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compute_erotate_asphere.cpp
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Sat, Jan 4, 20:26

compute_erotate_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.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "compute_erotate_asphere.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "atom_vec_line.h"
#include "atom_vec_tri.h"
#include "update.h"
#include "force.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeERotateAsphere::
ComputeERotateAsphere(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute erotate/asphere command");
scalar_flag = 1;
extscalar = 1;
// error check
avec_ellipsoid = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
avec_line = (AtomVecLine *) atom->style_match("line");
avec_tri = (AtomVecTri *) atom->style_match("tri");
if (!avec_ellipsoid && !avec_line && !avec_tri)
error->all(FLERR,"Compute erotate/asphere requires "
"atom style ellipsoid or line or tri");
}
/* ---------------------------------------------------------------------- */
void ComputeERotateAsphere::init()
{
// check that all particles are finite-size
// no point particles allowed, spherical is OK
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int flag;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
flag = 0;
if (ellipsoid && ellipsoid[i] >= 0) flag = 1;
if (line && line[i] >= 0) flag = 1;
if (tri && tri[i] >= 0) flag = 1;
if (!flag)
error->one(FLERR,"Compute erotate/asphere requires extended particles");
}
pfactor = 0.5 * force->mvv2e;
}
/* ---------------------------------------------------------------------- */
double ComputeERotateAsphere::compute_scalar()
{
invoked_scalar = update->ntimestep;
AtomVecEllipsoid::Bonus *ebonus;
if (avec_ellipsoid) ebonus = avec_ellipsoid->bonus;
AtomVecLine::Bonus *lbonus;
if (avec_line) lbonus = avec_line->bonus;
AtomVecTri::Bonus *tbonus;
if (avec_tri) tbonus = avec_tri->bonus;
int *ellipsoid = atom->ellipsoid;
int *line = atom->line;
int *tri = atom->tri;
double **omega = atom->omega;
double **angmom = atom->angmom;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// sum rotational energy for each particle
// no point particles since divide by inertia
double length;
double *shape,*quat;
double wbody[3],inertia[3];
double rot[3][3];
double erotate = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (ellipsoid && ellipsoid[i] >= 0) {
shape = ebonus[ellipsoid[i]].shape;
quat = ebonus[ellipsoid[i]].quat;
// principal moments of inertia
inertia[0] = rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]) / 5.0;
inertia[1] = rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]) / 5.0;
inertia[2] = rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]) / 5.0;
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
erotate += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
} else if (line && line[i] >= 0) {
length = lbonus[line[i]].length;
erotate += (omega[i][0]*omega[i][0] + omega[i][1]*omega[i][1] +
omega[i][2]*omega[i][2]) * length*length*rmass[i] / 12.0;
} else if (tri && tri[i] >= 0) {
// principal moments of inertia
inertia[0] = tbonus[tri[i]].inertia[0];
inertia[1] = tbonus[tri[i]].inertia[1];
inertia[2] = tbonus[tri[i]].inertia[2];
// wbody = angular velocity in body frame
MathExtra::quat_to_mat(tbonus[tri[i]].quat,rot);
MathExtra::transpose_matvec(rot,angmom[i],wbody);
wbody[0] /= inertia[0];
wbody[1] /= inertia[1];
wbody[2] /= inertia[2];
erotate += inertia[0]*wbody[0]*wbody[0] +
inertia[1]*wbody[1]*wbody[1] + inertia[2]*wbody[2]*wbody[2];
}
}
MPI_Allreduce(&erotate,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
scalar *= pfactor;
return scalar;
}

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