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compute_temp_drude.cpp
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Sat, Jun 1, 03:59

compute_temp_drude.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 <stdlib.h>
#include <string.h>
#include "compute_temp_drude.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
#include "comm.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempDrude::ComputeTempDrude(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute temp command");
vector_flag = 1;
scalar_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = -1;
extlist = new int[6];
extlist[0] = extlist[1] = 0;
extlist[2] = extlist[3] = extlist[4] = extlist[5] = 1;
tempflag = 0; // because does not compute a single temperature (scalar and vector)
vector = new double[6];
fix_drude = NULL;
id_temp = NULL;
temperature = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeTempDrude::~ComputeTempDrude()
{
delete [] vector;
delete [] extlist;
delete [] id_temp;
}
/* ---------------------------------------------------------------------- */
void ComputeTempDrude::init()
{
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
if (ifix == modify->nfix) error->all(FLERR, "compute temp/drude requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
if (!comm->ghost_velocity)
error->all(FLERR,"compute temp/drude requires ghost velocities. Use comm_modify vel yes");
}
/* ---------------------------------------------------------------------- */
void ComputeTempDrude::setup()
{
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempDrude::dof_compute()
{
int nlocal = atom->nlocal;
int *type = atom->type;
int dim = domain->dimension;
int *drudetype = fix_drude->drudetype;
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
bigint dof_core_loc = 0, dof_drude_loc = 0;
for (int i = 0; i < nlocal; i++) {
if (atom->mask[i] & groupbit) {
if (drudetype[type[i]] == DRUDE_TYPE) // Non-polarizable atom
dof_drude_loc++;
else
dof_core_loc++;
}
}
dof_core_loc *= dim;
dof_drude_loc *= dim;
MPI_Allreduce(&dof_core_loc, &dof_core, 1, MPI_LMP_BIGINT, MPI_SUM, world);
MPI_Allreduce(&dof_drude_loc, &dof_drude, 1, MPI_LMP_BIGINT, MPI_SUM, world);
dof_core -= fix_dof;
vector[2] = dof_core;
vector[3] = dof_drude;
}
/* ---------------------------------------------------------------------- */
int ComputeTempDrude::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void ComputeTempDrude::compute_vector()
{
invoked_vector = update->ntimestep;
int nlocal = atom->nlocal;
int *mask = atom->mask;
int *type = atom->type;
double *rmass = atom->rmass, *mass = atom->mass;
double **v = atom->v;
tagint *drudeid = fix_drude->drudeid;
int *drudetype = fix_drude->drudetype;
int dim = domain->dimension;
double mvv2e = force->mvv2e, kb = force->boltz;
double mcore, mdrude;
double ecore, edrude;
double *vcore, *vdrude;
double kineng_core_loc = 0., kineng_drude_loc = 0.;
for (int i=0; i<nlocal; i++){
if (groupbit & mask[i] && drudetype[type[i]] != DRUDE_TYPE){
if (drudetype[type[i]] == NOPOL_TYPE) {
ecore = 0.;
vcore = v[i];
if (temperature) temperature->remove_bias(i, vcore);
for (int k=0; k<dim; k++) ecore += vcore[k]*vcore[k];
if (temperature) temperature->restore_bias(i, vcore);
if (rmass) mcore = rmass[i];
else mcore = mass[type[i]];
kineng_core_loc += mcore * ecore;
} else { // CORE_TYPE
int j = atom->map(drudeid[i]);
if (rmass) {
mcore = rmass[i];
mdrude = rmass[j];
} else {
mcore = mass[type[i]];
mdrude = mass[type[j]];
}
double mtot_inv = 1. / (mcore + mdrude);
ecore = 0.;
edrude = 0.;
vcore = v[i];
vdrude = v[j];
if (temperature) {
temperature->remove_bias(i, vcore);
temperature->remove_bias(j, vdrude);
}
for (int k=0; k<dim; k++) {
double v1 = mdrude * vdrude[k] + mcore * vcore[k];
ecore += v1 * v1;
double v2 = vdrude[k] - vcore[k];
edrude += v2 * v2;
}
if (temperature) {
temperature->restore_bias(i, vcore);
temperature->restore_bias(j, vdrude);
}
kineng_core_loc += mtot_inv * ecore;
kineng_drude_loc += mtot_inv * mcore * mdrude * edrude;
}
}
}
if (dynamic) dof_compute();
kineng_core_loc *= 0.5 * mvv2e;
kineng_drude_loc *= 0.5 * mvv2e;
MPI_Allreduce(&kineng_core_loc,&kineng_core,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&kineng_drude_loc,&kineng_drude,1,MPI_DOUBLE,MPI_SUM,world);
temp_core = 2.0 * kineng_core / (dof_core * kb);
temp_drude = 2.0 * kineng_drude / (dof_drude * kb);
vector[0] = temp_core;
vector[1] = temp_drude;
vector[4] = kineng_core;
vector[5] = kineng_drude;
}
double ComputeTempDrude::compute_scalar(){
compute_vector();
scalar = vector[0];
return scalar;
}

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