Homec4science
Diffusion lammps (efficient_neuronet) Browse

lammps/src/USER-EFF/fix_nh_eff.cpp
3c59b58794a8efficient_neuronet

Last Change
Raw File

fix_nh_eff.cpp
View Options

/* ----------------------------------------------------------------------
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: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */
#include "math.h"
#include "fix_nh_eff.h"
#include "atom.h"
#include "atom_vec.h"
#include "group.h"
#include "error.h"
#include "domain.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNHEff::FixNHEff(LAMMPS *lmp, int narg, char **arg) : FixNH(lmp, narg, arg)
{
if (!atom->electron_flag)
error->all(FLERR,"Fix nvt/nph/npt/eff requires atom style electron");
}
/* ----------------------------------------------------------------------
perform half-step update of electron radial velocities
-----------------------------------------------------------------------*/
void FixNHEff::nve_v()
{
// standard nve_v velocity update
FixNH::nve_v();
double *erforce = atom->erforce;
double *ervel = atom->ervel;
double *mass = atom->mass;
int *spin = atom->spin;
double mefactor = domain->dimension/4.0;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
double dtfm;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (fabs(spin[i])==1) {
dtfm = dtf / mass[type[i]];
ervel[i] = dtfm * erforce[i] / mefactor;
}
}
}
}
/* ----------------------------------------------------------------------
perform full-step update of electron radii
-----------------------------------------------------------------------*/
void FixNHEff::nve_x()
{
// standard nve_x position update
FixNH::nve_x();
double *eradius = atom->eradius;
double *ervel = atom->ervel;
int *spin = atom->spin;
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)
if (fabs(spin[i])==1) eradius[i] += dtv * ervel[i];
}
/* ----------------------------------------------------------------------
perform half-step scaling of electron radial velocities
-----------------------------------------------------------------------*/
void FixNHEff::nh_v_temp()
{
// standard nh_v_temp velocity scaling
FixNH::nh_v_temp();
double *ervel = atom->ervel;
int *spin = atom->spin;
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)
if (fabs(spin[i])==1) ervel[i] *= factor_eta;
}
c4science · Help