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fix_nve_asphere.cpp
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Thu, Jun 27, 10:03

fix_nve_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 <math.h>
#include <stdio.h>
#include <string.h>
#include "fix_nve_asphere.h"
#include "math_extra.h"
#include "atom.h"
#include "atom_vec_ellipsoid.h"
#include "force.h"
#include "update.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define INERTIA 0.2 // moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */
FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixNVEAsphere::init()
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Compute nve/asphere requires atom style ellipsoid");
// check that all particles are finite-size ellipsoids
// no point particles allowed, spherical is OK
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix nve/asphere requires extended particles");
FixNVE::init();
}
/* ---------------------------------------------------------------------- */
void FixNVEAsphere::initial_integrate(int vflag)
{
double dtfm;
double inertia[3],omega[3];
double *shape,*quat;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **angmom = atom->angmom;
double **torque = atom->torque;
double *rmass = atom->rmass;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// set timestep here since dt may have changed or come via rRESPA
dtq = 0.5 * dtv;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
// update angular momentum by 1/2 step
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
// principal moments of inertia
shape = bonus[ellipsoid[i]].shape;
quat = bonus[ellipsoid[i]].quat;
inertia[0] = INERTIA*rmass[i] * (shape[1]*shape[1]+shape[2]*shape[2]);
inertia[1] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[2]*shape[2]);
inertia[2] = INERTIA*rmass[i] * (shape[0]*shape[0]+shape[1]*shape[1]);
// compute omega at 1/2 step from angmom at 1/2 step and current q
// update quaternion a full step via Richardson iteration
// returns new normalized quaternion
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
MathExtra::richardson(quat,angmom[i],omega,inertia,dtq);
}
}
/* ---------------------------------------------------------------------- */
void FixNVEAsphere::final_integrate()
{
double dtfm;
double **v = atom->v;
double **f = atom->f;
double **angmom = atom->angmom;
double **torque = atom->torque;
double *rmass = atom->rmass;
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) {
dtfm = dtf / rmass[i];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
angmom[i][0] += dtf * torque[i][0];
angmom[i][1] += dtf * torque[i][1];
angmom[i][2] += dtf * torque[i][2];
}
}

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