forked from lijiext/lammps
removed extra file
This commit is contained in:
dstelter92
parent
dab232c542
commit
3dff9f2018
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@ -1,196 +0,0 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Ganga P Purja Pun (George Mason University, Fairfax)
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------------------------------------------------------------------------- */
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#include <math.h>
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include "pair_tersoff_mod_c.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "force.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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#include "math_const.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define MAXLINE 1024
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#define DELTA 4
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/* ---------------------------------------------------------------------- */
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void PairTersoffMODC::read_file(char *file)
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{
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int params_per_line = 21;
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char **words = new char*[params_per_line+1];
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memory->sfree(params);
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params = NULL;
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nparams = maxparam = 0;
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// open file on proc 0
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FILE *fp;
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if (comm->me == 0) {
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fp = force->open_potential(file);
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open Tersoff potential file %s",file);
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error->one(FLERR,str);
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}
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}
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// read each line out of file, skipping blank lines or leading '#'
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// store line of params if all 3 element tags are in element list
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int n,nwords,ielement,jelement,kelement;
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char line[MAXLINE],*ptr;
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int eof = 0;
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while (1) {
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if (comm->me == 0) {
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ptr = fgets(line,MAXLINE,fp);
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if (ptr == NULL) {
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eof = 1;
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fclose(fp);
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} else n = strlen(line) + 1;
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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if (eof) break;
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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// strip comment, skip line if blank
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = atom->count_words(line);
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if (nwords == 0) continue;
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// concatenate additional lines until have params_per_line words
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while (nwords < params_per_line) {
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n = strlen(line);
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if (comm->me == 0) {
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ptr = fgets(&line[n],MAXLINE-n,fp);
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if (ptr == NULL) {
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eof = 1;
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fclose(fp);
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} else n = strlen(line) + 1;
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}
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MPI_Bcast(&eof,1,MPI_INT,0,world);
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if (eof) break;
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MPI_Bcast(&n,1,MPI_INT,0,world);
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MPI_Bcast(line,n,MPI_CHAR,0,world);
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if ((ptr = strchr(line,'#'))) *ptr = '\0';
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nwords = atom->count_words(line);
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}
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if (nwords != params_per_line)
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error->all(FLERR,"Incorrect format in Tersoff potential file");
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// words = ptrs to all words in line
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nwords = 0;
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words[nwords++] = strtok(line," \t\n\r\f");
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while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
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// ielement,jelement,kelement = 1st args
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// if all 3 args are in element list, then parse this line
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// else skip to next line
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for (ielement = 0; ielement < nelements; ielement++)
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if (strcmp(words[0],elements[ielement]) == 0) break;
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if (ielement == nelements) continue;
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for (jelement = 0; jelement < nelements; jelement++)
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if (strcmp(words[1],elements[jelement]) == 0) break;
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if (jelement == nelements) continue;
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for (kelement = 0; kelement < nelements; kelement++)
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if (strcmp(words[2],elements[kelement]) == 0) break;
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if (kelement == nelements) continue;
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// load up parameter settings and error check their values
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if (nparams == maxparam) {
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maxparam += DELTA;
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params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
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"pair:params");
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}
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params[nparams].ielement = ielement;
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params[nparams].jelement = jelement;
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params[nparams].kelement = kelement;
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params[nparams].powerm = atof(words[3]);
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params[nparams].lam3 = atof(words[4]);
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params[nparams].h = atof(words[5]);
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params[nparams].powern = atof(words[6]);
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params[nparams].beta = atof(words[7]);
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params[nparams].lam2 = atof(words[8]);
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params[nparams].bigb = atof(words[9]);
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params[nparams].bigr = atof(words[10]);
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params[nparams].bigd = atof(words[11]);
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params[nparams].lam1 = atof(words[12]);
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params[nparams].biga = atof(words[13]);
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params[nparams].powern_del = atof(words[14]);
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params[nparams].c1 = atof(words[15]);
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params[nparams].c2 = atof(words[16]);
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params[nparams].c3 = atof(words[17]);
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params[nparams].c4 = atof(words[18]);
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params[nparams].c5 = atof(words[19]);
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params[nparams].c0 = atof(words[20]);
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// currently only allow m exponent of 1
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params[nparams].powermint = int(params[nparams].powerm);
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if (
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params[nparams].lam3 < 0.0 || params[nparams].powern < 0.0 ||
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params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
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params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
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params[nparams].bigd < 0.0 ||
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params[nparams].bigd > params[nparams].bigr ||
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params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
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params[nparams].powerm - params[nparams].powermint != 0.0 ||
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(params[nparams].powermint != 3 && params[nparams].powermint != 1))
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error->all(FLERR,"Illegal Tersoff parameter");
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nparams++;
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}
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delete [] words;
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}
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/* ---------------------------------------------------------------------- */
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void PairTersoffMODC::repulsive(Param *param, double rsq, double &fforce,
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int eflag, double &eng)
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{
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double r,tmp_fc,tmp_fc_d,tmp_exp;
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r = sqrt(rsq);
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tmp_fc = ters_fc(r,param);
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tmp_fc_d = ters_fc_d(r,param);
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tmp_exp = exp(-param->lam1 * r);
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fforce = -param->biga * tmp_exp * (tmp_fc_d - tmp_fc * param->lam1) / r - param->c0 * tmp_fc_d / r;
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if (eflag) eng = tmp_fc * param->biga * tmp_exp + param->c0 * tmp_fc;
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}
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@ -1,66 +0,0 @@
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/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(tersoff/mod/c,PairTersoffMODC)
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#else
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#ifndef LMP_PAIR_TERSOFF_MOD_C_H
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#define LMP_PAIR_TERSOFF_MOD_C_H
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#include "pair_tersoff_mod.h"
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namespace LAMMPS_NS {
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class PairTersoffMODC : public PairTersoffMOD {
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public:
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PairTersoffMODC(class LAMMPS *lmp) : PairTersoffMOD(lmp) {};
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~PairTersoffMODC() {}
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protected:
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void read_file(char *);
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void repulsive(Param *, double, double &, int, double &);
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Cannot open Tersoff potential file %s
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The specified potential file cannot be opened. Check that the path
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and name are correct.
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E: Incorrect format in Tersoff potential file
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Incorrect number of words per line in the potential file.
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E: Illegal Tersoff parameter
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One or more of the coefficients defined in the potential file is
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invalid.
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E: Potential file has duplicate entry
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The potential file has more than one entry for the same element.
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E: Potential file is missing an entry
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The potential file does not have a needed entry.
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*/
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