Homec4science
Diffusion lammps (lammm-devel) Browse

lammps/src/COLLOID/pair_yukawa_colloid.cpp
76fb4e08152flammm-devel

Last Change
Raw File

pair_yukawa_colloid.cpp
View Options

/* ----------------------------------------------------------------------
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 (Sandia)
------------------------------------------------------------------------- */
#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)
{
writedata = 1;
}
/* ---------------------------------------------------------------------- */
void PairYukawaColloid::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,radi,radj;
double rsq,r,rinv,screening,forceyukawa,factor;
int *ilist,*jlist,*numneigh,**firstneigh;
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_lj = force->special_lj;
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 = radius[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor = special_lj[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];
radj = radius[j];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*(r-(radi+radj)));
forceyukawa = a[itype][jtype] * screening;
fpair = factor*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) {
evdwl = a[itype][jtype]/kappa * screening - offset[itype][jtype];
evdwl *= factor;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairYukawaColloid::init_style()
{
if (!atom->sphere_flag)
error->all(FLERR,"Pair yukawa/colloid requires atom style sphere");
neighbor->request(this,instance_me);
// require that atom radii are identical within each type
for (int i = 1; i <= atom->ntypes; i++)
if (!atom->radius_consistency(i,rad[i]))
error->all(FLERR,"Pair yukawa/colloid requires atoms with same type "
"have same radius");
}
/* ----------------------------------------------------------------------
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 && (kappa != 0.0)) {
double screening = exp(-kappa * (cut[i][j] - (rad[i]+rad[j])));
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 r,rinv,screening,forceyukawa,phi;
r = sqrt(rsq);
rinv = 1.0/r;
screening = exp(-kappa*(r-(rad[itype]+rad[jtype])));
forceyukawa = a[itype][jtype] * screening;
fforce = factor_lj*forceyukawa * rinv;
phi = a[itype][jtype]/kappa * screening - offset[itype][jtype];
return factor_lj*phi;
}
c4science · Help