Merge pull request #1288 from jrgissing/bond/react-limit-total-number-of-reactions (a5ce656c) · Commits · 郑智淋 / lammps

doc/src/fix_bond_react.txt

+5 −2

Original line number	Diff line number	Diff line
		@@ -36,10 +36,12 @@ react = mandatory argument indicating new reaction specification :l
		template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
		map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
		zero or more individual keyword/value pairs may be appended to each react argument :l
		individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l
		individual_keyword = {prob} or {max_rxn} or {stabilize_steps} or {update_edges} :l
		{prob} values = fraction seed
		fraction = initiate reaction with this probability if otherwise eligible
		seed = random number seed (positive integer)
		{max_rxn} value = N
		N = maximum number of reactions allowed to occur
		{stabilize_steps} value = timesteps
		timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
		{update_edges} value = {none} or {charges} or {custom}
		@@ -285,7 +287,8 @@ The {prob} keyword can affect whether an eligible reaction actually
		occurs. The fraction setting must be a value between 0.0 and 1.0. A
		uniform random number between 0.0 and 1.0 is generated and the
		eligible reaction only occurs if the random number is less than the
		fraction.
		fraction. Up to N reactions are permitted to occur, as optionally
		specified by the {max_rxn} keyword.

		The {stabilize_steps} keyword allows for the specification of how many
		timesteps a reaction site is stabilized before being returned to the

src/USER-MISC/fix_bond_react.cpp

+16 −7

Original line number	Diff line number	Diff line
		@@ -161,6 +161,7 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		memory->create(unreacted_mol,nreacts,"bond/react:unreacted_mol");
		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(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");
		@@ -179,6 +180,7 @@ 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;
		stabilize_steps_flag[i] = 0;
		update_edges_flag[i] = 0;
		// set default limit duration to 60 timesteps
		@@ -244,6 +246,13 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :
		if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: "
		"probability seed must be positive");
		iarg += 3;
		} else if (strcmp(arg[iarg],"max_rxn") == 0) {
		if (iarg+2 > narg) error->all(FLERR,"Illegal fix bond/react command: "
		"'max_rxn' has too few arguments");
		max_rxn[rxn] = force->inumeric(FLERR,arg[iarg+1]);
		if (max_rxn[rxn] < 0) error->all(FLERR,"Illegal fix bond/react command: "
		"'max_rxn' cannot be negative");
		iarg += 2;
		} else if (strcmp(arg[iarg],"stabilize_steps") == 0) {
		if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword "
		"used without stabilization keyword");
		@@ -379,9 +388,6 @@ FixBondReact::FixBondReact(LAMMPS lmp, int narg, char *arg) :

		FixBondReact::~FixBondReact()
		{
		// unregister callbacks to this fix from Atom class
		atom->delete_callback(id,0);

		for (int i = 0; i < nreacts; i++) {
		delete random[i];
		}
		@@ -396,6 +402,7 @@ FixBondReact::~FixBondReact()
		memory->destroy(edge);
		memory->destroy(equivalences);
		memory->destroy(reverse_equiv);
		memory->destroy(landlocked_atoms);
		memory->destroy(custom_edges);
		memory->destroy(delete_atoms);

		@@ -405,6 +412,7 @@ FixBondReact::~FixBondReact()
		memory->destroy(reacted_mol);
		memory->destroy(fraction);
		memory->destroy(seed);
		memory->destroy(max_rxn);
		memory->destroy(limit_duration);
		memory->destroy(stabilize_steps_flag);
		memory->destroy(update_edges_flag);
		@@ -434,7 +442,6 @@ FixBondReact::~FixBondReact()
		memory->destroy(restore);
		memory->destroy(glove);
		memory->destroy(pioneers);
		memory->destroy(landlocked_atoms);
		memory->destroy(local_mega_glove);
		memory->destroy(ghostly_mega_glove);
		}
		@@ -452,7 +459,7 @@ FixBondReact::~FixBondReact()
		delete [] id_fix3;
		}

		if (id_fix2 == NULL && modify->nfix) modify->delete_fix(id_fix2);
		if (id_fix2 && modify->nfix) modify->delete_fix(id_fix2);
		delete [] id_fix2;

		delete [] statted_id;
		@@ -748,6 +755,7 @@ void FixBondReact::post_integrate()

		int j;
		for (rxnID = 0; rxnID < nreacts; rxnID++) {
		if (max_rxn[rxnID] <= reaction_count_total[rxnID]) continue;
		for (int ii = 0; ii < nall; ii++) {
		partner[ii] = 0;
		finalpartner[ii] = 0;
		@@ -1148,12 +1156,13 @@ void FixBondReact::superimpose_algorithm()
		for (int i = 0; i < nreacts; i++)
		reaction_count_total[i] += reaction_count[i];

		// this assumes compute_vector is called from process 0
		// ...so doesn't bother to bcast ghostly_rxn_count
		if (me == 0)
		for (int i = 0; i < nreacts; i++)
		reaction_count_total[i] += ghostly_rxn_count[i];

		// bcast ghostly_rxn_count
		MPI_Bcast(&reaction_count_total[0], nreacts, MPI_INT, 0, world);

		// this updates topology next step
		next_reneighbor = update->ntimestep;

src/USER-MISC/fix_bond_react.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -54,7 +54,7 @@ class FixBondReact : public Fix {
		FILE *fp;
		int iatomtype,jatomtype;
		int *seed;
		double *cutsq,fraction;
		double *cutsq,fraction,*max_rxn;
		tagint lastcheck;
		int stabilization_flag;
		int custom_exclude_flag;

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