       for (int m = 1; m < nwords; m++) {
-        special[i][m - 1] = values.next_tagint();
-        if (special[i][m - 1] <= 0 || special[i][m - 1] > natoms || special[i][m - 1] == i + 1)
-          error->all(FLERR, "Invalid atom index in Special Bonds section of molecule file");
+        int ival = values.next_tagint();
+        if ((ival <= 0) || (ival > natoms) || (ival == iatom + 1))
+          error->all(FLERR, "Invalid atom index {} in Special Bonds section of molecule file",
+                     ival);
+        special[iatom][m - 1] = ival;
       }
+      count[iatom]++;
     }
   } catch (TokenizerException &e) {
     error->all(FLERR, "Invalid line in Special Bonds section of molecule file: {}\n{}", e.what(),
                line);
   }
+  for (int i = 0; i < natoms; i++) {
+    if (count[i] == 0)
+      error->all(FLERR, "Atom {} missing in Special Bonds section of molecule file", i + 1);
+  }
 }
 
 /* ----------------------------------------------------------------------

unittest/python/python-open.py

@@ -7,8 +7,8 @@ has_mpi4py=False
 
 try:
     from mpi4py import __version__ as mpi4py_version
-    # tested to work with mpi4py versions 2 and 3
-    has_mpi4py = mpi4py_version.split('.')[0] in ['2','3']
+    # tested to work with mpi4py versions 2, 3, and 4
+    has_mpi4py = mpi4py_version.split('.')[0] in ['2','3','4']
 except:
     pass