diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index 3098a1bd67..1ec29efacd 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -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);