Homec4science
Diffusion lammps (master) Browse

lammps/src/USER-EFF/fix_langevin_eff.cpp
e368acdaeb22master

Last Change
Raw File

fix_langevin_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
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <string.h>
#include <stdlib.h>
#include "fix_langevin_eff.h"
#include "math_extra.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 "input.h"
#include "variable.h"
#include "random_mars.h"
#include "memory.h"
#include "error.h"
#include "group.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL,ATOM};
#define SINERTIA 0.4 // moment of inertia prefactor for sphere
#define EINERTIA 0.2 // moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */
FixLangevinEff::FixLangevinEff(LAMMPS *lmp, int narg, char **arg) :
FixLangevin(lmp, narg, arg)
{
erforcelangevin = NULL;
}
/* ---------------------------------------------------------------------- */
FixLangevinEff::~FixLangevinEff()
{
memory->destroy(erforcelangevin);
}
/* ---------------------------------------------------------------------- */
void FixLangevinEff::post_force(int vflag)
{
if (tallyflag) post_force_tally();
else post_force_no_tally();
}
/* ---------------------------------------------------------------------- */
void FixLangevinEff::post_force_no_tally()
{
double gamma1,gamma2,t_target;
double **v = atom->v;
double **f = atom->f;
double *ervel = atom->ervel;
double *erforce = atom->erforce;
int *spin = atom->spin;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double mefactor = domain->dimension/4.0;
double sqrtmefactor = sqrt(mefactor);
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
// set current t_target and t_sqrt
// if variable temp, evaluate variable, wrap with clear/add
// reallocate tforce array if necessary
if (tstyle == CONSTANT) {
t_target = t_start + delta * (t_stop-t_start);
tsqrt = sqrt(t_target);
} else {
modify->clearstep_compute();
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,"Fix langevin/eff variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (atom->nmax > maxatom2) {
maxatom2 = atom->nmax;
memory->destroy(tforce);
memory->create(tforce,maxatom2,"langevin/eff:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tforce[i] < 0.0)
error->one(FLERR,
"Fix langevin/eff variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
// 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
// for ZEROFLAG:
// sum random force over all atoms in group
// subtract sum/particles from each atom in group
double fran[4],fsum[4],fsumall[4];
fsum[0] = fsum[1] = fsum[2] = fsum[3] = 0.0;
int particles = group->count(igroup);
if (zeroflag) {
if (particles == 0)
error->all(FLERR,"Cannot zero Langevin force of 0 atoms/electrons");
}
// find number of electrons in group
int dof,fix_dof;
dof = domain->dimension * particles;
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
// extra_dof = domain->dimension
dof -= domain->dimension + fix_dof;
int one = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (abs(spin[i])==1) one++;
}
int nelectrons, dofelectrons, dofnuclei;
MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world);
dofelectrons = domain->dimension*nelectrons;
dofnuclei = dof-dofelectrons;
// thermal partitioning factor between nuclei and electrons
// extra dof from electron size
double gfactor3=(double) (dof+nelectrons)/dofnuclei;
if (tbiasflag == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = gfactor1[type[i]] * gfactor3;
gamma2 = gfactor2[type[i]] * tsqrt;
fran[0] = gamma2*(random->uniform()-0.5);
fran[1] = gamma2*(random->uniform()-0.5);
fran[2] = gamma2*(random->uniform()-0.5);
f[i][0] += gamma1*v[i][0] + fran[0];
f[i][1] += gamma1*v[i][1] + fran[1];
f[i][2] += gamma1*v[i][2] + fran[2];
fsum[0] += fran[0];
fsum[1] += fran[1];
fsum[2] += fran[2];
if (abs(spin[i])==1) {
fran[3] = sqrtmefactor*gamma2*(random->uniform()-0.5);
erforce[i] += mefactor*gamma1*ervel[i]+fran[3];
fsum[3] += fran[3];
}
}
}
} else if (tbiasflag == BIAS) {
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = gfactor1[type[i]] * gfactor3;
gamma2 = gfactor2[type[i]] * tsqrt;
temperature->remove_bias(i,v[i]);
fran[0] = gamma2*(random->uniform()-0.5);
fran[1] = gamma2*(random->uniform()-0.5);
fran[2] = gamma2*(random->uniform()-0.5);
if (v[i][0] != 0.0)
f[i][0] += gamma1*v[i][0] + fran[0];
if (v[i][1] != 0.0)
f[i][1] += gamma1*v[i][1] + fran[1];
if (v[i][2] != 0.0)
f[i][2] += gamma1*v[i][2] + fran[2];
fsum[0] += fran[0];
fsum[1] += fran[1];
fsum[2] += fran[2];
if (abs(spin[i])==1) {
fran[3] = sqrtmefactor*gamma2*(random->uniform()-0.5);
if (ervel[i] != 0.0) erforce[i] += mefactor*gamma1*ervel[i]+fran[3];
fsum[3] += fran[3];
}
temperature->restore_bias(i,v[i]);
}
}
}
// set total force to zero
if (zeroflag) {
MPI_Allreduce(fsum,fsumall,3,MPI_DOUBLE,MPI_SUM,world);
fsumall[0] /= particles;
fsumall[1] /= particles;
fsumall[2] /= particles;
fsumall[3] /= nelectrons;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
f[i][0] -= fsumall[0];
f[i][1] -= fsumall[1];
f[i][2] -= fsumall[2];
if (abs(spin[i])==1) erforce[i] -= fsumall[3];
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixLangevinEff::post_force_tally()
{
double gamma1,gamma2,t_target;
// reallocate flangevin and erforcelangevin if necessary
if (atom->nmax > maxatom1) {
memory->destroy(flangevin);
memory->destroy(erforcelangevin);
maxatom1 = atom->nmax;
memory->create(flangevin,maxatom1,3,"langevin/eff:flangevin");
memory->create(erforcelangevin,maxatom1,"langevin/eff:erforcelangevin");
}
double **v = atom->v;
double **f = atom->f;
double *erforce = atom->erforce;
double *ervel = atom->ervel;
int *spin = atom->spin;
double mefactor = domain->dimension/4.0;
double sqrtmefactor = sqrt(mefactor);
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double delta = update->ntimestep - update->beginstep;
delta /= update->endstep - update->beginstep;
// set current t_target and t_sqrt
// if variable temp, evaluate variable, wrap with clear/add
// reallocate tforce array if necessary
if (tstyle == CONSTANT) {
t_target = t_start + delta * (t_stop-t_start);
tsqrt = sqrt(t_target);
} else {
modify->clearstep_compute();
if (tstyle == EQUAL) {
t_target = input->variable->compute_equal(tvar);
if (t_target < 0.0)
error->one(FLERR,"Fix langevin/eff variable returned negative temperature");
tsqrt = sqrt(t_target);
} else {
if (atom->nmax > maxatom2) {
maxatom2 = atom->nmax;
memory->destroy(tforce);
memory->create(tforce,maxatom2,"langevin/eff:tforce");
}
input->variable->compute_atom(tvar,igroup,tforce,1,0);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (tforce[i] < 0.0)
error->one(FLERR,
"Fix langevin/eff variable returned negative temperature");
}
modify->addstep_compute(update->ntimestep + 1);
}
// 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
int particles = group->count(igroup);
if (zeroflag) {
if (particles == 0)
error->all(FLERR,"Cannot zero Langevin force of 0 atoms/electrons");
}
// find number of electrons in group
int dof,fix_dof;
dof = domain->dimension * particles;
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
// extra_dof = domain->dimension
dof -= domain->dimension + fix_dof;
int one = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (abs(spin[i])==1) one++;
}
int nelectrons, dofelectrons, dofnuclei;
MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world);
dofelectrons = domain->dimension*nelectrons;
dofnuclei = dof-dofelectrons;
// thermal partitioning factor between nuclei and electrons
// extra dof from electron size
double gfactor3=(double) (dof+nelectrons)/dofnuclei;
if (tbiasflag == NOBIAS) {
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = gfactor1[type[i]] * gfactor3;
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);
f[i][0] += flangevin[i][0];
f[i][1] += flangevin[i][1];
f[i][2] += flangevin[i][2];
if (abs(spin[i])==1) {
erforcelangevin[i] = mefactor*gamma1*ervel[i]+sqrtmefactor*gamma2*(random->uniform()-0.5);
erforce[i] += erforcelangevin[i];
}
}
}
} else if (tbiasflag == BIAS) {
temperature->compute_scalar();
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
if (tstyle == ATOM) tsqrt = sqrt(tforce[i]);
gamma1 = gfactor1[type[i]] * gfactor3;
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);
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) {
erforcelangevin[i] = mefactor*gamma1*ervel[i]+sqrtmefactor*gamma2*(random->uniform()-0.5);
if (ervel[i] != 0.0) erforce[i] += erforcelangevin[i];
else erforcelangevin[i] = 0.0;
}
temperature->restore_bias(i,v[i]);
}
}
}
}
/* ----------------------------------------------------------------------
tally energy transfer to thermal reservoir
------------------------------------------------------------------------- */
void FixLangevinEff::end_of_step()
{
if (!tallyflag) 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 (!tallyflag || flangevin == NULL || erforcelangevin == NULL) 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;
}
c4science · Help