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fix_wall_region_ees.cpp
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Fri, Jun 7, 06:04

fix_wall_region_ees.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 author: Abdoreza Ershadinia, a.ershadinia at gmail.com
------------------------------------------------------------------------- */
#include <math.h>
#include <stdlib.h>
#include <string.h>
#include "fix_wall_region_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;
/* ---------------------------------------------------------------------- */
FixWallRegionEES::FixWallRegionEES(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 7) error->all(FLERR,"Illegal fix wall/region/ees command");
scalar_flag = 1;
vector_flag = 1;
size_vector = 3;
global_freq = 1;
extscalar = 1;
extvector = 1;
// parse args
iregion = domain->find_region(arg[3]);
if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
int n = strlen(arg[3]) + 1;
idregion = new char[n];
strcpy(idregion,arg[3]);
epsilon = force->numeric(FLERR,arg[4]);
sigma = force->numeric(FLERR,arg[5]);
cutoff = force->numeric(FLERR,arg[6]);
if (cutoff <= 0.0) error->all(FLERR,"Fix wall/region/ees cutoff <= 0.0");
eflag = 0;
ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
}
/* ---------------------------------------------------------------------- */
FixWallRegionEES::~FixWallRegionEES()
{
delete [] idregion;
}
/* ---------------------------------------------------------------------- */
int FixWallRegionEES::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixWallRegionEES::init()
{
// set index and check validity of region
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR,"Region ID for fix wall/region/ees does not exist");
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
if (!avec)
error->all(FLERR,"Fix wall/region/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/region/ees requires extended particles");
// setup coefficients
coeff1 = ( 2. / 4725. ) * epsilon * pow(sigma,12.0);
coeff2 = ( 1. / 24. ) * epsilon * pow(sigma,6.0);
coeff3 = ( 2. / 315. ) * epsilon * pow(sigma,12.0);
coeff4 = ( 1. / 3. ) * epsilon * pow(sigma,6.0);
coeff5 = ( 4. / 315. ) * epsilon * pow(sigma,12.0);
coeff6 = ( 1. / 12. ) * epsilon * pow(sigma,6.0);
offset = 0;
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
}
/* ---------------------------------------------------------------------- */
void FixWallRegionEES::setup(int vflag)
{
if (strstr(update->integrate_style,"verlet"))
post_force(vflag);
else {
((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
post_force_respa(vflag,nlevels_respa-1,0);
((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
}
}
/* ---------------------------------------------------------------------- */
void FixWallRegionEES::min_setup(int vflag)
{
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixWallRegionEES::post_force(int vflag)
{
//sth is needed here, but I dont know what
//that is calculation of sn
int i,m,n;
double rinv,fx,fy,fz,sn,tooclose[3];
eflag = 0;
ewall[0] = ewall[1] = ewall[2] = ewall[3] = 0.0;
double **x = atom->x;
double **f = atom->f;
double **tor = atom->torque;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
int *mask = atom->mask;
int nlocal = atom->nlocal;
Region *region = domain->regions[iregion];
region->prematch();
int onflag = 0;
// region->match() insures particle is in region or on surface, else error
// if returned contact dist r = 0, is on surface, also an error
// in COLLOID case, r <= radius is an error
for (i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (!region->match(x[i][0],x[i][1],x[i][2])) {
onflag = 1;
continue;
}
double A[3][3] = {{0,0,0},{0,0,0},{0,0,0}};
double tempvec[3]= {0,0,0};
double sn2 = 0.0;
double nhat[3] = {0,0,0};
double* shape = bonus[ellipsoid[i]].shape;;
MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
for(int which = 0 ; which < 3; which ++){//me
nhat[which]=1;
nhat[(which+1)%3] = 0 ;
nhat[(which+2)%3] = 0 ;
sn2 = 0 ;
MathExtra::transpose_matvec(A,nhat,tempvec);
for(int k = 0; k<3; k++) tempvec[k] *= shape[k];
for(int k = 0; k<3 ; k++) sn2 += tempvec[k]*tempvec[k];
sn = sqrt(sn2);
tooclose[which] = sn;
}
n = region->surface(x[i][0],x[i][1],x[i][2],cutoff);
for (m = 0; m < n; m++) {
if (region->contact[m].delx != 0 && region->contact[m].r <= tooclose[0]){
onflag = 1;
continue;
} else if (region->contact[m].dely != 0 && region->contact[m].r <= tooclose[1]){
onflag = 1;
continue;
} else if (region->contact[m].delz !=0 && region->contact[m].r <= tooclose[2]){
onflag = 1;
continue;
} else rinv = 1.0/region->contact[m].r;
ees(m,i);
ewall[0] += eng;
fx = fwall * region->contact[m].delx * rinv;
fy = fwall * region->contact[m].dely * rinv;
fz = fwall * region->contact[m].delz * rinv;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
ewall[1] -= fx;
ewall[2] -= fy;
ewall[3] -= fz;
tor[i][0] += torque[0];
tor[i][1] += torque[1];
tor[i][2] += torque[2];
}
}
if (onflag) error->one(FLERR,"Particle on or inside surface of region "
"used in fix wall/region/ees");
}
/* ---------------------------------------------------------------------- */
void FixWallRegionEES::post_force_respa(int vflag, int ilevel, int iloop)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixWallRegionEES::min_post_force(int vflag)
{
post_force(vflag);
}
/* ----------------------------------------------------------------------
energy of wall interaction
------------------------------------------------------------------------- */
double FixWallRegionEES::compute_scalar()
{
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return ewall_all[0];
}
/* ----------------------------------------------------------------------
components of force on wall
------------------------------------------------------------------------- */
double FixWallRegionEES::compute_vector(int n)
{
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,4,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return ewall_all[n+1];
}
/* ----------------------------------------------------------------------
EES interaction for ellipsoid particle with wall
compute eng and fwall and twall = magnitude of wall force and torque
------------------------------------------------------------------------- */
void FixWallRegionEES::ees(int m, int i)
{
Region *region = domain->regions[iregion];
region->prematch();
double delta, delta2, delta3, delta4, delta5, delta6;
double sigman, sigman2 , sigman3, sigman4, sigman5, sigman6;
double hhss, hhss2, hhss4, hhss7, hhss8; //h^2 - s_n^2
double hps; //h+s_n
double hms; //h-s_n
double twall;
double A[3][3], nhat[3], SAn[3], that[3];
double tempvec[3]= {0,0,0};
double tempvec2[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}};
nhat[0] = region->contact[m].delx / region->contact[m].r;
nhat[1] = region->contact[m].dely / region->contact[m].r;
nhat[2] = region->contact[m].delz / region->contact[m].r;
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
int *ellipsoid = atom->ellipsoid;
double* shape = bonus[ellipsoid[i]].shape;;
MathExtra::quat_to_mat(bonus[ellipsoid[i]].quat,A);
sigman2 = 0.0;
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];
for(int k = 0; k<3; k++) SAn[k] = tempvec[k];
sigman = sqrt(sigman2);
delta = fabs(region->contact[m].r);
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 = -1*coeff4/hhss2 + coeff3
* (21*delta6 + 63*delta4*sigman2 + 27*delta2*sigman4 + sigman6) / hhss8;
eng = -1*coeff2 * (4*delta/sigman2/hhss + 2*log(hms/hps)/sigman3) +
coeff1 * (35*delta5 + 70*delta3*sigman2 + 15*delta*sigman4) / hhss7;
twall = coeff6 * (6*delta3/sigman4/hhss2 - 10*delta/sigman2/hhss2
+ 3*log(hms/hps)/sigman5)
+ coeff5 * (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++)
torque[j] = twall * that[j];
}

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