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fix_langevin_eff.cpp
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Sun, May 26, 10:40
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rLAMMPS lammps
fix_langevin_eff.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: Andres Jaramillo-Botero
------------------------------------------------------------------------- */
#include "mpi.h"
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "fix_langevin_eff.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "domain.h"
#include "region.h"
#include "respa.h"
#include "comm.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixLangevinEff::FixLangevinEff(LAMMPS *lmp, int narg, char **arg) :
FixLangevin(lmp, narg, arg)
{
erforcelangevin = NULL;
}
/* ---------------------------------------------------------------------- */
FixLangevinEff::~FixLangevinEff()
{
memory->destroy(erforcelangevin);
}
/* ---------------------------------------------------------------------- */
void FixLangevinEff::post_force_no_tally()
{
double gamma1,gamma2;
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *ervel = atom->ervel;
double *erforce = atom->erforce;
int *spin = atom->spin;
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);
// apply damping and thermostat to atoms in group
// for BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
// test v = 0 since some computes mask non-participating atoms via v = 0
// and added force has extra term not multiplied by v = 0
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
if (abs(spin[i])==1) erforce[i] += 0.75*gamma1*ervel[i] + 0.866025404*gamma2*(random->uniform()-0.5);
}
}
} else if (which == BIAS) {
double tmp = temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
temperature->remove_bias(i,v[i]);
if (v[i][0] != 0.0)
f[i][0] += gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
if (v[i][1] != 0.0)
f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
if (v[i][2] != 0.0)
f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
if (abs(spin[i])==1 && ervel[i] != 0.0)
erforce[i] += 0.75*gamma1*ervel[i] + 0.866025404*gamma2*(random->uniform()-0.5);
temperature->restore_bias(i,v[i]);
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixLangevinEff::post_force_tally()
{
double gamma1,gamma2;
// reallocate flangevin if necessary
if (atom->nmax > nmax) {
memory->destroy(flangevin);
memory->destroy(erforcelangevin);
nmax = atom->nmax;
memory->create(flangevin,nmax,3,"langevin:flangevin");
memory->create(erforcelangevin,nmax,"langevin/eff:erforcelangevin");
}
double **v = atom->v;
double **f = atom->f;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double *erforce = atom->erforce;
double *ervel = atom->ervel;
int *spin = atom->spin;
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);
// apply damping and thermostat to appropriate atoms
// for BIAS:
// calculate temperature since some computes require temp
// computed on current nlocal atoms to remove bias
// test v = 0 since some computes mask non-participating atoms via v = 0
// and added force has extra term not multiplied by v = 0
if (which == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
erforcelangevin[i] = 0.75*gamma1*ervel[i]+0.866025404*gamma2*(random->uniform()-0.5);
f[i][0] += flangevin[i][0];
f[i][1] += flangevin[i][1];
f[i][2] += flangevin[i][2];
if (abs(spin[i])==1) erforce[i] += erforcelangevin[i];
}
}
} else if (which == BIAS) {
double tmp = temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
gamma1 = gfactor1[type[i]];
gamma2 = gfactor2[type[i]] * tsqrt;
temperature->remove_bias(i,v[i]);
flangevin[i][0] = gamma1*v[i][0] + gamma2*(random->uniform()-0.5);
flangevin[i][1] = gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
flangevin[i][2] = gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
erforcelangevin[i] = 0.75*gamma1*ervel[i]+0.866025404*gamma2*(random->uniform()-0.5);
if (v[i][0] != 0.0) f[i][0] += flangevin[i][0];
else flangevin[i][0] = 0.0;
if (v[i][1] != 0.0) f[i][1] += flangevin[i][1];
else flangevin[i][1] = 0.0;
if (v[i][2] != 0.0) f[i][2] += flangevin[i][2];
else flangevin[i][2] = 0.0;
if (abs(spin[i])==1 && ervel[i] != 0.0) erforce[i] += erforcelangevin[i];
temperature->restore_bias(i,v[i]);
}
}
}
}
/* ----------------------------------------------------------------------
tally energy transfer to thermal reservoir
------------------------------------------------------------------------- */
void FixLangevinEff::end_of_step()
{
if (!tally) return;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *spin = atom->spin;
energy_onestep = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
flangevin[i][2]*v[i][2];
if (abs(spin[i])==1) energy_onestep += erforcelangevin[i];
}
energy += energy_onestep*update->dt;
}
/* ---------------------------------------------------------------------- */
double FixLangevinEff::compute_scalar()
{
if (!tally) return 0.0;
// capture the very first energy transfer to thermal reservoir
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *spin = atom->spin;
if (update->ntimestep == update->beginstep) {
energy_onestep = 0.0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
energy_onestep += flangevin[i][0]*v[i][0] + flangevin[i][1]*v[i][1] +
flangevin[i][2]*v[i][2];
if (abs(spin[i])==1) energy_onestep += erforcelangevin[i];
}
energy = 0.5*energy_onestep*update->dt;
}
double energy_me = energy - 0.5*energy_onestep*update->dt;
double energy_all;
MPI_Allreduce(&energy_me,&energy_all,1,MPI_DOUBLE,MPI_SUM,world);
return -energy_all;
}
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