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compute_temp_region_eff.cpp
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Wed, Nov 13, 08:31

compute_temp_region_eff.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 author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "compute_temp_region_eff.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "modify.h"
#include "domain.h"
#include "region.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempRegionEff::ComputeTempRegionEff(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (!atom->electron_flag)
error->all(FLERR,"Compute temp/region/eff requires atom style electron");
if (narg != 4) error->all(FLERR,"Illegal compute temp/region/eff command");
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for compute temp/region/eff does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeTempRegionEff::~ComputeTempRegionEff()
{
delete [] idregion;
memory->destroy(vbiasall);
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempRegionEff::init()
{
// set index and check validity of region
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for compute temp/region/eff does not exist");
}
/* ---------------------------------------------------------------------- */
void ComputeTempRegionEff::setup()
{
dynamic = 0;
if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
dof = 0.0;
}
/* ---------------------------------------------------------------------- */
void ComputeTempRegionEff::dof_remove_pre()
{
domain->regions[iregion]->prematch();
}
/* ---------------------------------------------------------------------- */
int ComputeTempRegionEff::dof_remove(int i)
{
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2])) return 0;
return 1;
}
/* ---------------------------------------------------------------------- */
double ComputeTempRegionEff::compute_scalar()
{
invoked_scalar = update->ntimestep;
double **x = atom->x;
double **v = atom->v;
double *ervel = atom->ervel;
double *mass = atom->mass;
int *spin = atom->spin;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double mefactor = domain->dimension/4.0;
Region *region = domain->regions[iregion];
region->prematch();
int count = 0;
int ecount = 0;
double t = 0.0;
if (mass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
count++;
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
if (abs(spin[i])==1) {
t += mefactor*mass[type[i]]*ervel[i]*ervel[i];
ecount++;
}
}
}
double tarray[2],tarray_all[2];
// Assume 3/2 k T per nucleus
tarray[0] = count-ecount;
tarray[1] = t;
MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
dof = domain->dimension * tarray_all[0] - extra_dof;
int one = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (abs(spin[i])==1) one++;
}
if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
else scalar = 0.0;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempRegionEff::compute_vector()
{
int i;
invoked_vector = update->ntimestep;
double **x = atom->x;
double **v = atom->v;
double *ervel = atom->ervel;
double *mass = atom->mass;
int *spin = atom->spin;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double mefactor = domain->dimension/4.0;
Region *region = domain->regions[iregion];
region->prematch();
double massone,t[6];
for (i = 0; i < 6; i++) t[i] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
massone = mass[type[i]];
t[0] += massone * v[i][0]*v[i][0];
t[1] += massone * v[i][1]*v[i][1];
t[2] += massone * v[i][2]*v[i][2];
t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2];
if (abs(spin[i])==1) {
t[0] += mefactor * massone * ervel[i]*ervel[i];
t[1] += mefactor * massone * ervel[i]*ervel[i];
t[2] += mefactor * massone * ervel[i]*ervel[i];
}
}
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
NOTE: the following commands do not bias the radial electron velocities
------------------------------------------------------------------------- */
void ComputeTempRegionEff::remove_bias(int i, double *v)
{
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2]))
vbias[0] = vbias[1] = vbias[2] = 0.0;
else {
vbias[0] = v[0];
vbias[1] = v[1];
vbias[2] = v[2];
v[0] = v[1] = v[2] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRegionEff::remove_bias_all()
{
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > maxbias) {
memory->destroy(vbiasall);
maxbias = atom->nmax;
memory->create(vbiasall,maxbias,3,"temp/region:vbiasall");
}
Region *region = domain->regions[iregion];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region->match(x[i][0],x[i][1],x[i][2]))
vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0;
else {
vbiasall[i][0] = v[i][0];
vbiasall[i][1] = v[i][1];
vbiasall[i][2] = v[i][2];
v[i][0] = v[i][1] = v[i][2] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempRegionEff::restore_bias(int i, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempRegionEff::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vbiasall[i][0];
v[i][1] += vbiasall[i][1];
v[i][2] += vbiasall[i][2];
}
}
/* ---------------------------------------------------------------------- */
double ComputeTempRegionEff::memory_usage()
{
double bytes = maxbias * sizeof(double);
return bytes;
}

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