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allow wildcards with "cutoff" keyword to fix reaxff/species

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this also switched to using fmtlib for column aligned output formatting
and re-applies clang-format.
This commit is contained in:
Axel Kohlmeyer
2023-06-08 09:46:33 -04:00
parent 2272d8dd20
commit d6ad52ea66
3 changed files with 71 additions and 60 deletions
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23
doc/src/fix_reaxff_species.rst
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@ -25,7 +25,7 @@ Syntax
.. parsed-literal::
*cutoff* value = I J Cutoff
I, J = atom types
I, J = atom types (see asterisk form below)
Cutoff = Bond-order cutoff value for this pair of atom types
*element* value = Element1, Element2, ...
*position* value = posfreq filepos
@ -49,7 +49,7 @@ Examples
.. code-block:: LAMMPS
fix 1 all reaxff/species 10 10 100 species.out
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2*3 0.55
fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
fix 1 all reaxff/species 1 100 100 species.out delete species.del masslimit 0 50
@ -88,13 +88,24 @@ If the filename ends with ".gz", the output file is written in gzipped
format. A gzipped dump file will be about 3x smaller than the text version,
but will also take longer to write.
.. versionadded:: TBD
Support for wildcards added
Optional keyword *cutoff* can be assigned to change the minimum
bond-order values used in identifying chemical bonds between pairs of
atoms. Bond-order cutoffs should be carefully chosen, as bond-order
cutoffs that are too small may include too many bonds (which will
result in an error), while cutoffs that are too large will result in
fragmented molecules. The default cutoff of 0.3 usually gives good
results.
cutoffs that are too small may include too many bonds (which will result
in an error), while cutoffs that are too large will result in fragmented
molecules. The default cutoff of 0.3 usually gives good results. A
wildcard asterisk can be used in place of or in conjunction with the I,J
arguments to set the bond-order cutoff for multiple pairs of atom types.
This takes the form "\*" or "\*n" or "n\*" or "m\*n". If :math:`N` is
the number of atom types, then an asterisk with no numeric values means
all types from 1 to :math:`N`. A leading asterisk means all types from
1 to n (inclusive). A trailing asterisk means all types from n to
:math:`N` (inclusive). A middle asterisk means all types from m to n
(inclusive).
The optional keyword *element* can be used to specify the chemical
symbol printed for each LAMMPS atom type. The number of symbols must

106
src/REAXFF/fix_reaxff_species.cpp
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@ -48,15 +48,16 @@ using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_reaxff_species_delete[] =
"fix reaxff/species, 'delete' keyword: https://doi.org/10.1016/j.carbon.2022.11.002\n\n"
"@Article{Gissinger23,\n"
" author = {J. R. Gissinger, S. R. Zavada, J. G. Smith, J. Kemppainen, I. Gallegos, G. M. Odegard, E. J. Siochi, K. E. Wise},\n"
" title = {Predicting char yield of high-temperature resins},\n"
" journal = {Carbon},\n"
" year = 2023,\n"
" volume = 202,\n"
" pages = {336-347}\n"
"}\n\n";
"fix reaxff/species, 'delete' keyword: https://doi.org/10.1016/j.carbon.2022.11.002\n\n"
"@Article{Gissinger23,\n"
" author = {J. R. Gissinger, S. R. Zavada, J. G. Smith, J. Kemppainen, I. Gallegos, G. M. "
"Odegard, E. J. Siochi, K. E. Wise},\n"
" title = {Predicting char yield of high-temperature resins},\n"
" journal = {Carbon},\n"
" year = 2023,\n"
" volume = 202,\n"
" pages = {336-347}\n"
"}\n\n";
/* ---------------------------------------------------------------------- */
@ -148,13 +149,11 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
setupflag = 0;
// set default bond order cutoff
int itype, jtype;
double bo_cut;
bg_cut = 0.30;
double bo_cut = 0.30;
int np1 = ntypes + 1;
memory->create(BOCut, np1, np1, "reaxff/species:BOCut");
for (int i = 1; i < np1; i++)
for (int j = 1; j < np1; j++) BOCut[i][j] = bg_cut;
for (int j = 1; j < np1; j++) BOCut[i][j] = bo_cut;
// optional args
eletype = nullptr;
@ -172,16 +171,19 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
// set BO cutoff
if (strcmp(arg[iarg], "cutoff") == 0) {
if (iarg + 4 > narg) utils::missing_cmd_args(FLERR, "fix reaxff/species cutoff", error);
itype = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
jtype = utils::inumeric(FLERR, arg[iarg + 2], false, lmp);
int ilo, ihi, jlo, jhi;
utils::bounds(FLERR, arg[iarg + 1], 1, atom->ntypes, ilo, ihi, error);
utils::bounds(FLERR, arg[iarg + 2], 1, atom->ntypes, jlo, jhi, error);
bo_cut = utils::numeric(FLERR, arg[iarg + 3], false, lmp);
if ((itype <= 0) || (jtype <= 0) || (itype > ntypes) || (jtype > ntypes))
error->all(FLERR, "Fix reaxff/species cutoff atom type(s) out of range");
if ((bo_cut > 1.0) || (bo_cut < 0.0))
error->all(FLERR, "Fix reaxff/species invalid cutoff value: {}", bo_cut);
BOCut[itype][jtype] = bo_cut;
BOCut[jtype][itype] = bo_cut;
for (int i = ilo; i <= ihi; ++i) {
for (int j = MAX(jlo, i); j <= jhi; ++j) {
BOCut[i][j] = bo_cut;
BOCut[j][i] = bo_cut;
}
}
iarg += 4;
// modify element type names
@ -240,17 +242,21 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR, "Unknown fix reaxff/species delete option: {}", arg[iarg]);
// 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);
if (iarg + 3 > narg)
utils::missing_cmd_args(FLERR, "fix reaxff/species delete_rate_limit", error);
delete_Nlimit_varid = -1;
if (strncmp(arg[iarg+1],"v_",2) == 0) {
delete_Nlimit_varname = &arg[iarg+1][2];
if (strncmp(arg[iarg + 1], "v_", 2) == 0) {
delete_Nlimit_varname = &arg[iarg + 1][2];
delete_Nlimit_varid = input->variable->find(delete_Nlimit_varname.c_str());
if (delete_Nlimit_varid < 0)
error->all(FLERR,"Fix reaxff/species: Variable name {} does not exist",delete_Nlimit_varname);
error->all(FLERR, "Fix reaxff/species: Variable name {} does not exist",
delete_Nlimit_varname);
if (!input->variable->equalstyle(delete_Nlimit_varid))
error->all(FLERR,"Fix reaxff/species: Variable {} is not equal-style",delete_Nlimit_varname);
} else delete_Nlimit = utils::numeric(FLERR, arg[iarg+1], false, lmp);
delete_Nsteps = utils::numeric(FLERR, arg[iarg+2], false, lmp);
error->all(FLERR, "Fix reaxff/species: Variable {} is not equal-style",
delete_Nlimit_varname);
} 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
} else if (strcmp(arg[iarg], "position") == 0) {
@ -292,10 +298,9 @@ FixReaxFFSpecies::FixReaxFFSpecies(LAMMPS *lmp, int narg, char **arg) :
if (delete_Nsteps > 0) {
if (lmp->citeme) lmp->citeme->add(cite_reaxff_species_delete);
memory->create(delete_Tcount,delete_Nsteps,"reaxff/species:delete_Tcount");
memory->create(delete_Tcount, delete_Nsteps, "reaxff/species:delete_Tcount");
for (int i = 0; i < delete_Nsteps; i++)
delete_Tcount[i] = -1;
for (int i = 0; i < delete_Nsteps; i++) delete_Tcount[i] = -1;
delete_Tcount[0] = 0;
}
@ -393,9 +398,11 @@ void FixReaxFFSpecies::init()
if (delete_Nsteps > 0) {
delete_Nlimit_varid = input->variable->find(delete_Nlimit_varname.c_str());
if (delete_Nlimit_varid < 0)
error->all(FLERR,"Fix reaxff/species: Variable name {} does not exist",delete_Nlimit_varname);
error->all(FLERR, "Fix reaxff/species: Variable name {} does not exist",
delete_Nlimit_varname);
if (!input->variable->equalstyle(delete_Nlimit_varid))
error->all(FLERR,"Fix reaxff/species: Variable {} is not equal-style",delete_Nlimit_varname);
error->all(FLERR, "Fix reaxff/species: Variable {} is not equal-style",
delete_Nlimit_varname);
}
}
@ -427,8 +434,7 @@ void FixReaxFFSpecies::Output_ReaxFF_Bonds(bigint ntimestep, FILE * /*fp*/)
if (ntimestep != nvalid) {
// push back delete_Tcount on every step
if (delete_Nsteps > 0)
for (int i = delete_Nsteps-1; i > 0; i--)
delete_Tcount[i] = delete_Tcount[i-1];
for (int i = delete_Nsteps - 1; i > 0; i--) delete_Tcount[i] = delete_Tcount[i - 1];
return;
}
@ -732,31 +738,31 @@ void FixReaxFFSpecies::WriteFormulas(int Nmole, int Nspec)
int i, j, itemp;
bigint ntimestep = update->ntimestep;
fprintf(fp, "# Timestep No_Moles No_Specs ");
fprintf(fp, "# Timestep No_Moles No_Specs");
Nmoltype = 0;
for (i = 0; i < Nspec; i++) nd[i] = CheckExistence(i, ntypes);
for (i = 0; i < Nmoltype; i++) {
std::string molname;
for (j = 0; j < ntypes; j++) {
itemp = MolType[ntypes * i + j];
if (itemp != 0) {
if (eletype)
fprintf(fp, "%s", eletype[j]);
molname += eletype[j];
else
fprintf(fp, "%c", ele[j]);
if (itemp != 1) fprintf(fp, "%d", itemp);
molname += ele[j];
if (itemp != 1) molname += std::to_string(itemp);
}
}
fputs("\t", fp);
fmt::print(fp, " {:>11}", molname);
}
fputs("\n", fp);
fmt::print(fp, "{} {:11} {:11}\t", ntimestep, Nmole, Nspec);
for (i = 0; i < Nmoltype; i++) fprintf(fp, " %d\t", NMol[i]);
fprintf(fp, "\n");
fmt::print(fp, "{:>11} {:>11} {:>11}", ntimestep, Nmole, Nspec);
for (i = 0; i < Nmoltype; i++) fmt::print(fp, " {:>11}", NMol[i]);
fputs("\n", fp);
}
/* ---------------------------------------------------------------------- */
@ -884,8 +890,8 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
int ndeletions;
int headroom = -1;
if (delete_Nsteps > 0) {
if (delete_Tcount[delete_Nsteps-1] == -1) return;
ndeletions = delete_Tcount[0] - delete_Tcount[delete_Nsteps-1];
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);
@ -925,13 +931,11 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
std::random_device rnd;
std::minstd_rand park_rng(rnd());
int *molrange;
memory->create(molrange,Nmole,"reaxff/species:molrange");
for (m = 0; m < Nmole; m++)
molrange[m] = m + 1;
memory->create(molrange, Nmole, "reaxff/species:molrange");
for (m = 0; m < Nmole; m++) molrange[m] = m + 1;
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);
if (comm->me == 0) std::shuffle(&molrange[0], &molrange[Nmole], park_rng);
MPI_Bcast(&molrange[0], Nmole, MPI_INT, 0, world);
}
@ -1060,11 +1064,9 @@ void FixReaxFFSpecies::DeleteSpecies(int Nmole, int Nspec)
}
}
// push back delete_Tcount on every step
if (delete_Nsteps > 0) {
for (i = delete_Nsteps-1; i > 0; i--)
delete_Tcount[i] = delete_Tcount[i-1];
for (i = delete_Nsteps - 1; i > 0; i--) delete_Tcount[i] = delete_Tcount[i - 1];
delete_Tcount[0] += this_delete_Tcount;
}

2
src/REAXFF/fix_reaxff_species.h
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@ -51,8 +51,6 @@ class FixReaxFFSpecies : public Fix {
int *Mol2Spec;
double *clusterID;
AtomCoord *x0;
double bg_cut;
double **BOCut;
std::vector<std::string> del_species;