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pair_thole.cpp
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Mon, May 27, 01:49

pair_thole.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 "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_thole.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "fix.h"
#include "fix_store.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairThole::PairThole(LAMMPS *lmp) : Pair(lmp) {
fix_drude = NULL;
}
/* ---------------------------------------------------------------------- */
PairThole::~PairThole()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(polar);
memory->destroy(thole);
memory->destroy(ascreen);
memory->destroy(cut);
memory->destroy(scale);
}
}
/* ---------------------------------------------------------------------- */
void PairThole::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qi,qj,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
double r,rsq,r2inv,rinv,forcecoul,factor_coul;
int *ilist,*jlist,*numneigh,**firstneigh;
double factor_f,factor_e;
int di,dj;
double dcoul,asr,exp_asr;
ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
int *drudetype = fix_drude->drudetype;
tagint *drudeid = fix_drude->drudeid;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
// only on core-drude pair
if (drudetype[type[i]] == NOPOL_TYPE)
continue;
di = domain->closest_image(i, atom->map(drudeid[i]));
// get dq of the core via the drude charge
if (drudetype[type[i]] == DRUDE_TYPE)
qi = q[i];
else
qi = -q[di];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
// only on core-drude pair, but not into the same pair
if (drudetype[type[j]] == NOPOL_TYPE || j == di)
continue;
// get dq of the core via the drude charge
if (drudetype[type[j]] == DRUDE_TYPE)
qj = q[j];
else {
dj = domain->closest_image(j, atom->map(drudeid[j]));
qj = -q[dj];
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
r = sqrt(rsq);
asr = ascreen[itype][jtype] * r;
exp_asr = exp(-asr);
dcoul = qqrd2e * qi * qj *scale[itype][jtype] * rinv;
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr)))) - factor_coul;
if(eflag) factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
fpair = factor_f * dcoul * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag)
ecoul = factor_e * dcoul;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0.0,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairThole::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(scale,n+1,n+1,"pair:scale");
memory->create(ascreen,n+1,n+1,"pair:ascreen");
memory->create(thole,n+1,n+1,"pair:thole");
memory->create(polar,n+1,n+1,"pair:polar");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairThole::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
thole_global = force->numeric(FLERR,arg[0]);
cut_global = force->numeric(FLERR,arg[1]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
thole[i][j] = thole_global;
cut[i][j] = cut_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairThole::coeff(int narg, char **arg)
{
if (narg < 3 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double polar_one = force->numeric(FLERR,arg[2]);
double thole_one = thole_global;
double cut_one = cut_global;
if (narg >=4) thole_one = force->numeric(FLERR,arg[3]);
if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
polar[i][j] = polar_one;
thole[i][j] = thole_one;
ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
cut[i][j] = cut_one;
scale[i][j] = 1.0;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairThole::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style thole requires atom attribute q");
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, "Pair thole requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairThole::init_one(int i, int j)
{
if (setflag[i][j] == 0)
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
polar[j][i] = polar[i][j];
thole[j][i] = thole[i][j];
ascreen[j][i] = ascreen[i][j];
scale[j][i] = scale[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairThole::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&polar[i][j],sizeof(double),1,fp);
fwrite(&thole[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairThole::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&polar[i][j],sizeof(double),1,fp);
fread(&thole[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
}
MPI_Bcast(&polar[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&thole[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&ascreen[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairThole::write_restart_settings(FILE *fp)
{
fwrite(&thole_global,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairThole::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&thole_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&thole_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairThole::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,rinv,r,forcecoul,phicoul;
double qi,qj,factor_f,factor_e,dcoul,asr,exp_asr;
int di, dj;
int *drudetype = fix_drude->drudetype;
tagint *drudeid = fix_drude->drudeid;
int *type = atom->type;
// only on core-drude pair, but not on the same pair
if (drudetype[type[i]] == NOPOL_TYPE || drudetype[type[j]] == NOPOL_TYPE ||
j == i)
return 0.0;
// get dq of the core via the drude charge
if (drudetype[type[i]] == DRUDE_TYPE)
qi = atom->q[i];
else {
di = domain->closest_image(i, atom->map(drudeid[i]));
qi = -atom->q[di];
}
if (drudetype[type[j]] == DRUDE_TYPE)
qj = atom->q[j];
else {
dj = domain->closest_image(j, atom->map(drudeid[j]));
qj = -atom->q[dj];
}
r2inv = 1.0/rsq;
if (rsq < cutsq[itype][jtype]) {
rinv = sqrt(r2inv);
r = sqrt(rsq);
asr = ascreen[itype][jtype] * r;
exp_asr = exp(-asr);
dcoul = force->qqrd2e * qi * qj * rinv;
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr)))) - factor_coul;
forcecoul += factor_f * dcoul;
factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
} else forcecoul= 0.0;
fforce = factor_f*forcecoul * r2inv;
if (rsq < cutsq[itype][jtype]) {
phicoul = factor_e * dcoul;
} else phicoul = 0.0;
return phicoul;
}
/* ---------------------------------------------------------------------- */
void *PairThole::extract(const char *str, int &dim)
{
dim = 4;
if (strcmp(str,"scale") == 0) return (void *) scale;
if (strcmp(str,"polar") == 0) return (void *) polar;
if (strcmp(str,"thole") == 0) return (void *) thole;
if (strcmp(str,"ascreen") == 0) return (void *) ascreen;
return NULL;
}

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