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lammps/src/USER-EFF/compute_temp_eff.cpp
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compute_temp_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 "compute_temp_eff.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempEff::ComputeTempEff(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
// error check
if (!atom->spin_flag || !atom->ervel_flag)
error->all("Compute temp/eff requires atom attributes spin, ervel");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
vector = new double[size_vector];
}
/* ---------------------------------------------------------------------- */
ComputeTempEff::~ComputeTempEff()
{
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempEff::init()
{
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempEff::dof_compute()
{
double natoms = group->count(igroup);
dof = domain->dimension * natoms;
dof -= extra_dof + fix_dof;
int *spin = atom->spin;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int one = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (fabs(spin[i])==1) one++;
}
int nelectrons;
MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world);
// average over nuclear dof only
dof -= domain->dimension * nelectrons;
if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempEff::compute_scalar()
{
invoked_scalar = update->ntimestep;
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 t = 0.0;
if (mass) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]];
if (fabs(spin[i])==1) t += 0.75*mass[type[i]]*ervel[i]*ervel[i];
}
}
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempEff::compute_vector()
{
int i;
invoked_vector = update->ntimestep;
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 massone,t[6];
for (i = 0; i < 6; i++) t[i] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
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 (fabs(spin[i])==1) {
t[0] += 0.75*massone*ervel[i]*ervel[i];
t[1] += 0.75*massone*ervel[i]*ervel[i];
t[2] += 0.75*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;
}
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