lammps-sys 0.6.0

/* ----------------------------------------------------------------------
   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 "pair_tersoff_mod_c.h"
#include <mpi.h>
#include <cmath>
#include <cstdlib>
#include <cstring>
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"

using namespace LAMMPS_NS;

#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];
      snprintf(str,128,"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 or 3

    params[nparams].powermint = int(params[nparams].powerm);

    if (
      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].lam1 < 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;
}