Page MenuHomec4science
Files F70153949

compute_heat_flux.cpp
No OneTemporary
Actions

File Metadata

Created
Fri, Jul 5, 12:38

compute_heat_flux.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-AC04-93AL85000 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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Reese Jones (Sandia)
Philip Howell (Siemens)
Vikas Varsney (Air Force Research Laboratory)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "compute_heat_flux.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "force.h"
#include "pair.h"
#include "modify.h"
#include "group.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{DUMMY0,INVOKED_SCALAR,INVOKED_VECTOR,DUMMMY3,INVOKED_PERATOM};
/* ---------------------------------------------------------------------- */
ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all("Illegal compute heat/flux command");
vector_flag = 1;
size_vector = 6;
extvector = 1;
// store pe/atom ID used by heat flux computation
// insure it is valid for pe/atom computation
int n = strlen(arg[3]) + 1;
id_atomPE = new char[n];
strcpy(id_atomPE,arg[3]);
int icompute = modify->find_compute(id_atomPE);
if (icompute < 0) error->all("Could not find compute heat/flux compute ID");
if (modify->compute[icompute]->peatomflag == 0)
error->all("Compute heat/flux compute ID does not compute pe/atom");
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeHeatFlux::~ComputeHeatFlux()
{
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeHeatFlux::init()
{
// error checks
if (atom->avec->ghost_velocity == 0)
error->all("Compute heat/flux requires ghost atoms store velocity");
if (force->pair == NULL || force->pair->single_enable == 0)
error->all("Pair style does not support compute heat/flux");
int icompute = modify->find_compute(id_atomPE);
if (icompute < 0)
error->all("Compute ID for compute heat/flux does not exist");
atomPE = modify->compute[icompute];
pair = force->pair;
cutsq = force->pair->cutsq;
// need an occasional half neighbor list
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->compute = 1;
neighbor->requests[irequest]->occasional = 1;
}
/* ---------------------------------------------------------------------- */
void ComputeHeatFlux::init_list(int id, NeighList *ptr)
{
list = ptr;
}
/* ---------------------------------------------------------------------- */
void ComputeHeatFlux::compute_vector()
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz;
double rsq,eng,fpair,factor_coul,factor_lj,factor;
double fdotv,massone,ke,pe;
int *ilist,*jlist,*numneigh,**firstneigh;
invoked_vector = update->ntimestep;
double **x = atom->x;
double **v = atom->v;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
// invoke half neighbor list (will copy or build if necessary)
neighbor->build_one(list->index);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// heat flux J = \sum_i e_i v_i + \sum_{i<j} (f_ij . v_j) x_ij
// virial-like contribution
// loop over neighbors of my atoms
// require either i or j be in compute group
double Jv[3] = {0.0,0.0,0.0};
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = factor_lj = 1.0;
else {
factor_coul = special_coul[j/nall];
factor_lj = special_lj[j/nall];
j %= nall;
}
if (!(mask[i] & groupbit) && !(mask[j] & groupbit)) continue;
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]) {
eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
if (newton_pair || j < nlocal) factor = 1.0;
else factor = 0.5;
// symmetrize velocities
double vx = 0.5*(v[i][0]+v[j][0]);
double vy = 0.5*(v[i][1]+v[j][1]);
double vz = 0.5*(v[i][2]+v[j][2]);
fdotv = factor * fpair * (delx*vx + dely*vy + delz*vz);
Jv[0] += fdotv*delx;
Jv[1] += fdotv*dely;
Jv[2] += fdotv*delz;
}
}
}
// energy convection contribution
// uses per-atom potential energy
if (!(atomPE->invoked_flag & INVOKED_PERATOM)) {
atomPE->compute_peratom();
atomPE->invoked_flag |= INVOKED_PERATOM;
}
double *mass = atom->mass;
double *rmass = atom->rmass;
double mvv2e = force->mvv2e;
double Jc[3] = {0.0,0.0,0.0};
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
massone = (rmass) ? rmass[i] : mass[type[i]];
ke = mvv2e * 0.5 * massone *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
pe = atomPE->scalar_atom[i];
eng = pe + ke;
Jc[0] += v[i][0]*eng;
Jc[1] += v[i][1]*eng;
Jc[2] += v[i][2]*eng;
}
}
// total flux
double data[6] = {Jv[0]+Jc[0],Jv[1]+Jc[1],Jv[2]+Jc[2],
Jc[0],Jc[1],Jc[2]};
MPI_Allreduce(data,vector,6,MPI_DOUBLE,MPI_SUM,world);
}

Event Timeline

c4science · Help