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lammps/src/ASPHERE/compute_temp_asphere.cpp
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compute_temp_asphere.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: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "compute_temp_asphere.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3 && narg != 4)
error->all("Illegal compute temp/asphere command");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 1;
tempflag = 1;
tempbias = 0;
id_bias = NULL;
if (narg == 4) {
tempbias = 1;
int n = strlen(arg[3]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[3]);
}
vector = new double[6];
inertia =
memory->create_2d_double_array(atom->ntypes+1,3,"fix_temp_sphere:inertia");
// error checks
if (!atom->angmom_flag || !atom->quat_flag ||
!atom->avec->shape_type)
error->all("Compute temp/asphere requires atom attributes "
"angmom, quat, shape");
if (atom->radius_flag || atom->rmass_flag)
error->all("Compute temp/asphere cannot be used with atom attributes "
"diameter or rmass");
}
/* ---------------------------------------------------------------------- */
ComputeTempAsphere::~ComputeTempAsphere()
{
delete [] id_bias;
delete [] vector;
memory->destroy_2d_double_array(inertia);
}
/* ---------------------------------------------------------------------- */
void ComputeTempAsphere::init()
{
// check that all particles are finite-size
// no point particles allowed, spherical is OK
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (shape[type[i]][0] == 0.0)
error->one("Compue temp/asphere requires extended particles");
if (tempbias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
if (tbias->tempflag == 0)
error->all("Bias compute does not calculate temperature");
if (tbias->tempbias == 0)
error->all("Bias compute does not calculate a velocity bias");
if (tbias->igroup != igroup)
error->all("Bias compute group does not match compute group");
tbias->init();
if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2;
else tempbias = 1;
}
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
dof_compute();
calculate_inertia();
}
/* ---------------------------------------------------------------------- */
void ComputeTempAsphere::dof_compute()
{
// 6 dof for 3d, 3 dof for 2d
// assume full rotation of extended particles
// user can correct this via compute_modify if needed
double natoms = group->count(igroup);
if (domain->dimension == 3) dof = 6*natoms;
else dof = 3*natoms;
// additional adjustments to dof
if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms;
else if (tempbias == 2) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
int count = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tbias->dof_remove(i)) count++;
int count_all;
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
if (domain->dimension == 3) dof -= 6*count_all;
else dof -= 3*count_all;
}
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempAsphere::compute_scalar()
{
invoked_scalar = update->ntimestep;
if (tempbias) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
double **quat = atom->quat;
double **angmom = atom->angmom;
double *mass = atom->mass;
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int itype;
double wbody[3];
double rot[3][3];
double t = 0.0;
// sum translationals and rotational energy for each particle
// no point particles since divide by inertia
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
itype = type[i];
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * mass[itype];
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat[i],rot);
MathExtra::transpose_times_column3(rot,angmom[i],wbody);
wbody[0] /= inertia[itype][0];
wbody[1] /= inertia[itype][1];
wbody[2] /= inertia[itype][2];
t += inertia[itype][0]*wbody[0]*wbody[0] +
inertia[itype][1]*wbody[1]*wbody[1] +
inertia[itype][2]*wbody[2]*wbody[2];
}
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic || tempbias == 2) dof_compute();
scalar *= tfactor;
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputeTempAsphere::compute_vector()
{
int i;
invoked_vector = update->ntimestep;
if (tempbias) {
if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double **quat = atom->quat;
double **angmom = atom->angmom;
double *mass = atom->mass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int itype;
double wbody[3];
double rot[3][3];
double massone,t[6];
for (i = 0; i < 6; i++) t[i] = 0.0;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// translational kinetic energy
itype = type[i];
massone = mass[itype];
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];
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat[i],rot);
MathExtra::transpose_times_column3(rot,angmom[i],wbody);
wbody[0] /= inertia[itype][0];
wbody[1] /= inertia[itype][1];
wbody[2] /= inertia[itype][2];
// rotational kinetic energy
t[0] += inertia[itype][0]*wbody[0]*wbody[0];
t[1] += inertia[itype][1]*wbody[1]*wbody[1];
t[2] += inertia[itype][2]*wbody[2]*wbody[2];
t[3] += inertia[itype][0]*wbody[0]*wbody[1];
t[4] += inertia[itype][1]*wbody[0]*wbody[2];
t[5] += inertia[itype][2]*wbody[1]*wbody[2];
}
if (tempbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
principal moments of inertia for ellipsoids
------------------------------------------------------------------------- */
void ComputeTempAsphere::calculate_inertia()
{
double *mass = atom->mass;
double **shape = atom->shape;
for (int i = 1; i <= atom->ntypes; i++) {
inertia[i][0] = mass[i] *
(shape[i][1]*shape[i][1]+shape[i][2]*shape[i][2]) / 5.0;
inertia[i][1] = mass[i] *
(shape[i][0]*shape[i][0]+shape[i][2]*shape[i][2]) / 5.0;
inertia[i][2] = mass[i] *
(shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]) / 5.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempAsphere::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempAsphere::restore_bias(int i, double *v)
{
if (tbias) tbias->restore_bias(i,v);
}
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