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pair_yukawa_colloid.cpp
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Fri, Nov 1, 04:29

pair_yukawa_colloid.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing authors: Randy Schunk (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdlib.h"
#include "pair_yukawa_colloid.h"
#include "atom.h"
#include "atom_vec.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairYukawaColloid::PairYukawaColloid(LAMMPS *lmp) : PairYukawa(lmp) {}
/* ---------------------------------------------------------------------- */
void PairYukawaColloid::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair,radi,radj;
double rsq,r2inv,r,rinv,screening,forceyukawa,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 **shape = atom->shape;
int *type = atom->type;
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
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];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
radi = shape[itype][0];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
if (j < nall) factor_coul = 1.0;
else {
factor_coul = special_coul[j/nall];
j %= nall;
}
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];
radj = shape[jtype][0];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*(r-(radi+radj)));
forceyukawa = a[itype][jtype] * screening;
fpair = factor_coul*forceyukawa * rinv;
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 = a[itype][jtype]/kappa * screening - 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_compute();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairYukawaColloid::init_style()
{
if (!atom->avec->shape_type)
error->all("Pair yukawa/colloid requires atom attribute shape");
if (atom->radius_flag)
error->all("Pair yukawa/colloid cannot be used with "
"atom attribute diameter");
// insure all particle shapes are spherical
// can be point particles or polydisperse
for (int i = 1; i <= atom->ntypes; i++)
if ((atom->shape[i][0] != atom->shape[i][1]) ||
(atom->shape[i][0] != atom->shape[i][2]) ||
(atom->shape[i][1] != atom->shape[i][2]))
error->all("Pair yukawa/colloid requires spherical particles");
int irequest = neighbor->request(this);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairYukawaColloid::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
a[i][j] = mix_energy(a[i][i],a[j][j],1.0,1.0);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
if (offset_flag) {
double radi = atom->shape[i][0];
double radj = atom->shape[j][0];
double screening = exp(-kappa * (cut[i][j] - (radi+radj)));
offset[i][j] = a[i][j]/kappa * screening;
} else offset[i][j] = 0.0;
a[j][i] = a[i][j];
offset[j][i] = offset[i][j];
return cut[i][j];
}
/* ---------------------------------------------------------------------- */
double PairYukawaColloid::single(int i, int j, int itype, int jtype,
double rsq,
double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,r,rinv,screening,forceyukawa,phi,radi,radj;
int *type = atom->type;
radi = atom->shape[itype][0];
radj = atom->shape[jtype][0];
r2inv = 1.0/rsq;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*(r-(radi+radj)));
forceyukawa = a[itype][jtype] * screening;
fforce = factor_coul*forceyukawa * rinv;
phi = a[itype][jtype]/kappa * screening - offset[itype][jtype];
return factor_coul*phi;
}

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