Merge pull request #1292 from jrgissing/bond/react-limit-total-number-of-reactions (3609a33e) · Commits · 郑智淋 / lammps

src/USER-MISC/fix_bond_react.cpp

+65 −23

Original line number	Diff line number	Diff line
		@@ -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;

		@@ -1957,6 +1991,7 @@ void FixBondReact::glove_ghostcheck()
		// 'ghosts of another' indication taken from comm->sendlist

		int ghostly = 0;
		#if !defined(MPI_STUBS)
		if (comm->style == 0) {
		for (int i = 0; i < onemol->natoms; i++) {
		int ilocal = atom->map(glove[i][1]);
		@@ -1966,10 +2001,9 @@ void FixBondReact::glove_ghostcheck()
		}
		}
		} else {
		#if !defined(MPI_STUBS)
		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++;
		}
		}

src/USER-MISC/fix_bond_react.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -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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