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fix_wall_colloid.cpp
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Mon, Aug 5, 15:11

fix_wall_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: Jeremy Lechman (SNL)
------------------------------------------------------------------------- */
#include <math.h>
#include <string.h>
#include "fix_wall_colloid.h"
#include "atom.h"
#include "atom_vec.h"
#include "update.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixWallColloid::FixWallColloid(LAMMPS *lmp, int narg, char **arg) :
FixWall(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixWallColloid::init()
{
if (!atom->sphere_flag)
error->all(FLERR,"Fix wall/colloid requires atom style sphere");
// insure all particles in group are extended particles
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (radius[i] == 0.0) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) error->all(FLERR,"Fix wall/colloid requires extended particles");
FixWall::init();
}
/* ---------------------------------------------------------------------- */
void FixWallColloid::precompute(int m)
{
coeff1[m] = 4.0/315.0 * epsilon[m] * pow(sigma[m],6.0);
coeff2[m] = 2.0/3.0 * epsilon[m];
coeff3[m] = epsilon[m] * pow(sigma[m],6.0)/7560.0;
coeff4[m] = epsilon[m]/6.0;
}
/* ----------------------------------------------------------------------
interaction of all particles in group with a wall
m = index of wall coeffs
which = xlo,xhi,ylo,yhi,zlo,zhi
error if any finite-size particle is touching or penetrating wall
------------------------------------------------------------------------- */
void FixWallColloid::wall_particle(int m, int which, double coord)
{
double delta,delta2,rinv,r2inv,r4inv,r8inv,fwall;
double r2,rinv2,r2inv2,r4inv2;
double r3,rinv3,r2inv3,r4inv3;
double rad,rad2,rad4,rad8,diam,new_coeff2;
double eoffset;
double **x = atom->x;
double **f = atom->f;
double *radius = atom->radius;
int *mask = atom->mask;
int nlocal = atom->nlocal;
int dim = which / 2;
int side = which % 2;
if (side == 0) side = -1;
int onflag = 0;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (side < 0) delta = x[i][dim] - coord;
else delta = coord - x[i][dim];
if (delta >= cutoff[m]) continue;
rad = radius[i];
if (rad >= delta) {
onflag = 1;
continue;
}
new_coeff2 = coeff2[m]*rad*rad*rad;
diam = 2.0*rad;
rad2 = rad*rad;
rad4 = rad2*rad2;
rad8 = rad4*rad4;
delta2 = rad2 - delta*delta;
rinv = 1.0/delta2;
r2inv = rinv*rinv;
r4inv = r2inv*r2inv;
r8inv = r4inv*r4inv;
fwall = side * (coeff1[m]*(rad8*rad + 27.0*rad4*rad2*rad*pow(delta,2.0)
+ 63.0*rad4*rad*pow(delta,4.0)
+ 21.0*rad2*rad*pow(delta,6.0))*r8inv -
new_coeff2*r2inv);
f[i][dim] -= fwall;
r2 = rad - delta;
rinv2 = 1.0/r2;
r2inv2 = rinv2*rinv2;
r4inv2 = r2inv2*r2inv2;
r3 = delta + rad;
rinv3 = 1.0/r3;
r2inv3 = rinv3*rinv3;
r4inv3 = r2inv3*r2inv3;
ewall[0] += coeff3[m]*((-3.5*diam+delta)*r4inv2*r2inv2*rinv2
+ (3.5*diam+delta)*r4inv3*r2inv3*rinv3) -
coeff4[m]*((diam*delta-r2*r3*(log(-r2)-log(r3)))*
(-rinv2)*rinv3);
// offset depends on particle size
r2 = rad - cutoff[m];
rinv2 = 1.0/r2;
r2inv2 = rinv2*rinv2;
r4inv2 = r2inv2*r2inv2;
r3 = cutoff[m] + rad;
rinv3 = 1.0/r3;
r2inv3 = rinv3*rinv3;
r4inv3 = r2inv3*r2inv3;
eoffset = coeff3[m]*((-3.5*diam+cutoff[m])*r4inv2*r2inv2*rinv2
+ (3.5*diam+cutoff[m])*r4inv3*r2inv3*rinv3) -
coeff4[m]*((diam*cutoff[m]-r2*r3*(log(-r2)-log(r3)))*
(-rinv2)*rinv3);
ewall[0] -= eoffset;
ewall[m+1] += fwall;
}
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
}

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