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make simpler, faster, more self-contained

Browse Source 
(and fix bugs)
This commit is contained in:
Jacob Gissinger
2022-06-07 11:10:36 -04:00
parent 5bc1fb1580
commit f024abfe34
2 changed files with 28 additions and 13 deletions
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35
src/replicate.cpp
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@ -166,7 +166,7 @@ void Replicate::command(int narg, char **arg)
// atom = new replicated atom class
// also set atomKK for Kokkos version of Atom class
old = atom;
Atom *old = atom;
atomKK = nullptr;
if (lmp->kokkos) atom = atomKK = new AtomKokkos(lmp);
else atom = new Atom(lmp);
@ -434,15 +434,22 @@ void Replicate::command(int narg, char **arg)
int num_replicas_added = 0;
// let's repurpose the old atom class to allow atom->map for all atoms
// tag and x for the whole system (before replication) stored in 'old'
// store x and tag for the whole system (before replication)
if (bondlist_flag) {
m = 0;
old->nlocal = 0;
while (m < size_buf_all) m += old_avec->unpack_restart(&buf_all[m],old);
old->map_init();
old->map_set();
memory->create(old_x,old->natoms,3,"replicate:old_x");
memory->create(old_tag,old->natoms,"replicate:old_tag");
i = m = 0;
while (m < size_buf_all) {
old_x[i][0] = buf_all[m+1];
old_x[i][1] = buf_all[m+2];
old_x[i][2] = buf_all[m+3];
old_tag[i] = (tagint) ubuf(buf_all[m+4]).i;
old_map.insert({old_tag[i],i});
m += static_cast<int> (buf_all[m]);
i++;
}
}
for (ix = 0; ix < nx; ix++) {
@ -698,6 +705,10 @@ void Replicate::command(int narg, char **arg)
memory->destroy(size_buf_rnk);
memory->destroy(disp_buf_rnk);
memory->destroy(buf_all);
if (bondlist_flag) {
memory->destroy(old_x);
memory->destroy(old_tag);
}
int sum = 0;
MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world);
@ -866,12 +877,12 @@ void Replicate::command(int narg, char **arg)
void Replicate::newtag(tagint atom0tag, tagint &tag2bond) {
double del;
int repshift,rep2bond[3];
int atom0 = old->map(atom0tag);
int atom2bond = old->map(tag2bond);
int atom0 = old_map.find(atom0tag)->second;
int atom2bond = old_map.find(tag2bond)->second;
for (int i = 0; i < 3; i++) {
del = fabs(old->x[atom0][i] - old->x[atom2bond][i]);
del = fabs(old_x[atom0][i] - old_x[atom2bond][i]);
if (del > old_prd_half[i]) {
if (old->x[atom0][i] > old_center[i]) repshift = 1;
if (old_x[atom0][i] > old_center[i]) repshift = 1;
else repshift = -1;
} else repshift = 0;
rep2bond[i] = thisrep[i] + repshift;