Homec4science
Diffusion lammps (master) Browse

lammps/src/USER-MISC/fix_wall_ees.cpp
15853a0e38dcmaster

Last Change
Raw File

fix_wall_ees.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 author: Abdoreza Ershadinia, a.ershadinia at gmail.com
------------------------------------------------------------------------- */
#include <math.h>
#include "math_extra.h"
#include "fix_wall_ees.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "domain.h"
#include "region.h"
#include "force.h"
#include "lattice.h"
#include "update.h"
#include "output.h"
#include "respa.h"
#include "error.h"
#include "math_extra.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixWallEES::FixWallEES(LAMMPS *lmp, int narg, char **arg) :
FixWall(lmp, narg, arg) {}
/* ---------------------------------------------------------------------- */
void FixWallEES::precompute(int m)
{
coeff1[m] = ( 2. / 4725. ) * epsilon[m] * pow(sigma[m],12.0);
coeff2[m] = ( 1. / 24. ) * epsilon[m] * pow(sigma[m],6.0);
coeff3[m] = ( 2. / 315. ) * epsilon[m] * pow(sigma[m],12.0);
coeff4[m] = ( 1. / 3. ) * epsilon[m] * pow(sigma[m],6.0);
coeff5[m] = ( 4. / 315. ) * epsilon[m] * pow(sigma[m],12.0);
coeff6[m] = ( 1. / 12. ) * epsilon[m] * pow(sigma[m],6.0);
}
/* ---------------------------------------------------------------------- */
void FixWallEES::init()
{
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Fix wall/ees requires atom style ellipsoid");
// check that all particles are finite-size ellipsoids
// no point particles allowed, spherical is OK
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
if (ellipsoid[i] < 0)
error->one(FLERR,"Fix wall/ees requires extended particles");
FixWall::init();
}
/* ----------------------------------------------------------------------
interaction of all particles in group with a wall
m = index of wall coeffs
which = xlo,xhi,ylo,yhi,zlo,zhi
error if any particle is on or behind wall
------------------------------------------------------------------------- */
void FixWallEES::wall_particle(int m, int which, double coord)
{
double delta;
double **x = atom->x;
double **f = atom->f;
double **tor = atom->torque;
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
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;
double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
double tempvec[3]= {0,0,0};
double sigman = 0.0, sigman2 = 0.0;
double nhat[3] = {0,0,0};
nhat[dim]=-1*side;
nhat[(dim+1)%3] = 0 ;
nhat[(dim+2)%3] = 0 ;
double* shape = bonus[ellipsoid[i]].shape;;
MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
MathExtra::transpose_matvec(A,nhat,tempvec);
for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
for(int k = 0; k<3 ; k++) sigman2 += tempvec[k]*tempvec[k];
sigman = sqrt(sigman2);
if (delta <= sigman) {
onflag = 1;
continue;
}
double fwall = 0.0, twall = 0.0;
double delta2 = 0.0, delta3 = 0.0, delta4 = 0.0, delta5 = 0.0, delta6 = 0.0;
double sigman3 = 0.0, sigman4 = 0.0, sigman5 = 0.0, sigman6 = 0.0;
double hhss = 0.0, hhss2 = 0.0, hhss4 = 0.0, hhss7 = 0.0, hhss8 = 0.0;
double hps = 0.0;
double hms = 0.0;
double tempvec2[3]= {0,0,0};
double SAn[3] = {0,0,0};
double that[3] = {0,0,0};
double Lx[3][3] = {{0,0,0},{0,0,-1},{0,1,0}};
double Ly[3][3] = {{0,0,1},{0,0,0},{-1,0,0}};
double Lz[3][3] = {{0,-1,0},{1,0,0},{0,0,0}};
for(int k = 0; k<3; k++) SAn[k] = tempvec[k];
sigman3 = sigman2 * sigman;
sigman4 = sigman2 * sigman2;
sigman5 = sigman4 * sigman;
sigman6 = sigman3 * sigman3;
delta2 = delta * delta;
delta3 = delta2 * delta;
delta4 = delta2 * delta2;
delta5 = delta3 * delta2;
delta6 = delta3 * delta3;
hhss = delta2 - sigman2;
hhss2 = hhss * hhss;
hhss4 = hhss2 * hhss2;
hhss8 = hhss4 * hhss4;
hhss7 = hhss4 * hhss2 * hhss;
hps = delta + sigman;
hms = delta - sigman;
fwall = side*(
-1*coeff4[m]/hhss2 +
coeff3[m] * ( 21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6 ) / hhss8
);
f[i][dim] -= fwall;
ewall[0] += -1*coeff2[m] * ( 4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3 ) +
coeff1[m] * ( 35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4 ) / hhss7;
ewall[m+1] += fwall;
twall = coeff6[m] * ( 6.*delta3/sigman4/hhss2 - 10.*delta/sigman2/hhss2 + 3.*log(hms/hps)/sigman5 ) +
coeff5[m] * ( 21.*delta5 + 30.*delta3*sigman2 + 5.*delta*sigman4 ) / hhss8 ;
MathExtra::matvec(Lx,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
that[0] = MathExtra::dot3(SAn,tempvec2);
MathExtra::matvec(Ly,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k<3; k++) tempvec2[k] *= shape[k];
that[1] = MathExtra::dot3(SAn,tempvec2);
MathExtra::matvec(Lz,nhat,tempvec);
MathExtra::transpose_matvec(A,tempvec,tempvec2);
for(int k = 0; k < 3; k++) tempvec2[k] *= shape[k];
that[2] = MathExtra::dot3(SAn,tempvec2);
for(int j = 0; j<3 ; j++)
tor[i][j] += twall * that[j];
}
if (onflag) error->one(FLERR,"Particle on or inside fix wall surface");
}
c4science · Help