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fix_nh_body.cpp
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Wed, Nov 6, 01:57

fix_nh_body.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: Trung Dac Nguyen (ndactrung@gmail.com)
based on FixNHAsphere
------------------------------------------------------------------------- */
#include <string.h>
#include <stdlib.h>
#include <math.h>
#include "math_extra.h"
#include "fix_nh_body.h"
#include "atom.h"
#include "atom_vec_body.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixNHBody::FixNHBody(LAMMPS *lmp, int narg, char **arg) :
FixNH(lmp, narg, arg)
{
}
/* ---------------------------------------------------------------------- */
void FixNHBody::init()
{
avec = (AtomVecBody *) atom->style_match("body");
if (!avec)
error->all(FLERR,
"Compute nvt/nph/npt body requires atom style body");
// check that all particles are finite-size
// no point particles allowed, spherical is OK
int *body = atom->body;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (body[i] < 0)
error->one(FLERR,"Fix nvt/nph/npt body requires bodies");
FixNH::init();
}
/* ----------------------------------------------------------------------
perform half-step update of angular momentum
-----------------------------------------------------------------------*/
void FixNHBody::nve_v()
{
// standard nve_v velocity update
FixNH::nve_v();
double **angmom = atom->angmom;
double **torque = atom->torque;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
// update angular momentum by 1/2 step for all particles
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
angmom[i][0] += dtf*torque[i][0];
angmom[i][1] += dtf*torque[i][1];
angmom[i][2] += dtf*torque[i][2];
}
}
}
/* ----------------------------------------------------------------------
perform full-step update of orientation
-----------------------------------------------------------------------*/
void FixNHBody::nve_x()
{
double omega[3];
double *quat,*inertia;
// standard nve_x position update
FixNH::nve_x();
AtomVecBody::Bonus *bonus = avec->bonus;
int *body = atom->body;
double **angmom = atom->angmom;
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;
// update quaternion a full step via Richardson iteration
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
// 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
inertia = bonus[body[i]].inertia;
quat = bonus[body[i]].quat;
MathExtra::mq_to_omega(angmom[i],quat,inertia,omega);
MathExtra::richardson(quat,angmom[i],omega,inertia,dtq);
}
}
/* ----------------------------------------------------------------------
perform half-step temperature scaling of angular momentum
-----------------------------------------------------------------------*/
void FixNHBody::nh_v_temp()
{
// standard nh_v_temp scaling
FixNH::nh_v_temp();
double **angmom = atom->angmom;
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) {
angmom[i][0] *= factor_eta;
angmom[i][1] *= factor_eta;
angmom[i][2] *= factor_eta;
}
}
}

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