use new bitmap accessor function and simplify code

src/atom.cpp

@@ -2284,7 +2284,7 @@ void Atom::first_reorder()
   // nfirst = index of first atom not in firstgroup
   // when find firstgroup atom out of place, swap it with atom nfirst
 
-  int bitmask = group->bitmask[firstgroup];
+  const int bitmask = group->get_bitmask_by_id(FLERR, firstgroupname, "Atom::first_reorder");
   nfirst = 0;
   while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
 

src/change_box.cpp

@@ -52,9 +52,7 @@ void ChangeBox::command(int narg, char **arg)
 
   // group
 
-  int igroup = group->find(arg[0]);
+  int groupbit = group->get_bitmask_by_id(FLERR, arg[0], "change_box");
-  if (igroup == -1) error->all(FLERR,"Could not find change_box group ID {}", arg[0]);
-  int groupbit = group->bitmask[igroup];
 
   // parse operation arguments
   // allocate ops to max possible length

src/compute.cpp

@@ -48,11 +48,11 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
 
   id = utils::strdup(arg[0]);
   if (!utils::is_id(id))
-    error->all(FLERR,"Compute ID must be alphanumeric or underscore characters");
+    error->all(FLERR,"Compute ID {} must only have alphanumeric or underscore characters", id);
 
+  groupbit = group->get_bitmask_by_id(FLERR, arg[1], fmt::format("compute {}", arg[2]));
   igroup = group->find(arg[1]);
-  if (igroup == -1) error->all(FLERR,"Could not find compute group ID");
+  if (igroup == -1) error->all(FLERR,"Could not find compute group ID {}", arg[1]);
-  groupbit = group->bitmask[igroup];
 
   style = utils::strdup(arg[2]);
 

src/compute_coord_atom.cpp

@@ -39,8 +39,7 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
 {
   if (narg < 5) error->all(FLERR, "Illegal compute coord/atom command");
 
-  jgroup = group->find("all");
+  jgroupbit = group->get_bitmask_by_id(FLERR, "all", "compute coord/atom");
-  jgroupbit = group->bitmask[jgroup];
   cstyle = NONE;
 
   if (strcmp(arg[3], "cutoff") == 0) {
@@ -50,11 +49,10 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
 
     int iarg = 5;
     if ((narg > 6) && (strcmp(arg[5], "group") == 0)) {
+      delete[] group2;
       group2 = utils::strdup(arg[6]);
       iarg += 2;
-      jgroup = group->find(group2);
+      jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute coord/atom");
-      if (jgroup == -1) error->all(FLERR, "Compute coord/atom group2 ID does not exist");
-      jgroupbit = group->bitmask[jgroup];
     }
 
     ncol = narg - iarg + 1;

src/compute_coord_atom.h

@@ -46,7 +46,7 @@ class ComputeCoordAtom : public Compute {
   double **carray;
 
   char *group2;
-  int jgroup, jgroupbit;
+  int jgroupbit;
 
   class ComputeOrientOrderAtom *c_orientorder;
   char *id_orientorder;

src/compute_group_group.cpp

@@ -54,9 +54,7 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
   extvector = 1;
 
   group2 = utils::strdup(arg[3]);
-  jgroup = group->find(group2);
+  jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute group/group");
-  if (jgroup == -1) error->all(FLERR, "Compute group/group group ID does not exist");
-  jgroupbit = group->bitmask[jgroup];
 
   pairflag = 1;
   kspaceflag = 0;
@@ -147,9 +145,7 @@ void ComputeGroupGroup::init()
 
   // recheck that group 2 has not been deleted
 
-  jgroup = group->find(group2);
+  jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute group/group");
-  if (jgroup == -1) error->all(FLERR, "Compute group/group group ID does not exist");
-  jgroupbit = group->bitmask[jgroup];
 
   // need an occasional half neighbor list
 

src/compute_group_group.h

@@ -35,7 +35,7 @@ class ComputeGroupGroup : public Compute {
 
  private:
   char *group2;
-  int jgroup, jgroupbit, othergroupbit;
+  int jgroupbit;
   double **cutsq;
   double e_self, e_correction;
   int pairflag, kspaceflag, boundaryflag, molflag;

src/create_bonds.cpp

@@ -59,12 +59,8 @@ void CreateBonds::command(int narg, char **arg)
   if (strcmp(arg[0], "many") == 0) {
     style = MANY;
     if (narg != 6) error->all(FLERR, "No optional keywords allowed with create_bonds many");
-    igroup = group->find(arg[1]);
+    group1bit = group->get_bitmask_by_id(FLERR, arg[1], "create_bonds");
-    if (igroup == -1) error->all(FLERR, "Cannot find create_bonds first group ID {}", arg[1]);
+    group2bit = group->get_bitmask_by_id(FLERR, arg[2], "create_bonds");
-    group1bit = group->bitmask[igroup];
-    igroup = group->find(arg[2]);
-    if (igroup == -1) error->all(FLERR, "Cannot find create_bonds second group ID {}", arg[2]);
-    group2bit = group->bitmask[igroup];
     btype = utils::inumeric(FLERR, arg[3], false, lmp);
     rmin = utils::numeric(FLERR, arg[4], false, lmp);
     rmax = utils::numeric(FLERR, arg[5], false, lmp);

src/create_bonds.h

@@ -30,7 +30,7 @@ class CreateBonds : public Command {
   void command(int, char **) override;
 
  private:
-  int igroup, group1bit, group2bit;
+  int group1bit, group2bit;
   int btype, atype, dtype;
   tagint batom1, batom2, aatom1, aatom2, aatom3, datom1, datom2, datom3, datom4;
   double rmin, rmax;

src/delete_atoms.cpp

@@ -86,8 +86,8 @@ void DeleteAtoms::command(int narg, char **arg)
     error->all(FLERR, "Unknown delete_atoms sub-command: {}", arg[0]);
 
   if (allflag) {
-    int igroup = group->find("all");
+    int igroupbit = group->get_bitmask_by_id(FLERR, "all", "delete_atoms");
-    if ((igroup >= 0) && modify->check_rigid_group_overlap(group->bitmask[igroup]))
+    if (modify->check_rigid_group_overlap(igroupbit))
       error->warning(FLERR, "Attempting to delete atoms in rigid bodies");
   } else {
     if (modify->check_rigid_list_overlap(dlist))
@@ -215,8 +215,7 @@ void DeleteAtoms::delete_group(int narg, char **arg)
 {
   if (narg < 2) utils::missing_cmd_args(FLERR, "delete_atoms group", error);
 
-  int igroup = group->find(arg[1]);
+  int groupbit = group->get_bitmask_by_id(FLERR, arg[1], "delete_atoms");
-  if (igroup == -1) error->all(FLERR, "Could not find delete_atoms group ID {}", arg[1]);
   options(narg - 2, &arg[2]);
 
   // check for special case of group = all
@@ -233,8 +232,6 @@ void DeleteAtoms::delete_group(int narg, char **arg)
   for (int i = 0; i < nlocal; i++) dlist[i] = 0;
 
   int *mask = atom->mask;
-  int groupbit = group->bitmask[igroup];
-
   for (int i = 0; i < nlocal; i++)
     if (mask[i] & groupbit) dlist[i] = 1;
 }
@@ -280,18 +277,11 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
 
   const double cut = utils::numeric(FLERR, arg[1], false, lmp);
   const double cutsq = cut * cut;
+  const int group1bit = group->get_bitmask_by_id(FLERR, arg[2], "delete_atoms");
+  const int group2bit = group->get_bitmask_by_id(FLERR, arg[3], "delete_atoms");
 
-  int igroup1 = group->find(arg[2]);
-  if (igroup1 < 0)
-    error->all(FLERR, "Could not find delete_atoms overlap first group ID {}", arg[2]);
-  int igroup2 = group->find(arg[3]);
-  if (igroup2 < 0)
-    error->all(FLERR, "Could not find delete_atoms overlap second group ID {}", arg[3]);
   options(narg - 4, &arg[4]);
 
-  const int group1bit = group->bitmask[igroup1];
-  const int group2bit = group->bitmask[igroup2];
-
   if (comm->me == 0) utils::logmesg(lmp, "System init for delete_atoms ...\n");
 
   // request a full neighbor list for use by this command
@@ -453,9 +443,7 @@ void DeleteAtoms::delete_random(int narg, char **arg)
     error->all(FLERR, "Unknown delete_atoms random style: {}", arg[1]);
   }
 
-  int igroup = group->find(arg[4]);
+  int groupbit = group->get_bitmask_by_id(FLERR, arg[4], "delete_atoms");
-  if (igroup == -1) error->all(FLERR, "Could not find delete_atoms random group ID {}", arg[4]);
-
   auto region = domain->get_region_by_id(arg[5]);
   if (!region && (strcmp(arg[5], "NULL") != 0))
     error->all(FLERR, "Could not find delete_atoms random region ID {}", arg[5]);
@@ -476,7 +464,6 @@ void DeleteAtoms::delete_random(int narg, char **arg)
   double **x = atom->x;
   int *mask = atom->mask;
 
-  int groupbit = group->bitmask[igroup];
   if (region) region->prematch();
 
   // delete approximate fraction of atoms in both group and region

src/delete_bonds.cpp

@@ -56,11 +56,9 @@ void DeleteBonds::command(int narg, char **arg)
 
   if (comm->me == 0) utils::logmesg(lmp,"Deleting bonds ...\n");
 
-  // identify group
+  // get group bitmask
 
-  int igroup = group->find(arg[0]);
+  int groupbit = group->get_bitmask_by_id(FLERR, arg[0], "delete_bonds");
-  if (igroup == -1) error->all(FLERR,"Cannot find delete_bonds group ID");
-  int groupbit = group->bitmask[igroup];
 
   // set style and which = type value