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reax/species: variable input for Nlimit keyword

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This commit is contained in:
jrgissing
2023-05-04 20:10:13 -04:00
parent 8054923941
commit 0b71371597
3 changed files with 21 additions and 8 deletions
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3
doc/src/fix_reaxff_species.rst
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@ -148,7 +148,8 @@ formulae). The *specieslist* and *masslimit* keywords cannot both be
used in the same *reaxff/species* fix. The *delete_rate_limit*
keyword can enforce an upper limit on the overall rate of molecule
deletion. The number of deletion occurrences is limited to Nlimit
within an interval of Nsteps timesteps. When using the
within an interval of Nsteps timesteps. Nlimit can be specified with
an equal-style :doc:`variable <variable>`. When using the
*delete_rate_limit* keyword, no deletions are permitted to occur
within the first Nsteps timesteps of the first run (after reading a
either a data or restart file).

23
src/REAXFF/fix_reaxff_species.cpp
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@ -28,11 +28,13 @@
#include "fix_ave_atom.h"
#include "force.h"
#include "group.h"
#include "input.h"
#include "memory.h"
#include "modify.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "update.h"
#include "variable.h"
#include "pair_reaxff.h"
#include "reaxff_defs.h"
@ -239,7 +241,14 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
// rate limit when deleting molecules
} else if (strcmp(arg[iarg], "delete_rate_limit") == 0) {
if (iarg + 3 > narg) utils::missing_cmd_args(FLERR, "fix reaxff/species delete_rate_limit", error);
delete_Nlimit = utils::numeric(FLERR, arg[iarg+1], false, lmp);
delete_Nlimit_varid = -1;
if (strncmp(arg[iarg+1],"v_",2) == 0) {
delete_Nlimit_varid = input->variable->find(&arg[iarg+1][2]);
if (delete_Nlimit_varid < 0)
error->all(FLERR,"Fix reaxff/species: Variable name {} does not exist",&arg[iarg+1][2]);
if (!input->variable->equalstyle(delete_Nlimit_varid))
error->all(FLERR,"Fix reaxff/species: Variable {} is not equal-style",&arg[iarg+1][2]);
} else delete_Nlimit = utils::numeric(FLERR, arg[iarg+1], false, lmp);
delete_Nsteps = utils::numeric(FLERR, arg[iarg+2], false, lmp);
iarg += 3;
// position of molecules
@ -280,7 +289,7 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
if (delflag && specieslistflag && masslimitflag)
error->all(FLERR, "Incompatible combination fix reaxff/species command options");
if (delete_Nlimit > 0) {
if (delete_Nsteps > 0) {
if (lmp->citeme) lmp->citeme->add(cite_reaxff_species_delete);
memory->create(delete_Tcount,delete_Nsteps,"reaxff/species:delete_Tcount");
@ -407,7 +416,7 @@ void FixReaxFFSpecies::Output_ReaxFF_Bonds(bigint ntimestep, FILE * /*fp*/)
if (ntimestep != nvalid) {
// push back delete_Tcount on every step
if (delete_Nlimit > 0)
if (delete_Nsteps > 0)
for (int i = delete_Nsteps-1; i > 0; i--)
delete_Tcount[i] = delete_Tcount[i-1];
return;
@ -864,9 +873,11 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
{
int ndeletions;
int headroom = -1;
if (delete_Nlimit > 0) {
if (delete_Nsteps > 0) {
if (delete_Tcount[delete_Nsteps-1] == -1) return;
ndeletions = delete_Tcount[0] - delete_Tcount[delete_Nsteps-1];
if (delete_Nlimit_varid > -1)
delete_Nlimit = input->variable->compute_equal(delete_Nlimit_varid);
headroom = MAX(0, delete_Nlimit - ndeletions);
if (headroom == 0) return;
}
@ -907,7 +918,7 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
memory->create(molrange,Nmole,"reaxff/species:molrange");
for (m = 0; m < Nmole; m++)
molrange[m] = m + 1;
if (delete_Nlimit > 0) {
if (delete_Nsteps > 0) {
// shuffle index when using rate_limit, in case order is biased
if (comm->me == 0)
std::shuffle(&molrange[0],&molrange[Nmole], park_rng);
@ -1041,7 +1052,7 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
// push back delete_Tcount on every step
if (delete_Nlimit > 0) {
if (delete_Nsteps > 0) {
for (i = delete_Nsteps-1; i > 0; i--)
delete_Tcount[i] = delete_Tcount[i-1];
delete_Tcount[0] += this_delete_Tcount;

3
src/REAXFF/fix_reaxff_species.h
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@ -60,7 +60,8 @@ class FixReaxFFSpecies : public Fix {
FILE *fp, *pos, *fdel;
int eleflag, posflag, multipos, padflag, setupflag;
int delflag, specieslistflag, masslimitflag;
int delete_Nlimit, delete_Nsteps, *delete_Tcount;
int delete_Nlimit, delete_Nlimit_varid;
int delete_Nsteps, *delete_Tcount;
double massmin, massmax;
int singlepos_opened, multipos_opened, del_opened;
char *ele, **eletype, *filepos, *filedel;