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add rigid body overlap warnings to change_box and delete_atoms

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This commit is contained in:
Axel Kohlmeyer
2017-06-13 16:26:49 -04:00
parent 4c69bbcf5c
commit 32b967ed9c
3 changed files with 19 additions and 7 deletions
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21
src/delete_atoms.cpp
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@ -69,6 +69,15 @@ void DeleteAtoms::command(int narg, char **arg)
else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
else error->all(FLERR,"Illegal delete_atoms command");
if (allflag) {
int igroup = group->find("all");
if ((igroup >= 0) && modify->check_rigid_group_overlap(group->bitmask[igroup]))
error->warning(FLERR,"Attempting to delete atoms in rigid bodies");
} else {
if (modify->check_rigid_list_overlap(dlist))
error->warning(FLERR,"Attempting to delete atoms in rigid bodies");
}
// if allflag = 1, just reset atom->nlocal
// else delete atoms one by one
@ -89,16 +98,16 @@ void DeleteAtoms::command(int narg, char **arg)
int i = 0;
while (i < nlocal) {
if (dlist[i]) {
avec->copy(nlocal-1,i,1);
dlist[i] = dlist[nlocal-1];
nlocal--;
avec->copy(nlocal-1,i,1);
dlist[i] = dlist[nlocal-1];
nlocal--;
} else i++;
}
atom->nlocal = nlocal;
memory->destroy(dlist);
}
// if non-molecular system and compress flag set,
// reset atom tags to be contiguous
// set all atom IDs to 0, call tag_extend()
@ -201,7 +210,7 @@ void DeleteAtoms::delete_group(int narg, char **arg)
allflag = 1;
return;
}
// allocate and initialize deletion list
int nlocal = atom->nlocal;