modernize and simplify

src/KOKKOS/comm_kokkos.cpp

@@ -125,19 +125,19 @@ void CommKokkos::init()
   if (force->pair && (force->pair->execution_space == Host))
     check_reverse += force->pair->comm_reverse;
 
-  for (int i = 0; i < modify->nfix; i++) {
-    check_forward += modify->fix[i]->comm_forward;
-    check_reverse += modify->fix[i]->comm_reverse;
+  for (const auto &fix : modify->get_fix_list()) {
+    check_forward += fix->comm_forward;
+    check_reverse += fix->comm_reverse;
   }
 
-  for (int i = 0; i < modify->ncompute; i++) {
-    check_forward += modify->compute[i]->comm_forward;
-    check_reverse += modify->compute[i]->comm_reverse;
+  for (const auto &compute : modify->get_compute_list()) {
+    check_forward += compute->comm_forward;
+    check_reverse += compute->comm_reverse;
   }
 
-  for (int i = 0; i < output->ndump; i++) {
-    check_forward += output->dump[i]->comm_forward;
-    check_reverse += output->dump[i]->comm_reverse;
+  for (const auto &dump : output->get_dump_list()) {
+    check_forward += dump->comm_forward;
+    check_reverse += dump->comm_reverse;
   }
 
   if (force->newton == 0) check_reverse = 0;

src/comm.cpp

@@ -226,14 +226,14 @@ void Comm::init()
     maxreverse = MAX(maxreverse, fix->comm_reverse);
   }
 
-  for (int i = 0; i < modify->ncompute; i++) {
-    maxforward = MAX(maxforward,modify->compute[i]->comm_forward);
-    maxreverse = MAX(maxreverse,modify->compute[i]->comm_reverse);
+  for (const auto &compute : modify->get_compute_list()) {
+    maxforward = MAX(maxforward,compute->comm_forward);
+    maxreverse = MAX(maxreverse,compute->comm_reverse);
   }
 
-  for (int i = 0; i < output->ndump; i++) {
-    maxforward = MAX(maxforward,output->dump[i]->comm_forward);
-    maxreverse = MAX(maxreverse,output->dump[i]->comm_reverse);
+  for (const auto &dump: output->get_dump_list()) {
+    maxforward = MAX(maxforward,dump->comm_forward);
+    maxreverse = MAX(maxreverse,dump->comm_reverse);
   }
 
   if (force->newton == 0) maxreverse = 0;
@@ -247,8 +247,7 @@ void Comm::init()
   maxexchange_atom = atom->avec->maxexchange;
 
   maxexchange_fix_dynamic = 0;
-  for (const auto &fix : fix_list)
-    if (fix->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
+  for (const auto &fix : fix_list) if (fix->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
 
   if ((mode == Comm::MULTI) && (neighbor->style != Neighbor::MULTI))
     error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists");
@@ -270,8 +269,7 @@ void Comm::init()
 void Comm::init_exchange()
 {
   maxexchange_fix = 0;
-  for (const auto &fix : modify->get_fix_list())
-    maxexchange_fix += fix->maxexchange;
+  for (const auto &fix : modify->get_fix_list()) maxexchange_fix += fix->maxexchange;
 
   maxexchange = maxexchange_atom + maxexchange_fix;
   bufextra = maxexchange + BUFEXTRA;

src/group.cpp

@@ -101,22 +101,21 @@ void Group::assign(int narg, char **arg)
   // clear mask of each atom assigned to this group
 
   if (strcmp(arg[1],"delete") == 0) {
-    if (narg != 2) error->all(FLERR,"Illegal group command");
+    if (narg != 2) error->all(FLERR,"Illegal group command: too many arguments");
     int igroup = find(arg[0]);
-    if (igroup == -1) error->all(FLERR,"Could not find group delete group ID");
+    if (igroup == -1) error->all(FLERR,"Could not find group delete group ID {}",arg[0]);
     if (igroup == 0) error->all(FLERR,"Cannot delete group all");
-    for (const auto &fix : modify->get_fix_list())
-      if (fix->igroup == igroup)
-        error->all(FLERR,"Cannot delete group currently used by a fix");
-    for (i = 0; i < modify->ncompute; i++)
-      if (modify->compute[i]->igroup == igroup)
-        error->all(FLERR,"Cannot delete group currently used by a compute");
-    for (i = 0; i < output->ndump; i++)
-      if (output->dump[i]->igroup == igroup)
-        error->all(FLERR,"Cannot delete group currently used by a dump");
+    for (const auto &i : modify->get_fix_list())
+      if (i->igroup == igroup)
+        error->all(FLERR,"Cannot delete group {} currently used by fix ID {}",arg[0],i->id);
+    for (const auto &i : modify->get_compute_list())
+      if (i->igroup == igroup)
+        error->all(FLERR,"Cannot delete group {} currently used by compute ID {}",arg[0],i->id);
+    for (const auto &i : output->get_dump_list())
+      if (i->igroup == igroup)
+        error->all(FLERR,"Cannot delete group {} currently used by dump ID {}",arg[0],i->id);
     if (atom->firstgroupname && strcmp(arg[0],atom->firstgroupname) == 0)
-      error->all(FLERR,
-                 "Cannot delete group currently used by atom_modify first");
+      error->all(FLERR,"Cannot delete group {} currently used by atom_modify first",arg[0]);
 
     int *mask = atom->mask;
     int nlocal = atom->nlocal;

src/library.cpp

@@ -4761,43 +4761,19 @@ int lammps_has_id(void *handle, const char *category, const char *name) {
   auto lmp = (LAMMPS *) handle;
 
   if (strcmp(category,"compute") == 0) {
-    int ncompute = lmp->modify->ncompute;
-    Compute **compute = lmp->modify->compute;
-    for (int i=0; i < ncompute; ++i) {
-      if (strcmp(name,compute[i]->id) == 0) return 1;
-    }
+    if (lmp->modify->get_compute_by_id(name)) return 1;
   } else if (strcmp(category,"dump") == 0) {
-    int ndump = lmp->output->ndump;
-    Dump **dump = lmp->output->dump;
-    for (int i=0; i < ndump; ++i) {
-      if (strcmp(name,dump[i]->id) == 0) return 1;
-    }
+    if (lmp->output->get_dump_by_id(name)) return 1;
   } else if (strcmp(category,"fix") == 0) {
-    for (auto &ifix : lmp->modify->get_fix_list()) {
-      if (strcmp(name,ifix->id) == 0) return 1;
-    }
+    if (lmp->modify->get_fix_by_id(name)) return 1;
   } else if (strcmp(category,"group") == 0) {
-    int ngroup = lmp->group->ngroup;
-    char **groups = lmp->group->names;
-    for (int i=0; i < ngroup; ++i) {
-      if (strcmp(groups[i],name) == 0) return 1;
-    }
+    if (lmp->group->find(name) >= 0) return 1;
   } else if (strcmp(category,"molecule") == 0) {
-    int nmolecule = lmp->atom->nmolecule;
-    Molecule **molecule = lmp->atom->molecules;
-    for (int i=0; i < nmolecule; ++i) {
-      if (strcmp(name,molecule[i]->id) == 0) return 1;
-    }
+    if (lmp->atom->find_molecule(name) >= 0) return 1;
   } else if (strcmp(category,"region") == 0) {
-    for (auto &reg : lmp->domain->get_region_list()) {
-      if (strcmp(name,reg->id) == 0) return 1;
-    }
+    if (lmp->domain->get_region_by_id(name)) return 1;
   } else if (strcmp(category,"variable") == 0) {
-    int nvariable = lmp->input->variable->nvar;
-    char **varnames = lmp->input->variable->names;
-    for (int i=0; i < nvariable; ++i) {
-      if (strcmp(name,varnames[i]) == 0) return 1;
-    }
+    if (lmp->input->variable->find(name) >= 0) return 1;
   }
   return 0;
 }
@@ -4823,11 +4799,11 @@ categories.
 int lammps_id_count(void *handle, const char *category) {
   auto lmp = (LAMMPS *) handle;
   if (strcmp(category,"compute") == 0) {
-    return lmp->modify->ncompute;
+    return lmp->modify->get_compute_list().size();
   } else if (strcmp(category,"dump") == 0) {
-    return lmp->output->ndump;
+    return lmp->output->get_dump_list().size();
   } else if (strcmp(category,"fix") == 0) {
-    return lmp->modify->nfix;
+    return lmp->modify->get_fix_list().size();
   } else if (strcmp(category,"group") == 0) {
     return lmp->group->ngroup;
   } else if (strcmp(category,"molecule") == 0) {