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add unit conversion support to pair style tersoff/table

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This commit is contained in:
Axel Kohlmeyer
2020-06-24 21:05:00 -04:00
parent 361f636700
commit 00332d299b
4 changed files with 154 additions and 124 deletions
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218
src/USER-MISC/pair_tersoff_table.cpp
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@ -33,6 +33,8 @@
#include "comm.h"
#include "memory.h"
#include "utils.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
#include "error.h"
@ -59,6 +61,7 @@ PairTersoffTable::PairTersoffTable(LAMMPS *lmp) : Pair(lmp)
restartinfo = 0;
one_coeff = 1;
manybody_flag = 1;
unit_convert_flag = utils::get_supported_conversions(utils::ENERGY);
nelements = 0;
elements = nullptr;
@ -840,146 +843,115 @@ double PairTersoffTable::init_one(int i, int j)
void PairTersoffTable::read_file(char *file)
{
int params_per_line = 17;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
params = nullptr;
nparams = maxparam = 0;
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
snprintf(str,128,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
PotentialFileReader reader(lmp, file, "TersoffTable", unit_convert_flag);
char *line;
// transparently convert units for supported conversions
// read each set of params from potential file
// one set of params can span multiple lines
// store params if all 3 element tags are in element list
int unit_convert = reader.get_unit_convert();
double conversion_factor = utils::get_conversion_factor(utils::ENERGY,
unit_convert);
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;
while((line = reader.next_line(NPARAMS_PER_LINE))) {
while (1) {
if (comm->me == 0) {
ptr = fgets(line,MAXLINE,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
try {
ValueTokenizer values(line);
// strip comment, skip line if blank
std::string iname = values.next_string();
std::string jname = values.next_string();
std::string kname = values.next_string();
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords == 0) continue;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next entry in file
// concatenate additional lines until have params_per_line words
int ielement, jelement, kelement;
while (nwords < params_per_line) {
n = strlen(line);
if (comm->me == 0) {
ptr = fgets(&line[n],MAXLINE-n,fp);
if (ptr == NULL) {
eof = 1;
fclose(fp);
} else n = strlen(line) + 1;
for (ielement = 0; ielement < nelements; ielement++)
if (iname == elements[ielement]) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (jname == elements[jelement]) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (kname == elements[kelement]) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
// some parameters are not used since only Tersoff_2 is implemented
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].powerm = values.next_double(); // not used
params[nparams].gamma = values.next_double(); // not used
params[nparams].lam3 = values.next_double(); // not used
params[nparams].c = values.next_double();
params[nparams].d = values.next_double();
params[nparams].h = values.next_double();
params[nparams].powern = values.next_double();
params[nparams].beta = values.next_double();
params[nparams].lam2 = values.next_double();
params[nparams].bigb = values.next_double();
double bigr = values.next_double();
double bigd = values.next_double();
params[nparams].cutoffR = bigr - bigd;
params[nparams].cutoffS = bigr + bigd;
params[nparams].lam1 = values.next_double();
params[nparams].biga = values.next_double();
if (unit_convert) {
params[nparams].biga *= conversion_factor;
params[nparams].bigb *= conversion_factor;
}
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}
MPI_Bcast(&eof,1,MPI_INT,0,world);
if (eof) break;
MPI_Bcast(&n,1,MPI_INT,0,world);
MPI_Bcast(line,n,MPI_CHAR,0,world);
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (params[nparams].c < 0.0 ||
params[nparams].d < 0.0 ||
params[nparams].powern < 0.0 ||
params[nparams].beta < 0.0 ||
params[nparams].lam2 < 0.0 ||
params[nparams].bigb < 0.0 ||
params[nparams].cutoffR < 0.0 ||
params[nparams].cutoffS < 0.0 ||
params[nparams].cutoffR > params[nparams].cutoffS ||
params[nparams].lam1 < 0.0 ||
params[nparams].biga < 0.0
) error->one(FLERR,"Illegal Tersoff parameter");
// only tersoff_2 parametrization is implemented
if (params[nparams].gamma != 1.0 || params[nparams].lam3 != 0.0)
error->one(FLERR,"Currently the tersoff/table pair_style only "
"implements the Tersoff_2 parametrization");
nparams++;
}
if (nwords != params_per_line)
error->all(FLERR,"Incorrect format in Tersoff potential file");
// words = ptrs to all words in line
nwords = 0;
words[nwords++] = strtok(line," \t\n\r\f");
while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next entry in file
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
maxparam += DELTA;
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
"pair:params");
}
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].powerm = atof(words[3]); // not used (only tersoff_2 is implemented)
params[nparams].gamma = atof(words[4]); // not used (only tersoff_2 is implemented)
params[nparams].lam3 = atof(words[5]); // not used (only tersoff_2 is implemented)
params[nparams].c = atof(words[6]);
params[nparams].d = atof(words[7]);
params[nparams].h = atof(words[8]);
params[nparams].powern = atof(words[9]);
params[nparams].beta = atof(words[10]);
params[nparams].lam2 = atof(words[11]);
params[nparams].bigb = atof(words[12]);
// current implementation is based on functional form
// of tersoff_2 as reported in the reference paper
double bigr = atof(words[13]);
double bigd = atof(words[14]);
params[nparams].cutoffR = bigr - bigd;
params[nparams].cutoffS = bigr + bigd;
params[nparams].lam1 = atof(words[15]);
params[nparams].biga = atof(words[16]);
if (params[nparams].c < 0.0 ||
params[nparams].d < 0.0 ||
params[nparams].powern < 0.0 ||
params[nparams].beta < 0.0 ||
params[nparams].lam2 < 0.0 ||
params[nparams].bigb < 0.0 ||
params[nparams].cutoffR < 0.0 ||
params[nparams].cutoffS < 0.0 ||
params[nparams].cutoffR > params[nparams].cutoffS ||
params[nparams].lam1 < 0.0 ||
params[nparams].biga < 0.0
) error->all(FLERR,"Illegal Tersoff parameter");
// only tersoff_2 parametrization is implemented
if (params[nparams].gamma != 1.0 || params[nparams].lam3 != 0.0)
error->all(FLERR,"Current tersoff/table pair_style implements only tersoff_2 parametrization");
nparams++;
}
delete [] words;
MPI_Bcast(&nparams, 1, MPI_INT, 0, world);
MPI_Bcast(&maxparam, 1, MPI_INT, 0, world);
if(comm->me != 0) {
params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params");
}
MPI_Bcast(params, maxparam*sizeof(Param), MPI_BYTE, 0, world);
}
/* ---------------------------------------------------------------------- */