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pair_tersoff_zbl_omp.cpp.orig
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Fri, Feb 28, 23:28

pair_tersoff_zbl_omp.cpp.orig
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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: Aidan Thompson (SNL) - original Tersoff implementation
David Farrell (NWU) - ZBL addition
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_tersoff_zbl_omp.h"
#include "atom.h"
#include "update.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"
#include "math_special.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
#define MAXLINE 1024
#define DELTA 4
/* ----------------------------------------------------------------------
Fermi-like smoothing function
------------------------------------------------------------------------- */
static double F_fermi(const double r, const double expsc, const double cut)
{
return 1.0 / (1.0 + exp(-expsc*(r-cut)));
}
/* ----------------------------------------------------------------------
Fermi-like smoothing function derivative with respect to r
------------------------------------------------------------------------- */
static double F_fermi_d(const double r, const double expsc, const double cut)
{
return expsc*exp(-expsc*(r-cut)) / square(1.0 + exp(-expsc*(r-cut)));
}
/* ---------------------------------------------------------------------- */
PairTersoffZBLOMP::PairTersoffZBLOMP(LAMMPS *lmp) : PairTersoffOMP(lmp)
{
// hard-wired constants in metal or real units
// a0 = Bohr radius
// epsilon0 = permittivity of vacuum = q / energy-distance units
// e = unit charge
// 1 Kcal/mole = 0.043365121 eV
if (strcmp(update->unit_style,"metal") == 0) {
global_a_0 = 0.529;
global_epsilon_0 = 0.00552635;
global_e = 1.0;
} else if (strcmp(update->unit_style,"real") == 0) {
global_a_0 = 0.529;
global_epsilon_0 = 0.00552635 * 0.043365121;
global_e = 1.0;
} else error->all(FLERR,"Pair tersoff/zbl requires metal or real units");
}
/* ---------------------------------------------------------------------- */
void PairTersoffZBLOMP::read_file(char *file)
{
int params_per_line = 21;
char **words = new char*[params_per_line+1];
memory->sfree(params);
params = NULL;
nparams = 0;
// open file on proc 0
FILE *fp;
if (comm->me == 0) {
fp = fopen(file,"r");
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].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].Z_i = atof(words[17]);
params[nparams].Z_j = atof(words[18]);
params[nparams].ZBLcut = atof(words[19]);
params[nparams].ZBLexpscale = atof(words[20]);
// currently only allow m exponent of 1 or 3
params[nparams].powermint = int(params[nparams].powerm);
if (
params[nparams].lam3 < 0.0 || 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].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) ||
params[nparams].gamma < 0.0 ||
params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
error->all(FLERR,"Illegal Tersoff parameter");
nparams++;
}
delete [] words;
}
/* ---------------------------------------------------------------------- */
void PairTersoffZBLOMP::force_zeta(Param *param, double rsq, double zeta_ij,
double &fforce, double &prefactor,
int eflag, double &eng)
{
double r,fa,fa_d,bij;
r = sqrt(rsq);
fa = (r > param->bigr + param->bigd) ? 0.0 :
-param->bigb * exp(-param->lam2 * r) * ters_fc(r,param) *
F_fermi(r,param->ZBLexpscale,param->ZBLcut);
fa_d = (r > param->bigr + param->bigd) ? 0.0 :
param->bigb * exp(-param->lam2 * r) *
(param->lam2 * ters_fc(r,param) *
F_fermi(r,param->ZBLexpscale,param->ZBLcut) -
ters_fc_d(r,param) * F_fermi(r,param->ZBLexpscale,param->ZBLcut)
- ters_fc(r,param) * F_fermi_d(r,param->ZBLexpscale,param->ZBLcut));
bij = ters_bij(zeta_ij,param);
fforce = 0.5*bij*fa_d / r;
prefactor = -0.5*fa * ters_bij_d(zeta_ij,param);
if (eflag) eng = 0.5*bij*fa;
}
/* ---------------------------------------------------------------------- */
void PairTersoffZBLOMP::repulsive(Param *param, double rsq, double &fforce,
int eflag, double &eng)
{
double r,tmp_fc,tmp_fc_d,tmp_exp;
// Tersoff repulsive portion
r = sqrt(rsq);
tmp_fc = ters_fc(r,param);
tmp_fc_d = ters_fc_d(r,param);
tmp_exp = exp(-param->lam1 * r);
double fforce_ters = param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1);
double eng_ters = tmp_fc * param->biga * tmp_exp;
// ZBL repulsive portion
double esq = square(global_e);
double a_ij = (0.8854*global_a_0) /
(pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0);
double r_ov_a = r/a_ij;
double phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*r_ov_a);
double dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
0.9423*0.5099*exp(-0.9423*r_ov_a) -
0.4029*0.2802*exp(-0.4029*r_ov_a) -
0.2016*0.02817*exp(-0.2016*r_ov_a));
double fforce_ZBL = premult*-rsq* phi + premult/r*dphi;
double eng_ZBL = premult/r*phi;
// combine two parts with smoothing by Fermi-like function
fforce = -(-F_fermi_d(r,param->ZBLexpscale,param->ZBLcut) * eng_ZBL +
(1.0 - F_fermi(r,param->ZBLexpscale,param->ZBLcut))*fforce_ZBL +
F_fermi_d(r,param->ZBLexpscale,param->ZBLcut)*eng_ters +
F_fermi(r,param->ZBLexpscale,param->ZBLcut)*fforce_ters) / r;
if (eflag)
eng = (1.0 - F_fermi(r,param->ZBLexpscale,param->ZBLcut))*eng_ZBL +
F_fermi(r,param->ZBLexpscale,param->ZBLcut)*eng_ters;
}

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