From 94dc5e1133dd647adce23dbdeae12b926c4a6ed0 Mon Sep 17 00:00:00 2001
From: jrgissing <jrgiss05@gmail.com>
Date: Thu, 17 Jan 2019 23:13:21 -0700
Subject: [PATCH] bond/react: strict reaction limit
also, fixes a bug in the 'serial' build introduced in #1099, wherein no reactions could occur in some cases
---
src/USER-MISC/fix_bond_react.cpp | 88 +++++++++++++++++++++++---------
src/USER-MISC/fix_bond_react.h | 3 +-
2 files changed, 67 insertions(+), 24 deletions(-)
diff --git a/src/USER-MISC/fix_bond_react.cpp b/src/USER-MISC/fix_bond_react.cpp
index 4d4642f102..4b15f50d7d 100644
--- a/src/USER-MISC/fix_bond_react.cpp
+++ b/src/USER-MISC/fix_bond_react.cpp
@@ -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++;
}
}
diff --git a/src/USER-MISC/fix_bond_react.h b/src/USER-MISC/fix_bond_react.h
index 2b85bbd281..fffdfe4369 100644
--- a/src/USER-MISC/fix_bond_react.h
+++ b/src/USER-MISC/fix_bond_react.h
@@ -54,7 +54,8 @@ class FixBondReact : public Fix {
FILE *fp;
int *iatomtype,*jatomtype;
int *seed;
- double **cutsq,*fraction,*max_rxn;
+ double **cutsq,*fraction;
+ int *max_rxn,*nlocalskips,*nghostlyskips;
tagint lastcheck;
int stabilization_flag;
int custom_exclude_flag;
--
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