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compute_temp_rotate.cpp
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Wed, Apr 2, 13:14

compute_temp_rotate.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: Laurent Joly (U Lyon, France), ljoly.ulyon@gmail.com
------------------------------------------------------------------------- */
#include <mpi.h>
#include <stdlib.h>
#include <string.h>
#include "compute_temp_rotate.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "domain.h"
#include "lattice.h"
#include "error.h"
#include "memory.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempRotate::ComputeTempRotate(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute temp/rotate command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 1;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
/* ---------------------------------------------------------------------- */
ComputeTempRotate::~ComputeTempRotate()
{
memory->destroy(vbiasall);
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempRotate::init()
{
masstotal = group->mass(igroup);
}
/* ---------------------------------------------------------------------- */
void ComputeTempRotate::setup()
{
dynamic = 0;
if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempRotate::dof_compute()
{
adjust_dof_fix();
natoms_temp = group->count(igroup);
dof = domain->dimension * natoms_temp;
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempRotate::compute_scalar()
{
double vthermal[3];
double vcm[3],xcm[3],inertia[3][3],angmom[3],omega[3];
double dx,dy,dz;
double unwrap[3];
invoked_scalar = update->ntimestep;
if (dynamic) masstotal = group->mass(igroup);
group->vcm(igroup,masstotal,vcm);
group->xcm(igroup,masstotal,xcm);
group->inertia(igroup,xcm,inertia);
group->angmom(igroup,xcm,angmom);
group->omega(angmom,inertia,omega);
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
imageint *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (atom->nmax > maxbias) {
memory->destroy(vbiasall);
maxbias = atom->nmax;
memory->create(vbiasall,maxbias,3,"temp/rotate:vbiasall");
}
double t = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xcm[0];
dy = unwrap[1] - xcm[1];
dz = unwrap[2] - xcm[2];
vbiasall[i][0] = vcm[0] + dz*omega[1]-dy*omega[2];
vbiasall[i][1] = vcm[1] + dx*omega[2]-dz*omega[0];
vbiasall[i][2] = vcm[2] + dy*omega[0]-dx*omega[1];
vthermal[0] = v[i][0] - vbiasall[i][0];
vthermal[1] = v[i][1] - vbiasall[i][1];
vthermal[2] = v[i][2] - vbiasall[i][2];
if (rmass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[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 ComputeTempRotate::compute_vector()
{
double vthermal[3];
double vcm[3],xcm[3],inertia[3][3],angmom[3],omega[3];
double dx,dy,dz;
double unwrap[3];
invoked_vector = update->ntimestep;
if (dynamic) masstotal = group->mass(igroup);
group->vcm(igroup,masstotal,vcm);
group->xcm(igroup,masstotal,xcm);
group->inertia(igroup,xcm,inertia);
group->angmom(igroup,xcm,angmom);
group->omega(angmom,inertia,omega);
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
imageint *image = atom->image;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (atom->nmax > maxbias) {
memory->destroy(vbiasall);
maxbias = atom->nmax;
memory->create(vbiasall,maxbias,3,"temp/rotate:vbiasall");
}
double massone,t[6];
for (int i = 0; i < 6; i++) t[i] = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - xcm[0];
dy = unwrap[1] - xcm[1];
dz = unwrap[2] - xcm[2];
vbiasall[i][0] = vcm[0] + dz*omega[1]-dy*omega[2];
vbiasall[i][1] = vcm[1] + dx*omega[2]-dz*omega[0];
vbiasall[i][2] = vcm[2] + dy*omega[0]-dx*omega[1];
vthermal[0] = v[i][0] - vbiasall[i][0];
vthermal[1] = v[i][1] - vbiasall[i][1];
vthermal[2] = v[i][2] - vbiasall[i][2];
if (rmass) massone = rmass[i];
else massone = mass[type[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 (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRotate::remove_bias(int i, double *v)
{
v[0] -= vbiasall[i][0];
v[1] -= vbiasall[i][1];
v[2] -= vbiasall[i][2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRotate::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] -= vbiasall[i][0];
v[i][1] -= vbiasall[i][1];
v[i][2] -= vbiasall[i][2];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempRotate::restore_bias(int i, double *v)
{
v[0] += vbiasall[i][0];
v[1] += vbiasall[i][1];
v[2] += vbiasall[i][2];
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempRotate::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 ComputeTempRotate::memory_usage()
{
double bytes = maxbias * sizeof(double);
return bytes;
}

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