192 lines
6.1 KiB
C++
192 lines
6.1 KiB
C++
// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing authors: German Samolyuk (ORNL) and
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Mario Pinto (Computational Research Lab, Pune, India)
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------------------------------------------------------------------------- */
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#include "compute_heat_flux.h"
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#include <cstring>
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#include "atom.h"
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#include "update.h"
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#include "modify.h"
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#include "force.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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ComputeHeatFlux::ComputeHeatFlux(LAMMPS *lmp, int narg, char **arg) :
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Compute(lmp, narg, arg),
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id_ke(nullptr), id_pe(nullptr), id_stress(nullptr)
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{
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if (narg != 6) error->all(FLERR,"Illegal compute heat/flux command");
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vector_flag = 1;
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size_vector = 6;
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extvector = 1;
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// store ke/atom, pe/atom, stress/atom IDs used by heat flux computation
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// insure they are valid for these computations
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id_ke = utils::strdup(arg[3]);
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id_pe = utils::strdup(arg[4]);
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id_stress = utils::strdup(arg[5]);
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int ike = modify->find_compute(id_ke);
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int ipe = modify->find_compute(id_pe);
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int istress = modify->find_compute(id_stress);
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if (ike < 0 || ipe < 0 || istress < 0)
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error->all(FLERR,"Could not find compute heat/flux compute ID");
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if (strcmp(modify->compute[ike]->style,"ke/atom") != 0)
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error->all(FLERR,"Compute heat/flux compute ID does not compute ke/atom");
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if (modify->compute[ipe]->peatomflag == 0)
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error->all(FLERR,"Compute heat/flux compute ID does not compute pe/atom");
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if (modify->compute[istress]->pressatomflag != 1
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&& modify->compute[istress]->pressatomflag != 2)
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error->all(FLERR,
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"Compute heat/flux compute ID does not compute stress/atom or centroid/stress/atom");
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vector = new double[size_vector];
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}
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/* ---------------------------------------------------------------------- */
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ComputeHeatFlux::~ComputeHeatFlux()
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{
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delete [] id_ke;
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delete [] id_pe;
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delete [] id_stress;
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delete [] vector;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeHeatFlux::init()
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{
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// error checks
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int ike = modify->find_compute(id_ke);
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int ipe = modify->find_compute(id_pe);
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int istress = modify->find_compute(id_stress);
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if (ike < 0 || ipe < 0 || istress < 0)
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error->all(FLERR,"Could not find compute heat/flux compute ID");
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c_ke = modify->compute[ike];
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c_pe = modify->compute[ipe];
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c_stress = modify->compute[istress];
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}
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/* ---------------------------------------------------------------------- */
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void ComputeHeatFlux::compute_vector()
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{
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invoked_vector = update->ntimestep;
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// invoke 3 computes if they haven't been already
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if (!(c_ke->invoked_flag & Compute::INVOKED_PERATOM)) {
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c_ke->compute_peratom();
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c_ke->invoked_flag |= Compute::INVOKED_PERATOM;
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}
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if (!(c_pe->invoked_flag & Compute::INVOKED_PERATOM)) {
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c_pe->compute_peratom();
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c_pe->invoked_flag |= Compute::INVOKED_PERATOM;
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}
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if (!(c_stress->invoked_flag & Compute::INVOKED_PERATOM)) {
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c_stress->compute_peratom();
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c_stress->invoked_flag |= Compute::INVOKED_PERATOM;
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}
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// heat flux vector = jc[3] + jv[3]
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// jc[3] = convective portion of heat flux = sum_i (ke_i + pe_i) v_i[3]
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// jv[3] = virial portion of heat flux = sum_i (stress_tensor_i . v_i[3])
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// normalization by volume is not included
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double *ke = c_ke->vector_atom;
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double *pe = c_pe->vector_atom;
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double **stress = c_stress->array_atom;
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double **v = atom->v;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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double jc[3] = {0.0,0.0,0.0};
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double jv[3] = {0.0,0.0,0.0};
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double eng;
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// heat flux via centroid atomic stress
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if (c_stress->pressatomflag == 2) {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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eng = pe[i] + ke[i];
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jc[0] += eng*v[i][0];
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jc[1] += eng*v[i][1];
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jc[2] += eng*v[i][2];
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// stress[0]: rijx*fijx
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// stress[1]: rijy*fijy
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// stress[2]: rijz*fijz
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// stress[3]: rijx*fijy
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// stress[4]: rijx*fijz
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// stress[5]: rijy*fijz
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// stress[6]: rijy*fijx
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// stress[7]: rijz*fijx
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// stress[8]: rijz*fijy
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// jv[0] = rijx fijx vjx + rijx fijy vjy + rijx fijz vjz
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jv[0] -= stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
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stress[i][4]*v[i][2];
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// jv[1] = rijy fijx vjx + rijy fijy vjy + rijy fijz vjz
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jv[1] -= stress[i][6]*v[i][0] + stress[i][1]*v[i][1] +
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stress[i][5]*v[i][2];
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// jv[2] = rijz fijx vjx + rijz fijy vjy + rijz fijz vjz
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jv[2] -= stress[i][7]*v[i][0] + stress[i][8]*v[i][1] +
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stress[i][2]*v[i][2];
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}
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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eng = pe[i] + ke[i];
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jc[0] += eng*v[i][0];
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jc[1] += eng*v[i][1];
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jc[2] += eng*v[i][2];
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jv[0] -= stress[i][0]*v[i][0] + stress[i][3]*v[i][1] +
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stress[i][4]*v[i][2];
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jv[1] -= stress[i][3]*v[i][0] + stress[i][1]*v[i][1] +
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stress[i][5]*v[i][2];
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jv[2] -= stress[i][4]*v[i][0] + stress[i][5]*v[i][1] +
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stress[i][2]*v[i][2];
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}
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}
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}
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// convert jv from stress*volume to energy units via nktv2p factor
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double nktv2p = force->nktv2p;
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jv[0] /= nktv2p;
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jv[1] /= nktv2p;
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jv[2] /= nktv2p;
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// sum across all procs
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// 1st 3 terms are total heat flux
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// 2nd 3 terms are just conductive portion
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double data[6] = {jc[0]+jv[0],jc[1]+jv[1],jc[2]+jv[2],jc[0],jc[1],jc[2]};
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MPI_Allreduce(data,vector,6,MPI_DOUBLE,MPI_SUM,world);
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}
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