forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2121 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
24732209b8
commit
f62f8fc6e6
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@ -10,6 +10,7 @@ if ($1 == 1) then
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cp pair_eam_fs.cpp ..
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cp pair_sw.cpp ..
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cp pair_tersoff.cpp ..
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cp pair_tersoff_zbl.cpp ..
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cp pair_airebo.h ..
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cp pair_eam.h ..
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@ -17,6 +18,7 @@ if ($1 == 1) then
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cp pair_eam_fs.h ..
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cp pair_sw.h ..
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cp pair_tersoff.h ..
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cp pair_tersoff_zbl.h ..
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else if ($1 == 0) then
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@ -29,6 +31,7 @@ else if ($1 == 0) then
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rm ../pair_eam_fs.cpp
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rm ../pair_sw.cpp
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rm ../pair_tersoff.cpp
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rm ../pair_tersoff_zbl.cpp
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rm ../pair_airebo.h
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rm ../pair_eam.h
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@ -36,5 +39,6 @@ else if ($1 == 0) then
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rm ../pair_eam_fs.h
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rm ../pair_sw.h
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rm ../pair_tersoff.h
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rm ../pair_tersoff_zbl.h
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endif
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@ -41,6 +41,7 @@ PairTersoff::PairTersoff(LAMMPS *lmp) : Pair(lmp)
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single_enable = 0;
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one_coeff = 1;
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PI = 4.0*atan(1.0);
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PI2 = 2.0*atan(1.0);
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PI4 = atan(1.0);
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@ -21,14 +21,14 @@ namespace LAMMPS_NS {
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class PairTersoff : public Pair {
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public:
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PairTersoff(class LAMMPS *);
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~PairTersoff();
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virtual ~PairTersoff();
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void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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void init_style();
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double init_one(int, int);
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private:
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protected:
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struct Param {
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double lam1,lam2,lam3;
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double c,d,h;
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@ -39,9 +39,11 @@ 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 ZBLcut,ZBLexpscale;
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};
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double PI2,PI4;
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double PI,PI2,PI4;
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double cutmax; // max cutoff for all elements
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int nelements; // # of unique elements
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char **elements; // names of unique elements
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@ -52,9 +54,9 @@ class PairTersoff : public Pair {
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Param *params; // parameter set for an I-J-K interaction
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void allocate();
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void read_file(char *);
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virtual void read_file(char *);
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void setup();
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void repulsive(Param *, double, double &, int, double &);
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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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void force_zeta(Param *, double, double, double &, double &, int, double &);
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void attractive(Param *, double, double, double, double *, double *,
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@ -62,14 +64,14 @@ class PairTersoff : public Pair {
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double ters_fc(double, Param *);
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double ters_fc_d(double, Param *);
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double ters_fa(double, Param *);
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double ters_fa_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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double ters_gijk(double, Param *);
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double ters_gijk_d(double, Param *);
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void ters_zetaterm_d(double, double *, double, double *, double,
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double *, double *, double *, Param *);
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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 +1,285 @@
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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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David Farrell (NWU) - ZBL 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_zbl.h"
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#include "atom.h"
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#include "update.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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using namespace LAMMPS_NS;
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#define MAXLINE 1024
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#define DELTA 4
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/* ---------------------------------------------------------------------- */
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PairTersoffZBL::PairTersoffZBL(LAMMPS *lmp) : PairTersoff(lmp)
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{
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// hard-wired constants in metal or real units
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// a0 = Bohr radius
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// epsilon0 = permittivity of vacuum = q / energy-distance units
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// e = unit charge
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// 1 Kcal/mole = 0.043365121 eV
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if (strcmp(update->unit_style,"metal") == 0) {
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global_a_0 = 0.529;
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global_epsilon_0 = 0.00552635;
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global_e = 1.0;
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} else if (strcmp(update->unit_style,"real") == 0) {
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global_a_0 = 0.529;
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global_epsilon_0 = 0.00552635 * 0.043365121;
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global_e = 1.0;
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} else error->all("Pair tersoff/zbl requires metal or real units");
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}
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/* ---------------------------------------------------------------------- */
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void PairTersoffZBL::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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if (params) delete [] params;
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params = NULL;
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nparams = 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(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("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].gamma = atof(words[4]);
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params[nparams].lam3 = atof(words[5]);
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params[nparams].c = atof(words[6]);
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params[nparams].d = atof(words[7]);
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params[nparams].h = atof(words[8]);
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params[nparams].powern = atof(words[9]);
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params[nparams].beta = atof(words[10]);
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params[nparams].lam2 = atof(words[11]);
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params[nparams].bigb = atof(words[12]);
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params[nparams].bigr = atof(words[13]);
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params[nparams].bigd = atof(words[14]);
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params[nparams].lam1 = atof(words[15]);
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params[nparams].biga = atof(words[16]);
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params[nparams].Z_i = atof(words[17]);
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params[nparams].Z_j = atof(words[18]);
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params[nparams].ZBLcut = atof(words[19]);
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params[nparams].ZBLexpscale = atof(words[20]);
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// currently only allow m exponent of 1 or 3
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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].c < 0.0 ||
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params[nparams].d < 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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params[nparams].gamma < 0.0 ||
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params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
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params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
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error->all("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 PairTersoffZBL::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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// Tersoff repulsive portion
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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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double fforce_ters = param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1);
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double eng_ters = tmp_fc * param->biga * tmp_exp;
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// ZBL repulsive portion
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double esq = pow(global_e,2.0);
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double a_ij = (0.8854*global_a_0) /
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(pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
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double premult = (param->Z_i * param->Z_j * esq)/(4.0*PI*global_epsilon_0);
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double r_ov_a = r/a_ij;
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double phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
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0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*r_ov_a);
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double dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
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0.9423*0.5099*exp(-0.9423*r_ov_a) -
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0.4029*0.2802*exp(-0.4029*r_ov_a) -
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0.2016*0.02817*exp(-0.2016*r_ov_a));
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double fforce_ZBL = premult*-pow(r,-2.0)* phi + premult*pow(r,-1.0)*dphi;
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double eng_ZBL = premult*(1.0/r)*phi;
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// combine two parts with smoothing by Fermi-like function
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fforce = -(-F_fermi_d(r,param) * eng_ZBL +
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(1.0 - F_fermi(r,param))*fforce_ZBL +
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F_fermi_d(r,param)*eng_ters + F_fermi(r,param)*fforce_ters) / r;
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if (eflag)
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eng = (1.0 - F_fermi(r,param))*eng_ZBL + F_fermi(r,param)*eng_ters;
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffZBL::ters_fa(double r, Param *param)
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{
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if (r > param->bigr + param->bigd) return 0.0;
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return -param->bigb * exp(-param->lam2 * r) * ters_fc(r,param) *
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F_fermi(r,param);
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}
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/* ---------------------------------------------------------------------- */
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double PairTersoffZBL::ters_fa_d(double r, Param *param)
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{
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if (r > param->bigr + param->bigd) return 0.0;
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return param->bigb * exp(-param->lam2 * r) *
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(param->lam2 * ters_fc(r,param) * F_fermi(r,param) -
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ters_fc_d(r,param) * F_fermi(r,param) - ters_fc(r,param) *
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F_fermi_d(r,param));
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}
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/* ----------------------------------------------------------------------
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Fermi-like smoothing function
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------------------------------------------------------------------------- */
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double PairTersoffZBL::F_fermi(double r, Param *param)
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{
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return 1.0 / (1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)));
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}
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/* ----------------------------------------------------------------------
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Fermi-like smoothing function derivative with respect to r
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------------------------------------------------------------------------- */
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double PairTersoffZBL::F_fermi_d(double r, Param *param)
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{
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return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) /
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pow(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)),2.0);
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}
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@ -0,0 +1,43 @@
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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
|
||||
|
||||
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.
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------------------------------------------------------------------------- */
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#ifndef PAIR_TERSOFF_ZBL_H
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#define PAIR_TERSOFF_ZBL_H
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#include "pair_tersoff.h"
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namespace LAMMPS_NS {
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class PairTersoffZBL : public PairTersoff {
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public:
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PairTersoffZBL(class LAMMPS *);
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~PairTersoffZBL() {}
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private:
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double global_a_0; // Bohr radius for Coulomb repulsion
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double global_epsilon_0; // permittivity of vacuum for Coulomb repulsion
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double global_e; // proton charge (negative of electron charge)
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void read_file(char *);
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void repulsive(Param *, double, double &, int, double &);
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double ters_fa(double, Param *);
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double ters_fa_d(double, Param *);
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double F_fermi(double, Param *);
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double F_fermi_d(double, Param *);
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};
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}
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#endif
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@ -18,6 +18,7 @@
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#include "pair_eam_fs.h"
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||||
#include "pair_sw.h"
|
||||
#include "pair_tersoff.h"
|
||||
#include "pair_tersoff_zbl.h"
|
||||
#endif
|
||||
|
||||
#ifdef PairClass
|
||||
|
|
@ -27,4 +28,5 @@ PairStyle(eam/alloy,PairEAMAlloy)
|
|||
PairStyle(eam/fs,PairEAMFS)
|
||||
PairStyle(sw,PairSW)
|
||||
PairStyle(tersoff,PairTersoff)
|
||||
PairStyle(tersoff/zbl,PairTersoffZBL)
|
||||
#endif
|
||||
|
|
|
|||
|
|
@ -18,6 +18,7 @@
|
|||
#include "pair_eam_fs.h"
|
||||
#include "pair_sw.h"
|
||||
#include "pair_tersoff.h"
|
||||
#include "pair_tersoff_zbl.h"
|
||||
#endif
|
||||
|
||||
#ifdef PairClass
|
||||
|
|
@ -27,4 +28,5 @@ PairStyle(eam/alloy,PairEAMAlloy)
|
|||
PairStyle(eam/fs,PairEAMFS)
|
||||
PairStyle(sw,PairSW)
|
||||
PairStyle(tersoff,PairTersoff)
|
||||
PairStyle(tersoff/zbl,PairTersoffZBL)
|
||||
#endif
|
||||
|
|
|
|||
Loading…
Reference in New Issue