git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2952 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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src/compute_heat_flux.cpp
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src/compute_heat_flux.cpp
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, 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-AC04-93AL85000 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: Reese Jones (Sandia)
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Philip Howell (Siemens)
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Vikas Varsney (Air Force Research Laboratory)
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "compute_heat_flux.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "update.h"
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#include "force.h"
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#include "pair.h"
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#include "modify.h"
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#include "group.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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enum{DUMMY0,INVOKED_SCALAR,INVOKED_VECTOR,DUMMMY3,INVOKED_PERATOM};
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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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{
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if (narg != 4) error->all("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 pe/atom ID used by heat flux computation
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// insure it is valid for pe/atom computation
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int n = strlen(arg[3]) + 1;
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id_atomPE = new char[n];
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strcpy(id_atomPE,arg[3]);
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int icompute = modify->find_compute(id_atomPE);
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if (icompute < 0) error->all("Could not find compute heat/flux pe/atom ID");
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if (modify->compute[icompute]->peatomflag == 0)
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error->all("Compute heat/flux compute ID does not compute pe/atom");
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vector = new double[6];
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}
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/* ---------------------------------------------------------------------- */
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ComputeHeatFlux::~ComputeHeatFlux()
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{
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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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if (atom->avec->ghost_velocity == 0)
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error->all("Compute heat/flux requires ghost atoms store velocity");
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if (force->pair == NULL || force->pair->single_enable == 0)
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error->all("Pair style does not support compute heat/flux");
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int icompute = modify->find_compute(id_atomPE);
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if (icompute < 0)
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error->all("Pe/atom ID for compute heat/flux does not exist");
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atomPE = modify->compute[icompute];
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pair = force->pair;
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cutsq = force->pair->cutsq;
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// need an occasional half neighbor list
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int irequest = neighbor->request((void *) this);
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neighbor->requests[irequest]->pair = 0;
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neighbor->requests[irequest]->compute = 1;
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neighbor->requests[irequest]->occasional = 1;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeHeatFlux::init_list(int id, NeighList *ptr)
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{
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list = ptr;
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}
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/* ---------------------------------------------------------------------- */
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void ComputeHeatFlux::compute_vector()
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{
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int i,j,ii,jj,inum,jnum,itype,jtype;
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double xtmp,ytmp,ztmp,delx,dely,delz;
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double rsq,eng,fpair,factor_coul,factor_lj,factor;
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double fdotv,massone,ke,pe;
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int *ilist,*jlist,*numneigh,**firstneigh;
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invoked_vector = update->ntimestep;
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double **x = atom->x;
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double **v = atom->v;
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int *type = atom->type;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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int nall = nlocal + atom->nghost;
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double *special_coul = force->special_coul;
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double *special_lj = force->special_lj;
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int newton_pair = force->newton_pair;
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// invoke half neighbor list (will copy or build if necessary)
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neighbor->build_one(list->index);
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inum = list->inum;
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ilist = list->ilist;
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numneigh = list->numneigh;
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firstneigh = list->firstneigh;
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// heat flux J = \sum_i e_i v_i + \sum_{i<j} (f_ij . v_j) x_ij
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// virial-like contribution
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// loop over neighbors of my atoms
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// require either i or j be in compute group
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double Jv[3] = {0.0,0.0,0.0};
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for (ii = 0; ii < inum; ii++) {
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i = ilist[ii];
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xtmp = x[i][0];
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ytmp = x[i][1];
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ztmp = x[i][2];
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itype = type[i];
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jlist = firstneigh[i];
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jnum = numneigh[i];
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for (jj = 0; jj < jnum; jj++) {
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j = jlist[jj];
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if (j < nall) factor_coul = factor_lj = 1.0;
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else {
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factor_coul = special_coul[j/nall];
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factor_lj = special_lj[j/nall];
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j %= nall;
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}
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if (!(mask[i] & groupbit) && !(mask[j] & groupbit)) continue;
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delx = xtmp - x[j][0];
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dely = ytmp - x[j][1];
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delz = ztmp - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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jtype = type[j];
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if (rsq < cutsq[itype][jtype]) {
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eng = pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
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if (newton_pair || j < nlocal) factor = 1.0;
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else factor = 0.5;
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// symmetrize velocities
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double vx = 0.5*(v[i][0]+v[j][0]);
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double vy = 0.5*(v[i][1]+v[j][1]);
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double vz = 0.5*(v[i][2]+v[j][2]);
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fdotv = factor * fpair * (delx*vx + dely*vy + delz*vz);
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Jv[0] += fdotv*delx;
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Jv[1] += fdotv*dely;
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Jv[2] += fdotv*delz;
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}
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}
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}
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// energy convection contribution
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// uses per-atom potential energy
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if (!(atomPE->invoked_flag & INVOKED_PERATOM)) {
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atomPE->compute_peratom();
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atomPE->invoked_flag |= INVOKED_PERATOM;
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}
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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double mvv2e = force->mvv2e;
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double Jc[3] = {0.0,0.0,0.0};
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for (int i = 0; i < nlocal; i++) {
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if (mask[i] & groupbit) {
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massone = (rmass) ? rmass[i] : mass[type[i]];
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ke = mvv2e * 0.5 * massone *
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(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
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pe = atomPE->scalar_atom[i];
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eng = pe + ke;
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Jc[0] += v[i][0]*eng;
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Jc[1] += v[i][1]*eng;
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Jc[2] += v[i][2]*eng;
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}
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}
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// total flux
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double data[6] = {Jv[0]+Jc[0],Jv[1]+Jc[1],Jv[2]+Jc[2],
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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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