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compute_stress_tally.cpp
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Wed, Nov 13, 03:07

compute_stress_tally.cpp
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include <string.h>
#include "compute_stress_tally.h"
#include "atom.h"
#include "group.h"
#include "pair.h"
#include "update.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeStressTally::ComputeStressTally(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute stress/tally command");
igroup2 = group->find(arg[3]);
if (igroup2 == -1)
error->all(FLERR,"Could not find compute stress/tally second group ID");
groupbit2 = group->bitmask[igroup2];
scalar_flag = 1;
vector_flag = 0;
peratom_flag = 1;
timeflag = 1;
comm_reverse = size_peratom_cols = 6;
extscalar = 0;
peflag = 1; // we need Pair::ev_tally() to be run
did_compute = 0;
invoked_peratom = invoked_scalar = -1;
nmax = -1;
stress = NULL;
vector = new double[size_peratom_cols];
}
/* ---------------------------------------------------------------------- */
ComputeStressTally::~ComputeStressTally()
{
if (force && force->pair) force->pair->del_tally_callback(this);
memory->destroy(stress);
delete[] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeStressTally::init()
{
if (force->pair == NULL)
error->all(FLERR,"Trying to use compute stress/tally with no pair style");
else
force->pair->add_tally_callback(this);
if (force->pair->single_enable == 0 || force->pair->manybody_flag)
error->all(FLERR,"Compute stress/tally used with incompatible pair style.");
if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
|| force->improper || force->kspace))
error->warning(FLERR,"Compute stress/tally only called from pair style");
did_compute = -1;
}
/* ---------------------------------------------------------------------- */
void ComputeStressTally::pair_tally_callback(int i, int j, int nlocal, int newton,
double, double, double fpair,
double dx, double dy, double dz)
{
const int ntotal = atom->nlocal + atom->nghost;
const int * const mask = atom->mask;
// do setup work that needs to be done only once per timestep
if (did_compute != update->ntimestep) {
did_compute = update->ntimestep;
// grow local stress array if necessary
// needs to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(stress);
nmax = atom->nmax;
memory->create(stress,nmax,size_peratom_cols,"stress/tally:stress");
array_atom = stress;
}
// clear storage as needed
if (newton) {
for (int i=0; i < ntotal; ++i)
for (int j=0; j < size_peratom_cols; ++j)
stress[i][j] = 0.0;
} else {
for (int i=0; i < atom->nlocal; ++i)
for (int j=0; j < size_peratom_cols; ++j)
stress[i][j] = 0.0;
}
for (int i=0; i < size_peratom_cols; ++i)
vector[i] = virial[i] = 0.0;
}
if ( ((mask[i] & groupbit) && (mask[j] & groupbit2))
|| ((mask[i] & groupbit2) && (mask[j] & groupbit)) ) {
fpair *= 0.5;
const double v0 = dx*dx*fpair;
const double v1 = dy*dy*fpair;
const double v2 = dz*dz*fpair;
const double v3 = dx*dy*fpair;
const double v4 = dx*dz*fpair;
const double v5 = dy*dz*fpair;
if (newton || i < nlocal) {
virial[0] += v0; stress[i][0] += v0;
virial[1] += v1; stress[i][1] += v1;
virial[2] += v2; stress[i][2] += v2;
virial[3] += v3; stress[i][3] += v3;
virial[4] += v4; stress[i][4] += v4;
virial[5] += v5; stress[i][5] += v5;
}
if (newton || j < nlocal) {
virial[0] += v0; stress[j][0] += v0;
virial[1] += v1; stress[j][1] += v1;
virial[2] += v2; stress[j][2] += v2;
virial[3] += v3; stress[j][3] += v3;
virial[4] += v4; stress[j][4] += v4;
virial[5] += v5; stress[j][5] += v5;
}
}
}
/* ---------------------------------------------------------------------- */
int ComputeStressTally::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 m;
}
/* ---------------------------------------------------------------------- */
void ComputeStressTally::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++];
}
}
/* ---------------------------------------------------------------------- */
double ComputeStressTally::compute_scalar()
{
invoked_scalar = update->ntimestep;
if ((did_compute != invoked_scalar) || (update->eflag_global != invoked_scalar))
error->all(FLERR,"Energy was not tallied on needed timestep");
// sum accumulated forces across procs
MPI_Allreduce(virial,vector,size_peratom_cols,MPI_DOUBLE,MPI_SUM,world);
if (domain->dimension == 3)
scalar = (vector[0]+vector[1]+vector[2])/3.0;
else
scalar = (vector[0]+vector[1])/2.0;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeStressTally::compute_peratom()
{
invoked_peratom = update->ntimestep;
if ((did_compute != invoked_peratom) || (update->eflag_global != invoked_peratom))
error->all(FLERR,"Energy was not tallied on needed timestep");
// collect contributions from ghost atoms
if (force->newton_pair) {
comm->reverse_comm_compute(this);
const int nall = atom->nlocal + atom->nghost;
for (int i = atom->nlocal; i < nall; ++i)
for (int j = 0; j < size_peratom_cols; ++j)
stress[i][j] = 0.0;
}
// convert to stress*volume units = -pressure*volume
const double nktv2p = -force->nktv2p;
for (int i = 0; i < atom->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;
}
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeStressTally::memory_usage()
{
double bytes = nmax*size_peratom_cols * sizeof(double);
return bytes;
}

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