forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10700 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
afd85b2934
commit
270d94c5ef
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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: Julien Devemy (ICCF)
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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_nm_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 "neigh_list.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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PairNMCut::PairNMCut(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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PairNMCut::~PairNMCut()
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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(e0);
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memory->destroy(r0);
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memory->destroy(nn);
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memory->destroy(mm);
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memory->destroy(nm);
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memory->destroy(e0nm);
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memory->destroy(r0n);
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memory->destroy(r0m);
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memory->destroy(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairNMCut::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,factor_lj;
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double r,forcenm,rminv,rninv;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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factor_lj = special_lj[sbmask(j)];
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j &= NEIGHMASK;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r2inv = 1.0/rsq;
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r = sqrt(rsq);
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rminv = pow(r2inv,mm[itype][jtype]/2.0);
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rninv = pow(r2inv,nn[itype][jtype]/2.0);
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forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
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(r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
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r0m[itype][jtype]/pow(r,mm[itype][jtype]));
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fpair = factor_lj*forcenm*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 = e0nm[itype][jtype] *
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(mm[itype][jtype]*r0n[itype][jtype]*rninv -
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nn[itype][jtype]*r0m[itype][jtype]*rminv) - offset[itype][jtype];
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evdwl *= factor_lj;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,0.0,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_fdotr_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairNMCut::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(e0,n+1,n+1,"pair:e0");
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memory->create(r0,n+1,n+1,"pair:r0");
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memory->create(nn,n+1,n+1,"pair:nn");
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memory->create(mm,n+1,n+1,"pair:mm");
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memory->create(nm,n+1,n+1,"pair:nm");
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memory->create(e0nm,n+1,n+1,"pair:e0nm");
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memory->create(r0n,n+1,n+1,"pair:r0n");
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memory->create(r0m,n+1,n+1,"pair:r0m");
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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 PairNMCut::settings(int narg, char **arg)
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{
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if (narg != 1) error->all(FLERR,"Illegal pair_style command");
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cut_global = force->numeric(FLERR,arg[0]);
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i+1; j <= atom->ntypes; j++)
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if (setflag[i][j]) cut[i][j] = cut_global;
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one or more type pairs
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------------------------------------------------------------------------- */
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void PairNMCut::coeff(int narg, char **arg)
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{
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if (narg < 6 || narg > 7)
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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(arg[0],atom->ntypes,ilo,ihi);
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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double e0_one = force->numeric(FLERR,arg[2]);
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double r0_one = force->numeric(FLERR,arg[3]);
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double nn_one = force->numeric(FLERR,arg[4]);
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double mm_one = force->numeric(FLERR,arg[5]);
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double cut_one = cut_global;
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if (narg == 7) cut_one = force->numeric(FLERR,arg[6]);
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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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e0[i][j] = e0_one;
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r0[i][j] = r0_one;
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nn[i][j] = nn_one;
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mm[i][j] = mm_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 PairNMCut::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
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nm[i][j] = nn[i][j]*mm[i][j];
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e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]);
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r0n[i][j] = pow(r0[i][j],nn[i][j]);
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r0m[i][j] = pow(r0[i][j],mm[i][j]);
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if (offset_flag) {
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offset[i][j] = e0nm[i][j] *
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((mm[i][j]*r0n[i][j] / pow(cut[i][j],nn[i][j])) -
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(nn[i][j]*r0m[i][j] / pow(cut[i][j],mm[i][j])));
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} else offset[i][j] = 0.0;
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e0[j][i] = e0[i][j];
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nn[j][i] = nn[i][j];
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mm[j][i] = mm[i][j];
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nm[j][i] = nm[i][j];
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r0[j][i] = r0[i][j];
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e0nm[j][i] = e0nm[i][j];
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r0n[j][i] = r0n[i][j];
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r0m[j][i] = r0m[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 rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
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double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
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double p1 = 1-nn[i][j];
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double p2 = 1-mm[i][j];
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double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
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double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
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etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
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(rr1*pow(cut[i][j],p1)-rr2*pow(cut[i][j],p2));
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ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
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nn[i][j]*mm[i][j]*(rrr1*pow(cut[i][j],p1)-rrr2*pow(cut[i][j],p2));
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}
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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 PairNMCut::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(&e0[i][j],sizeof(double),1,fp);
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fwrite(&r0[i][j],sizeof(double),1,fp);
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fwrite(&nn[i][j],sizeof(double),1,fp);
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fwrite(&mm[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 PairNMCut::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(&e0[i][j],sizeof(double),1,fp);
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fread(&r0[i][j],sizeof(double),1,fp);
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fread(&nn[i][j],sizeof(double),1,fp);
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fread(&mm[i][j],sizeof(double),1,fp);
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fread(&cut[i][j],sizeof(double),1,fp);
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}
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MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&nn[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&mm[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 PairNMCut::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&offset_flag,sizeof(int),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
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fwrite(&tail_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 PairNMCut::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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fread(&cut_global,sizeof(double),1,fp);
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fread(&offset_flag,sizeof(int),1,fp);
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fread(&mix_flag,sizeof(int),1,fp);
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fread(&tail_flag,sizeof(int),1,fp);
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}
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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MPI_Bcast(&tail_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 PairNMCut::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 %g %g\n",i,e0[i][i],r0[i][i],nn[i][i],mm[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 PairNMCut::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 %g\n",i,j,
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e0[i][j],r0[i][j],nn[i][j],mm[i][j],cut[i][j]);
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}
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/* ---------------------------------------------------------------------- */
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double PairNMCut::single(int i, int j, int itype, int jtype,
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double rsq, double factor_coul, double factor_lj,
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double &fforce)
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{
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double r2inv,r,forcenm,phinm;
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r2inv = 1.0/rsq;
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r = sqrt(rsq);
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forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
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(r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
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r0m[itype][jtype]/pow(r,mm[itype][jtype]));
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fforce = factor_lj*forcenm*r2inv;
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phinm = e0nm[itype][jtype] *
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(mm[itype][jtype] * r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
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nn[itype][jtype]*r0m[itype][jtype] /pow(r,mm[itype][jtype])) -
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offset[itype][jtype];
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return factor_lj*phinm;
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}
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/* ---------------------------------------------------------------------- */
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void *PairNMCut::extract(const char *str, int &dim)
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{
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dim = 2;
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if (strcmp(str,"e0") == 0) return (void *) e0;
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if (strcmp(str,"r0") == 0) return (void *) r0;
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if (strcmp(str,"nn") == 0) return (void *) nn;
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if (strcmp(str,"mm") == 0) return (void *) mm;
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return NULL;
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}
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@ -0,0 +1,57 @@
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/* ----------------------------------------------------------------------
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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(nm/cut,PairNMCut)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_NM_CUT_H
|
||||
#define LMP_PAIR_NM_CUT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairNMCut : public Pair {
|
||||
public:
|
||||
PairNMCut(class LAMMPS *);
|
||||
virtual ~PairNMCut();
|
||||
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **e0,**r0,**nn, **mm;
|
||||
double **nm,**e0nm,**r0n,**r0m,**offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,506 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing Author: Julien Devemy (ICCF)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair_nm_cut_coul_cut.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairNMCutCoulCut::PairNMCutCoulCut(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
writedata = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairNMCutCoulCut::~PairNMCutCoulCut()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(cut_coul);
|
||||
memory->destroy(cut_coulsq);
|
||||
memory->destroy(e0);
|
||||
memory->destroy(r0);
|
||||
memory->destroy(nn);
|
||||
memory->destroy(mm);
|
||||
memory->destroy(nm);
|
||||
memory->destroy(e0nm);
|
||||
memory->destroy(r0n);
|
||||
memory->destroy(r0m);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double rsq,r2inv,factor_coul,factor_lj;
|
||||
double r,forcecoul,forcenm,rminv,rninv;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_coul = force->special_coul;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
if (rsq < cut_coulsq[itype][jtype])
|
||||
forcecoul = qqrd2e * qtmp*q[j]*sqrt(r2inv);
|
||||
else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r = sqrt(rsq);
|
||||
rminv = pow(r2inv,mm[itype][jtype]/2.0);
|
||||
rninv = pow(r2inv,nn[itype][jtype]/2.0);
|
||||
forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
|
||||
(r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
|
||||
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
|
||||
} else forcenm = 0.0;
|
||||
|
||||
fpair = (factor_coul*forcecoul + factor_lj*forcenm) * r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < cut_coulsq[itype][jtype])
|
||||
ecoul = factor_coul * qqrd2e * qtmp*q[j]*sqrt(r2inv);
|
||||
else ecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = e0nm[itype][jtype]*(mm[itype][jtype] *
|
||||
r0n[itype][jtype]*rninv -
|
||||
nn[itype][jtype] *
|
||||
r0m[itype][jtype]*rminv) -
|
||||
offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
|
||||
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
|
||||
memory->create(cut_coul,n+1,n+1,"pair:cut_coul");
|
||||
memory->create(cut_coulsq,n+1,n+1,"pair:cut_coulsq");
|
||||
memory->create(e0,n+1,n+1,"pair:e0");
|
||||
memory->create(r0,n+1,n+1,"pair:r0");
|
||||
memory->create(nn,n+1,n+1,"pair:nn");
|
||||
memory->create(mm,n+1,n+1,"pair:mm");
|
||||
memory->create(nm,n+1,n+1,"pair:nm");
|
||||
memory->create(e0nm,n+1,n+1,"pair:e0nm");
|
||||
memory->create(r0n,n+1,n+1,"pair:r0n");
|
||||
memory->create(r0m,n+1,n+1,"pair:r0m");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_lj_global = force->numeric(FLERR,arg[0]);
|
||||
if (narg == 1) cut_coul_global = cut_lj_global;
|
||||
else cut_coul_global = force->numeric(FLERR,arg[1]);
|
||||
|
||||
// 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_lj[i][j] = cut_lj_global;
|
||||
cut_coul[i][j] = cut_coul_global;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 6 || narg > 8)
|
||||
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 e0_one = force->numeric(FLERR,arg[2]);
|
||||
double r0_one = force->numeric(FLERR,arg[3]);
|
||||
double nn_one = force->numeric(FLERR,arg[4]);
|
||||
double mm_one = force->numeric(FLERR,arg[5]);
|
||||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
double cut_coul_one = cut_coul_global;
|
||||
if (narg >= 7) cut_coul_one = cut_lj_one = force->numeric(FLERR,arg[4]);
|
||||
if (narg == 8) cut_coul_one = force->numeric(FLERR,arg[5]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
e0[i][j] = e0_one;
|
||||
r0[i][j] = r0_one;
|
||||
nn[i][j] = nn_one;
|
||||
mm[i][j] = mm_one;
|
||||
cut_lj[i][j] = cut_lj_one;
|
||||
cut_coul[i][j] = cut_coul_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,"Pair style nm/cut/coul/cut requires atom attribute q");
|
||||
|
||||
neighbor->request(this);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairNMCutCoulCut::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
double cut = MAX(cut_lj[i][j],cut_coul[i][j]);
|
||||
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
|
||||
cut_coulsq[i][j] = cut_coul[i][j] * cut_coul[i][j];
|
||||
|
||||
nm[i][j] = nn[i][j]*mm[i][j];
|
||||
e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]);
|
||||
r0n[i][j] = pow(r0[i][j],nn[i][j]);
|
||||
r0m[i][j] = pow(r0[i][j],mm[i][j]);
|
||||
|
||||
if (offset_flag) {
|
||||
offset[i][j] = e0nm[i][j] *
|
||||
((mm[i][j]*r0n[i][j] / pow(cut_lj[i][j],nn[i][j])) -
|
||||
(nn[i][j]*r0m[i][j] / pow(cut_lj[i][j],mm[i][j])));
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
cut_ljsq[j][i] = cut_ljsq[i][j];
|
||||
cut_coulsq[j][i] = cut_coulsq[i][j];
|
||||
e0[j][i] = e0[i][j];
|
||||
nn[j][i] = nn[i][j];
|
||||
mm[j][i] = mm[i][j];
|
||||
nm[j][i] = nm[i][j];
|
||||
r0[j][i] = r0[i][j];
|
||||
e0nm[j][i] = e0nm[i][j];
|
||||
r0n[j][i] = r0n[i][j];
|
||||
r0m[j][i] = r0m[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// 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 rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
|
||||
double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
|
||||
double p1 = 1-nn[i][j];
|
||||
double p2 = 1-mm[i][j];
|
||||
|
||||
double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
|
||||
double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
|
||||
|
||||
etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
|
||||
(rr1*pow(cut_lj[i][j],p1)-rr2*pow(cut_lj[i][j],p2));
|
||||
ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
|
||||
nn[i][j]*mm[i][j]*(rrr1*pow(cut_lj[i][j],p1)-rrr2*pow(cut_lj[i][j],p2));
|
||||
|
||||
}
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::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(&e0[i][j],sizeof(double),1,fp);
|
||||
fwrite(&r0[i][j],sizeof(double),1,fp);
|
||||
fwrite(&nn[i][j],sizeof(double),1,fp);
|
||||
fwrite(&mm[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_coul[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::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(&e0[i][j],sizeof(double),1,fp);
|
||||
fread(&r0[i][j],sizeof(double),1,fp);
|
||||
fread(&nn[i][j],sizeof(double),1,fp);
|
||||
fread(&mm[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_coul[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&nn[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&mm[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_lj_global,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul_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 PairNMCutCoulCut::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&cut_lj_global,sizeof(double),1,fp);
|
||||
fread(&cut_coul_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_lj_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul_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);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g\n",i,e0[i][i],r0[i][i],nn[i][i],mm[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulCut::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp,"%d %d %g %g %g %g %g\n",i,j,
|
||||
e0[i][j],r0[i][j],nn[i][j],mm[i][j],cut_lj[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairNMCutCoulCut::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r,forcecoul,forcenm,phicoul,phinm;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
if (rsq < cut_coulsq[itype][jtype])
|
||||
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
|
||||
else forcecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r = sqrt(rsq);
|
||||
forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
|
||||
(r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
|
||||
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
|
||||
} else forcenm = 0.0;
|
||||
fforce = (factor_coul*forcecoul + factor_lj*forcenm) * r2inv;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq[itype][jtype]) {
|
||||
phicoul = force->qqrd2e * atom->q[i]*atom->q[j]*sqrt(r2inv);
|
||||
eng += factor_coul*phicoul;
|
||||
}
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
phinm = e0nm[itype][jtype] *
|
||||
(mm[itype][jtype]*r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
|
||||
nn[itype][jtype]*r0m[itype][jtype]/pow(r,mm[itype][jtype])) -
|
||||
offset[itype][jtype];
|
||||
eng += factor_lj*phinm;
|
||||
}
|
||||
|
||||
return eng;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairNMCutCoulCut::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 0;
|
||||
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||
dim = 2;
|
||||
if (strcmp(str,"e0") == 0) return (void *) e0;
|
||||
if (strcmp(str,"r0") == 0) return (void *) r0;
|
||||
if (strcmp(str,"nn") == 0) return (void *) nn;
|
||||
if (strcmp(str,"mm") == 0) return (void *) mm;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,78 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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(nm/cut/coul/cut,PairNMCutCoulCut)
|
||||
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_NM_CUT_COUL_CUT_H
|
||||
#define LMP_PAIR_NM_CUT_COUL_CUT_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairNMCutCoulCut : public Pair {
|
||||
public:
|
||||
PairNMCutCoulCut(class LAMMPS *);
|
||||
virtual ~PairNMCutCoulCut();
|
||||
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_lj_global,cut_coul_global;
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double **cut_coul,**cut_coulsq;
|
||||
double **e0,**r0,**nn, **mm;
|
||||
double **nm,**e0nm,**r0n,**r0m,**offset;
|
||||
|
||||
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 style nm/cut/coul/cut requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,590 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Contributing Author: Julien Devemy (ICCF)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair_nm_cut_coul_long.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "kspace.h"
|
||||
#include "update.h"
|
||||
#include "integrate.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "neigh_request.h"
|
||||
#include "math_const.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define EWALD_F 1.12837917
|
||||
#define EWALD_P 0.3275911
|
||||
#define A1 0.254829592
|
||||
#define A2 -0.284496736
|
||||
#define A3 1.421413741
|
||||
#define A4 -1.453152027
|
||||
#define A5 1.061405429
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairNMCutCoulLong::PairNMCutCoulLong(LAMMPS *lmp) : Pair(lmp)
|
||||
{
|
||||
ewaldflag = pppmflag = 1;
|
||||
ftable = NULL;
|
||||
qdist = 0.0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairNMCutCoulLong::~PairNMCutCoulLong()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(cutsq);
|
||||
|
||||
memory->destroy(cut_lj);
|
||||
memory->destroy(cut_ljsq);
|
||||
memory->destroy(e0);
|
||||
memory->destroy(r0);
|
||||
memory->destroy(nn);
|
||||
memory->destroy(mm);
|
||||
memory->destroy(nm);
|
||||
memory->destroy(e0nm);
|
||||
memory->destroy(r0n);
|
||||
memory->destroy(r0m);
|
||||
memory->destroy(offset);
|
||||
}
|
||||
if (ftable) free_tables();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
|
||||
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
|
||||
double fraction,table;
|
||||
double r,r2inv,factor_coul,factor_lj;
|
||||
double forcecoul,forcenm,rminv,rninv;
|
||||
double grij,expm2,prefactor,t,erfc;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
double rsq;
|
||||
|
||||
evdwl = ecoul = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
double *q = atom->q;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
double *special_coul = force->special_coul;
|
||||
double *special_lj = force->special_lj;
|
||||
int newton_pair = force->newton_pair;
|
||||
double qqrd2e = force->qqrd2e;
|
||||
|
||||
inum = list->inum;
|
||||
ilist = list->ilist;
|
||||
numneigh = list->numneigh;
|
||||
firstneigh = list->firstneigh;
|
||||
|
||||
// loop over neighbors of my atoms
|
||||
|
||||
for (ii = 0; ii < inum; ii++) {
|
||||
i = ilist[ii];
|
||||
qtmp = q[i];
|
||||
xtmp = x[i][0];
|
||||
ytmp = x[i][1];
|
||||
ztmp = x[i][2];
|
||||
itype = type[i];
|
||||
jlist = firstneigh[i];
|
||||
jnum = numneigh[i];
|
||||
|
||||
for (jj = 0; jj < jnum; jj++) {
|
||||
j = jlist[jj];
|
||||
factor_lj = special_lj[sbmask(j)];
|
||||
factor_coul = special_coul[sbmask(j)];
|
||||
j &= NEIGHMASK;
|
||||
|
||||
delx = xtmp - x[j][0];
|
||||
dely = ytmp - x[j][1];
|
||||
delz = ztmp - x[j][2];
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
jtype = type[j];
|
||||
|
||||
if (rsq < cutsq[itype][jtype]) {
|
||||
r2inv = 1.0/rsq;
|
||||
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = qqrd2e * qtmp*q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else {
|
||||
union_int_float_t rsq_lookup;
|
||||
rsq_lookup.f = rsq;
|
||||
itable = rsq_lookup.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = qtmp*q[j] * table;
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = qtmp*q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r = sqrt(rsq);
|
||||
rminv = pow(r2inv,mm[itype][jtype]/2.0);
|
||||
rninv = pow(r2inv,nn[itype][jtype]/2.0);
|
||||
forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
|
||||
(r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
|
||||
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
|
||||
} else forcenm = 0.0;
|
||||
|
||||
fpair = (forcecoul + factor_lj*forcenm) * r2inv;
|
||||
|
||||
f[i][0] += delx*fpair;
|
||||
f[i][1] += dely*fpair;
|
||||
f[i][2] += delz*fpair;
|
||||
if (newton_pair || j < nlocal) {
|
||||
f[j][0] -= delx*fpair;
|
||||
f[j][1] -= dely*fpair;
|
||||
f[j][2] -= delz*fpair;
|
||||
}
|
||||
|
||||
if (eflag) {
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq)
|
||||
ecoul = prefactor*erfc;
|
||||
else {
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
ecoul = qtmp*q[j] * table;
|
||||
}
|
||||
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else ecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
evdwl = e0nm[itype][jtype] *
|
||||
(mm[itype][jtype]*r0n[itype][jtype]*rninv -
|
||||
nn[itype][jtype]*r0m[itype][jtype]*rminv) - offset[itype][jtype];
|
||||
evdwl *= factor_lj;
|
||||
} else evdwl = 0.0;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,ecoul,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_fdotr_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = i; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
|
||||
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
|
||||
memory->create(e0,n+1,n+1,"pair:e0");
|
||||
memory->create(r0,n+1,n+1,"pair:r0");
|
||||
memory->create(nn,n+1,n+1,"pair:nn");
|
||||
memory->create(mm,n+1,n+1,"pair:mm");
|
||||
memory->create(nm,n+1,n+1,"pair:nm");
|
||||
memory->create(e0nm,n+1,n+1,"pair:e0nm");
|
||||
memory->create(r0n,n+1,n+1,"pair:r0n");
|
||||
memory->create(r0m,n+1,n+1,"pair:r0m");
|
||||
memory->create(offset,n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg < 1 || narg > 2) error->all(FLERR,"Illegal pair_style command");
|
||||
|
||||
cut_lj_global = force->numeric(FLERR,arg[0]);
|
||||
if (narg == 1) cut_coul = cut_lj_global;
|
||||
else cut_coul = force->numeric(FLERR,arg[1]);
|
||||
|
||||
// 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_lj[i][j] = cut_lj_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::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 e0_one = force->numeric(FLERR,arg[2]);
|
||||
double r0_one = force->numeric(FLERR,arg[3]);
|
||||
double nn_one = force->numeric(FLERR,arg[4]);
|
||||
double mm_one = force->numeric(FLERR,arg[5]);
|
||||
|
||||
double cut_lj_one = cut_lj_global;
|
||||
if (narg == 7) cut_lj_one = force->numeric(FLERR,arg[4]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||
e0[i][j] = e0_one;
|
||||
r0[i][j] = r0_one;
|
||||
nn[i][j] = nn_one;
|
||||
mm[i][j] = mm_one;
|
||||
cut_lj[i][j] = cut_lj_one;
|
||||
setflag[i][j] = 1;
|
||||
count++;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init specific to this pair style
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::init_style()
|
||||
{
|
||||
if (!atom->q_flag)
|
||||
error->all(FLERR,"Pair style nm/cut/coul/long requires atom attribute q");
|
||||
|
||||
neighbor->request(this);
|
||||
|
||||
cut_coulsq = cut_coul * cut_coul;
|
||||
// insure use of KSpace long-range solver, set g_ewald
|
||||
|
||||
if (force->kspace == NULL)
|
||||
error->all(FLERR,"Pair style requires a KSpace style");
|
||||
g_ewald = force->kspace->g_ewald;
|
||||
|
||||
// setup force tables
|
||||
|
||||
if (ncoultablebits) init_tables(cut_coul,NULL);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairNMCutCoulLong::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
|
||||
|
||||
// include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P
|
||||
|
||||
double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist);
|
||||
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
|
||||
|
||||
nm[i][j] = nn[i][j]*mm[i][j];
|
||||
e0nm[i][j] = e0[i][j]/(nn[i][j]-mm[i][j]);
|
||||
r0n[i][j] = pow(r0[i][j],nn[i][j]);
|
||||
r0m[i][j] = pow(r0[i][j],mm[i][j]);
|
||||
|
||||
if (offset_flag) {
|
||||
offset[i][j] = e0nm[i][j] *
|
||||
((mm[i][j]*r0n[i][j] / pow(cut_lj[i][j],nn[i][j])) -
|
||||
(nn[i][j]*r0m[i][j] / pow(cut_lj[i][j],mm[i][j])));
|
||||
} else offset[i][j] = 0.0;
|
||||
|
||||
cut_ljsq[j][i] = cut_ljsq[i][j];
|
||||
e0[j][i] = e0[i][j];
|
||||
nn[j][i] = nn[i][j];
|
||||
mm[j][i] = mm[i][j];
|
||||
nm[j][i] = nm[i][j];
|
||||
r0[j][i] = r0[i][j];
|
||||
e0nm[j][i] = e0nm[i][j];
|
||||
r0n[j][i] = r0n[i][j];
|
||||
r0m[j][i] = r0m[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
// 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 rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
|
||||
double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
|
||||
double p1 = 1-nn[i][j];
|
||||
double p2 = 1-mm[i][j];
|
||||
|
||||
double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
|
||||
double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
|
||||
|
||||
etail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j] *
|
||||
(rr1*pow(cut_lj[i][j],p1)-rr2*pow(cut_lj[i][j],p2));
|
||||
ptail_ij = 2.0*MY_PI*all[0]*all[1]*e0nm[i][j]*nn[i][j]*mm[i][j] *
|
||||
(rrr1*pow(cut_lj[i][j],p1)-rrr2*pow(cut_lj[i][j],p2));
|
||||
}
|
||||
|
||||
return cut;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::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(&e0[i][j],sizeof(double),1,fp);
|
||||
fwrite(&r0[i][j],sizeof(double),1,fp);
|
||||
fwrite(&nn[i][j],sizeof(double),1,fp);
|
||||
fwrite(&mm[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::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(&e0[i][j],sizeof(double),1,fp);
|
||||
fread(&r0[i][j],sizeof(double),1,fp);
|
||||
fread(&nn[i][j],sizeof(double),1,fp);
|
||||
fread(&mm[i][j],sizeof(double),1,fp);
|
||||
fread(&cut_lj[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&e0[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&nn[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&mm[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_lj_global,sizeof(double),1,fp);
|
||||
fwrite(&cut_coul,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);
|
||||
fwrite(&ncoultablebits,sizeof(int),1,fp);
|
||||
fwrite(&tabinner,sizeof(double),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&cut_lj_global,sizeof(double),1,fp);
|
||||
fread(&cut_coul,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);
|
||||
fread(&ncoultablebits,sizeof(int),1,fp);
|
||||
fread(&tabinner,sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut_coul,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);
|
||||
MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g %g %g\n",i,e0[i][i],r0[i][i],nn[i][i],mm[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes all pairs to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairNMCutCoulLong::write_data_all(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp,"%d %d %g %g %g %g %g\n",i,j,
|
||||
e0[i][j],r0[i][j],nn[i][j],mm[i][j],cut_lj[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairNMCutCoulLong::single(int i, int j, int itype, int jtype,
|
||||
double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r,grij,expm2,t,erfc,prefactor;
|
||||
double fraction,table,forcecoul,forcenm,phicoul,phinm;
|
||||
int itable;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq) {
|
||||
r = sqrt(rsq);
|
||||
grij = g_ewald * r;
|
||||
expm2 = exp(-grij*grij);
|
||||
t = 1.0 / (1.0 + EWALD_P*grij);
|
||||
erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
|
||||
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
|
||||
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
} else {
|
||||
union_int_float_t rsq_lookup_single;
|
||||
rsq_lookup_single.f = rsq;
|
||||
itable = rsq_lookup_single.i & ncoulmask;
|
||||
itable >>= ncoulshiftbits;
|
||||
fraction = (rsq_lookup_single.f - rtable[itable]) * drtable[itable];
|
||||
table = ftable[itable] + fraction*dftable[itable];
|
||||
forcecoul = atom->q[i]*atom->q[j] * table;
|
||||
if (factor_coul < 1.0) {
|
||||
table = ctable[itable] + fraction*dctable[itable];
|
||||
prefactor = atom->q[i]*atom->q[j] * table;
|
||||
forcecoul -= (1.0-factor_coul)*prefactor;
|
||||
}
|
||||
}
|
||||
} else forcecoul = 0.0;
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r = sqrt(rsq);
|
||||
forcenm = e0nm[itype][jtype]*nm[itype][jtype] *
|
||||
(r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
|
||||
r0m[itype][jtype]/pow(r,mm[itype][jtype]));
|
||||
} else forcenm = 0.0;
|
||||
|
||||
fforce = (forcecoul + factor_lj*forcenm) * r2inv;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq) {
|
||||
if (!ncoultablebits || rsq <= tabinnersq)
|
||||
phicoul = prefactor*erfc;
|
||||
else {
|
||||
table = etable[itable] + fraction*detable[itable];
|
||||
phicoul = atom->q[i]*atom->q[j] * table;
|
||||
}
|
||||
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
|
||||
eng += phicoul;
|
||||
}
|
||||
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
phinm = e0nm[itype][jtype] *
|
||||
(mm[itype][jtype]*r0n[itype][jtype]/pow(r,nn[itype][jtype]) -
|
||||
nn[itype][jtype]*r0m[itype][jtype]/pow(r,mm[itype][jtype])) -
|
||||
offset[itype][jtype];
|
||||
eng += factor_lj*phinm;
|
||||
}
|
||||
|
||||
return eng;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairNMCutCoulLong::extract(const char *str, int &dim)
|
||||
{
|
||||
dim = 0;
|
||||
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||
dim = 2;
|
||||
if (strcmp(str,"e0") == 0) return (void *) e0;
|
||||
if (strcmp(str,"r0") == 0) return (void *) r0;
|
||||
if (strcmp(str,"nn") == 0) return (void *) nn;
|
||||
if (strcmp(str,"mm") == 0) return (void *) mm;
|
||||
return NULL;
|
||||
}
|
||||
|
|
@ -0,0 +1,84 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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(nm/cut/coul/long,PairNMCutCoulLong)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_PAIR_NM_CUT_COUL_LONG_H
|
||||
#define LMP_PAIR_NM_CUT_COUL_LONG_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairNMCutCoulLong : public Pair {
|
||||
public:
|
||||
PairNMCutCoulLong(class LAMMPS *);
|
||||
virtual ~PairNMCutCoulLong();
|
||||
|
||||
virtual void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double init_one(int, int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_restart_settings(FILE *);
|
||||
void read_restart_settings(FILE *);
|
||||
void write_data(FILE *);
|
||||
void write_data_all(FILE *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
void *extract(const char *, int &);
|
||||
|
||||
protected:
|
||||
double cut_lj_global;
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double cut_coul,cut_coulsq;
|
||||
double **e0,**r0,**nn, **mm;
|
||||
double **nm,**e0nm,**r0n,**r0m,**offset;
|
||||
double qdist; // TIP4P distance from O site to negative charge
|
||||
double g_ewald;
|
||||
|
||||
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 style nm/cut/coul/long requires atom attribute q
|
||||
|
||||
The atom style defined does not have this attribute.
|
||||
|
||||
E: Pair style requires a KSpace style
|
||||
|
||||
No kspace style is defined.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue