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Merge pull request #2600 from jrgissing/bond/react-same-type-initiators-fix

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bond/react: same-type initiators fix
This commit is contained in:
Axel Kohlmeyer
2021-02-16 12:14:22 -05:00
committed by GitHub
parent f6454dce64 91f74cf956
commit 4af8de3287
1 changed files with 21 additions and 10 deletions
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31
src/USER-REACTION/fix_bond_react.cpp
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@ -1031,23 +1031,28 @@ void FixBondReact::post_integrate()
if (finalpartner[i] == 0) continue;
j = atom->map(finalpartner[i]);
// if (j < 0 || tag[i] < tag[j]) {
if (tag[i] < tag[j]) { //atom->map(std::min(tag[i],tag[j])) <= nlocal &&
if (nattempt[rxnID] == maxattempt) {
if (tag[i] < tag[j]) {
if (nattempt[rxnID] > maxattempt-2) {
maxattempt += DELTA;
// third column of 'attempt': bond/react integer ID
// third dim of 'attempt': bond/react integer ID
memory->grow(attempt,maxattempt,2,nreacts,"bond/react:attempt");
}
// to ensure types remain in same order
// unnecessary now taken from reaction map file
if (iatomtype[rxnID] == type[i]) {
attempt[nattempt[rxnID]][0][rxnID] = tag[i];
attempt[nattempt[rxnID]][1][rxnID] = finalpartner[i];
nattempt[rxnID]++;
// add another attempt if initiator atoms are same type
if (iatomtype[rxnID] == jatomtype[rxnID]) {
attempt[nattempt[rxnID]][0][rxnID] = finalpartner[i];
attempt[nattempt[rxnID]][1][rxnID] = tag[i];
nattempt[rxnID]++;
}
} else {
attempt[nattempt[rxnID]][0][rxnID] = finalpartner[i];
attempt[nattempt[rxnID]][1][rxnID] = tag[i];
nattempt[rxnID]++;
}
nattempt[rxnID]++;
}
}
}
@ -2705,7 +2710,7 @@ update molecule IDs, charges, types, special lists and all topology
void FixBondReact::update_everything()
{
int nlocal; // must be defined after create_atoms
int nlocal = atom->nlocal; // must be redefined after create atoms
int *type = atom->type;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
@ -2717,6 +2722,9 @@ void FixBondReact::update_everything()
// used when deleting atoms
int ndel,ndelone;
int *mark;
int nmark = nlocal;
memory->create(mark,nmark,"bond/react:mark");
for (int i = 0; i < nmark; i++) mark[i] = 0;
tagint *tag = atom->tag;
AtomVec *avec = atom->avec;
@ -2778,8 +2786,11 @@ void FixBondReact::update_everything()
// mark to-delete atoms
nlocal = atom->nlocal;
mark = new int[nlocal];
for (int i = 0; i < nlocal; i++) mark[i] = 0;
if (nlocal > nmark) {
memory->grow(mark,nlocal,"bond/react:mark");
for (int i = nmark; i < nlocal; i++) mark[i] = 0;
nmark = nlocal;
}
for (int i = 0; i < update_num_mega; i++) {
rxnID = update_mega_glove[0][i];
onemol = atom->molecules[unreacted_mol[rxnID]];
@ -3228,7 +3239,7 @@ void FixBondReact::update_everything()
}
}
}
delete [] mark;
memory->destroy(mark);
MPI_Allreduce(&ndelone,&ndel,1,MPI_INT,MPI_SUM,world);