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lammps/src/compute_heat_flux.cpp
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compute_heat_flux.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: German Samolyuk (ORNL) and
Mario Pinto (Computational Research Lab, Pune, India)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include "compute_heat_flux.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "force.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
#define INVOKED_PERATOM 8
/* ---------------------------------------------------------------------- */
ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
id_ke(NULL), id_pe(NULL), id_stress(NULL)
{
if (narg != 6) error->all(FLERR,"Illegal compute heat/flux command");
vector_flag = 1;
size_vector = 6;
extvector = 1;
// store ke/atom, pe/atom, stress/atom IDs used by heat flux computation
// insure they are valid for these computations
int n = strlen(arg[3]) + 1;
id_ke = new char[n];
strcpy(id_ke,arg[3]);
n = strlen(arg[4]) + 1;
id_pe = new char[n];
strcpy(id_pe,arg[4]);
n = strlen(arg[5]) + 1;
id_stress = new char[n];
strcpy(id_stress,arg[5]);
int ike = modify->find_compute(id_ke);
int ipe = modify->find_compute(id_pe);
int istress = modify->find_compute(id_stress);
if (ike < 0 || ipe < 0 || istress < 0)
error->all(FLERR,"Could not find compute heat/flux compute ID");
if (strcmp(modify->compute[ike]->style,"ke/atom") != 0)
error->all(FLERR,"Compute heat/flux compute ID does not compute ke/atom");
if (modify->compute[ipe]->peatomflag == 0)
error->all(FLERR,"Compute heat/flux compute ID does not compute pe/atom");
if (modify->compute[istress]->pressatomflag == 0)
error->all(FLERR,
"Compute heat/flux compute ID does not compute stress/atom");
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeHeatFlux::~ComputeHeatFlux()
{
delete [] id_ke;
delete [] id_pe;
delete [] id_stress;
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeHeatFlux::init()
{
// error checks
int ike = modify->find_compute(id_ke);
int ipe = modify->find_compute(id_pe);
int istress = modify->find_compute(id_stress);
if (ike < 0 || ipe < 0 || istress < 0)
error->all(FLERR,"Could not find compute heat/flux compute ID");
c_ke = modify->compute[ike];
c_pe = modify->compute[ipe];
c_stress = modify->compute[istress];
}
/* ---------------------------------------------------------------------- */
void ComputeHeatFlux::compute_vector()
{
invoked_vector = update->ntimestep;
// invoke 3 computes if they haven't been already
if (!(c_ke->invoked_flag & INVOKED_PERATOM)) {
c_ke->compute_peratom();
c_ke->invoked_flag |= INVOKED_PERATOM;
}
if (!(c_pe->invoked_flag & INVOKED_PERATOM)) {
c_pe->compute_peratom();
c_pe->invoked_flag |= INVOKED_PERATOM;
}
if (!(c_stress->invoked_flag & INVOKED_PERATOM)) {
c_stress->compute_peratom();
c_stress->invoked_flag |= INVOKED_PERATOM;
}
// 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
double *ke = c_ke->vector_atom;
double *pe = c_pe->vector_atom;
double **stress = c_stress->array_atom;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double jc[3] = {0.0,0.0,0.0};
double jv[3] = {0.0,0.0,0.0};
double eng;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
eng = pe[i] + ke[i];
jc[0] += eng*v[i][0];
jc[1] += eng*v[i][1];
jc[2] += eng*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];
}
}
// convert jv from stress*volume to energy units via nktv2p factor
double nktv2p = force->nktv2p;
jv[0] /= nktv2p;
jv[1] /= nktv2p;
jv[2] /= nktv2p;
// sum across all procs
// 1st 3 terms are total heat flux
// 2nd 3 terms are just conductive portion
double data[6] = {jc[0]+jv[0],jc[1]+jv[1],jc[2]+jv[2],jc[0],jc[1],jc[2]};
MPI_Allreduce(data,vector,6,MPI_DOUBLE,MPI_SUM,world);
}
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