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fix_drude_transform.cpp
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Mon, Nov 11, 02:19

fix_drude_transform.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.
------------------------------------------------------------------------- */
/** Fix Drude Transform ******************************************************/
#include <math.h>
#include "fix_drude_transform.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "error.h"
#include "modify.h"
#include "force.h"
#include <string.h>
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
template <bool inverse>
FixDrudeTransform<inverse>::FixDrudeTransform(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), mcoeff(NULL)
{
if (narg != 3) error->all(FLERR,"Illegal fix drude/transform command");
comm_forward = 9;
fix_drude = NULL;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
FixDrudeTransform<inverse>::~FixDrudeTransform()
{
if (mcoeff) delete [] mcoeff;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::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, "fix drude/transform requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
int FixDrudeTransform<inverse>::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::setup(int) {
int nlocal = atom->nlocal;
int ntypes = atom->ntypes;
int * type = atom->type;
double * rmass = atom->rmass, * mass = atom->mass;
tagint * drudeid = fix_drude->drudeid;
int * drudetype = fix_drude->drudetype;
if (!rmass) {
if (!mcoeff) mcoeff = new double[ntypes+1];
double mcoeff_loc[ntypes+1];
for (int itype=0; itype<=ntypes; itype++) mcoeff_loc[itype] = 2.; // an impossible value: mcoeff is at most 1.
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) {
int j = atom->map(drudeid[i]);
// i is drude, j is core
if (mcoeff_loc[type[i]] < 1.5) { // already done
if (mcoeff_loc[type[j]] > 1.5){ // not yet done ??
error->all(FLERR,"There must be one Drude type per core type");}
continue;
}
mcoeff_loc[type[i]] = mass[type[i]] / (mass[type[i]] + mass[type[j]]);
mcoeff_loc[type[j]] = -mass[type[i]] / mass[type[j]];
}
}
MPI_Allreduce(mcoeff_loc, mcoeff, ntypes+1, MPI_DOUBLE, MPI_MIN, world);
// mcoeff is 2 for non polarizable
// 0 < mcoeff < 1 for drude
// mcoeff < 0 for core
}
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS { // required for specialization
template <>
void FixDrudeTransform<false>::initial_integrate(int){
comm->forward_comm_fix(this);
real_to_reduced();
//comm->forward_comm_fix(this); // Normally not needed
}
template <>
void FixDrudeTransform<false>::final_integrate(){
comm->forward_comm_fix(this);
real_to_reduced();
//comm->forward_comm_fix(this); // Normally not needed
}
template <>
void FixDrudeTransform<true>::initial_integrate(int){
comm->forward_comm_fix(this);
reduced_to_real();
//comm->forward_comm_fix(this); // Normally not needed
}
template <>
void FixDrudeTransform<true>::final_integrate(){
comm->forward_comm_fix(this);
reduced_to_real();
//comm->forward_comm_fix(this); // Normally not needed
}
} // end of namespace
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::real_to_reduced()
{
int nlocal = atom->nlocal;
int ntypes = atom->ntypes;
int dim = domain->dimension;
int * mask = atom->mask, * type = atom->type;
double ** x = atom->x, ** v = atom->v, ** f = atom->f;
double * rmass = atom->rmass, * mass = atom->mass;
double mcore, mdrude, coeff;
int icore, idrude;
tagint * drudeid = fix_drude->drudeid;
int * drudetype = fix_drude->drudetype;
if (!rmass) { // TODO: maybe drudetype can be used instead?
for (int itype=1; itype<=ntypes; itype++)
if (mcoeff[itype] < 1.5) mass[itype] *= 1. - mcoeff[itype];
}
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
drudeid[i] = (tagint) domain->closest_image(i, atom->map(drudeid[i]));
}
}
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
int j = (int) drudeid[i];
if (drudetype[type[i]] == DRUDE_TYPE && j < nlocal) continue;
if (drudetype[type[i]] == DRUDE_TYPE) {
idrude = i;
icore = j;
} else {
icore = i;
idrude = j;
}
if (rmass) {
mcore = rmass[icore];
mdrude = rmass[idrude];
rmass[icore] += mdrude;
rmass[idrude] *= mcore / rmass[icore];
coeff = mdrude / (mcore + mdrude);
} else { // TODO check that all atoms of this types are in the group
coeff = mcoeff[type[idrude]];
}
for (int k=0; k<dim; k++) {
x[idrude][k] -= x[icore][k];
x[icore][k] += coeff * x[idrude][k];
v[idrude][k] -= v[icore][k];
v[icore][k] += coeff * v[idrude][k];
f[icore][k] += f[idrude][k];
f[idrude][k] -= coeff * f[icore][k];
}
}
}
fix_drude->is_reduced = true;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::reduced_to_real()
{
int nlocal = atom->nlocal;
int ntypes = atom->ntypes;
int dim = domain->dimension;
int * mask = atom->mask, * type = atom->type;
double ** x = atom->x, ** v = atom->v, ** f = atom->f;
double * rmass = atom->rmass, * mass = atom->mass;
double mcore, mdrude, coeff;
int icore, idrude;
tagint * drudeid = fix_drude->drudeid;
int * drudetype = fix_drude->drudetype;
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
int j = (int) drudeid[i]; // local index of drude partner because drudeid is in reduced form
if (drudetype[type[i]] == DRUDE_TYPE && j < nlocal) continue;
if (drudetype[type[i]] == DRUDE_TYPE) {
idrude = i;
icore = j;
} else {
icore = i;
idrude = j;
}
if (rmass) {
double s = sqrt(1. - rmass[idrude]/rmass[icore]);
rmass[idrude] = 0.5 * rmass[icore] * (1. - s);
mdrude = rmass[idrude];
rmass[icore] -= mdrude;
mcore = rmass[icore];
coeff = mdrude / (mcore + mdrude);
} else {
if (!mcoeff[type[icore]]) { // TODO: should it be > 1.5 ?
double s = sqrt(1. - mass[type[idrude]] / mass[type[icore]]);
mass[type[idrude]] = 0.5 * mass[type[icore]] * (1. - s);
mdrude = mass[type[idrude]];
mass[type[icore]] -= mdrude;
mcore = mass[type[icore]];
mcoeff[type[icore]] = mdrude / (mcore + mdrude);
}
coeff = mcoeff[type[idrude]];
}
for (int k=0; k<dim; k++) {
x[icore][k] -= coeff * x[idrude][k];
x[idrude][k] += x[icore][k];
v[icore][k] -= coeff * v[idrude][k];
v[idrude][k] += v[icore][k];
f[idrude][k] += coeff * f[icore][k];
f[icore][k] -= f[idrude][k];
}
}
}
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
drudeid[i] = atom->tag[(int) drudeid[i]];
}
}
if (!rmass) {
for (int itype=1; itype<=ntypes; itype++)
if (mcoeff[itype] < 1.5) mass[itype] /= 1. - mcoeff[itype];
}
fix_drude->is_reduced = false;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
int FixDrudeTransform<inverse>::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
double ** x = atom->x, ** v = atom->v, ** f = atom->f;
int * type = atom->type, * drudetype = fix_drude->drudetype;
double dx,dy,dz;
int dim = domain->dimension;
int m = 0;
for (int i=0; i<n; i++) {
int j = list[i];
if (pbc_flag == 0 ||
(fix_drude->is_reduced && drudetype[type[j]] == DRUDE_TYPE)) {
for (int k=0; k<dim; k++) buf[m++] = x[j][k];
}
else {
if (domain->triclinic != 0) {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy;
dy = pbc[1]*domain->yprd;
if (dim == 3) {
dx += + pbc[4]*domain->xz;
dy += pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
}
else {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
if (dim == 3)
dz = pbc[2]*domain->zprd;
}
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
if (dim == 3)
buf[m++] = x[j][2] + dz;
}
for (int k=0; k<dim; k++) buf[m++] = v[j][k];
for (int k=0; k<dim; k++) buf[m++] = f[j][k];
}
return m;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::unpack_forward_comm(int n, int first, double *buf)
{
double ** x = atom->x, ** v = atom->v, ** f = atom->f;
int dim = domain->dimension;
int m = 0;
int last = first + n;
for (int i=first; i<last; i++) {
for (int k=0; k<dim; k++) x[i][k] = buf[m++];
for (int k=0; k<dim; k++) v[i][k] = buf[m++];
for (int k=0; k<dim; k++) f[i][k] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
template class FixDrudeTransform<false>;
template class FixDrudeTransform<true>;

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