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pair_tersoff_mod_c.cpp
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Fri, Nov 8, 07:14

pair_tersoff_mod_c.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ganga P Purja Pun (George Mason University, Fairfax)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_tersoff_mod_c.h"
#include "atom.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define MAXLINE 1024
#define DELTA 4
/* ---------------------------------------------------------------------- */
void PairTersoffMODC::read_file(char *file)
{
int params_per_line = 21;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
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];
sprintf(str,"Cannot open Tersoff potential file %s",file);
error->one(FLERR,str);
}
}
// read each line out of file, skipping blank lines or leading '#'
// store line of params if all 3 element tags are in element list
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 = atom->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 = atom->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;
// ielement,jelement,kelement = 1st args
// if all 3 args are in element list, then parse this line
// else skip to next line
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]);
params[nparams].lam3 = atof(words[4]);
params[nparams].h = atof(words[5]);
params[nparams].powern = atof(words[6]);
params[nparams].beta = atof(words[7]);
params[nparams].lam2 = atof(words[8]);
params[nparams].bigb = atof(words[9]);
params[nparams].bigr = atof(words[10]);
params[nparams].bigd = atof(words[11]);
params[nparams].lam1 = atof(words[12]);
params[nparams].biga = atof(words[13]);
params[nparams].powern_del = atof(words[14]);
params[nparams].c1 = atof(words[15]);
params[nparams].c2 = atof(words[16]);
params[nparams].c3 = atof(words[17]);
params[nparams].c4 = atof(words[18]);
params[nparams].c5 = atof(words[19]);
params[nparams].c0 = atof(words[20]);
// currently only allow m exponent of 1
params[nparams].powermint = int(params[nparams].powerm);
if (
params[nparams].lam3 < 0.0 || params[nparams].powern < 0.0 ||
params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
params[nparams].bigd < 0.0 ||
params[nparams].bigd > params[nparams].bigr ||
params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
params[nparams].powerm - params[nparams].powermint != 0.0 ||
(params[nparams].powermint != 3 && params[nparams].powermint != 1))
error->all(FLERR,"Illegal Tersoff parameter");
nparams++;
}
delete [] words;
}
/* ---------------------------------------------------------------------- */
void PairTersoffMODC::repulsive(Param *param, double rsq, double &fforce,
int eflag, double &eng)
{
double r,tmp_fc,tmp_fc_d,tmp_exp;
r = sqrt(rsq);
tmp_fc = ters_fc(r,param);
tmp_fc_d = ters_fc_d(r,param);
tmp_exp = exp(-param->lam1 * r);
fforce = -param->biga * tmp_exp * (tmp_fc_d - tmp_fc * param->lam1) / r - param->c0 * tmp_fc_d / r;
if (eflag) eng = tmp_fc * param->biga * tmp_exp + param->c0 * tmp_fc;
}

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