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new group arg for delete_atoms porosity

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This commit is contained in:
Steve Plimpton
2021-10-05 13:07:34 -06:00
parent ab51c1bd3d
commit fc5920812f
2 changed files with 41 additions and 18 deletions
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35
src/delete_atoms.cpp
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@ -422,15 +422,23 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
void DeleteAtoms::delete_porosity(int narg, char **arg)
{
if (narg < 4) error->all(FLERR,"Illegal delete_atoms command");
if (narg < 5) error->all(FLERR,"Illegal delete_atoms command");
int iregion = domain->find_region(arg[1]);
if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
domain->regions[iregion]->prematch();
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find delete_atoms group ID");
double porosity_fraction = utils::numeric(FLERR,arg[2],false,lmp);
int seed = utils::inumeric(FLERR,arg[3],false,lmp);
options(narg-4,&arg[4]);
int iregion,regionflag;
if (strcmp(arg[2],"NULL") == 0) regionflag = 0;
else {
regionflag = 1;
int iregion = domain->find_region(arg[2]);
if (iregion == -1) error->all(FLERR,"Could not find delete_atoms region ID");
domain->regions[iregion]->prematch();
}
double porosity_fraction = utils::numeric(FLERR,arg[3],false,lmp);
int seed = utils::inumeric(FLERR,arg[4],false,lmp);
options(narg-5,&arg[5]);
RanMars *random = new RanMars(lmp,seed + comm->me);
@ -440,11 +448,18 @@ void DeleteAtoms::delete_porosity(int narg, char **arg)
memory->create(dlist,nlocal,"delete_atoms:dlist");
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
double **x = atom->x;
// delete fraction of atoms in both group and region
for (int i = 0; i < nlocal; i++)
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
double **x = atom->x;
int *mask = atom->mask;
int groupbit = group->bitmask[igroup];
for (int i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
if (regionflag && domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (random->uniform() <= porosity_fraction) dlist[i] = 1;
}
delete random;
}