forked from lijiext/lammps
442 lines
14 KiB
C++
442 lines
14 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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/* ----------------------------------------------------------------------
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Contributing author: Mark Stevens (SNL)
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------------------------------------------------------------------------- */
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#include "pair_lj_gromacs.h"
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#include <mpi.h>
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#include <cmath>
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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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#include "utils.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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PairLJGromacs::PairLJGromacs(LAMMPS *lmp) : Pair(lmp)
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{
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writedata = 1;
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}
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/* ---------------------------------------------------------------------- */
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PairLJGromacs::~PairLJGromacs()
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{
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if (copymode) return;
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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(cut_inner);
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memory->destroy(cut_inner_sq);
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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(ljsw1);
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memory->destroy(ljsw2);
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memory->destroy(ljsw3);
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memory->destroy(ljsw4);
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memory->destroy(ljsw5);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairLJGromacs::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,r6inv,forcelj,factor_lj;
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double r,t,fswitch,eswitch;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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ev_init(eflag,vflag);
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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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forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
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if (rsq > cut_inner_sq[itype][jtype]) {
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r = sqrt(rsq);
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t = r - cut_inner[itype][jtype];
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fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
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forcelj += fswitch;
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}
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fpair = 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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evdwl = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
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evdwl += ljsw5[itype][jtype];
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if (rsq > cut_inner_sq[itype][jtype]) {
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eswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);
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evdwl += eswitch;
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}
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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 PairLJGromacs::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(cut_inner,n+1,n+1,"pair:cut_inner");
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memory->create(cut_inner_sq,n+1,n+1,"pair:cut_inner_sq");
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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(ljsw1,n+1,n+1,"pair:ljsw1");
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memory->create(ljsw2,n+1,n+1,"pair:ljsw2");
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memory->create(ljsw3,n+1,n+1,"pair:ljsw3");
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memory->create(ljsw4,n+1,n+1,"pair:ljsw4");
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memory->create(ljsw5,n+1,n+1,"pair:ljsw5");
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairLJGromacs::settings(int narg, char **arg)
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{
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if (narg != 2) error->all(FLERR,"Illegal pair_style command");
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cut_inner_global = force->numeric(FLERR,arg[0]);
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cut_global = force->numeric(FLERR,arg[1]);
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if (cut_inner_global <= 0.0 || cut_inner_global > cut_global)
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error->all(FLERR,"Illegal pair_style command");
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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; j <= atom->ntypes; j++)
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if (setflag[i][j]) {
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cut_inner[i][j] = cut_inner_global;
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cut[i][j] = cut_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 PairLJGromacs::coeff(int narg, char **arg)
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{
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if (narg != 4 && narg != 6)
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error->all(FLERR,"Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,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 epsilon_one = force->numeric(FLERR,arg[2]);
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double sigma_one = force->numeric(FLERR,arg[3]);
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double cut_inner_one = cut_inner_global;
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double cut_one = cut_global;
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if (narg == 6) {
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cut_inner_one = force->numeric(FLERR,arg[4]);
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cut_one = force->numeric(FLERR,arg[5]);
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}
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if (cut_inner_one <= 0.0 || cut_inner_one > cut_one)
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error->all(FLERR,"Incorrect args for pair coefficients");
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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_inner[i][j] = cut_inner_one;
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cut[i][j] = cut_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 PairLJGromacs::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_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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}
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cut_inner_sq[i][j] = cut_inner[i][j]*cut_inner[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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double r6inv = 1.0/pow(cut[i][j],6.0);
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double r8inv = 1.0/pow(cut[i][j],8.0);
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double t = cut[i][j] - cut_inner[i][j];
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double t2inv = 1.0/(t*t);
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double t3inv = t2inv/t;
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double t3 = 1.0/t3inv;
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double a6 = (7.0*cut_inner[i][j] - 10.0*cut[i][j])*r8inv*t2inv;
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double b6 = (9.0*cut[i][j] - 7.0*cut_inner[i][j])*r8inv*t3inv;
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double a12 = (13.0*cut_inner[i][j] - 16.0*cut[i][j])*r6inv*r8inv*t2inv;
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double b12 = (15.0*cut[i][j] - 13.0*cut_inner[i][j])*r6inv*r8inv*t3inv;
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double c6 = r6inv - t3*(6.0*a6/3.0 + 6.0*b6*t/4.0);
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double c12 = r6inv*r6inv - t3*(12.0*a12/3.0 + 12.0*b12*t/4.0);
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ljsw1[i][j] = lj1[i][j]*a12 - lj2[i][j]*a6;
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ljsw2[i][j] = lj1[i][j]*b12 - lj2[i][j]*b6;
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ljsw3[i][j] = -lj3[i][j]*12.0*a12/3.0 + lj4[i][j]*6.0*a6/3.0;
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ljsw4[i][j] = -lj3[i][j]*12.0*b12/4.0 + lj4[i][j]*6.0*b6/4.0;
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ljsw5[i][j] = -lj3[i][j]*c12 + lj4[i][j]*c6;
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cut_inner[j][i] = cut_inner[i][j];
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cut_inner_sq[j][i] = cut_inner_sq[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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ljsw1[j][i] = ljsw1[i][j];
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ljsw2[j][i] = ljsw2[i][j];
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ljsw3[j][i] = ljsw3[i][j];
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ljsw4[j][i] = ljsw4[i][j];
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ljsw5[j][i] = ljsw5[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 PairLJGromacs::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_inner[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 PairLJGromacs::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) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,NULL,error);
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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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utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,NULL,error);
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utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,NULL,error);
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utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,NULL,error);
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utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,NULL,error);
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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_inner[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 PairLJGromacs::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_inner_global,sizeof(double),1,fp);
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fwrite(&cut_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 PairLJGromacs::read_restart_settings(FILE *fp)
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{
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int me = comm->me;
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if (me == 0) {
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utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,NULL,error);
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utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,NULL,error);
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utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,NULL,error);
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utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,NULL,error);
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}
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MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_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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proc 0 writes to data file
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------------------------------------------------------------------------- */
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void PairLJGromacs::write_data(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++)
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fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
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}
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/* ----------------------------------------------------------------------
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proc 0 writes all pairs to data file
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------------------------------------------------------------------------- */
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void PairLJGromacs::write_data_all(FILE *fp)
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{
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for (int i = 1; i <= atom->ntypes; i++)
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for (int j = i; j <= atom->ntypes; j++)
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fprintf(fp,"%d %d %g %g %g %g\n",i,j,
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epsilon[i][j],sigma[i][j],cut_inner[i][j],cut[i][j]);
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}
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/* ---------------------------------------------------------------------- */
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double PairLJGromacs::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,forcelj,philj;
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double r,t,fswitch,phiswitch;
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r2inv = 1.0/rsq;
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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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if (rsq > cut_inner_sq[itype][jtype]) {
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r = sqrt(rsq);
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t = r - cut_inner[itype][jtype];
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fswitch = r*t*t*(ljsw1[itype][jtype] + ljsw2[itype][jtype]*t);
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forcelj += fswitch;
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}
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fforce = factor_lj*forcelj*r2inv;
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philj = r6inv * (lj3[itype][jtype]*r6inv - lj4[itype][jtype]);
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philj += ljsw5[itype][jtype];
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if (rsq > cut_inner_sq[itype][jtype]) {
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phiswitch = t*t*t*(ljsw3[itype][jtype] + ljsw4[itype][jtype]*t);
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philj += phiswitch;
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}
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return factor_lj*philj;
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}
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