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fix_nh_sphere.cpp
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Tue, Oct 8, 12:58

fix_nh_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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Mike Brown (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include "fix_nh_sphere.h"
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
#define INERTIA 0.4 // moment of inertia prefactor for sphere
/* ---------------------------------------------------------------------- */
FixNHSphere::FixNHSphere(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg)
{
if (!atom->sphere_flag)
error->all(FLERR,"Fix nvt/nph/npt sphere requires atom style sphere");
}
/* ---------------------------------------------------------------------- */
void FixNHSphere::init()
{
// check that all particles are finite-size
// no point particles allowed
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0)
error->one(FLERR,"Fix nvt/sphere requires extended particles");
FixNH::init();
}
/* ----------------------------------------------------------------------
perform half-step update of rotational velocities
-----------------------------------------------------------------------*/
void FixNHSphere::nve_v()
{
// standard nve_v velocity update
FixNH::nve_v();
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
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
double dtfrotate = dtf / INERTIA;
double dtirotate;
// update omega for all particles
// d_omega/dt = torque / inertia
// 4 cases depending on radius vs shape and rmass vs mass
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dtirotate = dtfrotate / (radius[i]*radius[i]*rmass[i]);
omega[i][0] += dtirotate*torque[i][0];
omega[i][1] += dtirotate*torque[i][1];
omega[i][2] += dtirotate*torque[i][2];
}
}
/* ----------------------------------------------------------------------
perform full-step update of position with dipole orientation, if requested
-----------------------------------------------------------------------*/
void FixNHSphere::nve_x()
{
// standard nve_x position update
FixNH::nve_x();
// update mu for dipoles
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
if (dipole_flag) {
double msq,scale,g[3];
double **mu = atom->mu;
double **omega = atom->omega;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (mu[i][3] > 0.0) {
g[0] = mu[i][0] + dtv * (omega[i][1]*mu[i][2]-omega[i][2]*mu[i][1]);
g[1] = mu[i][1] + dtv * (omega[i][2]*mu[i][0]-omega[i][0]*mu[i][2]);
g[2] = mu[i][2] + dtv * (omega[i][0]*mu[i][1]-omega[i][1]*mu[i][0]);
msq = g[0]*g[0] + g[1]*g[1] + g[2]*g[2];
scale = mu[i][3]/sqrt(msq);
mu[i][0] = g[0]*scale;
mu[i][1] = g[1]*scale;
mu[i][2] = g[2]*scale;
}
}
}
/* ----------------------------------------------------------------------
perform half-step scaling of rotatonal velocities
-----------------------------------------------------------------------*/
void FixNHSphere::nh_v_temp()
{
// standard nh_v_temp scaling
FixNH::nh_v_temp();
double **omega = atom->omega;
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) {
omega[i][0] *= factor_eta;
omega[i][1] *= factor_eta;
omega[i][2] *= factor_eta;
}
}
}

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