git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@255 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/compute_stress_atom.cpp
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255
src/compute_stress_atom.cpp
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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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#include "string.h"
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#include "compute_stress_atom.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "modify.h"
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#include "comm.h"
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#include "update.h"
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#include "force.h"
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#include "pair.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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ComputeStressAtom::ComputeStressAtom(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg)
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{
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if (narg != 3) error->all("Illegal compute stress/atom command");
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peratom_flag = 1;
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size_peratom = 6;
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comm_reverse = 6;
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neigh_half_once = 1;
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nmax = 0;
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stress = NULL;
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}
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/* ---------------------------------------------------------------------- */
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ComputeStressAtom::~ComputeStressAtom()
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{
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memory->destroy_2d_double_array(stress);
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}
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/* ---------------------------------------------------------------------- */
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void ComputeStressAtom::init()
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{
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if (force->pair == NULL || force->pair->single_enable == 0)
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error->all("Pair style does not support computing per-atom stress");
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int count = 0;
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for (int i = 0; i < modify->ncompute; i++)
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if (strcmp(modify->compute[i]->style,"stress/atom") == 0) count++;
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if (count > 1 && comm->me == 0)
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error->warning("More than one compute stress/atom defined");
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}
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/* ---------------------------------------------------------------------- */
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void ComputeStressAtom::compute_peratom()
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{
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int i,j,k,n,itype,jtype,numneigh;
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double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
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double factor_coul,factor_lj,fforce,rmass;
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int *neighs;
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Pair::One one;
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// grow stress array if necessary
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if (atom->nmax > nmax) {
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memory->destroy_2d_double_array(stress);
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nmax = atom->nmax;
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stress =
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memory->create_2d_double_array(nmax,6,"compute/stress/atom:stress");
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vector_atom = stress;
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}
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// clear stress array
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// n includes ghosts only if newton_pair flag is set
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if (force->newton_pair) n = atom->nlocal + atom->nghost;
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else n = atom->nlocal;
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for (i = 0; i < n; i++) {
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stress[i][0] = 0.0;
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stress[i][1] = 0.0;
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stress[i][2] = 0.0;
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stress[i][3] = 0.0;
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stress[i][4] = 0.0;
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stress[i][5] = 0.0;
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}
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// if needed, build a half neighbor list
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if (!neighbor->half_every) neighbor->build_half();
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// compute pairwise stress for all atoms via pair->single()
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// use half neighbor list
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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double **cutsq = force->pair->cutsq;
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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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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_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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force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
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fforce = one.fforce;
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stress[i][0] -= delx*delx*fforce;
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stress[i][1] -= dely*dely*fforce;
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stress[i][2] -= delz*delz*fforce;
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stress[i][3] -= delx*dely*fforce;
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stress[i][4] -= delx*delz*fforce;
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stress[i][5] -= dely*delz*fforce;
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if (force->newton_pair || j < nlocal) {
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stress[j][0] -= delx*delx*fforce;
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stress[j][1] -= dely*dely*fforce;
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stress[j][2] -= delz*delz*fforce;
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stress[j][3] -= delx*dely*fforce;
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stress[j][4] -= delx*delz*fforce;
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stress[j][5] -= dely*delz*fforce;
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}
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}
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}
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}
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// communicate stress between neighbor procs
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if (force->newton_pair) comm->reverse_comm_compute(this);
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// remove double counting of per-atom stress
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for (i = 0; i < nlocal; i++) {
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stress[i][0] *= 0.5;
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stress[i][1] *= 0.5;
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stress[i][2] *= 0.5;
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stress[i][3] *= 0.5;
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stress[i][4] *= 0.5;
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stress[i][5] *= 0.5;
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}
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// include kinetic energy term for each atom
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// mvv2e converts mv^2 to energy
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double **v = atom->v;
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double *mass = atom->mass;
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double mvv2e = force->mvv2e;
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for (i = 0; i < nlocal; i++) {
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rmass = mvv2e * mass[type[i]];
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stress[i][0] -= rmass*v[i][0]*v[i][0];
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stress[i][1] -= rmass*v[i][1]*v[i][1];
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stress[i][2] -= rmass*v[i][2]*v[i][2];
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stress[i][3] -= rmass*v[i][0]*v[i][1];
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stress[i][4] -= rmass*v[i][0]*v[i][2];
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stress[i][5] -= rmass*v[i][1]*v[i][2];
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}
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// convert to pressure units (actually stress/volume = pressure)
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double nktv2p = force->nktv2p;
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for (i = 0; i < nlocal; i++) {
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stress[i][0] *= nktv2p;
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stress[i][1] *= nktv2p;
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stress[i][2] *= nktv2p;
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stress[i][3] *= nktv2p;
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stress[i][4] *= nktv2p;
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stress[i][5] *= nktv2p;
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}
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}
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/* ---------------------------------------------------------------------- */
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int ComputeStressAtom::pack_reverse_comm(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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buf[m++] = stress[i][0];
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buf[m++] = stress[i][1];
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buf[m++] = stress[i][2];
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buf[m++] = stress[i][3];
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buf[m++] = stress[i][4];
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buf[m++] = stress[i][5];
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}
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return 6;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeStressAtom::unpack_reverse_comm(int n, int *list, double *buf)
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{
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int i,j,m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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stress[j][0] += buf[m++];
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stress[j][1] += buf[m++];
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stress[j][2] += buf[m++];
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stress[j][3] += buf[m++];
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stress[j][4] += buf[m++];
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stress[j][5] += buf[m++];
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}
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based array
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------------------------------------------------------------------------- */
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int ComputeStressAtom::memory_usage()
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{
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int bytes = nmax*6 * sizeof(double);
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return bytes;
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}
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