mirror of https://github.com/lammps/lammps.git
434 lines
13 KiB
C++
434 lines
13 KiB
C++
/* ----------------------------------------------------------------------
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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 "string.h"
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#include "pair_lj_cut_coul_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 "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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/* ---------------------------------------------------------------------- */
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PairLJCutCoulCut::PairLJCutCoulCut(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairLJCutCoulCut::~PairLJCutCoulCut()
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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_lj);
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memory->destroy(cut_ljsq);
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memory->destroy(cut_coul);
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memory->destroy(cut_coulsq);
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memory->destroy(epsilon);
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memory->destroy(sigma);
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memory->destroy(lj1);
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memory->destroy(lj2);
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memory->destroy(lj3);
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memory->destroy(lj4);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJCutCoulCut::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 qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
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double rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = ecoul = 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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double *q = atom->q;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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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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qtmp = q[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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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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factor_coul = special_coul[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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if (rsq < cut_coulsq[itype][jtype])
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forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
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else forcecoul = 0.0;
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if (rsq < cut_ljsq[itype][jtype]) {
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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} else forcelj = 0.0;
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fpair = (factor_coul*forcecoul + factor_lj*forcelj) * 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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if (rsq < cut_coulsq[itype][jtype])
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ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
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else ecoul = 0.0;
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if (rsq < cut_ljsq[itype][jtype]) {
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evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
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offset[itype][jtype];
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evdwl *= factor_lj;
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} else evdwl = 0.0;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,ecoul,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_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 PairLJCutCoulCut::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_lj,n+1,n+1,"pair:cut_lj");
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memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
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memory->create(cut_coul,n+1,n+1,"pair:cut_coul");
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memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq");
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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(lj1,n+1,n+1,"pair:lj1");
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memory->create(lj2,n+1,n+1,"pair:lj2");
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memory->create(lj3,n+1,n+1,"pair:lj3");
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memory->create(lj4,n+1,n+1,"pair:lj4");
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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 PairLJCutCoulCut::settings(int narg, char **arg)
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{
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if (narg < 1 || narg > 2) error->all("Illegal pair_style command");
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cut_lj_global = force->numeric(arg[0]);
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if (narg == 1) cut_coul_global = cut_lj_global;
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else cut_coul_global = force->numeric(arg[1]);
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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]) {
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cut_lj[i][j] = cut_lj_global;
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cut_coul[i][j] = cut_coul_global;
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}
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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 PairLJCutCoulCut::coeff(int narg, char **arg)
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{
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if (narg < 4 || narg > 6) error->all("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(arg[0],atom->ntypes,ilo,ihi);
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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double epsilon_one = force->numeric(arg[2]);
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double sigma_one = force->numeric(arg[3]);
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double cut_lj_one = cut_lj_global;
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double cut_coul_one = cut_coul_global;
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if (narg >= 5) cut_coul_one = cut_lj_one = force->numeric(arg[4]);
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if (narg == 6) cut_coul_one = force->numeric(arg[5]);
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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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epsilon[i][j] = epsilon_one;
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sigma[i][j] = sigma_one;
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cut_lj[i][j] = cut_lj_one;
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cut_coul[i][j] = cut_coul_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("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 PairLJCutCoulCut::init_style()
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{
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if (!atom->q_flag)
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error->all("Pair style lj/cut/coul/cut requires atom attribute q");
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int irequest = neighbor->request(this);
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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 PairLJCutCoulCut::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
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sigma[i][i],sigma[j][j]);
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sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
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cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
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cut_coul[i][j] = mix_distance(cut_coul[i][i],cut_coul[j][j]);
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}
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double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
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cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
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cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j];
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lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
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lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
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if (offset_flag) {
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double ratio = sigma[i][j] / cut_lj[i][j];
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offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
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} else offset[i][j] = 0.0;
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cut_ljsq[j][i] = cut_ljsq[i][j];
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cut_coulsq[j][i] = cut_coulsq[i][j];
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lj1[j][i] = lj1[i][j];
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lj2[j][i] = lj2[i][j];
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lj3[j][i] = lj3[i][j];
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lj4[j][i] = lj4[i][j];
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offset[j][i] = offset[i][j];
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// compute I,J contribution to long-range tail correction
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// count total # of atoms of type I and J via Allreduce
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if (tail_flag) {
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double count[2],all[2];
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count[0] = count[1] = 0.0;
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for (int k = 0; k < nlocal; k++) {
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if (type[k] == i) count[0] += 1.0;
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if (type[k] == j) count[1] += 1.0;
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}
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MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
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double PI = 4.0*atan(1.0);
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double sig2 = sigma[i][j]*sigma[i][j];
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double sig6 = sig2*sig2*sig2;
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double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
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double rc6 = rc3*rc3;
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double rc9 = rc3*rc6;
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etail_ij = 8.0*PI*all[0]*all[1]*epsilon[i][j] *
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sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
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ptail_ij = 16.0*PI*all[0]*all[1]*epsilon[i][j] *
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sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
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}
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return cut;
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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 PairLJCutCoulCut::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(&epsilon[i][j],sizeof(double),1,fp);
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fwrite(&sigma[i][j],sizeof(double),1,fp);
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fwrite(&cut_lj[i][j],sizeof(double),1,fp);
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fwrite(&cut_coul[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 PairLJCutCoulCut::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(&epsilon[i][j],sizeof(double),1,fp);
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fread(&sigma[i][j],sizeof(double),1,fp);
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fread(&cut_lj[i][j],sizeof(double),1,fp);
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fread(&cut_coul[i][j],sizeof(double),1,fp);
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}
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MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_coul[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 PairLJCutCoulCut::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_lj_global,sizeof(double),1,fp);
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fwrite(&cut_coul_global,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 PairLJCutCoulCut::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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fread(&cut_lj_global,sizeof(double),1,fp);
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fread(&cut_coul_global,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_lj_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_coul_global,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 PairLJCutCoulCut::single(int i, int j, int itype, int jtype,
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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 r2inv,r6inv,forcecoul,forcelj,phicoul,philj;
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r2inv = 1.0/rsq;
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if (rsq < cut_coulsq[itype][jtype])
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forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
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else forcecoul = 0.0;
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if (rsq < cut_ljsq[itype][jtype]) {
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r6inv = r2inv*r2inv*r2inv;
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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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} else forcelj = 0.0;
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fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
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double eng = 0.0;
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if (rsq < cut_coulsq[itype][jtype]) {
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phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
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eng += factor_coul*phicoul;
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}
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if (rsq < cut_ljsq[itype][jtype]) {
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philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
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offset[itype][jtype];
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eng += factor_lj*philj;
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}
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return eng;
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}
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