Unverified Commit a5ce656c authored by Axel Kohlmeyer's avatar Axel Kohlmeyer Committed by GitHub
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Merge pull request #1288 from jrgissing/bond/react-limit-total-number-of-reactions 

Bond/react: limit number of reactions, bugfixes
parents 3cbf009c b0af54ac

doc/src/fix_bond_react.txt

+5 −2
Original line number Original line 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

  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

  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

  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

    {prob} values = fraction seed

      fraction = initiate reaction with this probability if otherwise eligible

      fraction = initiate reaction with this probability if otherwise eligible

      seed = random number seed (positive integer)

      seed = random number seed (positive integer)

    {max_rxn} value = N

      N = maximum number of reactions allowed to occur

    {stabilize_steps} value = timesteps

    {stabilize_steps} value = timesteps

      timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms

      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}

    {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

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

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

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

The {stabilize_steps} keyword allows for the specification of how many

timesteps a reaction site is stabilized before being returned to the

timesteps a reaction site is stabilized before being returned to the

src/USER-MISC/fix_bond_react.cpp

+16 −7
Original line number Original line 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(unreacted_mol,nreacts,"bond/react:unreacted_mol");

  memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");

  memory->create(reacted_mol,nreacts,"bond/react:reacted_mol");

  memory->create(fraction,nreacts,"bond/react:fraction");

  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(seed,nreacts,"bond/react:seed");

  memory->create(limit_duration,nreacts,"bond/react:limit_duration");

  memory->create(limit_duration,nreacts,"bond/react:limit_duration");

  memory->create(stabilize_steps_flag,nreacts,"bond/react:stabilize_steps_flag");

  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++) {

  for (int i = 0; i < nreacts; i++) {

    fraction[i] = 1;

    fraction[i] = 1;

    seed[i] = 12345;

    seed[i] = 12345;

    max_rxn[i] = BIG;

    stabilize_steps_flag[i] = 0;

    stabilize_steps_flag[i] = 0;

    update_edges_flag[i] = 0;

    update_edges_flag[i] = 0;

    // set default limit duration to 60 timesteps

    // 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: "

        if (seed[rxn] <= 0) error->all(FLERR,"Illegal fix bond/react command: "

                                       "probability seed must be positive");

                                       "probability seed must be positive");

        iarg += 3;

        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) {

      } else if (strcmp(arg[iarg],"stabilize_steps") == 0) {

        if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword "

        if (stabilization_flag == 0) error->all(FLERR,"Stabilize_steps keyword "

                                                "used without stabilization keyword");

                                                "used without stabilization keyword");
@@ -379,9 +388,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) : 




FixBondReact::~FixBondReact()

FixBondReact::~FixBondReact()

{

{

  // unregister callbacks to this fix from Atom class

  atom->delete_callback(id,0);



  for (int i = 0; i < nreacts; i++) {

  for (int i = 0; i < nreacts; i++) {

    delete random[i];

    delete random[i];

  }

  }
@@ -396,6 +402,7 @@ FixBondReact::~FixBondReact() 
  memory->destroy(edge);

  memory->destroy(edge);

  memory->destroy(equivalences);

  memory->destroy(equivalences);

  memory->destroy(reverse_equiv);

  memory->destroy(reverse_equiv);

  memory->destroy(landlocked_atoms);

  memory->destroy(custom_edges);

  memory->destroy(custom_edges);

  memory->destroy(delete_atoms);

  memory->destroy(delete_atoms);
@@ -405,6 +412,7 @@ FixBondReact::~FixBondReact() 
  memory->destroy(reacted_mol);

  memory->destroy(reacted_mol);

  memory->destroy(fraction);

  memory->destroy(fraction);

  memory->destroy(seed);

  memory->destroy(seed);

  memory->destroy(max_rxn);

  memory->destroy(limit_duration);

  memory->destroy(limit_duration);

  memory->destroy(stabilize_steps_flag);

  memory->destroy(stabilize_steps_flag);

  memory->destroy(update_edges_flag);

  memory->destroy(update_edges_flag);
@@ -434,7 +442,6 @@ FixBondReact::~FixBondReact() 
    memory->destroy(restore);

    memory->destroy(restore);

    memory->destroy(glove);

    memory->destroy(glove);

    memory->destroy(pioneers);

    memory->destroy(pioneers);

    memory->destroy(landlocked_atoms);

    memory->destroy(local_mega_glove);

    memory->destroy(local_mega_glove);

    memory->destroy(ghostly_mega_glove);

    memory->destroy(ghostly_mega_glove);

  }

  }
@@ -452,7 +459,7 @@ FixBondReact::~FixBondReact() 
    delete [] id_fix3;

    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 [] id_fix2;





  delete [] statted_id;

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




  int j;

  int j;

  for (rxnID = 0; rxnID < nreacts; rxnID++) {

  for (rxnID = 0; rxnID < nreacts; rxnID++) {

    if (max_rxn[rxnID] <= reaction_count_total[rxnID]) continue;

    for (int ii = 0; ii < nall; ii++) {

    for (int ii = 0; ii < nall; ii++) {

      partner[ii] = 0;

      partner[ii] = 0;

      finalpartner[ii] = 0;

      finalpartner[ii] = 0;
@@ -1148,12 +1156,13 @@ void FixBondReact::superimpose_algorithm() 
  for (int i = 0; i < nreacts; i++)

  for (int i = 0; i < nreacts; i++)

    reaction_count_total[i] += reaction_count[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)

  if (me == 0)

    for (int i = 0; i < nreacts; i++)

    for (int i = 0; i < nreacts; i++)

      reaction_count_total[i] += ghostly_rxn_count[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

  // this updates topology next step

  next_reneighbor = update->ntimestep;

  next_reneighbor = update->ntimestep;

src/USER-MISC/fix_bond_react.h

+1 −1
Original line number Original line Diff line number Diff line
@@ -54,7 +54,7 @@ class FixBondReact : public Fix { 
  FILE *fp;

  FILE *fp;

  int *iatomtype,*jatomtype;

  int *iatomtype,*jatomtype;

  int *seed;

  int *seed;

  double **cutsq,*fraction;

  double **cutsq,*fraction,*max_rxn;

  tagint lastcheck;

  tagint lastcheck;

  int stabilization_flag;

  int stabilization_flag;

  int custom_exclude_flag;

  int custom_exclude_flag;

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