forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9071 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
81cddd4f1d
commit
8da7579a57
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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: Cassiano Aimoli (aimoli@gmail.com)
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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_mie_cut.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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using namespace LAMMPS_NS;
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using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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PairMIECut::PairMIECut(LAMMPS *lmp) : Pair(lmp)
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{
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respa_enable = 1;
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}
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/* ---------------------------------------------------------------------- */
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PairMIECut::~PairMIECut()
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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(epsilon);
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memory->destroy(sigma);
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memory->destroy(gamR);
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memory->destroy(gamA);
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memory->destroy(Cmie);
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memory->destroy(mie1);
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memory->destroy(mie2);
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memory->destroy(mie3);
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memory->destroy(mie4);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairMIECut::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,r2inv,rgamR,rgamA,forcemie,factor_mie;
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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_mie = 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_mie = special_mie[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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rgamA = pow(r2inv,(gamA[itype][jtype]/2.0));
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rgamR = pow(r2inv,(gamR[itype][jtype]/2.0));
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forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA);
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fpair = factor_mie*forcemie*r2inv;
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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 = (mie3[itype][jtype]*rgamR - mie4[itype][jtype]*rgamA) -
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offset[itype][jtype];
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evdwl *= factor_mie;
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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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void PairMIECut::compute_inner()
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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,fpair;
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double rsq,r2inv,rgamR,rgamA,forcemie,factor_mie,rsw;
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int *ilist,*jlist,*numneigh,**firstneigh;
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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_mie = force->special_lj;
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int newton_pair = force->newton_pair;
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inum = listinner->inum;
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ilist = listinner->ilist;
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numneigh = listinner->numneigh;
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firstneigh = listinner->firstneigh;
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double cut_out_on = cut_respa[0];
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double cut_out_off = cut_respa[1];
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double cut_out_diff = cut_out_off - cut_out_on;
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double cut_out_on_sq = cut_out_on*cut_out_on;
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double cut_out_off_sq = cut_out_off*cut_out_off;
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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_mie = special_mie[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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if (rsq < cut_out_off_sq) {
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r2inv = 1.0/rsq;
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rgamA = pow(r2inv,(gamA[itype][jtype]/2.0));
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rgamR = pow(r2inv,(gamR[itype][jtype]/2.0));
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jtype = type[j];
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forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA);
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fpair = factor_mie*forcemie*r2inv;
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if (rsq > cut_out_on_sq) {
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rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
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fpair *= 1.0 - rsw*rsw*(3.0 - 2.0*rsw);
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}
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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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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairMIECut::compute_middle()
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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,fpair;
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double rsq,r2inv,rgamR,rgamA,forcemie,factor_mie,rsw;
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int *ilist,*jlist,*numneigh,**firstneigh;
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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_mie = force->special_lj;
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int newton_pair = force->newton_pair;
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inum = listmiddle->inum;
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ilist = listmiddle->ilist;
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numneigh = listmiddle->numneigh;
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firstneigh = listmiddle->firstneigh;
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double cut_in_off = cut_respa[0];
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double cut_in_on = cut_respa[1];
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double cut_out_on = cut_respa[2];
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double cut_out_off = cut_respa[3];
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double cut_in_diff = cut_in_on - cut_in_off;
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double cut_out_diff = cut_out_off - cut_out_on;
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double cut_in_off_sq = cut_in_off*cut_in_off;
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double cut_in_on_sq = cut_in_on*cut_in_on;
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double cut_out_on_sq = cut_out_on*cut_out_on;
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double cut_out_off_sq = cut_out_off*cut_out_off;
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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_mie = special_mie[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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if (rsq < cut_out_off_sq && rsq > cut_in_off_sq) {
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r2inv = 1.0/rsq;
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rgamA = pow(r2inv,(gamA[itype][jtype]/2.0));
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rgamR = pow(r2inv,(gamR[itype][jtype]/2.0));
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jtype = type[j];
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forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA);
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fpair = factor_mie*forcemie*r2inv;
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if (rsq < cut_in_on_sq) {
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rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
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fpair *= rsw*rsw*(3.0 - 2.0*rsw);
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}
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if (rsq > cut_out_on_sq) {
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rsw = (sqrt(rsq) - cut_out_on)/cut_out_diff;
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fpair *= 1.0 + rsw*rsw*(2.0*rsw - 3.0);
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}
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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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}
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}
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairMIECut::compute_outer(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,r2inv,rgamR,rgamA,forcemie,factor_mie,rsw;
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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 = 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_mie = force->special_lj;
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int newton_pair = force->newton_pair;
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inum = listouter->inum;
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ilist = listouter->ilist;
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numneigh = listouter->numneigh;
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firstneigh = listouter->firstneigh;
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double cut_in_off = cut_respa[2];
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double cut_in_on = cut_respa[3];
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double cut_in_diff = cut_in_on - cut_in_off;
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double cut_in_off_sq = cut_in_off*cut_in_off;
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double cut_in_on_sq = cut_in_on*cut_in_on;
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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_mie = special_mie[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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if (rsq > cut_in_off_sq) {
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r2inv = 1.0/rsq;
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rgamA = pow(r2inv,(gamA[itype][jtype]/2.0));
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rgamR = pow(r2inv,(gamR[itype][jtype]/2.0));
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forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA);
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fpair = factor_mie*forcemie*r2inv;
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if (rsq < cut_in_on_sq) {
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rsw = (sqrt(rsq) - cut_in_off)/cut_in_diff;
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fpair *= rsw*rsw*(3.0 - 2.0*rsw);
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}
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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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}
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if (eflag) {
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r2inv = 1.0/rsq;
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rgamA = pow(r2inv,(gamA[itype][jtype]/2.0));
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rgamR = pow(r2inv,(gamR[itype][jtype]/2.0));
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evdwl = (mie3[itype][jtype]*rgamR - mie4[itype][jtype]*rgamA) -
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offset[itype][jtype];
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evdwl *= factor_mie;
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}
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if (vflag) {
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if (rsq <= cut_in_off_sq) {
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r2inv = 1.0/rsq;
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rgamA = pow(r2inv,(gamA[itype][jtype]/2.0));
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rgamR = pow(r2inv,(gamR[itype][jtype]/2.0));
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forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA);
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fpair = factor_mie*forcemie*r2inv;
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} else if (rsq < cut_in_on_sq)
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fpair = factor_mie*forcemie*r2inv;
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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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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairMIECut::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(epsilon,n+1,n+1,"pair:epsilon");
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memory->create(sigma,n+1,n+1,"pair:sigma");
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memory->create(gamR,n+1,n+1,"pair:gamR");
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memory->create(gamA,n+1,n+1,"pair:gamA");
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memory->create(Cmie,n+1,n+1,"pair:Cmie");
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memory->create(mie1,n+1,n+1,"pair:mie1");
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memory->create(mie2,n+1,n+1,"pair:mie2");
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memory->create(mie3,n+1,n+1,"pair:mie3");
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memory->create(mie4,n+1,n+1,"pair:mie4");
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memory->create(offset,n+1,n+1,"pair:offset");
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}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMIECut::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_global = force->numeric(arg[0]);
|
||||
|
||||
// reset cutoffs that have been explicitly set
|
||||
|
||||
if (allocated) {
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i+1; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMIECut::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 6 || narg > 7)
|
||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi,jlo,jhi;
|
||||
force->bounds(arg[0],atom->ntypes,ilo,ihi);
|
||||
force->bounds(arg[1],atom->ntypes,jlo,jhi);
|
||||
|
||||
double epsilon_one = force->numeric(arg[2]);
|
||||
double sigma_one = force->numeric(arg[3]);
|
||||
double gamR_one = force->numeric(arg[4]);
|
||||
double gamA_one = force->numeric(arg[5]);
|
||||
|
||||
double cut_one = cut_global;
|
||||
if (narg == 7) cut_one = force->numeric(arg[6]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
epsilon[i][j] = epsilon_one;
|
||||
sigma[i][j] = sigma_one;
|
||||
gamR[i][j] = gamR_one;
|
||||
gamA[i][j] = gamA_one;
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMIECut::init_style()
|
||||
{
|
||||
// request regular or rRESPA neighbor lists
|
||||
|
||||
int irequest;
|
||||
|
||||
if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
|
||||
int respa = 0;
|
||||
if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
|
||||
if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
|
||||
|
||||
if (respa == 0) irequest = neighbor->request(this);
|
||||
else if (respa == 1) {
|
||||
irequest = neighbor->request(this);
|
||||
neighbor->requests[irequest]->id = 1;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->respainner = 1;
|
||||
irequest = neighbor->request(this);
|
||||
neighbor->requests[irequest]->id = 3;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->respaouter = 1;
|
||||
} else {
|
||||
irequest = neighbor->request(this);
|
||||
neighbor->requests[irequest]->id = 1;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->respainner = 1;
|
||||
irequest = neighbor->request(this);
|
||||
neighbor->requests[irequest]->id = 2;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->respamiddle = 1;
|
||||
irequest = neighbor->request(this);
|
||||
neighbor->requests[irequest]->id = 3;
|
||||
neighbor->requests[irequest]->half = 0;
|
||||
neighbor->requests[irequest]->respaouter = 1;
|
||||
}
|
||||
|
||||
} else irequest = neighbor->request(this);
|
||||
|
||||
// set rRESPA cutoffs
|
||||
|
||||
if (strstr(update->integrate_style,"respa") &&
|
||||
((Respa *) update->integrate)->level_inner >= 0)
|
||||
cut_respa = ((Respa *) update->integrate)->cutoff;
|
||||
else cut_respa = NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
neighbor callback to inform pair style of neighbor list to use
|
||||
regular or rRESPA
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMIECut::init_list(int id, NeighList *ptr)
|
||||
{
|
||||
if (id == 0) list = ptr;
|
||||
else if (id == 1) listinner = ptr;
|
||||
else if (id == 2) listmiddle = ptr;
|
||||
else if (id == 3) listouter = ptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairMIECut::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) {
|
||||
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
|
||||
sigma[i][i],sigma[j][j]);
|
||||
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
|
||||
gamR[i][j] = mix_distance(gamR[i][i],gamR[j][j]);
|
||||
gamA[i][j] = mix_distance(gamA[i][i],gamA[j][j]);
|
||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
||||
}
|
||||
|
||||
gamA[j][i] = gamA[i][j];
|
||||
gamR[j][i] = gamR[i][j];
|
||||
Cmie[i][j] = (gamR[i][j]/(gamR[i][j]-gamA[i][j]) *
|
||||
pow((gamR[i][j]/gamA[i][j]),
|
||||
(gamA[i][j]/(gamR[i][j]-gamA[i][j]))));
|
||||
mie1[i][j] = Cmie[i][j] * gamR[i][j]* epsilon[i][j] *
|
||||
pow(sigma[i][j],gamR[i][j]);
|
||||
mie2[i][j] = Cmie[i][j] * gamA[i][j] * epsilon[i][j] *
|
||||
pow(sigma[i][j],gamA[i][j]);
|
||||
mie3[i][j] = Cmie[i][j] * epsilon[i][j] * pow(sigma[i][j],gamR[i][j]);
|
||||
mie4[i][j] = Cmie[i][j] * epsilon[i][j] * pow(sigma[i][j],gamA[i][j]);
|
||||
|
||||
if (offset_flag) {
|
||||
double ratio = sigma[i][j] / cut[i][j];
|
||||
offset[i][j] = Cmie[i][j] * epsilon[i][j] *
|
||||
(pow(ratio,gamR[i][j]) - pow(ratio,gamA[i][j]));
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
mie1[j][i] = mie1[i][j];
|
||||
mie2[j][i] = mie2[i][j];
|
||||
mie3[j][i] = mie3[i][j];
|
||||
mie4[j][i] = mie4[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// check interior rRESPA cutoff
|
||||
|
||||
if (cut_respa && cut[i][j] < cut_respa[3])
|
||||
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
|
||||
|
||||
// compute I,J contribution to long-range tail correction
|
||||
// count total # of atoms of type I and J via Allreduce
|
||||
|
||||
if (tail_flag) {
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double count[2],all[2];
|
||||
count[0] = count[1] = 0.0;
|
||||
for (int k = 0; k < nlocal; k++) {
|
||||
if (type[k] == i) count[0] += 1.0;
|
||||
if (type[k] == j) count[1] += 1.0;
|
||||
}
|
||||
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
double siggamA = pow(sigma[i][j],gamA[i][j]);
|
||||
double siggamR = pow(sigma[i][j],gamR[i][j]);
|
||||
double rcgamA = pow(cut[i][j],(gamA[i][j]-3.0));
|
||||
double rcgamR = pow(cut[i][j],(gamR[i][j]-3.0));
|
||||
etail_ij = Cmie[i][j]*2.0*MY_PI*all[0]*all[1]*epsilon[i][j]*
|
||||
(siggamR/((gamR[i][j]-3.0)*rcgamR)-siggamA/((gamA[i][j]-3.0)*rcgamA));
|
||||
ptail_ij = Cmie[i][j]*2.0*MY_PI*all[0]*all[1]*epsilon[i][j]/3.0*
|
||||
((gamR[i][j]/(gamR[i][j]-3.0))*siggamR/rcgamR-
|
||||
(gamA[i][j]/(gamA[i][j]-3.0))*siggamA/rcgamA);
|
||||
}
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMIECut::write_restart(FILE *fp)
|
||||
{
|
||||
write_restart_settings(fp);
|
||||
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||
if (setflag[i][j]) {
|
||||
fwrite(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||
fwrite(&gamR[i][j],sizeof(double),1,fp);
|
||||
fwrite(&gamA[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMIECut::read_restart(FILE *fp)
|
||||
{
|
||||
read_restart_settings(fp);
|
||||
allocate();
|
||||
|
||||
int i,j;
|
||||
int me = comm->me;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i; j <= atom->ntypes; j++) {
|
||||
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||
if (setflag[i][j]) {
|
||||
if (me == 0) {
|
||||
fread(&epsilon[i][j],sizeof(double),1,fp);
|
||||
fread(&sigma[i][j],sizeof(double),1,fp);
|
||||
fread(&gamR[i][j],sizeof(double),1,fp);
|
||||
fread(&gamA[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&gamR[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&gamA[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMIECut::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
fwrite(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairMIECut::read_restart_settings(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) {
|
||||
fread(&cut_global,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
fread(&tail_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairMIECut::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double factor_coul, double factor_mie,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,rgamR,rgamA,forcemie,phimie;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
rgamA = pow(r2inv,(gamA[itype][jtype]/2.0));
|
||||
rgamR = pow(r2inv,(gamR[itype][jtype]/2.0));
|
||||
forcemie = (mie1[itype][jtype]*rgamR - mie2[itype][jtype]*rgamA);
|
||||
fforce = factor_mie*forcemie*r2inv;
|
||||
|
||||
phimie = (mie3[itype][jtype]*rgamR - mie4[itype][jtype]*rgamA) -
|
||||
offset[itype][jtype];
|
||||
return factor_mie*phimie;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairMIECut::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 2;
|
||||
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
|
||||
if (strcmp(str,"sigma") == 0) return (void *) sigma;
|
||||
if (strcmp(str,"gamR") == 0) return (void *) gamR;
|
||||
if (strcmp(str,"gamA") == 0) return (void *) gamA;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,81 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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(mie/cut,PairMIECut)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_MIE_CUT_H
|
||||
#define LMP_PAIR_MIE_CUT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairMIECut : public Pair {
|
||||
public:
|
||||
PairMIECut(class LAMMPS *);
|
||||
virtual ~PairMIECut();
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
void init_list(int, class NeighList *);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
void compute_inner();
|
||||
void compute_middle();
|
||||
void compute_outer(int, int);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **epsilon,**sigma;
|
||||
double **gamR,**gamA,**Cmie;
|
||||
double **mie1,**mie2,**mie3,**mie4,**offset;
|
||||
double *cut_respa;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#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 cutoff < Respa interior cutoff
|
||||
|
||||
One or more pairwise cutoffs are too short to use with the specified
|
||||
rRESPA cutoffs.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue