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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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24
doc/src/delete_atoms.rst
View File

@ -20,8 +20,10 @@ Syntax
cutoff = delete one atom from pairs of atoms within the cutoff (distance units)
group1-ID = one atom in pair must be in this group
group2-ID = other atom in pair must be in this group
*porosity* args = region-ID fraction seed
*porosity* args = group-ID region-ID fraction seed
group-ID = group within which to perform deletions
region-ID = region within which to perform deletions
or NULL to only impose the group criterion
fraction = delete this fraction of atoms
seed = random number seed (positive integer)
@ -43,7 +45,8 @@ Examples
delete_atoms region sphere compress no
delete_atoms overlap 0.3 all all
delete_atoms overlap 0.5 solvent colloid
delete_atoms porosity cube 0.1 482793 bond yes
delete_atoms porosity all cube 0.1 482793 bond yes
delete_atoms porosity polymer cube 0.1 482793 bond yes
Description
"""""""""""
@ -76,12 +79,17 @@ have occurred that no atom pairs within the cutoff will remain
minimum number of atoms will be deleted, or that the same atoms will
be deleted when running on different numbers of processors.
For style *porosity* a specified *fraction* of atoms are deleted
within the specified region. For example, if fraction is 0.1, then
10% of the atoms will be deleted. The atoms to delete are chosen
randomly. There is no guarantee that the exact fraction of atoms will
be deleted, or that the same atoms will be deleted when running on
different numbers of processors.
For style *porosity* a specified *fraction* of atoms are deleted which
are both in the specified group and within the specified region. The
region-ID can be specified as NULL to only impose the group
criterion. Likewise, specifying the group-ID as *all* will only impose
the region criterion.
For example, if fraction is 0.1, then 10% of the eligible atoms will
be deleted. The atoms to delete are chosen randomly. There is no
guarantee that the exact fraction of atoms will be deleted, or that
the same atoms will be deleted when running on different numbers of
processors.
If the *compress* keyword is set to *yes*, then after atoms are
deleted, then atom IDs are re-assigned so that they run from 1 to the

31
src/delete_atoms.cpp
View File

@ -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]);
int igroup = group->find(arg[1]);
if (igroup == -1) error->all(FLERR,"Could not find delete_atoms group ID");
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[2],false,lmp);
int seed = utils::inumeric(FLERR,arg[3],false,lmp);
options(narg-4,&arg[4]);
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;
}