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fix_mvv_tdpd.cpp
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Thu, May 23, 23:51

fix_mvv_tdpd.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
This is a time integrator for position, velocity and concentration (x,
v and cc) using the modified velocity-Verlet (MVV) algorithm.
Setting verlet = 0.5 recovers the standard velocity-Verlet algorithm.
Contributing author: Zhen Li (Brown University)
Email: zhen_li@brown.edu
Please cite the related publication:
Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. "Transport
dissipative particle dynamics model for mesoscopic advection-diffusion
-reaction problems". The Journal of Chemical Physics, 2015, 143: 014101.
------------------------------------------------------------------------- */
#include <stdio.h>
#include <string.h>
#include "fix_mvv_tdpd.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixMvvTDPD::FixMvvTDPD(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (strcmp(style,"tdpd/verlet") != 0 && narg < 3)
error->all(FLERR,"Illegal fix mvv/tdpd command");
verlet = 0.5;
if(narg > 3) verlet = force->numeric(FLERR,arg[3]);
cc_species = atom->cc_species;
dynamic_group_allow = 1;
time_integrate = 1;
}
/* ---------------------------------------------------------------------- */
int FixMvvTDPD::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixMvvTDPD::init()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}
/* ----------------------------------------------------------------------
allow for both per-type and per-atom mass
------------------------------------------------------------------------- */
void FixMvvTDPD::initial_integrate(int vflag)
{
double dtfm;
// update v and x and cc of atoms in group
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **cc = atom->cc;
double **cc_flux = atom->cc_flux;
double **vest = atom->vest;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
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 (rmass) dtfm = dtf / rmass[i];
else dtfm = dtf / mass[type[i]];
vest[i][0] = v[i][0] + dtfm * f[i][0];
vest[i][1] = v[i][1] + dtfm * f[i][1];
vest[i][2] = v[i][2] + dtfm * f[i][2];
x[i][0] += dtv * vest[i][0];
x[i][1] += dtv * vest[i][1];
x[i][2] += dtv * vest[i][2];
v[i][0] += 2.0 * verlet * dtfm * f[i][0];
v[i][1] += 2.0 * verlet * dtfm * f[i][1];
v[i][2] += 2.0 * verlet * dtfm * f[i][2];
for(int k = 0; k < cc_species; k++)
cc[i][k] += 0.5 * dtv * cc_flux[i][k];
}
}
/* ---------------------------------------------------------------------- */
void FixMvvTDPD::final_integrate()
{
double dtfm;
// update v of atoms in group
double **v = atom->v;
double **f = atom->f;
double **cc = atom->cc;
double **cc_flux = atom->cc_flux;
double **vest = atom->vest;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
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 (rmass) dtfm = dtf / rmass[i];
else dtfm = dtf / mass[type[i]];
v[i][0] = vest[i][0] + dtfm * f[i][0];
v[i][1] = vest[i][1] + dtfm * f[i][1];
v[i][2] = vest[i][2] + dtfm * f[i][2];
for(int k = 0; k < cc_species; k++)
cc[i][k] += 0.5 * dtv * cc_flux[i][k];
}
}
/* ---------------------------------------------------------------------- */
void FixMvvTDPD::reset_dt()
{
dtv = update->dt;
dtf = 0.5 * update->dt * force->ftm2v;
}

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