forked from lijiext/lammps
add gao-weber potentials (regular and with ZBL core) with SiC potential files
NOTE: documentation is missing
This commit is contained in:
Axel Kohlmeyer
parent
06c151421c
commit
d9d4ef17c8
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# DATE: 2016-05-06 CONTRIBUTOR: German Samolyuk, samolyuk@gmail.com CITATION: ???
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# Gao-Weber parameters for various elements and mixtures
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units:
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# format of a single entry (one or more lines):
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# element 1, element 2, element 3,
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# m, gamma, lambda3, c, d, h, n, beta, lambda2, X_ij*B, R, D, lambda1, A
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#E1 E2 E3 m gamma lambda3 c d h n beta lambda2 B R D lambda1 A
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Si Si Si 1 0.013318 0 14 2.1 -1 0.78000 1 1.80821400248640 632.658058300867 2.35 0.15 2.38684248328205 1708.79738703139
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Si Si C 1 0.013318 0 14 2.1 -1 0.78000 1 1.80821400248640 632.658058300867 2.35 0.15 2.38684248328205 1708.79738703139
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Si C Si 1 0.013318 0 14 2.1 -1 0.78000 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234
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C Si Si 1 0.011304 0 19 2.5 -1 0.80468 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234
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C C Si 1 0.011304 0 19 2.5 -1 0.80469 1 1.76776695296637 203.208547714849 2.35 0.15 2.54558441227157 458.510465798439
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C Si C 1 0.011304 0 19 2.5 -1 0.80469 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234
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Si C C 1 0.013318 0 14 2.1 -1 0.78000 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234
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C C C 1 0.011304 0 19 2.5 -1 0.80469 1 1.76776695296637 203.208547714849 2.35 0.15 2.54558441227157 458.510465798439
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# DATE: 2016-05-06 CONTRIBUTOR: German Samolyuk, samolyuk@gmail.com CITATION: ???
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# Gao-Weber parameters for various elements and mixtures
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# multiple entries can be added to this file, LAMMPS reads the ones it needs
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# these entries are in LAMMPS "metal" units:
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# format of a single entry (one or more lines):
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# element 1, element 2, element 3,
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# m, gamma, lambda3, c, d, h, n, beta, lambda2, X_ij*B, R, D, lambda1, A
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#E1 E2 E3 m gamma lambda3 c d h n beta lambda2 B R D lambda1 A Z_i, Z_j, ZBLcut, ZBLexpscale
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Si Si Si 1 0.013318 0 14 2.1 -1 0.78000 1 1.80821400248640 632.658058300867 2.35 0.15 2.38684248328205 1708.79738703139 14 14 .95 14
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Si Si C 1 0.013318 0 14 2.1 -1 0.78000 1 1.80821400248640 632.658058300867 2.35 0.15 2.38684248328205 1708.79738703139 14 14 .95 14
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Si C Si 1 0.013318 0 14 2.1 -1 0.78000 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234 14 6 .95 14
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C Si Si 1 0.011304 0 19 2.5 -1 0.80468 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234 6 14 .95 14
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C C Si 1 0.011304 0 19 2.5 -1 0.80469 1 1.76776695296637 203.208547714849 2.35 0.15 2.54558441227157 458.510465798439 6 6 .95 14
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C Si C 1 0.011304 0 19 2.5 -1 0.80469 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234 6 14 .95 14
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Si C C 1 0.013318 0 14 2.1 -1 0.78000 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234 14 6 .95 14
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C C C 1 0.011304 0 19 2.5 -1 0.80469 1 1.76776695296637 203.208547714849 2.35 0.15 2.54558441227157 458.510465798439 6 6 .95 14
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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: German Samolyuk (ORNL)
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based on PairTersoff by Aidan Thompson (SNL)
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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_gw.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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PairGW::PairGW(LAMMPS *lmp) : Pair(lmp)
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{
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single_enable = 0;
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restartinfo = 0;
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one_coeff = 1;
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manybody_flag = 1;
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nelements = 0;
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elements = NULL;
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nparams = maxparam = 0;
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params = NULL;
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elem2param = NULL;
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map = NULL;
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}
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/* ----------------------------------------------------------------------
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check if allocated, since class can be destructed when incomplete
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------------------------------------------------------------------------- */
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PairGW::~PairGW()
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{
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if (elements)
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for (int i = 0; i < nelements; i++) delete [] elements[i];
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delete [] elements;
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memory->destroy(params);
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memory->destroy(elem2param);
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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delete [] map;
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairGW::compute(int eflag, int vflag)
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{
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int i,j,k,ii,jj,kk,inum,jnum;
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int itag,jtag,itype,jtype,ktype,iparam_ij,iparam_ijk;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,rsq1,rsq2;
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double delr1[3],delr2[3],fi[3],fj[3],fk[3];
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double zeta_ij, prefactor;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = vflag_atom = 0;
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double **x = atom->x;
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double **f = atom->f;
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tagint *tag = atom->tag;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int newton_pair = force->newton_pair;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over full neighbor list of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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itag = tag[i];
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itype = map[type[i]];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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// two-body interactions, skip half of them
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtag = tag[j];
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if (itag > jtag) {
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if ((itag+jtag) % 2 == 0) continue;
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} else if (itag < jtag) {
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if ((itag+jtag) % 2 == 1) continue;
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} else {
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if (x[j][2] < x[i][2]) continue;
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if (x[j][2] == ztmp && x[j][1] < ytmp) continue;
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if (x[j][2] == ztmp && x[j][1] == ytmp && x[j][0] < xtmp) continue;
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}
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jtype = map[type[j]];
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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iparam_ij = elem2param[itype][jtype][jtype];
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if (rsq > params[iparam_ij].cutsq) continue;
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repulsive(¶ms[iparam_ij],rsq,fpair,eflag,evdwl);
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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}
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// three-body interactions
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// skip immediately if I-J is not within cutoff
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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j &= NEIGHMASK;
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jtype = map[type[j]];
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iparam_ij = elem2param[itype][jtype][jtype];
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delr1[0] = x[j][0] - xtmp;
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delr1[1] = x[j][1] - ytmp;
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delr1[2] = x[j][2] - ztmp;
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rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2];
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if (rsq1 > params[iparam_ij].cutsq) continue;
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// accumulate bondorder zeta for each i-j interaction via loop over k
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zeta_ij = 1.0;
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for (kk = 0; kk < jnum; kk++) {
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if (jj == kk) continue;
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k = jlist[kk];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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iparam_ijk = elem2param[itype][jtype][ktype];
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delr2[0] = x[k][0] - xtmp;
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delr2[1] = x[k][1] - ytmp;
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delr2[2] = x[k][2] - ztmp;
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rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
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if (rsq2 > params[iparam_ijk].cutsq) continue;
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zeta_ij += zeta(¶ms[iparam_ijk],rsq1,rsq2,delr1,delr2);
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}
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// pairwise force due to zeta
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force_zeta(¶ms[iparam_ij],rsq1,zeta_ij,fpair,prefactor,eflag,evdwl);
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f[i][0] += delr1[0]*fpair;
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f[i][1] += delr1[1]*fpair;
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f[i][2] += delr1[2]*fpair;
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f[j][0] -= delr1[0]*fpair;
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f[j][1] -= delr1[1]*fpair;
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f[j][2] -= delr1[2]*fpair;
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,-fpair,-delr1[0],-delr1[1],-delr1[2]);
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// attractive term via loop over k
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for (kk = 0; kk < jnum; kk++) {
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if (jj == kk) continue;
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k = jlist[kk];
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k &= NEIGHMASK;
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ktype = map[type[k]];
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iparam_ijk = elem2param[itype][jtype][ktype];
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delr2[0] = x[k][0] - xtmp;
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delr2[1] = x[k][1] - ytmp;
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delr2[2] = x[k][2] - ztmp;
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rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2];
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if (rsq2 > params[iparam_ijk].cutsq) continue;
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attractive(¶ms[iparam_ijk],prefactor,
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rsq1,rsq2,delr1,delr2,fi,fj,fk);
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f[i][0] += fi[0];
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f[i][1] += fi[1];
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f[i][2] += fi[2];
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f[j][0] += fj[0];
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f[j][1] += fj[1];
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f[j][2] += fj[2];
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f[k][0] += fk[0];
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f[k][1] += fk[1];
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f[k][2] += fk[2];
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if (vflag_atom) v_tally3(i,j,k,fj,fk,delr1,delr2);
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} // kk
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} // jj
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} // ii
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ---------------------------------------------------------------------- */
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void PairGW::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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memory->create(setflag,n+1,n+1,"pair:setflag");
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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map = new int[n+1];
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairGW::settings(int narg, char **arg)
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{
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if (narg != 0) error->all(FLERR,"Illegal pair_style command");
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairGW::coeff(int narg, char **arg)
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{
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int i,j,n;
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if (!allocated) allocate();
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if (narg != 3 + atom->ntypes)
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error->all(FLERR,"Incorrect args for pair coefficients");
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// insure I,J args are * *
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if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
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error->all(FLERR,"Incorrect args for pair coefficients");
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// read args that map atom types to elements in potential file
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// map[i] = which element the Ith atom type is, -1 if NULL
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// nelements = # of unique elements
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// elements = list of element names
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if (elements) {
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for (i = 0; i < nelements; i++) delete [] elements[i];
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delete [] elements;
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}
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elements = new char*[atom->ntypes];
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for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
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nelements = 0;
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for (i = 3; i < narg; i++) {
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if (strcmp(arg[i],"NULL") == 0) {
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map[i-2] = -1;
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continue;
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}
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for (j = 0; j < nelements; j++)
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if (strcmp(arg[i],elements[j]) == 0) break;
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map[i-2] = j;
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if (j == nelements) {
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n = strlen(arg[i]) + 1;
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elements[j] = new char[n];
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strcpy(elements[j],arg[i]);
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nelements++;
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}
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}
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// read potential file and initialize potential parameters
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read_file(arg[2]);
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setup_params();
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// clear setflag since coeff() called once with I,J = * *
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n = atom->ntypes;
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for (i = 1; i <= n; i++)
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for (j = i; j <= n; j++)
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setflag[i][j] = 0;
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// set setflag i,j for type pairs where both are mapped to elements
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int count = 0;
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for (i = 1; i <= n; i++)
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for (j = i; j <= n; j++)
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if (map[i] >= 0 && map[j] >= 0) {
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setflag[i][j] = 1;
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count++;
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}
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if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairGW::init_style()
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{
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if (atom->tag_enable == 0)
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error->all(FLERR,"Pair style GW requires atom IDs");
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if (force->newton_pair == 0)
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error->all(FLERR,"Pair style GW requires newton pair on");
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// need a full neighbor list
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int irequest = neighbor->request(this,instance_me);
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neighbor->requests[irequest]->half = 0;
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neighbor->requests[irequest]->full = 1;
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairGW::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
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return cutmax;
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}
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/* ---------------------------------------------------------------------- */
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void PairGW::read_file(char *file)
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{
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int params_per_line = 17;
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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;
|
||||
if (comm->me == 0) {
|
||||
fp = force->open_potential(file);
|
||||
if (fp == NULL) {
|
||||
char str[128];
|
||||
sprintf(str,"Cannot open GW 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 GW 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]);
|
||||
|
||||
// currently only allow m exponent of 1 or 3
|
||||
|
||||
params[nparams].powermint = int(params[nparams].powerm);
|
||||
|
||||
if (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].lam1 < 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)
|
||||
error->all(FLERR,"Illegal GW parameter");
|
||||
|
||||
nparams++;
|
||||
}
|
||||
|
||||
delete [] words;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGW::setup_params()
|
||||
{
|
||||
int i,j,k,m,n;
|
||||
|
||||
// set elem2param for all element triplet combinations
|
||||
// must be a single exact match to lines read from file
|
||||
// do not allow for ACB in place of ABC
|
||||
|
||||
memory->destroy(elem2param);
|
||||
memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
|
||||
|
||||
for (i = 0; i < nelements; i++)
|
||||
for (j = 0; j < nelements; j++)
|
||||
for (k = 0; k < nelements; k++) {
|
||||
n = -1;
|
||||
for (m = 0; m < nparams; m++) {
|
||||
if (i == params[m].ielement && j == params[m].jelement &&
|
||||
k == params[m].kelement) {
|
||||
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
|
||||
n = m;
|
||||
}
|
||||
}
|
||||
if (n < 0) error->all(FLERR,"Potential file is missing an entry");
|
||||
elem2param[i][j][k] = n;
|
||||
}
|
||||
|
||||
|
||||
// compute parameter values derived from inputs
|
||||
|
||||
for (m = 0; m < nparams; m++) {
|
||||
params[m].cut = params[m].bigr + params[m].bigd;
|
||||
params[m].cutsq = params[m].cut*params[m].cut;
|
||||
|
||||
params[m].c1 = pow(2.0*params[m].powern*1.0e-16,-1.0/params[m].powern);
|
||||
params[m].c2 = pow(2.0*params[m].powern*1.0e-8,-1.0/params[m].powern);
|
||||
params[m].c3 = 1.0/params[m].c2;
|
||||
params[m].c4 = 1.0/params[m].c1;
|
||||
}
|
||||
|
||||
// set cutmax to max of all params
|
||||
|
||||
cutmax = 0.0;
|
||||
for (m = 0; m < nparams; m++)
|
||||
if (params[m].cut > cutmax) cutmax = params[m].cut;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGW::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 = gw_fc(r,param);
|
||||
tmp_fc_d = gw_fc_d(r,param);
|
||||
tmp_exp = exp(-param->lam1 * r);
|
||||
fforce = -param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1) / r;
|
||||
if (eflag) eng = tmp_fc * param->biga * tmp_exp;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGW::zeta(Param *param, double rsqij, double rsqik,
|
||||
double *delrij, double *delrik)
|
||||
{
|
||||
double rij,rik,costheta,arg,ex_delr;
|
||||
|
||||
rij = sqrt(rsqij);
|
||||
rik = sqrt(rsqik);
|
||||
costheta = (delrij[0]*delrik[0] + delrij[1]*delrik[1] +
|
||||
delrij[2]*delrik[2]) / (rij*rik);
|
||||
|
||||
if (param->powermint == 3) arg = pow(param->lam3 * (rij-rik),3.0);
|
||||
else arg = param->lam3 * (rij-rik);
|
||||
|
||||
if (arg > 69.0776) ex_delr = 1.e30;
|
||||
else if (arg < -69.0776) ex_delr = 0.0;
|
||||
else ex_delr = exp(arg);
|
||||
|
||||
return gw_fc(rik,param) * gw_gijk(costheta,param) * ex_delr;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGW::force_zeta(Param *param_i, double rsq, double zeta_ij,
|
||||
double &fforce, double &prefactor,
|
||||
int eflag, double &eng)
|
||||
{
|
||||
double r,fa,fa_d,bij;
|
||||
|
||||
r = sqrt(rsq);
|
||||
fa = gw_fa(r,param_i);
|
||||
fa_d = gw_fa_d(r,param_i);
|
||||
bij = gw_bij(zeta_ij,param_i);
|
||||
fforce = 0.5*bij*fa_d / r;
|
||||
prefactor = -0.5*fa * gw_bij_d(zeta_ij,param_i);
|
||||
if (eflag) eng = 0.5*bij*fa;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
attractive term
|
||||
use param_ij cutoff for rij test
|
||||
use param_ijk cutoff for rik test
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGW::attractive(Param *param, double prefactor,
|
||||
double rsqij, double rsqik,
|
||||
double *delrij, double *delrik,
|
||||
double *fi, double *fj, double *fk)
|
||||
{
|
||||
double rij_hat[3],rik_hat[3];
|
||||
double rij,rijinv,rik,rikinv;
|
||||
|
||||
rij = sqrt(rsqij);
|
||||
rijinv = 1.0/rij;
|
||||
vec3_scale(rijinv,delrij,rij_hat);
|
||||
|
||||
rik = sqrt(rsqik);
|
||||
rikinv = 1.0/rik;
|
||||
vec3_scale(rikinv,delrik,rik_hat);
|
||||
|
||||
gw_zetaterm_d(prefactor,rij_hat,rij,rik_hat,rik,fi,fj,fk,param);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGW::gw_fc(double r, Param *param)
|
||||
{
|
||||
double gw_R = param->bigr;
|
||||
double gw_D = param->bigd;
|
||||
|
||||
if (r < gw_R-gw_D) return 1.0;
|
||||
if (r > gw_R+gw_D) return 0.0;
|
||||
return 0.5*(1.0 - sin(MY_PI2*(r - gw_R)/gw_D));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGW::gw_fc_d(double r, Param *param)
|
||||
{
|
||||
double gw_R = param->bigr;
|
||||
double gw_D = param->bigd;
|
||||
|
||||
if (r < gw_R-gw_D) return 0.0;
|
||||
if (r > gw_R+gw_D) return 0.0;
|
||||
return -(MY_PI4/gw_D) * cos(MY_PI2*(r - gw_R)/gw_D);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGW::gw_fa(double r, Param *param)
|
||||
{
|
||||
if (r > param->bigr + param->bigd) return 0.0;
|
||||
return -param->bigb * exp(-param->lam2 * r) * gw_fc(r,param);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGW::gw_fa_d(double r, Param *param)
|
||||
{
|
||||
if (r > param->bigr + param->bigd) return 0.0;
|
||||
return param->bigb * exp(-param->lam2 * r) *
|
||||
(param->lam2 * gw_fc(r,param) - gw_fc_d(r,param));
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGW::gw_bij(double zeta_ij, Param *param_i)
|
||||
{
|
||||
double tmp = param_i->beta * zeta_ij;
|
||||
return pow(tmp,-param_i->powern);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGW::gw_bij_d(double zeta_ij, Param *param_i)
|
||||
{
|
||||
double tmp = param_i->beta * zeta_ij;
|
||||
return - param_i->powern * pow(tmp,-param_i->powern-1)*tmp / zeta_ij;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGW::gw_zetaterm_d(double prefactor,
|
||||
double *rij_hat, double rij,
|
||||
double *rik_hat, double rik,
|
||||
double *dri, double *drj, double *drk,
|
||||
Param *param)
|
||||
{
|
||||
double gijk,gijk_d,ex_delr,ex_delr_d,fc,dfc,cos_theta,tmp;
|
||||
double dcosdri[3],dcosdrj[3],dcosdrk[3];
|
||||
|
||||
fc = gw_fc(rik,param);
|
||||
dfc = gw_fc_d(rik,param);
|
||||
if (param->powermint == 3) tmp = pow(param->lam3 * (rij-rik),3.0);
|
||||
else tmp = param->lam3 * (rij-rik);
|
||||
|
||||
if (tmp > 69.0776) ex_delr = 1.e30;
|
||||
else if (tmp < -69.0776) ex_delr = 0.0;
|
||||
else ex_delr = exp(tmp);
|
||||
|
||||
if (param->powermint == 3)
|
||||
ex_delr_d = 3.0*pow(param->lam3,3.0) * pow(rij-rik,2.0)*ex_delr;
|
||||
else ex_delr_d = param->lam3 * ex_delr;
|
||||
|
||||
cos_theta = vec3_dot(rij_hat,rik_hat);
|
||||
gijk = gw_gijk(cos_theta,param);
|
||||
gijk_d = gw_gijk_d(cos_theta,param);
|
||||
costheta_d(rij_hat,rij,rik_hat,rik,dcosdri,dcosdrj,dcosdrk);
|
||||
|
||||
// compute the derivative wrt Ri
|
||||
// dri = -dfc*gijk*ex_delr*rik_hat;
|
||||
// dri += fc*gijk_d*ex_delr*dcosdri;
|
||||
// dri += fc*gijk*ex_delr_d*(rik_hat - rij_hat);
|
||||
|
||||
vec3_scale(-dfc*gijk*ex_delr,rik_hat,dri);
|
||||
vec3_scaleadd(fc*gijk_d*ex_delr,dcosdri,dri,dri);
|
||||
vec3_scaleadd(fc*gijk*ex_delr_d,rik_hat,dri,dri);
|
||||
vec3_scaleadd(-fc*gijk*ex_delr_d,rij_hat,dri,dri);
|
||||
vec3_scale(prefactor,dri,dri);
|
||||
|
||||
// compute the derivative wrt Rj
|
||||
// drj = fc*gijk_d*ex_delr*dcosdrj;
|
||||
// drj += fc*gijk*ex_delr_d*rij_hat;
|
||||
|
||||
vec3_scale(fc*gijk_d*ex_delr,dcosdrj,drj);
|
||||
vec3_scaleadd(fc*gijk*ex_delr_d,rij_hat,drj,drj);
|
||||
vec3_scale(prefactor,drj,drj);
|
||||
|
||||
// compute the derivative wrt Rk
|
||||
// drk = dfc*gijk*ex_delr*rik_hat;
|
||||
// drk += fc*gijk_d*ex_delr*dcosdrk;
|
||||
// drk += -fc*gijk*ex_delr_d*rik_hat;
|
||||
|
||||
vec3_scale(dfc*gijk*ex_delr,rik_hat,drk);
|
||||
vec3_scaleadd(fc*gijk_d*ex_delr,dcosdrk,drk,drk);
|
||||
vec3_scaleadd(-fc*gijk*ex_delr_d,rik_hat,drk,drk);
|
||||
vec3_scale(prefactor,drk,drk);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGW::costheta_d(double *rij_hat, double rij,
|
||||
double *rik_hat, double rik,
|
||||
double *dri, double *drj, double *drk)
|
||||
{
|
||||
// first element is devative wrt Ri, second wrt Rj, third wrt Rk
|
||||
|
||||
double cos_theta = vec3_dot(rij_hat,rik_hat);
|
||||
|
||||
vec3_scaleadd(-cos_theta,rij_hat,rik_hat,drj);
|
||||
vec3_scale(1.0/rij,drj,drj);
|
||||
vec3_scaleadd(-cos_theta,rik_hat,rij_hat,drk);
|
||||
vec3_scale(1.0/rik,drk,drk);
|
||||
vec3_add(drj,drk,dri);
|
||||
vec3_scale(-1.0,dri,dri);
|
||||
}
|
||||
|
|
@ -0,0 +1,196 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(gw,PairGW)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_GW_H
|
||||
#define LMP_PAIR_GW_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairGW : public Pair {
|
||||
public:
|
||||
PairGW(class LAMMPS *);
|
||||
virtual ~PairGW();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
|
||||
protected:
|
||||
struct Param {
|
||||
double lam1,lam2,lam3;
|
||||
double c,d,h;
|
||||
double gamma,powerm;
|
||||
double powern,beta;
|
||||
double biga,bigb,bigd,bigr;
|
||||
double cut,cutsq;
|
||||
double c1,c2,c3,c4;
|
||||
int ielement,jelement,kelement;
|
||||
int powermint;
|
||||
double Z_i,Z_j;
|
||||
double ZBLcut,ZBLexpscale;
|
||||
};
|
||||
|
||||
Param *params; // parameter set for an I-J-K interaction
|
||||
char **elements; // names of unique elements
|
||||
int ***elem2param; // mapping from element triplets to paramegw
|
||||
int *map; // mapping from atom types to elements
|
||||
double cutmax; // max cutoff for all elements
|
||||
int nelements; // # of unique elements
|
||||
int nparams; // # of stored parameter sets
|
||||
int maxparam; // max # of parameter sets
|
||||
|
||||
int **pages; // neighbor list pages
|
||||
int maxlocal; // size of numneigh, firstneigh arrays
|
||||
int maxpage; // # of pages currently allocated
|
||||
int pgsize; // size of neighbor page
|
||||
int oneatom; // max # of neighbors for one atom
|
||||
|
||||
|
||||
int *GW_numneigh; // # of pair neighbors for each atom
|
||||
int **GW_firstneigh; // ptr to 1st neighbor of each atom
|
||||
|
||||
void GW_neigh();
|
||||
void add_pages(int howmany = 1);
|
||||
|
||||
void allocate();
|
||||
virtual void read_file(char *);
|
||||
void setup_params();
|
||||
virtual void repulsive(Param *, double, double &, int, double &);
|
||||
double zeta(Param *, double, double, double *, double *);
|
||||
virtual void force_zeta(Param *, double, double, double &,
|
||||
double &, int, double &);
|
||||
void attractive(Param *, double, double, double, double *, double *,
|
||||
double *, double *, double *);
|
||||
|
||||
double gw_fc(double, Param *);
|
||||
double gw_fc_d(double, Param *);
|
||||
virtual double gw_fa(double, Param *);
|
||||
virtual double gw_fa_d(double, Param *);
|
||||
double gw_bij(double, Param *);
|
||||
double gw_bij_d(double, Param *);
|
||||
|
||||
void gw_zetaterm_d(double, double *, double, double *, double,
|
||||
double *, double *, double *, Param *);
|
||||
void costheta_d(double *, double, double *, double,
|
||||
double *, double *, double *);
|
||||
|
||||
// inlined functions for efficiency
|
||||
|
||||
inline double gw_gijk(const double costheta,
|
||||
const Param * const param) const {
|
||||
const double gw_c = param->c * param->c;
|
||||
const double gw_d = param->d * param->d;
|
||||
const double hcth = param->h - costheta;
|
||||
|
||||
//printf("gw_gijk: gw_c=%f gw_d=%f hcth=%f=%f-%f\n", gw_c, gw_d, hcth, param->h, costheta);
|
||||
|
||||
return param->gamma*(1.0 + gw_c/gw_d - gw_c / (gw_d + hcth*hcth));
|
||||
}
|
||||
|
||||
inline double gw_gijk_d(const double costheta,
|
||||
const Param * const param) const {
|
||||
const double gw_c = param->c * param->c;
|
||||
const double gw_d = param->d * param->d;
|
||||
const double hcth = param->h - costheta;
|
||||
const double numerator = -2.0 * gw_c * hcth;
|
||||
const double denominator = 1.0/(gw_d + hcth*hcth);
|
||||
return param->gamma*numerator*denominator*denominator;
|
||||
}
|
||||
|
||||
inline double vec3_dot(const double x[3], const double y[3]) const {
|
||||
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
|
||||
}
|
||||
|
||||
inline void vec3_add(const double x[3], const double y[3],
|
||||
double * const z) const {
|
||||
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
|
||||
}
|
||||
|
||||
inline void vec3_scale(const double k, const double x[3],
|
||||
double y[3]) const {
|
||||
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
|
||||
}
|
||||
|
||||
inline void vec3_scaleadd(const double k, const double x[3],
|
||||
const double y[3], double * const z) const {
|
||||
z[0] = k*x[0]+y[0];
|
||||
z[1] = k*x[1]+y[1];
|
||||
z[2] = k*x[2]+y[2];
|
||||
}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Pair style GW requires atom IDs
|
||||
|
||||
This is a requirement to use the GW potential.
|
||||
|
||||
E: Pair style GW requires newton pair on
|
||||
|
||||
See the newton command. This is a restriction to use the GW
|
||||
potential.
|
||||
|
||||
E: All pair coeffs are not set
|
||||
|
||||
All pair coefficients must be set in the data file or by the
|
||||
pair_coeff command before running a simulation.
|
||||
|
||||
E: Cannot open GW potential file %s
|
||||
|
||||
The specified GW potential file cannot be opened. Check that the
|
||||
path and name are correct.
|
||||
|
||||
E: Incorrect format in GW potential file
|
||||
|
||||
Incorrect number of words per line in the potential file.
|
||||
|
||||
E: Illegal GW parameter
|
||||
|
||||
One or more of the coefficients defined in the potential file is
|
||||
invalid.
|
||||
|
||||
E: Potential file has duplicate entry
|
||||
|
||||
The potential file for a SW or GW potential has more than
|
||||
one entry for the same 3 ordered elements.
|
||||
|
||||
E: Potential file is missing an entry
|
||||
|
||||
The potential file for a SW or GW potential does not have a
|
||||
needed entry.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,287 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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: German Samolyuk (ORNL)
|
||||
Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include <math.h>
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include "pair_gw_zbl.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"
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define MAXLINE 1024
|
||||
#define DELTA 4
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairGWZBL::PairGWZBL(LAMMPS *lmp) : PairGW(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 gw/zbl requires metal or real units");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGWZBL::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];
|
||||
sprintf(str,"Cannot open GW 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 GW 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 GW parameter");
|
||||
|
||||
nparams++;
|
||||
}
|
||||
|
||||
delete [] words;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGWZBL::repulsive(Param *param, double rsq, double &fforce,
|
||||
int eflag, double &eng)
|
||||
{
|
||||
double r,tmp_fc,tmp_fc_d,tmp_exp;
|
||||
|
||||
// GW repulsive portion
|
||||
|
||||
r = sqrt(rsq);
|
||||
tmp_fc = gw_fc(r,param);
|
||||
tmp_fc_d = gw_fc_d(r,param);
|
||||
tmp_exp = exp(-param->lam1 * r);
|
||||
double fforce_gw = param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1);
|
||||
double eng_gw = tmp_fc * param->biga * tmp_exp;
|
||||
|
||||
// ZBL repulsive portion
|
||||
|
||||
double esq = pow(global_e,2.0);
|
||||
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*-phi/rsq + premult*dphi/r;
|
||||
double eng_ZBL = premult*(1.0/r)*phi;
|
||||
|
||||
// combine two parts with smoothing by Fermi-like function
|
||||
|
||||
fforce = -(-F_fermi_d(r,param) * eng_ZBL +
|
||||
(1.0 - F_fermi(r,param))*fforce_ZBL +
|
||||
F_fermi_d(r,param)*eng_gw + F_fermi(r,param)*fforce_gw) / r;
|
||||
|
||||
if (eflag)
|
||||
eng = (1.0 - F_fermi(r,param))*eng_ZBL + F_fermi(r,param)*eng_gw;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGWZBL::gw_fa(double r, Param *param)
|
||||
{
|
||||
if (r > param->bigr + param->bigd) return 0.0;
|
||||
return -param->bigb * exp(-param->lam2 * r) * gw_fc(r,param) *
|
||||
F_fermi(r,param);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGWZBL::gw_fa_d(double r, Param *param)
|
||||
{
|
||||
if (r > param->bigr + param->bigd) return 0.0;
|
||||
return param->bigb * exp(-param->lam2 * r) *
|
||||
(param->lam2 * gw_fc(r,param) * F_fermi(r,param) -
|
||||
gw_fc_d(r,param) * F_fermi(r,param) - gw_fc(r,param) *
|
||||
F_fermi_d(r,param));
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Fermi-like smoothing function
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairGWZBL::F_fermi(double r, Param *param)
|
||||
{
|
||||
return 1.0 / (1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)));
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Fermi-like smoothing function derivative with respect to r
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairGWZBL::F_fermi_d(double r, Param *param)
|
||||
{
|
||||
return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) /
|
||||
pow(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)),2.0);
|
||||
}
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef PAIR_CLASS
|
||||
|
||||
PairStyle(gw/zbl,PairGWZBL)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_GW_ZBL_H
|
||||
#define LMP_PAIR_GW_ZBL_H
|
||||
|
||||
#include "pair_gw.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairGWZBL : public PairGW {
|
||||
public:
|
||||
PairGWZBL(class LAMMPS *);
|
||||
~PairGWZBL() {}
|
||||
|
||||
private:
|
||||
double global_a_0; // Bohr radius for Coulomb repulsion
|
||||
double global_epsilon_0; // permittivity of vacuum for Coulomb repulsion
|
||||
double global_e; // proton charge (negative of electron charge)
|
||||
|
||||
void read_file(char *);
|
||||
void repulsive(Param *, double, double &, int, double &);
|
||||
|
||||
double gw_fa(double, Param *);
|
||||
double gw_fa_d(double, Param *);
|
||||
|
||||
double F_fermi(double, Param *);
|
||||
double F_fermi_d(double, Param *);
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Pair GW/zbl requires metal or real units
|
||||
|
||||
This is a current restriction of this pair potential.
|
||||
|
||||
E: Cannot open GW potential file %s
|
||||
|
||||
The specified GW potential file cannot be opened. Check that the
|
||||
path and name are correct.
|
||||
|
||||
E: Incorrect format in GW potential file
|
||||
|
||||
Incorrect number of words per line in the potential file.
|
||||
|
||||
E: Illegal GW parameter
|
||||
|
||||
One or more of the coefficients defined in the potential file is
|
||||
invalid.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue