Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-TALLY/compute_heat_flux_tally.cpp
e3d0a322729eefficient_neuronet

Last Change
Raw File

compute_heat_flux_tally.cpp
View Options

/* ----------------------------------------------------------------------
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_heat_flux_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;
/* ---------------------------------------------------------------------- */
ComputeHeatFluxTally::ComputeHeatFluxTally(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all(FLERR,"Illegal compute heat/flux/tally command");
igroup2 = group->find(arg[3]);
if (igroup2 == -1)
error->all(FLERR,"Could not find compute heat/flux/tally second group ID");
groupbit2 = group->bitmask[igroup2];
vector_flag = 1;
timeflag = 1;
comm_reverse = 7;
extvector = 1;
size_vector = 6;
peflag = 1; // we need Pair::ev_tally() to be run
did_compute = 0;
invoked_peratom = invoked_scalar = -1;
nmax = -1;
stress = NULL;
eatom = NULL;
vector = new double[size_vector];
}
/* ---------------------------------------------------------------------- */
ComputeHeatFluxTally::~ComputeHeatFluxTally()
{
if (force && force->pair) force->pair->del_tally_callback(this);
delete[] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeHeatFluxTally::init()
{
if (force->pair == NULL)
error->all(FLERR,"Trying to use compute heat/flux/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 heat/flux/tally used with incompatible pair style.");
if ((comm->me == 0) && (force->bond || force->angle || force->dihedral
|| force->improper || force->kspace))
error->warning(FLERR,"Compute heat/flux/tally only called from pair style");
did_compute = -1;
}
/* ---------------------------------------------------------------------- */
void ComputeHeatFluxTally::pair_tally_callback(int i, int j, int nlocal, int newton,
double evdwl, double ecoul, 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 and eatom arrays if necessary
// needs to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(stress);
nmax = atom->nmax;
memory->create(stress,nmax,6,"heat/flux/tally:stress");
memory->destroy(eatom);
nmax = atom->nmax;
memory->create(eatom,nmax,"heat/flux/tally:eatom");
}
// clear storage as needed
if (newton) {
for (int i=0; i < ntotal; ++i) {
eatom[i] = 0.0;
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;
}
} else {
for (int i=0; i < atom->nlocal; ++i) {
eatom[i] = 0.0;
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;
}
}
for (int i=0; i < size_vector; ++i)
vector[i] = heatj[i] = 0.0;
}
if ( ((mask[i] & groupbit) && (mask[j] & groupbit2))
|| ((mask[i] & groupbit2) && (mask[j] & groupbit)) ) {
const double epairhalf = 0.5 * (evdwl + ecoul);
fpair *= 0.5;
const double v0 = dx*dx*fpair; // dx*fpair = Fij_x
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) {
eatom[i] += epairhalf;
stress[i][0] += v0;
stress[i][1] += v1;
stress[i][2] += v2;
stress[i][3] += v3;
stress[i][4] += v4;
stress[i][5] += v5;
}
if (newton || j < nlocal) {
eatom[j] += epairhalf;
stress[j][0] += v0;
stress[j][1] += v1;
stress[j][2] += v2;
stress[j][3] += v3;
stress[j][4] += v4;
stress[j][5] += v5;
}
}
}
/* ---------------------------------------------------------------------- */
int ComputeHeatFluxTally::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++] = eatom[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 ComputeHeatFluxTally::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
eatom[j] += buf[m++];
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++];
}
}
/* ---------------------------------------------------------------------- */
void ComputeHeatFluxTally::compute_vector()
{
invoked_vector = update->ntimestep;
if ((did_compute != invoked_vector) || (update->eflag_global != invoked_vector))
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) {
eatom[i] = 0.0;
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;
}
}
// compute heat currents
// heat flux vector = jc[3] + jv[3]
// jc[3] = convective portion of heat flux = sum_i (ke_i + pe_i) v_i[3]
// jv[3] = virial portion of heat flux = sum_i (stress_tensor_i . v_i[3])
// normalization by volume is not included
// J = sum_i( (0.5*m*v_i^2 + 0.5*(evdwl_i+ecoul_i))*v_i +
// + (F_ij . v_i)*dR_ij/2 )
int nlocal = atom->nlocal;
int *mask = atom->mask;
const double pfactor = 0.5 * force->mvv2e;
double **v = atom->v;
double *mass = atom->mass;
int *type = atom->type;
double jc[3] = {0.0,0.0,0.0};
double jv[3] = {0.0,0.0,0.0};
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
double ke_i = pfactor * mass[type[i]] *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
jc[0] += (ke_i + eatom[i]) * v[i][0];
jc[1] += (ke_i + eatom[i]) * v[i][1];
jc[2] += (ke_i + eatom[i]) * v[i][2];
jv[0] += stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
stress[i][4]*v[i][2];
jv[1] += stress[i][3]*v[i][0] + stress[i][1]*v[i][1] +
stress[i][5]*v[i][2];
jv[2] += stress[i][4]*v[i][0] + stress[i][5]*v[i][1] +
stress[i][2]*v[i][2];
}
}
// sum accumulated heatj across procs
heatj[0] = jc[0] + jv[0];
heatj[1] = jc[1] + jv[1];
heatj[2] = jc[2] + jv[2];
heatj[3] = jc[0];
heatj[4] = jc[1];
heatj[5] = jc[2];
MPI_Allreduce(heatj,vector,size_vector,MPI_DOUBLE,MPI_SUM,world);
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double ComputeHeatFluxTally::memory_usage()
{
double bytes = nmax*comm_reverse * sizeof(double);
return bytes;
}
c4science · Help