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bond/react: strict reaction limit

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also, fixes a bug in the 'serial' build introduced in #1099, wherein no reactions could occur in some cases
This commit is contained in:
jrgissing
2019-01-17 23:13:21 -07:00
parent b0af54ac37
commit 94dc5e1133
2 changed files with 67 additions and 24 deletions
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88
src/USER-MISC/fix_bond_react.cpp
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@ -162,6 +162,8 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");
memory->create(fraction,nreacts,"bond/react:fraction");
memory->create(max_rxn,nreacts,"bond/react:max_rxn");
memory->create(nlocalskips,nreacts,"bond/react:nlocalskips");
memory->create(nghostlyskips,nreacts,"bond/react:nghostlyskips");
memory->create(seed,nreacts,"bond/react:seed");
memory->create(limit_duration,nreacts,"bond/react:limit_duration");
memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");
@ -180,7 +182,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
for (int i = 0; i < nreacts; i++) {
fraction[i] = 1;
seed[i] = 12345;
max_rxn[i] = BIG;
max_rxn[i] = INT_MAX;
stabilize_steps_flag[i] = 0;
update_edges_flag[i] = 0;
// set default limit duration to 60 timesteps
@ -413,6 +415,8 @@ FixBondReact::~FixBondReact()
memory->destroy(fraction);
memory->destroy(seed);
memory->destroy(max_rxn);
memory->destroy(nlocalskips);
memory->destroy(nghostlyskips);
memory->destroy(limit_duration);
memory->destroy(stabilize_steps_flag);
memory->destroy(update_edges_flag);
@ -684,6 +688,8 @@ void FixBondReact::post_integrate()
reaction_count[i] = 0;
local_rxn_count[i] = 0;
ghostly_rxn_count[i] = 0;
nlocalskips[i] = 0;
nghostlyskips[i] = 0;
}
if (nevery_check) {
@ -1153,16 +1159,44 @@ void FixBondReact::superimpose_algorithm()
MPI_Allreduce(&local_rxn_count[0],&reaction_count[0],nreacts,MPI_INT,MPI_SUM,world);
for (int i = 0; i < nreacts; i++)
reaction_count_total[i] += reaction_count[i];
if (me == 0)
for (int i = 0; i < nreacts; i++)
reaction_count_total[i] += ghostly_rxn_count[i];
reaction_count_total[i] += reaction_count[i] + ghostly_rxn_count[i];
// bcast ghostly_rxn_count
MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world);
// check if we overstepped our reaction limit
for (int i = 0; i < nreacts; i++) {
if (reaction_count_total[i] > max_rxn[i]) {
// let's randomly choose rxns to skip, unbiasedly from local and ghostly
int local_rxncounts[nprocs];
int all_localskips[nprocs];
MPI_Gather(&local_rxn_count[i],1,MPI_INT,local_rxncounts,1,MPI_INT,0,world);
if (me == 0) {
int overstep = reaction_count_total[i] - max_rxn[i];
int delta_rxn = reaction_count[i] + ghostly_rxn_count[i];
int rxn_by_proc[delta_rxn];
for (int j = 0; j < delta_rxn; j++)
rxn_by_proc[j] = -1; // corresponds to ghostly
int itemp = 0;
for (int j = 0; j < nprocs; j++)
for (int k = 0; k < local_rxn_count[j]; k++)
rxn_by_proc[itemp++] = j;
std::random_shuffle(&rxn_by_proc[0],&rxn_by_proc[delta_rxn]);
for (int j = 0; j < nprocs; j++)
all_localskips[j] = 0;
nghostlyskips[i] = 0;
for (int j = 0; j < overstep; j++) {
if (rxn_by_proc[j] == -1) nghostlyskips[i]++;
else all_localskips[rxn_by_proc[j]]++;
}
}
reaction_count_total[i] = max_rxn[i];
MPI_Scatter(&all_localskips[0],1,MPI_INT,&nlocalskips[i],1,MPI_INT,0,world);
MPI_Bcast(&nghostlyskips[i],1,MPI_INT,0,world);
}
}
// this updates topology next step
next_reneighbor = update->ntimestep;
@ -1957,19 +1991,19 @@ void FixBondReact::glove_ghostcheck()
// 'ghosts of another' indication taken from comm->sendlist
int ghostly = 0;
if (comm->style == 0) {
for (int i = 0; i < onemol->natoms; i++) {
int ilocal = atom->map(glove[i][1]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
ghostly = 1;
break;
#if !defined(MPI_STUBS)
if (comm->style == 0) {
for (int i = 0; i < onemol->natoms; i++) {
int ilocal = atom->map(glove[i][1]);
if (ilocal >= atom->nlocal || localsendlist[ilocal] == 1) {
ghostly = 1;
break;
}
}
}
} else {
#if !defined(MPI_STUBS)
} else {
ghostly = 1;
#endif
}
}
#endif
if (ghostly == 1) {
ghostly_mega_glove[0][ghostly_num_mega] = rxnID;
@ -2104,18 +2138,26 @@ void FixBondReact::update_everything()
memory->create(update_mega_glove,max_natoms+1,MAX(local_num_mega,global_megasize),"bond/react:update_mega_glove");
for (int pass = 0; pass < 2; pass++) {
update_num_mega = 0;
int iskip[nreacts];
for (int i = 0; i < nreacts; i++) iskip[i] = 0;
if (pass == 0) {
update_num_mega = local_num_mega;
for (int i = 0; i < update_num_mega; i++) {
for (int i = 0; i < local_num_mega; i++) {
rxnID = local_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
if (iskip[rxnID]++ < nlocalskips[rxnID]) continue;
for (int j = 0; j < max_natoms+1; j++)
update_mega_glove[j][i] = local_mega_glove[j][i];
update_mega_glove[j][update_num_mega] = local_mega_glove[j][i];
update_num_mega++;
}
} else if (pass == 1) {
update_num_mega = global_megasize;
for (int i = 0; i < global_megasize; i++) {
rxnID = global_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
if (iskip[rxnID]++ < nghostlyskips[rxnID]) continue;
for (int j = 0; j < max_natoms+1; j++)
update_mega_glove[j][i] = global_mega_glove[j][i];
update_mega_glove[j][update_num_mega] = global_mega_glove[j][i];
update_num_mega++;
}
}