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pair_coul_diel.cpp
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Mon, May 20, 21:31
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Wed, May 22, 21:31 (1 d, 23 h)
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rLAMMPS lammps
pair_coul_diel.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributiong authors: Arben Jusufi, Axel Kohlmeyer (Temple U.)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_coul_diel.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairCoulDiel::PairCoulDiel(LAMMPS *lmp) : Pair(lmp) {}
/* ---------------------------------------------------------------------- */
PairCoulDiel::~PairCoulDiel()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(sigmae);
memory->destroy(rme);
memory->destroy(offset);
memory->destroy(cutsq);
memory->destroy(cut);
allocated = 0;
}
}
/* ---------------------------------------------------------------------- */
void PairCoulDiel::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
double rsq,r,rarg,th,depsdr,epsr,forcecoul,factor_coul;
int *ilist,*jlist,*numneigh,**firstneigh;
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;
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];
qtmp = q[i];
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;
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]) {
r = sqrt(rsq);
rarg = (r-rme[itype][jtype])/sigmae[itype][jtype];
th=tanh(rarg);
epsr=a_eps+b_eps*th;
depsdr=b_eps * (1.0 - th*th) / sigmae[itype][jtype];
forcecoul = qqrd2e*qtmp*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
fpair = factor_coul*forcecoul/r;
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 = (qqrd2e*qtmp*q[j]*((eps_s/epsr) -1.)/r) - offset[itype][jtype];
ecoul *= factor_coul;
}
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 PairCoulDiel::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(sigmae,n+1,n+1,"pair:sigmae");
memory->create(rme,n+1,n+1,"pair:rme");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairCoulDiel::settings(int narg, char **arg)
{
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
cut_global = force->numeric(FLERR,arg[0]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++)
if (setflag[i][j]) cut[i][j] = cut_global;
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairCoulDiel::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 6) error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
eps_s = force->numeric(FLERR,arg[2]);
double rme_one =force->numeric(FLERR,arg[3]);
double sigmae_one = force->numeric(FLERR,arg[4]);
double cut_one = cut_global;
if (narg == 6) cut_one = force->numeric(FLERR,arg[5]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
sigmae[i][j] = sigmae_one;
rme[i][j] = rme_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
}
a_eps = 0.5*(5.2+eps_s);
b_eps = 0.5*(eps_s-5.2);
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairCoulDiel::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style coul/diel requires atom attribute q");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairCoulDiel::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
error->all(FLERR,"for pair style coul/diel, parameters need to be set explicitly for all pairs.");
}
double *q = atom->q;
double qqrd2e = force->qqrd2e;
if (offset_flag && (cut[i][j] > 0.0)) {
double rarg = (cut[i][j]-rme[i][j])/sigmae[i][j];
double epsr=a_eps+b_eps*tanh(rarg);
offset[i][j] = qqrd2e*q[i]*q[j]*((eps_s/epsr) -1.)/cut[i][j];
} else offset[i][j] = 0.0;
sigmae[j][i] = sigmae[i][j];
rme[j][i] = rme[i][j];
offset[j][i] = offset[i][j];
cut[j][i] = cut[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulDiel::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(&rme[i][j],sizeof(double),1,fp);
fwrite(&sigmae[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairCoulDiel::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 (setflag[i][j]) {
if (me == 0) {
fread(&rme[i][j],sizeof(double),1,fp);
fread(&sigmae[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&rme[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigmae[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairCoulDiel::write_restart_settings(FILE *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 PairCoulDiel::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
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 PairCoulDiel::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double r, rarg,forcedielec,phidielec;
double th,epsr,depsdr;
double *q = atom->q;
double qqrd2e = force->qqrd2e;
r=sqrt(rsq);
rarg = (r-rme[itype][jtype])/sigmae[itype][jtype];
th = tanh(rarg);
epsr=a_eps+b_eps*th;
depsdr=b_eps*(1.-th*th)/sigmae[itype][jtype];
forcedielec = qqrd2e*q[i]*q[j]*((eps_s*(epsr+r*depsdr)/epsr/epsr) -1.)/rsq;
fforce = factor_coul*forcedielec/r;
phidielec = (qqrd2e*q[i]*q[j]*((eps_s/epsr) -1.)/r)- offset[itype][jtype];
return factor_coul*phidielec;
}
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