From c5ce3ffe60e40f186cb8b63b4233ccfed7d229dd Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sun, 20 Aug 2017 09:18:04 -0400
Subject: [PATCH] use list of bonds per atom instead of bondlist, as that will
work with shake as well
---
src/compute_fragment_atom.cpp | 29 ++++++++++-------------------
1 file changed, 10 insertions(+), 19 deletions(-)
diff --git a/src/compute_fragment_atom.cpp b/src/compute_fragment_atom.cpp
index 02a0b8e7dc..5024ada4f4 100644
--- a/src/compute_fragment_atom.cpp
+++ b/src/compute_fragment_atom.cpp
@@ -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;
--
GitLab