when identifying molecules/clusters fall back to unfiltered coordinates for ghost atoms (d3a863e7) · Commits · 郑智淋 / lammps

src/USER-REAXC/fix_reaxc_species.cpp

+69 −55

Original line number	Diff line number	Diff line
		@@ -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;
		}
		}

Admin message