mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2853 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
0ddeb592a1
commit
d089e246b9
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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: Ahmed Ismail (SNL)
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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_born_coul_long.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 "kspace.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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#define EWALD_F 1.12837917
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#define EWALD_P 0.3275911
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#define A1 0.254829592
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#define A2 -0.284496736
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#define A3 1.421413741
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#define A4 -1.453152027
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#define A5 1.061405429
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/* ---------------------------------------------------------------------- */
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PairBornCoulLong::PairBornCoulLong(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairBornCoulLong::~PairBornCoulLong()
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{
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if (allocated) {
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memory->destroy_2d_int_array(setflag);
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memory->destroy_2d_double_array(cutsq);
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memory->destroy_2d_double_array(cut_lj);
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memory->destroy_2d_double_array(cut_ljsq);
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memory->destroy_2d_double_array(a);
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memory->destroy_2d_double_array(rho);
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memory->destroy_2d_double_array(sigma);
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memory->destroy_2d_double_array(c);
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memory->destroy_2d_double_array(d);
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memory->destroy_2d_double_array(rhoinv);
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memory->destroy_2d_double_array(born1);
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memory->destroy_2d_double_array(born2);
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memory->destroy_2d_double_array(born3);
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memory->destroy_2d_double_array(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairBornCoulLong::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
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double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
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double grij,expm2,prefactor,t,erfc;
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double r,rexp;
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int *ilist,*jlist,*numneigh,**firstneigh;
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evdwl = ecoul = 0.0;
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = vflag_fdotr = 0;
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double **x = atom->x;
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double **f = atom->f;
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double *q = atom->q;
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int *type = atom->type;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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double qqrd2e = force->qqrd2e;
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// loop over neighbors of my atoms
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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qtmp = q[i];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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if (j < nall) factor_coul = factor_lj = 1.0;
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else {
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factor_coul = special_coul[j/nall];
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factor_lj = special_lj[j/nall];
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j %= nall;
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}
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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r2inv = 1.0/rsq;
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if (rsq < cut_coulsq) {
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r = sqrt(rsq);
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grij = g_ewald * r;
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expm2 = exp(-grij*grij);
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t = 1.0 / (1.0 + EWALD_P*grij);
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erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
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prefactor = qqrd2e * qtmp*q[j]/r;
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forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
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if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
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} else forcecoul = 0.0;
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if (rsq < cut_ljsq[itype][jtype]) {
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r6inv = r2inv*r2inv*r2inv;
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r = sqrt(rsq);
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rexp = exp((sigma[itype][jtype]-r)*rhoinv[itype][jtype]);
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forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
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+ born3[itype][jtype]*r2inv*r6inv;
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} else forceborn = 0.0;
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fpair = (forcecoul + factor_lj*forceborn) * r2inv;
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f[i][0] += delx*fpair;
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f[i][1] += dely*fpair;
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f[i][2] += delz*fpair;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fpair;
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f[j][1] -= dely*fpair;
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f[j][2] -= delz*fpair;
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}
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if (eflag) {
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if (rsq < cut_coulsq) {
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ecoul = prefactor*erfc;
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if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
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} else ecoul = 0.0;
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if (rsq < cut_ljsq[itype][jtype]) {
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evdwl = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
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+ d[itype][jtype]*r6inv*r2inv - offset[itype][jtype];
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evdwl *= factor_lj;
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} else evdwl = 0.0;
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}
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if (evflag) ev_tally(i,j,nlocal,newton_pair,
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evdwl,ecoul,fpair,delx,dely,delz);
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}
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}
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}
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if (vflag_fdotr) virial_compute();
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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void PairBornCoulLong::allocate()
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{
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allocated = 1;
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int n = atom->ntypes;
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setflag = memory->create_2d_int_array(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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cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
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cut_lj = memory->create_2d_double_array(n+1,n+1,"pair:cut_lj");
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cut_ljsq = memory->create_2d_double_array(n+1,n+1,"pair:cut_ljsq");
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a = memory->create_2d_double_array(n+1,n+1,"pair:a");
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rho = memory->create_2d_double_array(n+1,n+1,"pair:rho");
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sigma = memory->create_2d_double_array(n+1,n+1,"pair:sigma");
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c = memory->create_2d_double_array(n+1,n+1,"pair:c");
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d = memory->create_2d_double_array(n+1,n+1,"pair:d");
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rhoinv = memory->create_2d_double_array(n+1,n+1,"pair:rhoinv");
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born1 = memory->create_2d_double_array(n+1,n+1,"pair:born1");
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born2 = memory->create_2d_double_array(n+1,n+1,"pair:born2");
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born3 = memory->create_2d_double_array(n+1,n+1,"pair:born3");
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offset = memory->create_2d_double_array(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 PairBornCoulLong::settings(int narg, char **arg)
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{
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if (narg < 1 || narg > 2) error->all("Illegal pair_style command");
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cut_lj_global = atof(arg[0]);
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if (narg == 1) cut_coul = cut_lj_global;
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else cut_coul = atof(arg[1]);
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// reset cutoffs that have been explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= atom->ntypes; i++)
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for (j = i+1; j <= atom->ntypes; j++)
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if (setflag[i][j]) cut_lj[i][j] = cut_lj_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 PairBornCoulLong::coeff(int narg, char **arg)
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{
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if (narg < 7 || narg > 8) error->all("Incorrect args for pair coefficients");
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if (!allocated) allocate();
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int ilo,ihi,jlo,jhi;
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force->bounds(arg[0],atom->ntypes,ilo,ihi);
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force->bounds(arg[1],atom->ntypes,jlo,jhi);
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double a_one = atof(arg[2]);
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double rho_one = atof(arg[3]);
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double sigma_one = atof(arg[4]);
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if (rho_one <= 0) error->all("Incorrect args for pair coefficients");
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double c_one = atof(arg[5]);
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double d_one = atof(arg[6]);
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double cut_lj_one = cut_lj_global;
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if (narg == 8) cut_lj_one = atof(arg[7]);
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int count = 0;
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for (int i = ilo; i <= ihi; i++) {
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for (int j = MAX(jlo,i); j <= jhi; j++) {
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a[i][j] = a_one;
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rho[i][j] = rho_one;
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sigma[i][j] = sigma_one;
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c[i][j] = c_one;
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d[i][j] = d_one;
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cut_lj[i][j] = cut_lj_one;
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setflag[i][j] = 1;
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count++;
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}
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}
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if (count == 0) error->all("Incorrect args for pair coefficients");
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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double PairBornCoulLong::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
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double cut = MAX(cut_lj[i][j],cut_coul);
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cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
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rhoinv[i][j] = 1.0/rho[i][j];
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born1[i][j] = a[i][j]/rho[i][j];
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born2[i][j] = 6.0*c[i][j];
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born3[i][j] = 8.0*d[i][j];
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if (offset_flag) {
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double rexp = exp(-cut_lj[i][j]/rho[i][j]);
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offset[i][j] = a[i][j]*rexp - c[i][j]/pow(cut_lj[i][j],6.0)
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+ d[i][j]/pow(cut_lj[i][j],8.0);
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} else offset[i][j] = 0.0;
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cut_ljsq[j][i] = cut_ljsq[i][j];
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a[j][i] = a[i][j];
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c[j][i] = c[i][j];
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d[j][i] = d[i][j];
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rhoinv[j][i] = rhoinv[i][j];
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sigma[j][i] = sigma[i][j];
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born1[j][i] = born1[i][j];
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born2[j][i] = born2[i][j];
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born3[j][i] = born3[i][j];
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offset[j][i] = offset[i][j];
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return cut;
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairBornCoulLong::init_style()
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{
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if (!atom->q_flag)
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error->all("Pair style born/coul/long requires atom attribute q");
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cut_coulsq = cut_coul * cut_coul;
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// insure use of KSpace long-range solver, set g_ewald
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if (force->kspace == NULL)
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error->all("Pair style is incompatible with KSpace style");
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g_ewald = force->kspace->g_ewald;
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int irequest = neighbor->request(this);
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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 PairBornCoulLong::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(&a[i][j],sizeof(double),1,fp);
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fwrite(&rho[i][j],sizeof(double),1,fp);
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fwrite(&sigma[i][j],sizeof(double),1,fp);
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fwrite(&c[i][j],sizeof(double),1,fp);
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fwrite(&d[i][j],sizeof(double),1,fp);
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fwrite(&cut_lj[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 PairBornCoulLong::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(&a[i][j],sizeof(double),1,fp);
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fread(&rho[i][j],sizeof(double),1,fp);
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fread(&sigma[i][j],sizeof(double),1,fp);
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fread(&c[i][j],sizeof(double),1,fp);
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fread(&d[i][j],sizeof(double),1,fp);
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fread(&cut_lj[i][j],sizeof(double),1,fp);
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}
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MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&rho[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(&c[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&d[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
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}
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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 PairBornCoulLong::write_restart_settings(FILE *fp)
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{
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fwrite(&cut_lj_global,sizeof(double),1,fp);
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fwrite(&cut_coul,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 PairBornCoulLong::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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fread(&cut_lj_global,sizeof(double),1,fp);
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fread(&cut_coul,sizeof(double),1,fp);
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fread(&offset_flag,sizeof(int),1,fp);
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fread(&mix_flag,sizeof(int),1,fp);
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}
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MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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}
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/* ---------------------------------------------------------------------- */
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double PairBornCoulLong::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,r,rexp,grij,expm2,t,erfc,prefactor;
|
||||
double forcecoul,forceborn,phicoul,phiborn;
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
if (rsq < cut_coulsq) {
|
||||
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 forcecoul = 0.0;
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
r6inv = r2inv*r2inv*r2inv;
|
||||
r = sqrt(rsq);
|
||||
rexp = exp(-r*rhoinv[itype][jtype]);
|
||||
forceborn = born1[itype][jtype]*r*rexp - born2[itype][jtype]*r6inv
|
||||
+ born3[itype][jtype]*r2inv*r6inv;
|
||||
} else forceborn = 0.0;
|
||||
fforce = (forcecoul + factor_lj*forceborn) * r2inv;
|
||||
|
||||
double eng = 0.0;
|
||||
if (rsq < cut_coulsq) {
|
||||
phicoul = prefactor*erfc;
|
||||
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
|
||||
eng += phicoul;
|
||||
}
|
||||
if (rsq < cut_ljsq[itype][jtype]) {
|
||||
phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv
|
||||
+ d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
|
||||
eng += factor_lj*phiborn;
|
||||
}
|
||||
return eng;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void *PairBornCoulLong::extract(char *str)
|
||||
{
|
||||
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||
return NULL;
|
||||
}
|
||||
|
||||
|
|
@ -0,0 +1,50 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef PAIR_BORN_COUL_LONG_H
|
||||
#define PAIR_BORN_COUL_LONG_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairBornCoulLong : public Pair {
|
||||
public:
|
||||
PairBornCoulLong(class LAMMPS *);
|
||||
~PairBornCoulLong();
|
||||
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 *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
void *extract(char *);
|
||||
|
||||
private:
|
||||
double cut_lj_global;
|
||||
double **cut_lj,**cut_ljsq;
|
||||
double cut_coul,cut_coulsq;
|
||||
double **a,**rho,**sigma,**c,**d;
|
||||
double **rhoinv,**born1,**born2,**born3,**offset;
|
||||
double g_ewald;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
Loading…
Reference in New Issue