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fix_stress.cpp
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Sun, Aug 25, 10:18

fix_stress.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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.
------------------------------------------------------------------------- */
#include "string.h"
#include "fix_stress.h"
#include "atom.h"
#include "neighbor.h"
#include "modify.h"
#include "comm.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "memory.h"
#include "error.h"
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))
/* ---------------------------------------------------------------------- */
FixStress::FixStress(int narg, char **arg) : Fix(narg, arg)
{
if (narg != 3) error->all("Illegal fix stress command");
neigh_half_once = 1;
nmax = 0;
stress = NULL;
}
/* ---------------------------------------------------------------------- */
FixStress::~FixStress()
{
memory->destroy_2d_double_array(stress);
}
/* ---------------------------------------------------------------------- */
int FixStress::setmask()
{
int mask = 0;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixStress::init()
{
if (force->pair == NULL || force->pair->single_enable == 0)
error->all("Pair style does not support dumping per-atom stress");
// set communication size in comm class
comm->maxreverse_fix = MAX(comm->maxreverse_fix,6);
// warn if more than one stress fix
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"STRESS") == 0) count++;
if (count > 1 && comm->me == 0)
error->warning("More than one dump custom with a stress attribute");
}
/* ---------------------------------------------------------------------- */
void FixStress::dump()
{
int i,j,k,n,itype,jtype,numneigh;
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
double factor_coul,factor_lj,fforce,rmass;
int *neighs;
Pair::One one;
// grow stress array if necessary
if (atom->nmax > nmax) {
memory->destroy_2d_double_array(stress);
nmax = atom->nmax;
stress = memory->create_2d_double_array(nmax,6,"stress:stress");
}
// clear stress array
// n includes ghosts only if newton_pair flag is set
if (force->newton_pair) n = atom->nlocal + atom->nghost;
else n = atom->nlocal;
for (i = 0; i < n; i++) {
stress[i][0] = 0.0;
stress[i][1] = 0.0;
stress[i][2] = 0.0;
stress[i][3] = 0.0;
stress[i][4] = 0.0;
stress[i][5] = 0.0;
}
// if needed, build a half neighbor list
if (!neighbor->half_every) neighbor->build_half();
// compute pairwise stress for all atoms via pair->single()
// use half neighbor list
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
double **cutsq = force->pair->cutsq;
double **x = atom->x;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = atom->nlocal + atom->nghost;
for (i = 0; i < nlocal; i++) {
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
neighs = neighbor->firstneigh[i];
numneigh = neighbor->numneigh[i];
for (k = 0; k < numneigh; k++) {
j = neighs[k];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
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]) {
force->pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,0,one);
fforce = one.fforce;
stress[i][0] -= delx*delx*fforce;
stress[i][1] -= dely*dely*fforce;
stress[i][2] -= delz*delz*fforce;
stress[i][3] -= delx*dely*fforce;
stress[i][4] -= delx*delz*fforce;
stress[i][5] -= dely*delz*fforce;
if (force->newton_pair || j < nlocal) {
stress[j][0] -= delx*delx*fforce;
stress[j][1] -= dely*dely*fforce;
stress[j][2] -= delz*delz*fforce;
stress[j][3] -= delx*dely*fforce;
stress[j][4] -= delx*delz*fforce;
stress[j][5] -= dely*delz*fforce;
}
}
}
}
// communicate stress between neighbor procs
if (force->newton_pair) comm->reverse_comm_fix(this);
// remove double counting of per-atom stress
for (i = 0; i < nlocal; i++) {
stress[i][0] *= 0.5;
stress[i][1] *= 0.5;
stress[i][2] *= 0.5;
stress[i][3] *= 0.5;
stress[i][4] *= 0.5;
stress[i][5] *= 0.5;
}
// include kinetic energy term for each atom
// mvv2e converts mv^2 to energy
double **v = atom->v;
double *mass = atom->mass;
double mvv2e = force->mvv2e;
for (i = 0; i < nlocal; i++) {
rmass = mvv2e * mass[type[i]];
stress[i][0] -= rmass*v[i][0]*v[i][0];
stress[i][1] -= rmass*v[i][1]*v[i][1];
stress[i][2] -= rmass*v[i][2]*v[i][2];
stress[i][3] -= rmass*v[i][0]*v[i][1];
stress[i][4] -= rmass*v[i][0]*v[i][2];
stress[i][5] -= rmass*v[i][1]*v[i][2];
}
// convert to pressure units (actually stress/volume = pressure)
double nktv2p = force->nktv2p;
for (i = 0; i < nlocal; i++) {
stress[i][0] *= nktv2p;
stress[i][1] *= nktv2p;
stress[i][2] *= nktv2p;
stress[i][3] *= nktv2p;
stress[i][4] *= nktv2p;
stress[i][5] *= nktv2p;
}
}
/* ---------------------------------------------------------------------- */
int FixStress::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = stress[i][0];
buf[m++] = stress[i][1];
buf[m++] = stress[i][2];
buf[m++] = stress[i][3];
buf[m++] = stress[i][4];
buf[m++] = stress[i][5];
}
return 6;
}
/* ---------------------------------------------------------------------- */
void FixStress::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
stress[j][0] += buf[m++];
stress[j][1] += buf[m++];
stress[j][2] += buf[m++];
stress[j][3] += buf[m++];
stress[j][4] += buf[m++];
stress[j][5] += buf[m++];
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
int FixStress::memory_usage()
{
int bytes = nmax*6 * sizeof(double);
return bytes;
}

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