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compute_temp_sphere.cpp
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Thu, Jun 27, 10:33

compute_temp_sphere.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 "string.h"
#include "compute_temp_sphere.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 "error.h"
using namespace LAMMPS_NS;
#define INERTIA 0.4 // moment of inertia for sphere
/* ---------------------------------------------------------------------- */
ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3 && narg != 4)
error->all("Illegal compute temp/sphere 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];
// error checks
if (!atom->omega_flag)
error->all("Compute temp/sphere requires atom attribute omega");
if (!atom->radius_flag && !atom->avec->shape_type)
error->all("Compute temp/sphere requires atom attribute "
"radius or shape");
}
/* ---------------------------------------------------------------------- */
ComputeTempSphere::~ComputeTempSphere()
{
delete [] id_bias;
delete [] vector;
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::init()
{
int i,itype;
// if shape used, check that all particles are spherical
// point particles are allowed
if (atom->radius == NULL) {
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
itype = type[i];
if (shape[itype][0] != shape[itype][1] ||
shape[itype][0] != shape[itype][2])
error->one("Compute temp/sphere requires "
"spherical particle shapes");
}
}
if (tempbias) {
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 (i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::dof_compute()
{
int count,count_all;
// 6 or 3 dof for extended/point particles for 3d
// 3 or 2 dof for extended/point particles for 2d
// assume full rotation of extended particles
// user should correct this via compute_modify if needed
int dimension = domain->dimension;
double *radius = atom->radius;
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
count = 0;
if (dimension == 3) {
if (radius) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (radius[i] == 0.0) count += 3;
else count += 6;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (shape[type[i]][0] == 0.0) count += 3;
else count += 6;
}
}
}
} else {
if (radius) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (radius[i] == 0.0) count += 2;
else count += 3;
}
}
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (shape[type[i]][0] == 0.0) count += 2;
else count += 3;
}
}
}
}
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof = count_all;
// additional adjustments to dof
if (tempbias == 1) {
double natoms = group->count(igroup);
dof -= tbias->dof_remove(-1) * natoms;
} else if (tempbias == 2) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
count = 0;
if (dimension == 3) {
if (radius) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbias->dof_remove(i)) {
if (radius[i] == 0.0) count += 3;
else count += 6;
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbias->dof_remove(i)) {
if (shape[type[i]][0] == 0.0) count += 3;
else count += 6;
}
}
}
} else {
if (radius) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbias->dof_remove(i)) {
if (radius[i] == 0.0) count += 2;
else count += 3;
}
}
} else {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (tbias->dof_remove(i)) {
if (shape[type[i]][0] == 0.0) count += 2;
else count += 3;
}
}
}
}
MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world);
dof -= count_all;
}
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
/* ---------------------------------------------------------------------- */
double ComputeTempSphere::compute_scalar()
{
int i,itype;
invoked_scalar = update->ntimestep;
if (tempbias) {
if (tbias->invoked_scalar != update->ntimestep) tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
double **omega = atom->omega;
double *radius = atom->radius;
double *rmass = atom->rmass;
double *mass = atom->mass;
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// 4 cases depending on radius vs shape and rmass vs mass
// point particles will not contribute rotation due to radius or shape = 0
double t = 0.0;
if (radius) {
if (rmass) {
for (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]) *
rmass[i];
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) *
INERTIA*radius[i]*radius[i]*rmass[i];
}
} else {
for (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];
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) *
INERTIA*radius[i]*radius[i]*mass[itype];
}
}
} else {
if (rmass) {
for (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]) *
rmass[i];
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) *
INERTIA*shape[itype][0]*shape[itype][0]*rmass[i];
}
} else {
for (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];
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) *
INERTIA*shape[itype][0]*shape[itype][0]*mass[itype];
}
}
}
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 ComputeTempSphere::compute_vector()
{
int i,itype;
invoked_vector = update->ntimestep;
if (tempbias) {
if (tbias->invoked_vector != update->ntimestep) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double **omega = atom->omega;
double *mass = atom->mass;
double *rmass = atom->rmass;
double *radius = atom->radius;
double **shape = atom->shape;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// 4 cases depending on radius vs shape and rmass vs mass
// point particles will not contribute rotation due to radius or shape = 0
double massone,inertiaone,t[6];
for (i = 0; i < 6; i++) t[i] = 0.0;
if (radius) {
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
massone = rmass[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];
inertiaone = INERTIA*radius[i]*radius[i]*rmass[i];
t[0] += inertiaone * omega[i][0]*omega[i][0];
t[1] += inertiaone * omega[i][1]*omega[i][1];
t[2] += inertiaone * omega[i][2]*omega[i][2];
t[3] += inertiaone * omega[i][0]*omega[i][1];
t[4] += inertiaone * omega[i][0]*omega[i][2];
t[5] += inertiaone * omega[i][1]*omega[i][2];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
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];
inertiaone = INERTIA*radius[i]*radius[i]*mass[itype];
t[0] += inertiaone * omega[i][0]*omega[i][0];
t[1] += inertiaone * omega[i][1]*omega[i][1];
t[2] += inertiaone * omega[i][2]*omega[i][2];
t[3] += inertiaone * omega[i][0]*omega[i][1];
t[4] += inertiaone * omega[i][0]*omega[i][2];
t[5] += inertiaone * omega[i][1]*omega[i][2];
}
}
} else {
if (rmass) {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
itype = type[i];
massone = rmass[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];
inertiaone = INERTIA*shape[itype][0]*shape[itype][0]*rmass[i];
t[0] += inertiaone * omega[i][0]*omega[i][0];
t[1] += inertiaone * omega[i][1]*omega[i][1];
t[2] += inertiaone * omega[i][2]*omega[i][2];
t[3] += inertiaone * omega[i][0]*omega[i][1];
t[4] += inertiaone * omega[i][0]*omega[i][2];
t[5] += inertiaone * omega[i][1]*omega[i][2];
}
} else {
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
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];
inertiaone = INERTIA*shape[itype][0]*shape[itype][0]*mass[itype];
t[0] += inertiaone * omega[i][0]*omega[i][0];
t[1] += inertiaone * omega[i][1]*omega[i][1];
t[2] += inertiaone * omega[i][2]*omega[i][2];
t[3] += inertiaone * omega[i][0]*omega[i][1];
t[4] += inertiaone * omega[i][0]*omega[i][2];
t[5] += inertiaone * omega[i][1]*omega[i][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;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempSphere::remove_bias(int i, double *v)
{
tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempSphere::restore_bias(int i, double *v)
{
tbias->restore_bias(i,v);
}

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