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compute_temp_com.cpp
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Sat, Jun 21, 22:16

compute_temp_com.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.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "compute_temp_com.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
ComputeTempCOM::ComputeTempCOM(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute temp command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeTempCOM::~ComputeTempCOM()
{
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCOM::init()
{
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
dof_compute();
masstotal = group->mass(igroup);
}
/* ---------------------------------------------------------------------- */
void ComputeTempCOM::dof_compute()
{
double natoms = group->count(igroup);
int nper = domain->dimension;
dof = nper * natoms;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempCOM::compute_scalar()
{
double vthermal[3];
invoked_scalar = update->ntimestep;
if (dynamic) masstotal = group->mass(igroup);
group->vcm(igroup,masstotal,vbias);
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double t = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
vthermal[0] = v[i][0] - vbias[0];
vthermal[1] = v[i][1] - vbias[1];
vthermal[2] = v[i][2] - vbias[2];
if (mass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempCOM::compute_vector()
{
int i;
double vthermal[3];
invoked_vector = update->ntimestep;
if (dynamic) masstotal = group->mass(igroup);
group->vcm(igroup,masstotal,vbias);
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
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) {
vthermal[0] = v[i][0] - vbias[0];
vthermal[1] = v[i][1] - vbias[1];
vthermal[2] = v[i][2] - vbias[2];
if (mass) massone = mass[type[i]];
else massone = rmass[i];
t[0] += massone * vthermal[0]*vthermal[0];
t[1] += massone * vthermal[1]*vthermal[1];
t[2] += massone * vthermal[2]*vthermal[2];
t[3] += massone * vthermal[0]*vthermal[1];
t[4] += massone * vthermal[0]*vthermal[2];
t[5] += massone * vthermal[1]*vthermal[2];
}
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
------------------------------------------------------------------------- */
void ComputeTempCOM::remove_bias(int i, double *v)
{
v[0] -= vbias[0];
v[1] -= vbias[1];
v[2] -= vbias[2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempCOM::remove_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] -= vbias[0];
v[i][1] -= vbias[1];
v[i][2] -= vbias[2];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempCOM::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 ComputeTempCOM::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] += vbias[0];
v[i][1] += vbias[1];
v[i][2] += vbias[2];
}
}

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