256 lines
7.2 KiB
C++
256 lines
7.2 KiB
C++
/* ----------------------------------------------------------------------
|
|
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 "compute_temp_sphere.h"
|
|
#include "atom.h"
|
|
#include "force.h"
|
|
#include "domain.h"
|
|
#include "modify.h"
|
|
#include "fix.h"
|
|
#include "group.h"
|
|
#include "error.h"
|
|
|
|
using namespace LAMMPS_NS;
|
|
|
|
#define INVOKED_SCALAR 1
|
|
#define INVOKED_VECTOR 2
|
|
|
|
#define INERTIA 0.4 // moment of inertia for sphere
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
ComputeTempSphere::ComputeTempSphere(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;
|
|
|
|
vector = new double[6];
|
|
inertia = new double[atom->ntypes+1];
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
ComputeTempSphere::~ComputeTempSphere()
|
|
{
|
|
delete [] vector;
|
|
delete [] inertia;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeTempSphere::init()
|
|
{
|
|
fix_dof = 0;
|
|
for (int i = 0; i < modify->nfix; i++)
|
|
fix_dof += modify->fix[i]->dof(igroup);
|
|
dof_compute();
|
|
|
|
tempbias = 0;
|
|
tbias = NULL;
|
|
if (id_bias) {
|
|
tempbias = 1;
|
|
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 (atom->mass) {
|
|
double *mass = atom->mass;
|
|
double **shape = atom->shape;
|
|
|
|
for (int i = 1; i <= atom->ntypes; i++) {
|
|
if (shape[i][0] != shape[i][1] || shape[i][0] != shape[i][2])
|
|
error->all("Compute temp/sphere requires spherical particle shapes");
|
|
inertia[i] = INERTIA * 0.25*shape[i][0]*shape[i][0] * mass[i];
|
|
}
|
|
}
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeTempSphere::dof_compute()
|
|
{
|
|
double natoms = group->count(igroup);
|
|
if (domain->dimension == 3) dof = 6.0 * natoms;
|
|
else dof = 3.0 * natoms;
|
|
if (tbias) dof -= tbias->dof_remove(natoms);
|
|
dof -= extra_dof + fix_dof;
|
|
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
|
|
else tfactor = 0.0;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
double ComputeTempSphere::compute_scalar()
|
|
{
|
|
invoked |= INVOKED_SCALAR;
|
|
|
|
if (tbias) {
|
|
if (!(tbias->invoked & INVOKED_SCALAR))
|
|
double tmp = tbias->compute_scalar();
|
|
tbias->remove_bias_all();
|
|
}
|
|
|
|
double **v = atom->v;
|
|
double **omega = atom->omega;
|
|
double *mass = atom->mass;
|
|
double *rmass = atom->rmass;
|
|
double *radius = atom->radius;
|
|
int *type = atom->type;
|
|
int *mask = atom->mask;
|
|
int nlocal = atom->nlocal;
|
|
|
|
double t = 0.0;
|
|
|
|
if (mass) {
|
|
for (int 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]) *
|
|
mass[type[i]];
|
|
t += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
|
|
omega[i][2]*omega[i][2]) * inertia[type[i]];
|
|
}
|
|
} else {
|
|
for (int 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];
|
|
}
|
|
}
|
|
|
|
if (tbias) tbias->restore_bias_all();
|
|
|
|
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
|
|
if (dynamic || tbias) dof_compute();
|
|
scalar *= tfactor;
|
|
return scalar;
|
|
}
|
|
|
|
/* ---------------------------------------------------------------------- */
|
|
|
|
void ComputeTempSphere::compute_vector()
|
|
{
|
|
int i;
|
|
|
|
invoked |= INVOKED_VECTOR;
|
|
|
|
if (tbias) {
|
|
if (!(tbias->invoked & INVOKED_VECTOR)) 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;
|
|
int *type = atom->type;
|
|
int *mask = atom->mask;
|
|
int nlocal = atom->nlocal;
|
|
|
|
double massone,inertiaone,t[6];
|
|
for (i = 0; i < 6; i++) t[i] = 0.0;
|
|
|
|
if (mass) {
|
|
for (i = 0; i < nlocal; i++)
|
|
if (mask[i] & groupbit) {
|
|
massone = mass[type[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[type[i]];
|
|
t[0] += massone * omega[i][0]*omega[i][0];
|
|
t[1] += massone * omega[i][1]*omega[i][1];
|
|
t[2] += massone * omega[i][2]*omega[i][2];
|
|
t[3] += massone * omega[i][0]*omega[i][1];
|
|
t[4] += massone * omega[i][0]*omega[i][2];
|
|
t[5] += massone * omega[i][1]*omega[i][2];
|
|
}
|
|
} else {
|
|
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] += massone * omega[i][0]*omega[i][0];
|
|
t[1] += massone * omega[i][1]*omega[i][1];
|
|
t[2] += massone * omega[i][2]*omega[i][2];
|
|
t[3] += massone * omega[i][0]*omega[i][1];
|
|
t[4] += massone * omega[i][0]*omega[i][2];
|
|
t[5] += massone * omega[i][1]*omega[i][2];
|
|
}
|
|
}
|
|
|
|
if (tbias) 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)
|
|
{
|
|
if (tbias) tbias->remove_bias(i,v);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
remove velocity bias from all atoms to leave thermal velocity
|
|
------------------------------------------------------------------------- */
|
|
|
|
void ComputeTempSphere::remove_bias_all()
|
|
{
|
|
if (tbias) tbias->remove_bias_all();
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
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)
|
|
{
|
|
if (tbias) tbias->restore_bias(i,v);
|
|
}
|
|
|
|
/* ----------------------------------------------------------------------
|
|
add back in velocity bias to all atoms removed by remove_bias_all()
|
|
assume remove_bias_all() was previously called
|
|
------------------------------------------------------------------------- */
|
|
|
|
void ComputeTempSphere::restore_bias_all()
|
|
{
|
|
if (tbias) tbias->restore_bias_all();
|
|
}
|
|
|