mirror of https://github.com/lammps/lammps.git
328 lines
8.9 KiB
C++
328 lines
8.9 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "stdlib.h"
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#include "pair_yukawa.h"
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#include "atom.h"
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#include "force.h"
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#include "comm.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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PairYukawa::PairYukawa(LAMMPS *lmp) : Pair(lmp) {}
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/* ---------------------------------------------------------------------- */
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PairYukawa::~PairYukawa()
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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(offset);
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}
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}
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/* ---------------------------------------------------------------------- */
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void PairYukawa::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;
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double rsq,r2inv,r,rinv,screening,forceyukawa,fforce,factor_coul,phi;
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int *ilist,*jlist,*numneigh,**firstneigh;
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eng_coul = 0.0;
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if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
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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 = atom->nlocal + atom->nghost;
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double *special_coul = force->special_coul;
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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_coul = 1.0;
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else {
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factor_coul = special_coul[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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r = sqrt(rsq);
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rinv = 1.0/r;
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screening = exp(-kappa*r);
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forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
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fforce = factor_coul*forceyukawa * r2inv;
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f[i][0] += delx*fforce;
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f[i][1] += dely*fforce;
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f[i][2] += delz*fforce;
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if (newton_pair || j < nlocal) {
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f[j][0] -= delx*fforce;
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f[j][1] -= dely*fforce;
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f[j][2] -= delz*fforce;
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}
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if (eflag) {
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phi = a[itype][jtype] * screening * rinv - offset[itype][jtype];
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if (newton_pair || j < nlocal) eng_coul += factor_coul*phi;
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else eng_coul += 0.5*factor_coul*phi;
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}
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if (vflag == 1) {
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if (newton_pair == 0 && j >= nlocal) fforce *= 0.5;
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virial[0] += delx*delx*fforce;
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virial[1] += dely*dely*fforce;
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virial[2] += delz*delz*fforce;
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virial[3] += delx*dely*fforce;
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virial[4] += delx*delz*fforce;
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virial[5] += dely*delz*fforce;
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}
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}
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}
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}
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if (vflag == 2) 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 PairYukawa::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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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 PairYukawa::settings(int narg, char **arg)
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{
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if (narg != 2) error->all("Illegal pair_style command");
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kappa = atof(arg[0]);
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cut_global = 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[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 PairYukawa::coeff(int narg, char **arg)
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{
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if (narg < 3 || narg > 4) 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 cut_one = cut_global;
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if (narg == 4) cut_one = atof(arg[3]);
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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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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 PairYukawa::init_one(int i, int j)
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{
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if (setflag[i][j] == 0) {
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a[i][j] = mix_energy(a[i][i],a[j][j],1.0,1.0);
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cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
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}
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if (offset_flag) {
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double screening = exp(-kappa * cut[i][j]);
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offset[i][j] = a[i][j] * screening / cut[i][j];
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} else offset[i][j] = 0.0;
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offset[j][i] = offset[i][j];
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return cut[i][j];
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void PairYukawa::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(&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 PairYukawa::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(&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(&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 PairYukawa::write_restart_settings(FILE *fp)
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{
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fwrite(&kappa,sizeof(double),1,fp);
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fwrite(&cut_global,sizeof(double),1,fp);
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fwrite(&offset_flag,sizeof(int),1,fp);
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fwrite(&mix_flag,sizeof(int),1,fp);
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void PairYukawa::read_restart_settings(FILE *fp)
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{
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if (comm->me == 0) {
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fread(&kappa,sizeof(double),1,fp);
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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(&kappa,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
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MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
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MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
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}
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/* ---------------------------------------------------------------------- */
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void PairYukawa::single(int i, int j, int itype, int jtype, double rsq,
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double factor_coul, double factor_lj,
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int eflag, One &one)
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{
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double r2inv,r,rinv,screening,forceyukawa,phi;
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r2inv = 1.0/rsq;
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r = sqrt(rsq);
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rinv = 1.0/r;
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screening = exp(-kappa*r);
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forceyukawa = a[itype][jtype] * screening * (kappa + rinv);
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one.fforce = factor_coul*forceyukawa * r2inv;
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if (eflag) {
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phi = a[itype][jtype] * screening * rinv - offset[itype][jtype];
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one.eng_coul = factor_coul*phi;
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one.eng_vdwl = 0.0;
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}
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}
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