Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/USER-MISC/fix_ti_rs.cpp
0f6d21acda7blammm-master-deprecated

Last Change
Raw File

fix_ti_rs.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 authors:
Rodrigo Freitas (Unicamp/Brazil) - rodrigohb@gmail.com
Maurice de Koning (Unicamp/Brazil) - dekoning@ifi.unicamp.br
------------------------------------------------------------------------- */
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "fix_ti_rs.h"
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
// Class constructor initialize all variables.
FixTIRS::FixTIRS(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{
// Checking the input information.
if (narg < 7 || narg > 9) error->all(FLERR,"Illegal fix ti/rs command");
// Fix flags.
vector_flag = 1;
size_vector = 2;
global_freq = 1;
extvector = 1;
// Time variables.
t_switch = force->bnumeric(FLERR,arg[5]);
t_equil = force->bnumeric(FLERR,arg[6]);
t0 = update->ntimestep;
if (t_switch <= 0) error->all(FLERR,"Illegal fix ti/rs command");
if (t_equil <= 0) error->all(FLERR,"Illegal fix ti/rs command");
// Coupling parameter limits and initialization.
l_initial = force->numeric(FLERR,arg[3]);
l_final = force->numeric(FLERR,arg[4]);
sf = 1;
if (narg > 7) {
if (strcmp(arg[7], "function") == 0) sf = force->inumeric(FLERR,arg[8]);
else error->all(FLERR,"Illegal fix ti/rs switching function");
if ((sf<1) || (sf>3))
error->all(FLERR,"Illegal fix ti/rs switching function");
}
lambda = switch_func(0);
dlambda = dswitch_func(0);
}
/* ---------------------------------------------------------------------- */
FixTIRS::~FixTIRS()
{
// unregister callbacks to this fix from Atom class
atom->delete_callback(id,0);
atom->delete_callback(id,1);
}
/* ---------------------------------------------------------------------- */
int FixTIRS::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixTIRS::init()
{
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixTIRS::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixTIRS::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTIRS::post_force(int vflag)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
double **f = atom->f;
// Scaling forces.
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
f[i][0] = lambda * f[i][0];
f[i][1] = lambda * f[i][1];
f[i][2] = lambda * f[i][2];
}
}
}
/* ---------------------------------------------------------------------- */
void FixTIRS::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTIRS::min_post_force(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixTIRS::initial_integrate(int vflag)
{
// Update the coupling parameter value.
const bigint t = update->ntimestep - (t0+t_equil);
const double r_switch = 1.0/t_switch;
if( (t >= 0) && (t <= t_switch) ) {
lambda = switch_func(t*r_switch);
dlambda = dswitch_func(t*r_switch);
}
if( (t >= t_equil+t_switch) && (t <= (t_equil+2*t_switch)) ) {
lambda = switch_func(1.0 - (t - t_switch - t_equil)*r_switch);
dlambda = - dswitch_func(1.0 - (t - t_switch - t_equil)*r_switch);
}
}
/* ---------------------------------------------------------------------- */
double FixTIRS::compute_vector(int n)
{
linfo[0] = lambda;
linfo[1] = dlambda;
return linfo[n];
}
/* ---------------------------------------------------------------------- */
double FixTIRS::switch_func(double t)
{
if (sf == 2) return l_initial / (1 + t * (l_initial/l_final - 1));
if (sf == 3) return l_initial / (1 + log2(1+t) * (l_initial/l_final - 1));
// Default option is sf = 1.
return l_initial + (l_final - l_initial) * t;
}
/* ---------------------------------------------------------------------- */
double FixTIRS::dswitch_func(double t)
{
double aux = (1.0/l_initial - 1.0/l_final);
if (sf == 2) return lambda * lambda * aux / t_switch;
if (sf == 3) return lambda * lambda * aux / (t_switch * log(2) * (1 + t));
// Default option is sf = 1.
return (l_final-l_initial)/t_switch;
}
c4science · Help