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Update pair tersoff

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This commit is contained in:
Richard Berger
2020-05-27 16:49:26 -04:00
parent dddc34e214
commit c22bbecb58
2 changed files with 86 additions and 128 deletions
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14
src/MANYBODY/pair_sw.cpp
View File

@ -349,7 +349,7 @@ double PairSW::init_one(int i, int j)
void PairSW::read_file(char *file)
{
memory->sfree(params);
params = NULL;
params = nullptr;
nparams = maxparam = 0;
// open file on proc 0
@ -362,9 +362,9 @@ void PairSW::read_file(char *file)
try {
ValueTokenizer values(line, " \t\n\r\f");
std::string iword = values.next_string();
std::string jword = values.next_string();
std::string kword = values.next_string();
std::string iname = values.next_string();
std::string jname = values.next_string();
std::string kname = values.next_string();
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
@ -372,13 +372,13 @@ void PairSW::read_file(char *file)
int ielement, jelement, kelement;
for (ielement = 0; ielement < nelements; ielement++)
if (iword == elements[ielement]) break;
if (iname == elements[ielement]) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (jword == elements[jelement]) break;
if (jname == elements[jelement]) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (kword == elements[kelement]) break;
if (kname == elements[kelement]) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values

132
src/MANYBODY/pair_tersoff.cpp
View File

@ -29,6 +29,8 @@
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
#include "math_const.h"
#include "math_special.h"
@ -392,93 +394,40 @@ double PairTersoff::init_one(int i, int j)
void PairTersoff::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, "Tersoff");
char * line;
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
while(line = reader.next_line(Param::NPARAMS_PER_LINE)) {
try {
ValueTokenizer values(line, " \t\n\r\f");
int n,nwords,ielement,jelement,kelement;
char line[MAXLINE],*ptr;
int eof = 0;
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);
// strip comment, skip line if blank
if ((ptr = strchr(line,'#'))) *ptr = '\0';
nwords = utils::count_words(line);
if (nwords == 0) continue;
// concatenate additional lines until have params_per_line words
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;
}
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 (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;
std::string iname = values.next_string();
std::string jname = values.next_string();
std::string kname = values.next_string();
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next line
// else skip to next entry in file
int ielement, jelement, kelement;
for (ielement = 0; ielement < nelements; ielement++)
if (strcmp(words[0],elements[ielement]) == 0) break;
if (iname == elements[ielement]) break;
if (ielement == nelements) continue;
for (jelement = 0; jelement < nelements; jelement++)
if (strcmp(words[1],elements[jelement]) == 0) break;
if (jname == elements[jelement]) break;
if (jelement == nelements) continue;
for (kelement = 0; kelement < nelements; kelement++)
if (strcmp(words[2],elements[kelement]) == 0) break;
if (kname == elements[kelement]) break;
if (kelement == nelements) continue;
// load up parameter settings and error check their values
if (nparams == maxparam) {
@ -490,25 +439,26 @@ void PairTersoff::read_file(char *file)
params[nparams].ielement = ielement;
params[nparams].jelement = jelement;
params[nparams].kelement = kelement;
params[nparams].powerm = atof(words[3]);
params[nparams].gamma = atof(words[4]);
params[nparams].lam3 = atof(words[5]);
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]);
params[nparams].bigr = atof(words[13]);
params[nparams].bigd = atof(words[14]);
params[nparams].lam1 = atof(words[15]);
params[nparams].biga = atof(words[16]);
params[nparams].powerm = values.next_double();
params[nparams].gamma = values.next_double();
params[nparams].lam3 = values.next_double();
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();
params[nparams].bigr = values.next_double();
params[nparams].bigd = values.next_double();
params[nparams].lam1 = values.next_double();
params[nparams].biga = values.next_double();
params[nparams].powermint = int(params[nparams].powerm);
} catch (TokenizerException & e) {
error->one(FLERR, e.what());
}
// currently only allow m exponent of 1 or 3
params[nparams].powermint = int(params[nparams].powerm);
if (params[nparams].c < 0.0 ||
params[nparams].d < 0.0 ||
params[nparams].powern < 0.0 ||
@ -524,12 +474,20 @@ void PairTersoff::read_file(char *file)
(params[nparams].powermint != 3 &&
params[nparams].powermint != 1) ||
params[nparams].gamma < 0.0)
error->all(FLERR,"Illegal Tersoff parameter");
error->one(FLERR,"Illegal Tersoff parameter");
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);
}
/* ---------------------------------------------------------------------- */