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Merge pull request #4548 from jrgissing/bond/react-create+rate_limit_bugfix

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bond/react: refactor reaction counting
This commit is contained in:
Axel Kohlmeyer
2025-04-14 09:38:10 -04:00
committed by GitHub
parent 994b7b4937 1eb61936ab
commit 0b0383bc64
1 changed files with 12 additions and 19 deletions
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31
src/REACTION/fix_bond_react.cpp
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@ -1475,15 +1475,14 @@ void FixBondReact::superimpose_algorithm()
int rxnflag = 0;
int *delta_rxn;
memory->create(delta_rxn,nreacts,"bond/react:delta_rxn");
memory->create(delta_rxn, nreacts, "bond/react:delta_rxn");
if (comm->me == 0)
for (int i = 0; i < nreacts; i++) {
delta_rxn[i] = reaction_count[i] + ghostly_rxn_count[i];
reaction_count_total[i] += delta_rxn[i];
rxnflag += delta_rxn[i];
}
MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world);
MPI_Bcast(&delta_rxn[0], nreacts, MPI_INT, 0, world);
MPI_Bcast(&rxnflag, 1, MPI_INT, 0, world);
if (!rxnflag) return;
@ -1495,12 +1494,12 @@ void FixBondReact::superimpose_algorithm()
// check if we overstepped our reaction limit, via either max_rxn or rate_limit
for (int i = 0; i < nreacts; i++) {
int overstep = 0;
int max_rxn_overstep = reaction_count_total[i] - max_rxn[i];
int max_rxn_overstep = reaction_count_total[i] + delta_rxn[i] - max_rxn[i];
overstep = MAX(overstep,max_rxn_overstep);
if (rate_limit[0][i] == 1) {
int myrxn_count = store_rxn_count[rate_limit[2][i]-1][i];
if (myrxn_count != -1) {
int nrxn_delta = reaction_count_total[i] - myrxn_count;
int nrxn_delta = reaction_count_total[i] + delta_rxn[i] - myrxn_count;
int my_nrate;
if (var_flag[NRATE][i] == 1) {
my_nrate = input->variable->compute_equal(var_id[NRATE][i]);
@ -1540,7 +1539,6 @@ void FixBondReact::superimpose_algorithm()
else all_localkeep[rxn_by_proc[j]]++;
}
memory->destroy(rxn_by_proc);
reaction_count_total[i] -= overstep;
}
MPI_Scatter(&all_localkeep[0],1,MPI_INT,&nlocalkeep[i],1,MPI_INT,0,world);
MPI_Bcast(&nghostlykeep[i],1,MPI_INT,0,world);
@ -1548,7 +1546,6 @@ void FixBondReact::superimpose_algorithm()
memory->destroy(all_localkeep);
}
}
MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world);
memory->destroy(delta_rxn);
// this updates topology next step
@ -3103,18 +3100,16 @@ void FixBondReact::update_everything()
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
if (insert_atoms_setup(update_mega_glove,update_num_mega)) {
inserted_atoms_flag = 1;
} else { // create aborted
reaction_count_total[rxnID]--;
continue;
}
if (insert_atoms_setup(update_mega_glove,update_num_mega)) inserted_atoms_flag = 1;
else continue;
}
noccur[rxnID]++;
if (rescale_charges_flag[rxnID]) sim_total_charges[update_num_mega] = local_mega_glove[1][i];
update_num_mega++;
}
MPI_Allreduce(MPI_IN_PLACE, &noccur[0], nreacts, MPI_INT, MPI_SUM, world);
reaction_count_total[rxnID] += noccur[rxnID];
} else if (pass == 1) {
for (int i = 0; i < global_megasize; i++) {
rxnID = (int) global_mega_glove[0][i];
@ -3129,17 +3124,15 @@ void FixBondReact::update_everything()
// we can insert atoms here, now that reactions are finalized
// can't do it any earlier, due to skipped reactions (max_rxn)
// for MPI build, reactions that create atoms are always treated as 'global'
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
if (insert_atoms_setup(update_mega_glove,update_num_mega)) {
inserted_atoms_flag = 1;
} else { // create aborted
reaction_count_total[rxnID]--;
continue;
}
if (insert_atoms_setup(update_mega_glove,update_num_mega)) inserted_atoms_flag = 1;
else continue;
}
noccur[rxnID]++;
reaction_count_total[rxnID]++;
if (rescale_charges_flag[rxnID]) sim_total_charges[update_num_mega] = global_mega_glove[1][i];
update_num_mega++;