forked from lijiext/lammps
move pair_zhou to USER-MISC and update USER-MISC/README
This commit is contained in:
Tonnam Balankura
parent
5be32f5d8d
commit
da81531906
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@ -69,4 +69,5 @@ pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
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pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16
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pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14
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pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11
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pair_style zhou, Kristen Fichthorn, fichthorn@psu.edu, 18 Mar 17
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temper/grem, David Stelter, dstelter@bu.edu, 22 Nov 16
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@ -0,0 +1,361 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdio.h"
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#include "stdlib.h"
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#include "pair_zhou.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 "neigh_list.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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/* ---------------------------------------------------------------------- */
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PairZhou::PairZhou(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairZhou::~PairZhou()
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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(cut);
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memory->destroy(d0);
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memory->destroy(alpha);
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memory->destroy(r0);
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memory->destroy(c);
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memory->destroy(rr);
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memory->destroy(morse1);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairZhou::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,dr,dexp,factor_lj,r2inv,r6inv,ddexp,invexp;
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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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double *special_lj = force->special_lj;
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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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factor_lj = special_lj[sbmask(j)];
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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 < cutsq[itype][jtype]) {
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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r = sqrt(rsq);
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dr = r - r0[itype][jtype];
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dexp = exp(-alpha[itype][jtype] * dr);
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ddexp = exp(-dscale * (r/rr[itype][jtype] - 1.0));
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invexp = 1.0/(1+ddexp);
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fpair = morse1[itype][jtype] * (dexp*dexp - dexp) / r;
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fpair -= sscale*c[itype][jtype] * (invexp*invexp*ddexp*(-dscale/rr[itype][jtype])*r6inv) / r;
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fpair -= sscale*c[itype][jtype] * (6.0 * invexp * r6inv * r2inv);
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fpair *= factor_lj;
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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 = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
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sscale*c[itype][jtype]*r6inv*invexp - offset[itype][jtype];
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evdwl *= factor_lj;
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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 PairZhou::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(cut,n+1,n+1,"pair:cut");
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memory->create(d0,n+1,n+1,"pair:d0");
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memory->create(alpha,n+1,n+1,"pair:alpha");
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memory->create(r0,n+1,n+1,"pair:r0");
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memory->create(c,n+1,n+1,"pair:c");
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memory->create(rr,n+1,n+1,"pair:rr");
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memory->create(morse1,n+1,n+1,"pair:morse1");
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memory->create(offset,n+1,n+1,"pair:offset");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairZhou::settings(int narg, char **arg)
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{
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if (narg != 3) error->all(FLERR,"Illegal pair_style command");
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cut_global = force->numeric(FLERR,arg[0]);
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sscale = force->numeric(FLERR,arg[1]);
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dscale = force->numeric(FLERR,arg[2]);
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i+1; j <= atom->ntypes; j++)
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if (setflag[i][j]) cut[i][j] = cut_global;
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}
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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 PairZhou::coeff(int narg, char **arg)
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{
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if (narg < 7 || narg > 8) error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
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force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
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double d0_one = force->numeric(FLERR,arg[2]);
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double alpha_one = force->numeric(FLERR,arg[3]);
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double r0_one = force->numeric(FLERR,arg[4]);
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double c_one = force->numeric(FLERR,arg[5]);
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double rr_one = force->numeric(FLERR,arg[6]);
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double cut_one = cut_global;
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if (narg == 8) cut_one = force->numeric(FLERR,arg[7]);
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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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d0[i][j] = d0_one;
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alpha[i][j] = alpha_one;
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r0[i][j] = r0_one;
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cut[i][j] = cut_one;
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c[i][j] = c_one;
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rr[i][j] = rr_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 for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairZhou::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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morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
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if (offset_flag) {
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double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
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offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
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} else offset[i][j] = 0.0;
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d0[j][i] = d0[i][j];
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alpha[j][i] = alpha[i][j];
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r0[j][i] = r0[i][j];
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c[j][i] = c[i][j];
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rr[j][i] = rr[i][j];
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morse1[j][i] = morse1[i][j];
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offset[j][i] = offset[i][j];
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return cut[i][j];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairZhou::write_restart(FILE *fp)
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{
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write_restart_settings(fp);
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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fwrite(&setflag[i][j],sizeof(int),1,fp);
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if (setflag[i][j]) {
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fwrite(&d0[i][j],sizeof(double),1,fp);
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fwrite(&alpha[i][j],sizeof(double),1,fp);
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fwrite(&r0[i][j],sizeof(double),1,fp);
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fwrite(&c[i][j],sizeof(double),1,fp);
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fwrite(&rr[i][j],sizeof(double),1,fp);
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fwrite(&cut[i][j],sizeof(double),1,fp);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairZhou::read_restart(FILE *fp)
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{
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read_restart_settings(fp);
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allocate();
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int i,j;
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int me = comm->me;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i; j <= atom->ntypes; j++) {
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if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
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MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
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if (setflag[i][j]) {
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if (me == 0) {
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fread(&d0[i][j],sizeof(double),1,fp);
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fread(&alpha[i][j],sizeof(double),1,fp);
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fread(&r0[i][j],sizeof(double),1,fp);
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fread(&c[i][j],sizeof(double),1,fp);
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fread(&rr[i][j],sizeof(double),1,fp);
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fread(&cut[i][j],sizeof(double),1,fp);
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}
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MPI_Bcast(&d0[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&c[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&rr[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
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}
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairZhou::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&sscale,sizeof(double),1,fp);
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fwrite(&dscale,sizeof(double),1,fp);
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fwrite(&offset_flag,sizeof(int),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairZhou::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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fread(&cut_global,sizeof(double),1,fp);
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fread(&sscale,sizeof(double),1,fp);
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fread(&dscale,sizeof(double),1,fp);
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fread(&offset_flag,sizeof(int),1,fp);
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fread(&mix_flag,sizeof(int),1,fp);
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}
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&sscale,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&dscale,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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}
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/* ---------------------------------------------------------------------- */
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double PairZhou::single(int i, int j, int itype, int jtype, double rsq,
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double factor_coul, double factor_lj,
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double &fforce)
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{
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double r,dr,dexp,phi,r2inv,r6inv,ddexp,invexp;
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r2inv = 1.0/rsq;
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r6inv = r2inv*r2inv*r2inv;
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r = sqrt(rsq);
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dr = r - r0[itype][jtype];
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dexp = exp(-alpha[itype][jtype] * dr);
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ddexp = exp(-dscale * (r/rr[itype][jtype] - 1.0));
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invexp = 1.0/(1+ddexp);
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fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
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fforce -= factor_lj * sscale* c[itype][jtype] * (invexp*invexp*ddexp*(-dscale/rr[itype][jtype])*r6inv) / r;
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fforce -= factor_lj * sscale* c[itype][jtype] * (6.0 * invexp * r6inv * r2inv);
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phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - sscale*c[itype][jtype]*r6inv*invexp - offset[itype][jtype];
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return factor_lj*phi;
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}
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@ -0,0 +1,75 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
|
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(zhou,PairZhou)
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#else
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#ifndef LMP_PAIR_ZHOU_H
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#define LMP_PAIR_ZHOU_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairZhou : public Pair {
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public:
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PairZhou(class LAMMPS *);
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virtual ~PairZhou();
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virtual void compute(int, int);
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virtual void settings(int, char **);
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void coeff(int, char **);
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virtual double init_one(int, int);
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void write_restart(FILE *);
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void read_restart(FILE *);
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void write_restart_settings(FILE *);
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void read_restart_settings(FILE *);
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virtual double single(int, int, int, int, double, double, double, double &);
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protected:
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double cut_global;
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double **cut;
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double sscale,dscale;
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double **d0,**alpha,**r0,**c,**rr;
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double **morse1;
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double **offset;
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void allocate();
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Incorrect args for pair coefficients
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Self-explanatory. Check the input script or data file.
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E: All pair coeffs are not set
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All pair coefficients must be set in the data file or by the
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pair_coeff command before running a simulation.
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*/
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