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when identifying molecules/clusters fall back to unfiltered coordinates for ghost atoms

This commit is contained in:
Axel Kohlmeyer 2017-06-09 14:35:12 -04:00
parent 64e8000720
commit d3a863e7af
1 changed files with 69 additions and 55 deletions
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20
src/USER-REAXC/fix_reaxc_species.cpp
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@ -520,6 +520,8 @@ void FixReaxCSpecies::FindMolecule ()
int *ilist;
double bo_tmp,bo_cut;
double **spec_atom = f_SPECBOND->array_atom;
const double * const * const x = atom->x;
const int nlocal = atom->nlocal;
inum = reaxc->list->inum;
ilist = reaxc->list->ilist;
@ -553,11 +555,14 @@ void FixReaxCSpecies::FindMolecule ()
for (jj = 0; jj < MAXSPECBOND; jj++) {
j = reaxc->tmpid[i][jj];
if (j < i) continue;
if ((j == 0) || (j < i)) continue;
if (!(mask[j] & groupbit)) continue;
if (clusterID[i] == clusterID[j] && PBCconnected[i] == PBCconnected[j]
&& x0[i].x == x0[j].x && x0[i].y == x0[j].y && x0[i].z == x0[j].z) continue;
if (clusterID[i] == clusterID[j]
&& PBCconnected[i] == PBCconnected[j]
&& x0[i].x == x0[j].x
&& x0[i].y == x0[j].y
&& x0[i].z == x0[j].z) continue;
jtype = atom->type[j];
bo_cut = BOCut[itype][jtype];
@ -567,10 +572,19 @@ void FixReaxCSpecies::FindMolecule ()
clusterID[i] = clusterID[j] = MIN(clusterID[i], clusterID[j]);
PBCconnected[i] = PBCconnected[j] = MAX(PBCconnected[i], PBCconnected[j]);
x0[i] = x0[j] = chAnchor(x0[i], x0[j]);
// spec_atom[][] contains filtered coordinates only for local atoms,
// so we have to use unfiltered ones for ghost atoms.
if (j < nlocal) {
if ((fabs(spec_atom[i][1] - spec_atom[j][1]) > reaxc->control->bond_cut)
|| (fabs(spec_atom[i][2] - spec_atom[j][2]) > reaxc->control->bond_cut)
|| (fabs(spec_atom[i][3] - spec_atom[j][3]) > reaxc->control->bond_cut))
PBCconnected[i] = PBCconnected[j] = 1;
} else {
if ((fabs(spec_atom[i][1] - x[j][1]) > reaxc->control->bond_cut)
|| (fabs(spec_atom[i][2] - x[j][2]) > reaxc->control->bond_cut)
|| (fabs(spec_atom[i][3] - x[j][3]) > reaxc->control->bond_cut))
PBCconnected[i] = PBCconnected[j] = 1;
}
done = 0;
}
}