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fix_nve_dipole.cpp
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Sat, Nov 16, 09:32

fix_nve_dipole.cpp
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
www.cs.sandia.gov/~sjplimp/lammps.html
Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
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 "math.h"
#include "string.h"
#include "fix_nve_dipole.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
// moment of inertia for a sphere
#define INERTIA 0.4
/* ---------------------------------------------------------------------- */
FixNVEDipole::FixNVEDipole(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal fix nve/dipole command");
if (!atom->mu_flag || !atom->omega_flag ||
!atom->torque_flag || atom->shape == NULL)
error->all("Fix nve/dipole requires atom attributes "
"mu, omega, torque, shape");
inertia = new double[atom->ntypes+1];
}
/* ---------------------------------------------------------------------- */
FixNVEDipole::~FixNVEDipole()
{
delete [] inertia;
}
/* ---------------------------------------------------------------------- */
int FixNVEDipole::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= INITIAL_INTEGRATE_RESPA;
mask |= FINAL_INTEGRATE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixNVEDipole::init()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
if (strcmp(update->integrate_style,"respa") == 0)
step_respa = ((Respa *) update->integrate)->step;
// moment of inertia for each particle type
double *mass = atom->mass;
double **shape = atom->shape;
for (int i = 1; i <= atom->ntypes; i++)
inertia[i] = INERTIA * mass[i] * 0.25*shape[i][0]*shape[i][0];
}
/* ---------------------------------------------------------------------- */
void FixNVEDipole::initial_integrate()
{
double dtfm,msq,scale;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **mu = atom->mu;
double **omega = atom->omega;
double **torque = atom->torque;
double *mass = atom->mass;
double *dipole = atom->dipole;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double g[3];
// update v,x for all particles
// update omega,mu for all dipoles
// d_omega/dt = torque / inertia
// d_mu/dt = omega cross mu
// renormalize mu to dipole length
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[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];
if (dipole[type[i]] > 0.0) {
dtfm = dtf / inertia[type[i]];
omega[i][0] += dtfm * torque[i][0];
omega[i][1] += dtfm * torque[i][1];
omega[i][2] += dtfm * torque[i][2];
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 = dipole[type[i]]/sqrt(msq);
mu[i][0] = g[0]*scale;
mu[i][1] = g[1]*scale;
mu[i][2] = g[2]*scale;
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVEDipole::final_integrate()
{
double dtfm;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *mass = atom->mass;
double *dipole = atom->dipole;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// update v for all particles
// update omega for all dipoles
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf / mass[type[i]];
v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2];
if (dipole[type[i]] > 0.0) {
dtfm = dtf / inertia[type[i]];
omega[i][0] += dtfm * torque[i][0];
omega[i][1] += dtfm * torque[i][1];
omega[i][2] += dtfm * torque[i][2];
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixNVEDipole::initial_integrate_respa(int ilevel, int flag)
{
if (flag) return; // only used by NPT,NPH
dtv = step_respa[ilevel];
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
if (ilevel == 0) initial_integrate();
else final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixNVEDipole::final_integrate_respa(int ilevel)
{
dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
final_integrate();
}
/* ---------------------------------------------------------------------- */
void FixNVEDipole::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}

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