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fix_langevin.cpp
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Wed, Oct 16, 15:36
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Fri, Oct 18, 15:36 (1 d, 23 h)
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rLAMMPS lammps
fix_langevin.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.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_langevin.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "random_mars.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 7) error->all("Illegal fix langevin command");
t_start = atof(arg[3]);
t_stop = atof(arg[4]);
t_period = atof(arg[5]);
int seed = atoi(arg[6]);
if (t_period <= 0.0) error->all("Fix langevin period must be > 0.0");
if (seed <= 0 || seed > 900000000)
error->all("Illegal fix langevin command");
// initialize Marsaglia RNG with processor-unique seed
random = new RanMars(lmp,seed + comm->me);
// allocate per-type arrays for force prefactors
gfactor1 = new double[atom->ntypes+1];
gfactor2 = new double[atom->ntypes+1];
ratio = new double[atom->ntypes+1];
// optional args
flagx = flagy = flagz = 1;
for (int i = 1; i <= atom->ntypes; i++) ratio[i] = 1.0;
iregion = -1;
int iarg = 7;
while (iarg < narg) {
if (strcmp(arg[iarg],"axes") == 0) {
if (iarg+4 > narg) error->all("Illegal fix langevin command");
flagx = atoi(arg[iarg+1]);
flagy = atoi(arg[iarg+2]);
flagz = atoi(arg[iarg+3]);
iarg += 4;
} else if (strcmp(arg[iarg],"scale") == 0) {
if (iarg+3 > narg) error->all("Illegal fix langevin command");
int itype = atoi(arg[iarg+1]);
double scale = atof(arg[iarg+2]);
if (itype <= 0 || itype > atom->ntypes)
error->all("Illegal fix langevin command");
ratio[itype] = scale;
iarg += 3;
} else if (strcmp(arg[iarg],"region") == 0) {
for (iregion = 0; iregion < domain->nregion; iregion++)
if (strcmp(arg[iarg+1],domain->regions[iregion]->id) == 0) break;
if (iregion == domain->nregion)
error->all("Fix langevin region ID does not exist");
iarg += 2;
} else error->all("Illegal fix langevin command");
}
}
/* ---------------------------------------------------------------------- */
FixLangevin::~FixLangevin()
{
delete random;
delete [] gfactor1;
delete [] gfactor2;
delete [] ratio;
}
/* ---------------------------------------------------------------------- */
int FixLangevin::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixLangevin::init()
{
// set force prefactors
for (int i = 1; i <= atom->ntypes; i++) {
gfactor1[i] = - atom->mass[i] / t_period / force->ftm2v;
gfactor2[i] = sqrt(atom->mass[i]) *
sqrt(24.0*force->boltz/t_period/update->dt/force->mvv2e) / force->ftm2v;
gfactor1[i] *= 1.0/ratio[i];
gfactor2[i] *= 1.0/sqrt(ratio[i]);
}
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixLangevin::setup()
{
if (strcmp(update->integrate_style,"verlet") == 0)
post_force(1);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(1,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixLangevin::post_force(int vflag)
{
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
double t_target = t_start + delta * (t_stop-t_start);
double tsqrt = sqrt(t_target);
double gamma1,gamma2;
// apply damping and thermostat to all atoms in fix group
if (iregion == -1) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
if (flagx) f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
if (flagy) f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
if (flagz) f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
}
}
// apply damping and thermostat to all atoms in fix group and in region
} else {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit &&
domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
if (flagx) f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
if (flagy) f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
if (flagz) f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixLangevin::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixLangevin::reset_target(double t_new)
{
t_start = t_stop = t_new;
}
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