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add delete_atoms "variable" option

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This commit is contained in:
Axel Kohlmeyer
2022-04-29 21:53:38 -04:00
parent 87b0939fe7
commit 31d6af6114
3 changed files with 47 additions and 2 deletions
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37
src/delete_atoms.cpp
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@ -24,6 +24,8 @@
#include "domain.h"
#include "error.h"
#include "force.h"
#include "input.h"
#include "variable.h"
#include "group.h"
#include "memory.h"
#include "modify.h"
@ -69,7 +71,8 @@ void DeleteAtoms::command(int narg, char **arg)
else if (strcmp(arg[0],"region") == 0) delete_region(narg,arg);
else if (strcmp(arg[0],"overlap") == 0) delete_overlap(narg,arg);
else if (strcmp(arg[0],"porosity") == 0) delete_porosity(narg,arg);
else error->all(FLERR,"Illegal delete_atoms command");
else if (strcmp(arg[0],"variable") == 0) delete_variable(narg,arg);
else error->all(FLERR,"Unknown delete_atoms sub-command: {}", arg[0]);
if (allflag) {
int igroup = group->find("all");
@ -453,6 +456,38 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
delete random;
}
/* ----------------------------------------------------------------------
delete all as flagged by non-zero atom style variable
------------------------------------------------------------------------- */
void DeleteAtoms::delete_variable(int narg, char **arg)
{
if (narg < 2) utils::missing_cmd_args(FLERR,"delete_atoms variable", error);
int ivar = input->variable->find(arg[1]);
if (ivar < 0) error->all(FLERR, "Variable name {} for delete_atoms does not exist", arg[1]);
if (!input->variable->atomstyle(ivar))
error->all(FLERR,"Variable {} for delete_atoms is invalid style", arg[1]);
// consume remaining options
options(narg-2,&arg[2]);
// aflag = evaluation of per-atom variable
const int nlocal = atom->nlocal;
double *aflag;
memory->create(dlist,nlocal,"delete_atoms:dlist");
memory->create(aflag,nlocal,"group:aflag");
input->variable->compute_atom(ivar,0,aflag,1,0);
// delete if per-atom variable evaluated to non-zero
for (int i = 0; i < nlocal; i++) dlist[i] = (aflag[i] == 0.0) ? 0 : 1;
memory->destroy(aflag);
}
/* ----------------------------------------------------------------------
delete all topology interactions that include deleted atoms
------------------------------------------------------------------------- */