forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10420 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
5a0cd49c32
commit
ab39e9a6ae
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@ -45,8 +45,10 @@ class PairTersoff : public Pair {
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double c1,c2,c3,c4;
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int ielement,jelement,kelement;
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int powermint;
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double Z_i,Z_j;
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double Z_i,Z_j; // added for TersoffZBL
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double ZBLcut,ZBLexpscale;
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double c5,ca1,ca4; // added for TersoffMOD
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double powern_del;
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};
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Param *params; // parameter set for an I-J-K interaction
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@ -60,22 +62,22 @@ class PairTersoff : public Pair {
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void allocate();
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virtual void read_file(char *);
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void setup();
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virtual void setup();
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virtual void repulsive(Param *, double, double &, int, double &);
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double zeta(Param *, double, double, double *, double *);
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virtual double zeta(Param *, double, double, double *, double *);
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virtual void force_zeta(Param *, double, double, double &,
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double &, int, double &);
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void attractive(Param *, double, double, double, double *, double *,
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double *, double *, double *);
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double ters_fc(double, Param *);
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double ters_fc_d(double, Param *);
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virtual double ters_fc(double, Param *);
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virtual double ters_fc_d(double, Param *);
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virtual double ters_fa(double, Param *);
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virtual double ters_fa_d(double, Param *);
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double ters_bij(double, Param *);
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double ters_bij_d(double, Param *);
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virtual double ters_bij(double, Param *);
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virtual double ters_bij_d(double, Param *);
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void ters_zetaterm_d(double, double *, double, double *, double,
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virtual void ters_zetaterm_d(double, double *, double, double *, double,
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double *, double *, double *, Param *);
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void costheta_d(double *, double, double *, double,
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double *, double *, double *);
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@ -0,0 +1,361 @@
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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: Aidan Thompson (SNL) - original Tersoff implementation
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Vitaly Dozhdikov (JIHT of RAS) - MOD addition
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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.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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PairTersoffMOD::PairTersoffMOD(LAMMPS *lmp) : PairTersoff(lmp) {}
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/* ---------------------------------------------------------------------- */
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void PairTersoffMOD::read_file(char *file)
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{
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int params_per_line = 20;
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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 = fopen(file,"r");
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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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// 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 PairTersoffMOD::setup()
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{
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int i,j,k,m,n;
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// set elem2param for all element triplet combinations
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// must be a single exact match to lines read from file
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// do not allow for ACB in place of ABC
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memory->destroy(elem2param);
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memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
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for (i = 0; i < nelements; i++)
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for (j = 0; j < nelements; j++)
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for (k = 0; k < nelements; k++) {
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n = -1;
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for (m = 0; m < nparams; m++) {
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if (i == params[m].ielement && j == params[m].jelement &&
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k == params[m].kelement) {
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if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
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n = m;
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}
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}
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if (n < 0) error->all(FLERR,"Potential file is missing an entry");
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elem2param[i][j][k] = n;
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}
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// compute parameter values derived from inputs
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for (m = 0; m < nparams; m++) {
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params[m].cut = params[m].bigr + params[m].bigd;
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params[m].cutsq = params[m].cut*params[m].cut;
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params[m].ca1 = pow(2.0*params[m].powern_del*1.0e-16,-1.0/params[m].powern);
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params[m].ca4 = 1.0/params[m].ca1;
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}
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// set cutmax to max of all params
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cutmax = 0.0;
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for (m = 0; m < nparams; m++)
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if (params[m].cut > cutmax) cutmax = params[m].cut;
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::zeta(Param *param, double rsqij, double rsqik,
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double *delrij, double *delrik)
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{
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double rij,rik,costheta,arg,ex_delr;
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rij = sqrt(rsqij);
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rik = sqrt(rsqik);
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costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
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delrij[2]*delrik[2]) / (rij*rik);
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if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
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else arg = param->lam3 * (rij-rik);
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if (arg > 69.0776) ex_delr = 1.e30;
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else if (arg < -69.0776) ex_delr = 0.0;
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else ex_delr = exp(arg);
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return ters_fc(rik,param) * ters_gijk_mod(costheta,param) * ex_delr;
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::ters_fc(double r, Param *param)
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{
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double ters_R = param->bigr;
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double ters_D = param->bigd;
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if (r < ters_R-ters_D) return 1.0;
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if (r > ters_R+ters_D) return 0.0;
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return 0.5*(1.0 - 1.125*sin(MY_PI2*(r - ters_R)/ters_D) -
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0.125*sin(3*MY_PI2*(r - ters_R)/ters_D));
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::ters_fc_d(double r, Param *param)
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{
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double ters_R = param->bigr;
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double ters_D = param->bigd;
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if (r < ters_R-ters_D) return 0.0;
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if (r > ters_R+ters_D) return 0.0;
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return -(0.375*MY_PI4/ters_D) * (3*cos(MY_PI2*(r - ters_R)/ters_D) +
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cos(3*MY_PI2*(r - ters_R)/ters_D));
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::ters_bij(double zeta, Param *param)
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{
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double tmp = param->beta * zeta;
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if (tmp > param->ca1) return pow(tmp, -param->powern/(2.0*param->powern_del));
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if (tmp < param->ca4) return 1.0;
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return pow(1.0 + pow(tmp,param->powern), -1.0/(2.0*param->powern_del));
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffMOD::ters_bij_d(double zeta, Param *param)
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{
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double tmp = param->beta * zeta;
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if (tmp > param->ca1) return -0.5*(param->powern/param->powern_del)*
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pow(tmp,-0.5*(param->powern/param->powern_del)) / zeta;
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if (tmp < param->ca4) return 0.0;
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double tmp_n = pow(tmp,param->powern);
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return -0.5 *(param->powern/param->powern_del)*
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pow(1.0+tmp_n, -1.0-(1.0/(2.0*param->powern_del)))*tmp_n / zeta;
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}
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/* ---------------------------------------------------------------------- */
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void PairTersoffMOD::ters_zetaterm_d(double prefactor,
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double *rij_hat, double rij,
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double *rik_hat, double rik,
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double *dri, double *drj, double *drk,
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Param *param)
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{
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double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
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double dcosdri[3],dcosdrj[3],dcosdrk[3];
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fc = ters_fc(rik,param);
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dfc = ters_fc_d(rik,param);
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if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
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else tmp = param->lam3 * (rij-rik);
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if (tmp > 69.0776) ex_delr = 1.e30;
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else if (tmp < -69.0776) ex_delr = 0.0;
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else ex_delr = exp(tmp);
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if (param->powermint == 3)
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ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
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else ex_delr_d = param->lam3 * ex_delr;
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cos_theta = vec3_dot(rij_hat,rik_hat);
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gijk = ters_gijk_mod(cos_theta,param);
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gijk_d = ters_gijk_d_mod(cos_theta,param);
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costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
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// compute the derivative wrt Ri
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// dri = -dfc*gijk*ex_delr*rik_hat;
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// dri += fc*gijk_d*ex_delr*dcosdri;
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// dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
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vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
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vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
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vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
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vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
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vec3_scale(prefactor,dri,dri);
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// compute the derivative wrt Rj
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// drj = fc*gijk_d*ex_delr*dcosdrj;
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// drj += fc*gijk*ex_delr_d*rij_hat;
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vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
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vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
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vec3_scale(prefactor,drj,drj);
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// compute the derivative wrt Rk
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// drk = dfc*gijk*ex_delr*rik_hat;
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// drk += fc*gijk_d*ex_delr*dcosdrk;
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// drk += -fc*gijk*ex_delr_d*rik_hat;
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vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
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vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
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vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
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vec3_scale(prefactor,drk,drk);
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}
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@ -0,0 +1,78 @@
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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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#ifdef PAIR_CLASS
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PairStyle(tersoff/mod,PairTersoffMOD)
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#else
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#ifndef LMP_PAIR_TERSOFF_MOD_H
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#define LMP_PAIR_TERSOFF_MOD_H
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||||
#include "pair_tersoff.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairTersoffMOD : public PairTersoff {
|
||||
public:
|
||||
PairTersoffMOD(class LAMMPS *);
|
||||
~PairTersoffMOD() {}
|
||||
|
||||
protected:
|
||||
void read_file(char *);
|
||||
void setup();
|
||||
double zeta(Param *, double, double, double *, double *);
|
||||
|
||||
double ters_fc(double, Param *);
|
||||
double ters_fc_d(double, Param *);
|
||||
double ters_bij(double, Param *);
|
||||
double ters_bij_d(double, Param *);
|
||||
void ters_zetaterm_d(double, double *, double, double *, double,
|
||||
double *, double *, double *, Param *);
|
||||
|
||||
// inlined functions for efficiency
|
||||
// these replace but do not override versions in PairTersoff
|
||||
// since overriding virtual inlined functions is best avoided
|
||||
|
||||
inline double ters_gijk_mod(const double costheta,
|
||||
const Param * const param) const {
|
||||
const double ters_c1 = param->c1;
|
||||
const double ters_c2 = param->c2;
|
||||
const double ters_c3 = param->c3;
|
||||
const double ters_c4 = param->c4;
|
||||
const double ters_c5 = param->c5;
|
||||
const double tmp_h = (param->h - costheta)*(param->h - costheta);
|
||||
|
||||
return ters_c1 + (ters_c2*tmp_h/(ters_c3 + tmp_h)) *
|
||||
(1.0 + ters_c4*exp(-ters_c5*tmp_h));
|
||||
}
|
||||
|
||||
inline double ters_gijk_d_mod(const double costheta,
|
||||
const Param * const param) const {
|
||||
const double ters_c2 = param->c2;
|
||||
const double ters_c3 = param->c3;
|
||||
const double ters_c4 = param->c4;
|
||||
const double ters_c5 = param->c5;
|
||||
const double tmp_h = (param->h - costheta)*(param->h - costheta);
|
||||
const double g1 = (param->h - costheta)/(ters_c3 + tmp_h);
|
||||
const double g2 = exp(-ters_c5*tmp_h);
|
||||
|
||||
return -2.0*ters_c2*g1*((1 + ters_c4*g2)*(1 + g1*(costheta - param->h)) -
|
||||
tmp_h*ters_c4*ters_c5*g2);
|
||||
}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue