Added pair style ZBL
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10790 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
428
src/pair_zbl.cpp
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428
src/pair_zbl.cpp
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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 authors: Stephen Foiles, 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_zbl.h"
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#include "atom.h"
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#include "comm.h"
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#include "force.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 "update.h"
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#include "integrate.h"
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#include "respa.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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// From J.F. Zeigler, J. P. Biersack and U. Littmark,
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// "The Stopping and Range of Ions in Matter" volume 1, Pergamon, 1985.
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using namespace LAMMPS_NS;
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using namespace MathConst;
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using namespace PairZBLConstants;
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/* ---------------------------------------------------------------------- */
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PairZBL::PairZBL(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairZBL::~PairZBL()
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{
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(cutsq);
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memory->destroy(z);
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memory->destroy(d1a);
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memory->destroy(d2a);
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memory->destroy(d3a);
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memory->destroy(d4a);
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memory->destroy(zze);
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memory->destroy(sw1);
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memory->destroy(sw2);
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memory->destroy(sw3);
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memory->destroy(sw4);
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memory->destroy(sw5);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairZBL::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,r,t,fswitch,eswitch;
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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 = 0;
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double **x = atom->x;
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double **f = atom->f;
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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 neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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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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itype = type[i];
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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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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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jtype = type[j];
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if (rsq < cut_globalsq) {
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r = sqrt(rsq);
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fpair = dzbldr(r, itype, jtype);
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if (rsq > cut_innersq) {
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t = r - cut_inner;
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fswitch = t*t *
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(sw1[itype][jtype] + sw2[itype][jtype]*t);
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fpair += fswitch;
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}
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fpair *= -1.0/r;
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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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if (newton_pair || j < nlocal) {
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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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}
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if (eflag) {
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evdwl = e_zbl(r, itype, jtype);
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evdwl += sw5[itype][jtype];
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if (rsq > cut_innersq) {
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eswitch = t*t*t *
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(sw3[itype][jtype] + sw4[itype][jtype]*t);
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evdwl += eswitch;
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}
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}
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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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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairZBL::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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for (int i = 1; i <= n; i++)
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for (int j = i; j <= n; j++)
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setflag[i][j] = 0;
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memory->create(cutsq,n+1,n+1,"pair:cutsq");
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memory->create(z,n+1,"pair:z");
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memory->create(d1a,n+1,n+1,"pair:d1a");
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memory->create(d2a,n+1,n+1,"pair:d2a");
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memory->create(d3a,n+1,n+1,"pair:d3a");
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memory->create(d4a,n+1,n+1,"pair:d4a");
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memory->create(zze,n+1,n+1,"pair:zze");
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memory->create(sw1,n+1,n+1,"pair:sw1");
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memory->create(sw2,n+1,n+1,"pair:sw2");
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memory->create(sw3,n+1,n+1,"pair:sw3");
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memory->create(sw4,n+1,n+1,"pair:sw4");
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memory->create(sw5,n+1,n+1,"pair:sw5");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairZBL::settings(int narg, char **arg)
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{
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if (narg != 2) error->all(FLERR,"Illegal pair_style command");
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cut_inner = force->numeric(FLERR,arg[0]);
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cut_global = force->numeric(FLERR,arg[1]);
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if (cut_inner <= 0.0 )
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error->all(FLERR,"Illegal pair_style command");
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if (cut_inner > cut_global)
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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 PairZBL::coeff(int narg, char **arg)
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{
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if (narg != 3)
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error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(arg[0],atom->ntypes,ilo,ihi);
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int jlo,jhi;
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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double z_one = force->numeric(FLERR,arg[2]);
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// Set flag for each i-j pair
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// Set z-parameter only for i-i pairs
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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if (i == j) z[i] = z_one;
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setflag[i][j] = 1;
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count++;
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}
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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 PairZBL::init_style()
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{
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neighbor->request(this);
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cut_innersq = cut_inner * cut_inner;
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cut_globalsq = cut_global * cut_global;
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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 PairZBL::init_one(int i, int j)
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{
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double ainv = (pow(z[i],pzbl) + pow(z[j],pzbl))/a0;
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d1a[i][j] = d1*ainv;
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d2a[i][j] = d2*ainv;
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d3a[i][j] = d3*ainv;
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d4a[i][j] = d4*ainv;
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zze[i][j] = z[i]*z[j]*econv;
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d1a[j][i] = d1a[i][j];
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d2a[j][i] = d2a[i][j];
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d3a[j][i] = d3a[i][j];
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d4a[j][i] = d4a[i][j];
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zze[j][i] = zze[i][j];
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// e = t^3 (sw3 + sw4*t) + sw5
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// = A/3*t^3 + B/4*t^4 + C
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// sw3 = A/3
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// sw4 = B/4
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// sw5 = C
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// dedr = t^2 (sw1 + sw2*t)
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// = A*t^2 + B*t^3
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// sw1 = A
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// sw2 = B
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// A = (-3Fc' + tc*Fc'')/tc^2
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// B = ( 2Fc' - tc*Fc'')/tc^3
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// C = = -Fc + tc/2*Fc' - tc^2/12*Fc''
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double tc = cut_global - cut_inner;
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double fc = e_zbl(cut_global, i, j);
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double fcp = dzbldr(cut_global, i, j);
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double fcpp = d2zbldr2(cut_global, i, j);
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double swa = (-3.0*fcp + tc*fcpp)/(tc*tc);
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double swb = ( 2.0*fcp - tc*fcpp)/(tc*tc*tc);
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double swc = -fc + (tc/2.0)*fcp - (tc*tc/12.0)*fcpp;
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sw1[i][j] = swa;
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sw2[i][j] = swb;
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sw3[i][j] = swa/3.0;
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sw4[i][j] = swb/4.0;
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sw5[i][j] = swc;
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sw1[j][i] = sw1[i][j];
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sw2[j][i] = sw2[i][j];
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sw3[j][i] = sw3[i][j];
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sw4[j][i] = sw4[i][j];
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sw5[j][i] = sw5[i][j];
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return cut_global;
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}
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/* ---------------------------------------------------------------------- */
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double PairZBL::single(int i, int j, int itype, int jtype, double rsq,
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double dummy1, double dummy2,
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double &fforce)
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{
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double phi,r,t,eswitch,fswitch;
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r = sqrt(rsq);
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fforce = dzbldr(r, itype, jtype);
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if (rsq > cut_innersq) {
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t = r - cut_inner;
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fswitch = t*t *
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(sw1[itype][jtype] + sw2[itype][jtype]*t);
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fforce += fswitch;
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}
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fforce *= -1.0/r;
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phi = e_zbl(r, itype, jtype);
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phi += sw5[itype][jtype];
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if (rsq > cut_innersq) {
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eswitch = t*t*t *
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(sw3[itype][jtype] + sw4[itype][jtype]*t);
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phi += eswitch;
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}
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return phi;
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}
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/* ----------------------------------------------------------------------
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compute ZBL pair energy
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------------------------------------------------------------------------- */
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double PairZBL::e_zbl(double r, int i, int j) {
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double d1aij = d1a[i][j];
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double d2aij = d2a[i][j];
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double d3aij = d3a[i][j];
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double d4aij = d4a[i][j];
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double zzeij = zze[i][j];
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double rinv = 1.0/r;
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double sum = c1*exp(-d1aij*r);
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sum += c2*exp(-d2aij*r);
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sum += c3*exp(-d3aij*r);
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sum += c4*exp(-d4aij*r);
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double result = zzeij*sum*rinv;
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return result;
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};
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/* ----------------------------------------------------------------------
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compute ZBL first derivative
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------------------------------------------------------------------------- */
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double PairZBL::dzbldr(double r, int i, int j) {
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double d1aij = d1a[i][j];
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double d2aij = d2a[i][j];
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double d3aij = d3a[i][j];
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double d4aij = d4a[i][j];
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double zzeij = zze[i][j];
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double rinv = 1.0/r;
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double e1 = exp(-d1aij*r);
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double e2 = exp(-d2aij*r);
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double e3 = exp(-d3aij*r);
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double e4 = exp(-d4aij*r);
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double sum = c1*e1;
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sum += c2*e2;
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sum += c3*e3;
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sum += c4*e4;
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double sum_p = -c1*d1aij*e1;
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sum_p -= c2*d2aij*e2;
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sum_p -= c3*d3aij*e3;
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sum_p -= c4*d4aij*e4;
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double result = zzeij*(sum_p - sum*rinv)*rinv;
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return result;
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};
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/* ----------------------------------------------------------------------
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compute ZBL second derivative
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------------------------------------------------------------------------- */
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double PairZBL::d2zbldr2(double r, int i, int j) {
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double d1aij = d1a[i][j];
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double d2aij = d2a[i][j];
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double d3aij = d3a[i][j];
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double d4aij = d4a[i][j];
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double zzeij = zze[i][j];
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double rinv = 1.0/r;
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double e1 = exp(-d1aij*r);
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double e2 = exp(-d2aij*r);
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double e3 = exp(-d3aij*r);
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double e4 = exp(-d4aij*r);
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double sum = c1*e1;
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sum += c2*e2;
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sum += c3*e3;
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sum += c4*e4;
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double sum_p = c1*e1*d1aij;
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sum_p += c2*e2*d2aij;
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sum_p += c3*e3*d3aij;
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sum_p += c4*e4*d4aij;
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double sum_pp = c1*e1*d1aij*d1aij;
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sum_pp += c2*e2*d2aij*d2aij;
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sum_pp += c3*e3*d3aij*d3aij;
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sum_pp += c4*e4*d4aij*d4aij;
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double result = zzeij*(sum_pp + 2.0*sum_p*rinv +
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2.0*sum*rinv*rinv)*rinv;
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return result;
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};
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