forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5010 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
4e67191e82
commit
becdcdb27d
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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: Sai Jayaraman (U Notre Dame)
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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.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 "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MIN(a,b) ((a) < (b) ? (a) : (b))
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#define MAX(a,b) ((a) > (b) ? (a) : (b))
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/* ---------------------------------------------------------------------- */
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PairBorn::PairBorn(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairBorn::~PairBorn()
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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);
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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 PairBorn::compute(int eflag, int vflag)
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
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double rsq,r2inv,r6inv,force_tf,factor_lj;
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double r,rexp;
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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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int nall = nlocal + atom->nghost;
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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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if (j < nall) factor_lj = 1.0;
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else {
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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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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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fpair = 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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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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}
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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_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 PairBorn::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 = memory->create_2d_double_array(n+1,n+1,"pair:cut");
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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 PairBorn::settings(int narg, char **arg)
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{
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if (narg != 1) error->all("Illegal pair_style command");
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cut_global = atof(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 PairBorn::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 = force->numeric(arg[2]);
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double rho_one = force->numeric(arg[3]);
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double sigma_one = force->numeric(arg[4]);
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if (rho_one <= 0) error->all("Incorrect args for pair coefficients");
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double c_one = force->numeric(arg[5]);
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double d_one = force->numeric(arg[6]);
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double cut_one = cut_global;
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if (narg == 8) cut_one = force->numeric(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[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("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 PairBorn::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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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((sigma[i][j]-cut_lj[i][j])*rhoinv[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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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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// compute I,J contribution to long-range tail correction
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// count total # of atoms of type I and J via Allreduce
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if (tail_flag) {
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int *type = atom->type;
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int nlocal = atom->nlocal;
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double count[2],all[2];
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count[0] = count[1] = 0.0;
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for (int k = 0; k < nlocal; k++) {
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if (type[k] == i) count[0] += 1.0;
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if (type[k] == j) count[1] += 1.0;
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}
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MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
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double PI = 4.0*atan(1.0);
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double rho1 = rho[i][j];
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double rho2 = rho1*rho1;
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double rho3 = rho2*rho1;
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double rc = sigma[i][j] - cut[i][j];
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double rc2 = rc*rc;
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double rc3 = rc2*rc;
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double rc5 = rc3*rc2;
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etail_ij = 2.0*PI*all[0]*all[1] *
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(a[i][j]*exp(-rc/rho1)*rho1* (rc2 + 2.0*rho1*rc + 2.0*rho2) -
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c[i][j]/(3.0*rc3) + d[i][j]/(5.0*rc5));
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ptail_ij = (-1/3.0)*2.0*PI*all[0]*all[1] *
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(-a[i][j]*exp(-rc/rho1) *
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(rc3 + 3.0*rho1*rc2 + 6.0*rho2*rc + 6.0*rho3) +
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2.0*c[i][j]/rc3 - 8.0*d[i][j]/(5.0*rc5));
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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 PairBorn::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[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 PairBorn::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[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[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 PairBorn::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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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairBorn::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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}
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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}
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/* ---------------------------------------------------------------------- */
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double PairBorn::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,r6inv,r,rexp,forceborn,phiborn;
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r2inv = 1.0/rsq;
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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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fforce = factor_lj*force_born*r2inv;
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phiborn = a[itype][jtype]*rexp - c[itype][jtype]*r6inv +
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d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
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return factor_lj*phiborn;
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}
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@ -0,0 +1,54 @@
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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
|
||||
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.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(born,PairBorn)
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#else
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#ifndef PAIR_BORN_H
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#define PAIR_BORN_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairBorn : public Pair {
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public:
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PairBorn(class LAMMPS *);
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~PairBorn();
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||||
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 *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
private:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **a,**rho,**sigma,**c, **d;
|
||||
double **rhoinv,**tf1,**tf2,**tf3,**offset;
|
||||
double **rhoinv,**born1,**born2,**born3,**offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
|
@ -0,0 +1,320 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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: Sai Jayaraman (University of Notre Dame)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "pair_gauss.h"
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "neighbor.h"
|
||||
#include "neigh_list.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define MIN(a,b) ((a) < (b) ? (a) : (b))
|
||||
#define MAX(a,b) ((a) > (b) ? (a) : (b))
|
||||
|
||||
#define EPSILON 1.0e-10
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairGauss::PairGauss(LAMMPS *lmp) :Pair(lmp) {}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
PairGauss::~PairGauss()
|
||||
{
|
||||
if (allocated) {
|
||||
memory->destroy_2d_int_array(setflag);
|
||||
memory->destroy_2d_double_array(cutsq);
|
||||
|
||||
memory->destroy_2d_double_array(cut);
|
||||
memory->destroy_2d_double_array(a);
|
||||
memory->destroy_2d_double_array(b);
|
||||
memory->destroy_2d_double_array(offset);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void PairGauss::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
|
||||
double r,rsq,r2inv,r6inv,forcelj,rexp;
|
||||
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||
|
||||
evdwl = 0.0;
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = vflag_fdotr = 0;
|
||||
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *type = atom->type;
|
||||
int nlocal = atom->nlocal;
|
||||
int nall = nlocal + atom->nghost;
|
||||
int newton_pair = force->newton_pair;
|
||||
|
||||
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];
|
||||
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];
|
||||
|
||||
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;
|
||||
r = sqrt(rsq);
|
||||
forcelj = - 2.0*a[itype][jtype]*b[itype][jtype] * rsq *
|
||||
exp(-b[itype][jtype]*rsq);
|
||||
if (r < 0.00001) forcelj = 0.0;
|
||||
fpair = forcelj*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) {
|
||||
evdwl = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) -
|
||||
offset[itype][jtype]);
|
||||
evdwl *= MAX(EPSILON,latscale);
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||
evdwl,0.0,fpair,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_fdotr) virial_compute();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
allocate all arrays
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGauss::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ntypes;
|
||||
|
||||
setflag = memory->create_2d_int_array(n+1,n+1,"pair:setflag");
|
||||
for (int i = 1; i <= n; i++)
|
||||
for (int j = 1; j <= n; j++)
|
||||
setflag[i][j] = 0;
|
||||
|
||||
cutsq = memory->create_2d_double_array(n+1,n+1,"pair:cutsq");
|
||||
|
||||
cut = memory->create_2d_double_array(n+1,n+1,"pair:cut_gauss");
|
||||
a = memory->create_2d_double_array(n+1,n+1,"pair:a");
|
||||
b = memory->create_2d_double_array(n+1,n+1,"pair:b");
|
||||
offset = memory->create_2d_double_array(n+1,n+1,"pair:offset");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
global settings
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGauss::settings(int narg, char **arg)
|
||||
{
|
||||
if (narg != 1) error->all("Illegal pair_style command");
|
||||
|
||||
cut_global = atof(arg[0]);
|
||||
|
||||
// reset cutoffs that have been explicity set
|
||||
|
||||
if (allocated) {
|
||||
int i,j;
|
||||
for (i = 1; i <= atom->ntypes; i++)
|
||||
for (j = i+1; j <= atom->ntypes; j++)
|
||||
if (setflag[i][j]) cut[i][j] = cut_global;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more type pairs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGauss::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg < 4 || narg > 5) error->all("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 a_one = atof(arg[2]);
|
||||
double b_one = atof(arg[3]);
|
||||
|
||||
double cut_one = cut_global;
|
||||
if (narg == 5) cut_one = atof(arg[4]);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
for (int j = MAX(jlo,i); j<=jhi; j++) {
|
||||
a[i][j] = a_one;
|
||||
b[i][j] = b_one;
|
||||
cut[i][j] = cut_one;
|
||||
setflag[i][j] = 1;
|
||||
count++ ;
|
||||
}
|
||||
}
|
||||
|
||||
if (count == 0) error->all("Incorrect args for pair coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
init for one type pair i,j and corresponding j,i
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double PairGauss::init_one(int i, int j)
|
||||
{
|
||||
if (setflag[i][j] == 0) error->all("All pair coeffs are not set");
|
||||
|
||||
if (offset_flag) offset[i][j] = a[i][j]*exp(-b[i][j]*cut[i][j]*cut[i][j]);
|
||||
else offset[i][j] = 0.0;
|
||||
|
||||
a[j][i] = a[i][j];
|
||||
b[j][i] = b[i][j];
|
||||
offset[j][i] = offset[i][j];
|
||||
|
||||
return cut[i][j];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGauss::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(&a[i][j],sizeof(double),1,fp);
|
||||
fwrite(&b[i][j],sizeof(double),1,fp);
|
||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGauss::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(&a[i][j],sizeof(double),1,fp);
|
||||
fread(&b[i][j],sizeof(double),1,fp);
|
||||
fread(&cut[i][j],sizeof(double),1,fp);
|
||||
}
|
||||
MPI_Bcast(&a[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&b[i][j],1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGauss::write_restart_settings(FILE *fp)
|
||||
{
|
||||
fwrite(&cut_global,sizeof(double),1,fp);
|
||||
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void PairGauss::read_restart_settings(FILE *fp)
|
||||
{
|
||||
if (comm->me == 0) {
|
||||
fread(&cut_global,sizeof(double),1,fp);
|
||||
fread(&offset_flag,sizeof(int),1,fp);
|
||||
fread(&mix_flag,sizeof(int),1,fp);
|
||||
}
|
||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double PairGauss::single(int i, int j, int itype, int jtype, double rsq,
|
||||
double factor_coul, double factor_lj,
|
||||
double &fforce)
|
||||
{
|
||||
double r2inv,r6inv,forcelj,philj,r;
|
||||
|
||||
r = sqrt(rsq);
|
||||
|
||||
r2inv = 1.0/rsq;
|
||||
philj = -(a[itype][jtype]*exp(-b[itype][jtype]*rsq) - offset[itype][jtype]);
|
||||
philj *= MAX(eps,latscale);
|
||||
|
||||
forcelj = -2.0*a[itype][jtype]*b[itype][jtype]*rsq*exp(-b[itype][jtype]*rsq);
|
||||
fforce = forcelj*r2inv;
|
||||
return philj;
|
||||
}
|
||||
|
|
@ -0,0 +1,52 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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(gauss,PairGauss)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef PAIR_GAUSS_H
|
||||
#define PAIR_GAUSS_H
|
||||
|
||||
#include "pair.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class PairGauss : public Pair {
|
||||
public:
|
||||
PairGauss(class LAMMPS *);
|
||||
~PairGauss();
|
||||
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 *);
|
||||
double single(int, int, int, int, double, double, double, double &);
|
||||
|
||||
private:
|
||||
double cut_global;
|
||||
double **cut;
|
||||
double **a,**b;
|
||||
double **offset;
|
||||
|
||||
void allocate();
|
||||
};
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue