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compute_temp_partial.cpp
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Fri, Jul 4, 00:37

compute_temp_partial.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 "compute_temp_partial.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 6) error->all(FLERR,"Illegal compute temp/partial command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
xflag = force->inumeric(FLERR,arg[3]);
yflag = force->inumeric(FLERR,arg[4]);
zflag = force->inumeric(FLERR,arg[5]);
if (zflag && domain->dimension == 2)
error->all(FLERR,"Compute temp/partial cannot use vz for 2d systemx");
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeTempPartial::~ComputeTempPartial()
{
memory->destroy(vbiasall);
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempPartial::setup()
{
dynamic = 0;
if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
dof_compute();
}
/* ----------------------------------------------------------------------
DOF for a body of N atoms with S constraints (e.g. from SHAKE)
DOF = nper/dim (dim*N - S), where dim = dimensionality = 2 or 3
------------------------------------------------------------------------- */
void ComputeTempPartial::dof_compute()
{
adjust_dof_fix();
natoms_temp = group->count(igroup);
int nper = xflag+yflag+zflag;
dof = nper * natoms_temp;
dof -= (1.0*nper/domain->dimension)*fix_dof + extra_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
int ComputeTempPartial::dof_remove(int i)
{
int nper = xflag+yflag+zflag;
return (domain->dimension - nper);
}
/* ---------------------------------------------------------------------- */
double ComputeTempPartial::compute_scalar()
{
invoked_scalar = update->ntimestep;
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;
if (rmass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] +
zflag*v[i][2]*v[i][2]) * rmass[i];
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
t += (xflag*v[i][0]*v[i][0] + yflag*v[i][1]*v[i][1] +
zflag*v[i][2]*v[i][2]) * mass[type[i]];
}
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) dof_compute();
if (dof < 0.0 && natoms_temp > 0.0)
error->all(FLERR,"Temperature compute degrees of freedom < 0");
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempPartial::compute_vector()
{
int i;
invoked_vector = update->ntimestep;
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) {
if (rmass) massone = rmass[i];
else massone = mass[type[i]];
t[0] += massone * xflag*v[i][0]*v[i][0];
t[1] += massone * yflag*v[i][1]*v[i][1];
t[2] += massone * zflag*v[i][2]*v[i][2];
t[3] += massone * xflag*yflag*v[i][0]*v[i][1];
t[4] += massone * xflag*zflag*v[i][0]*v[i][2];
t[5] += massone * yflag*zflag*v[i][1]*v[i][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 ComputeTempPartial::remove_bias(int i, double *v)
{
if (!xflag) {
vbias[0] = v[0];
v[0] = 0.0;
}
if (!yflag) {
vbias[1] = v[1];
v[1] = 0.0;
}
if (!zflag) {
vbias[2] = v[2];
v[2] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempPartial::remove_bias_all()
{
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/partial:vbiasall");
}
if (!xflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
vbiasall[i][0] = v[i][0];
v[i][0] = 0.0;
}
}
if (!yflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
vbiasall[i][1] = v[i][1];
v[i][1] = 0.0;
}
}
if (!zflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
vbiasall[i][2] = v[i][2];
v[i][2] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
reset thermal velocity of all atoms to be consistent with bias
called from velocity command after it creates thermal velocities
this re-zero components that should stay zero
------------------------------------------------------------------------- */
void ComputeTempPartial::reapply_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (!xflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) v[i][0] = 0.0;
}
if (!yflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) v[i][1] = 0.0;
}
if (!zflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) v[i][2] = 0.0;
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempPartial::restore_bias(int i, double *v)
{
if (!xflag) v[0] += vbias[0];
if (!yflag) v[1] += vbias[1];
if (!zflag) 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 ComputeTempPartial::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (!xflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
v[i][0] += vbiasall[i][0];
}
if (!yflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
v[i][1] += vbiasall[i][1];
}
if (!zflag) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
v[i][2] += vbiasall[i][2];
}
}
/* ---------------------------------------------------------------------- */
double ComputeTempPartial::memory_usage()
{
double bytes = 3*maxbias * sizeof(double);
return bytes;
}

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