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use list of bonds per atom instead of bondlist, as that will work with shake as well

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This commit is contained in:
Axel Kohlmeyer
2017-08-20 09:18:04 -04:00
parent 6f66e6c454
commit c5ce3ffe60
1 changed files with 10 additions and 19 deletions
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29
src/compute_fragment_atom.cpp
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@ -90,9 +90,6 @@ void ComputeFragmentAtom::compute_peratom()
vector_atom = fragmentID;
}
int nbondlist = neighbor->nbondlist;
int **bondlist = neighbor->bondlist;
// if group is dynamic, insure ghost atom masks are current
if (group->dynamic[igroup]) {
@ -100,21 +97,17 @@ void ComputeFragmentAtom::compute_peratom()
comm->forward_comm_compute(this);
}
// every bond starts in its own fragment,
// with fragmentID = MIN(b1atomID,b2atomID)
// only bonds wholly contained in the group are considered
// each atom starts in its own fragment,
int nlocal = atom->nlocal;
tagint *tag = atom->tag;
int *mask = atom->mask;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
for (i = 0; i < nbondlist; i++) {
const int b1 = bondlist[i][0];
const int b2 = bondlist[i][1];
if ((mask[b1] & groupbit) && (mask[b2] & groupbit))
fragmentID[b1] = fragmentID[b2] = MIN(tag[b1],tag[b2]);
else fragmentID[b1] = fragmentID[b2] = 0;
}
for (i = 0; i < nlocal + atom->nghost; i++)
if (mask[i] & groupbit) fragmentID[i] = tag[i];
else fragmentID[i] = 0;
// loop until no more changes on any proc:
// acquire fragmentIDs of ghost atoms
@ -124,9 +117,6 @@ void ComputeFragmentAtom::compute_peratom()
// then check if any proc made changes
commflag = 1;
int nlocal = atom->nlocal;
int *num_bond = atom->num_bond;
tagint **bond_atom = atom->bond_atom;
int change,done,anychange;
@ -138,9 +128,10 @@ void ComputeFragmentAtom::compute_peratom()
done = 1;
for (i = 0; i < nlocal; i++) {
if (!(mask[i] & groupbit)) continue;
for (j = 0; j < num_bond[i]; j++) {
k = bond_atom[i][j];
k = atom->map(bond_atom[i][j]);
if (k < 0) continue;
if (!(mask[k] & groupbit)) continue;
if (fragmentID[i] == fragmentID[k]) continue;