git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@26 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
341
src/pair_morse.cpp
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341
src/pair_morse.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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www.cs.sandia.gov/~sjplimp/lammps.html
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Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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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 "stdio.h"
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#include "stdlib.h"
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#include "pair_morse.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 "update.h"
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#include "memory.h"
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#include "neighbor.h"
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#include "error.h"
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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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free all arrays
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------------------------------------------------------------------------- */
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PairMorse::~PairMorse()
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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(d0);
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memory->destroy_2d_double_array(alpha);
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memory->destroy_2d_double_array(r0);
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memory->destroy_2d_double_array(morse1);
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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 PairMorse::compute(int eflag, int vflag)
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{
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int i,j,k,numneigh,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz;
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double rsq,r,dr,dexp,fforce,factor_lj,phi;
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int *neighs;
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double **f;
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eng_vdwl = 0.0;
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if (vflag) for (i = 0; i < 6; i++) virial[i] = 0.0;
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if (vflag == 2) f = update->f_pair;
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else f = atom->f;
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double **x = atom->x;
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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_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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// loop over neighbors of my atoms
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for (i = 0; i < nlocal; 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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neighs = neighbor->firstneigh[i];
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numneigh = neighbor->numneigh[i];
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for (k = 0; k < numneigh; k++) {
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j = neighs[k];
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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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r = sqrt(rsq);
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dr = r - r0[itype][jtype];
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dexp = exp(-alpha[itype][jtype] * dr);
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fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
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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 = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) -
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offset[itype][jtype];
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if (newton_pair || j < nlocal) eng_vdwl += factor_lj*phi;
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else eng_vdwl += 0.5*factor_lj*phi;
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}
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if (vflag == 1) {
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if (newton_pair || j < nlocal) {
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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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} else {
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virial[0] += 0.5*delx*delx*fforce;
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virial[1] += 0.5*dely*dely*fforce;
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virial[2] += 0.5*delz*delz*fforce;
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virial[3] += 0.5*delx*dely*fforce;
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virial[4] += 0.5*delx*delz*fforce;
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virial[5] += 0.5*dely*delz*fforce;
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}
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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 PairMorse::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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d0 = memory->create_2d_double_array(n+1,n+1,"pair:d0");
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alpha = memory->create_2d_double_array(n+1,n+1,"pair:alpha");
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r0 = memory->create_2d_double_array(n+1,n+1,"pair:r0");
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morse1 = memory->create_2d_double_array(n+1,n+1,"pair:morse1");
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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 PairMorse::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 PairMorse::coeff(int narg, char **arg)
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{
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if (narg < 5 || narg > 6) 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 d0_one = atof(arg[2]);
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double alpha_one = atof(arg[3]);
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double r0_one = atof(arg[4]);
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double cut_one = cut_global;
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if (narg == 6) cut_one = atof(arg[5]);
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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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d0[i][j] = d0_one;
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alpha[i][j] = alpha_one;
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r0[i][j] = r0_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 PairMorse::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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morse1[i][j] = 2.0*d0[i][j]*alpha[i][j];
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if (offset_flag) {
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double alpha_dr = -alpha[i][j] * (cut[i][j] - r0[i][j]);
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offset[i][j] = d0[i][j] * (exp(2.0*alpha_dr) - 2.0*exp(alpha_dr));
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} else offset[i][j] = 0.0;
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d0[j][i] = d0[i][j];
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alpha[j][i] = alpha[i][j];
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r0[j][i] = r0[i][j];
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morse1[j][i] = morse1[i][j];
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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 PairMorse::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(&d0[i][j],sizeof(double),1,fp);
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fwrite(&alpha[i][j],sizeof(double),1,fp);
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fwrite(&r0[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 PairMorse::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(&d0[i][j],sizeof(double),1,fp);
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fread(&alpha[i][j],sizeof(double),1,fp);
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fread(&r0[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(&d0[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&alpha[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&r0[i][j],1,MPI_DOUBLE,0,world);
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MPI_Bcast(&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 PairMorse::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 PairMorse::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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void PairMorse::single(int i, int j, int itype, int jtype, double rsq,
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double factor_coul, double factor_lj, int eflag,
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One &one)
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{
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double r,dr,dexp,phi;
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r = sqrt(rsq);
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dr = r - r0[itype][jtype];
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dexp = exp(-alpha[itype][jtype] * dr);
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one.fforce = factor_lj * morse1[itype][jtype] * (dexp*dexp - dexp) / r;
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if (eflag) {
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phi = d0[itype][jtype] * (dexp*dexp - 2.0*dexp) - offset[itype][jtype];
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one.eng_vdwl = factor_lj*phi;
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one.eng_coul = 0.0;
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}
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}
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