Homec4science
Diffusion lammps (master) Browse

lammps/src/FLD/pair_brownian_poly.cpp
597e68a377a1master

Last Change
Raw File

pair_brownian_poly.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: Amit Kumar and Michael Bybee (UIUC)
Dave Heine (Corning), polydispersity
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_brownian_poly.h"
#include "atom.h"
#include "atom_vec.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "domain.h"
#include "update.h"
#include "memory.h"
#include "random_mars.h"
#include "math_const.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
/* ---------------------------------------------------------------------- */
PairBrownianPoly::PairBrownianPoly(LAMMPS *lmp) : PairBrownian(lmp)
{
no_virial_fdotr_compute = 1;
}
/* ---------------------------------------------------------------------- */
void PairBrownianPoly::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz,tx,ty,tz;
double rsq,r,h_sep,beta0,beta1,radi,radj;
int *ilist,*jlist,*numneigh,**firstneigh;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **torque = atom->torque;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
double vxmu2f = force->vxmu2f;
int overlaps = 0;
double randr;
double prethermostat;
double xl[3],a_sq,a_sh,a_pu,Fbmag;
double p1[3],p2[3],p3[3];
// scale factor for Brownian moments
prethermostat = sqrt(24.0*force->boltz*t_target/update->dt);
prethermostat *= sqrt(force->vxmu2f/force->ftm2v/force->mvv2e);
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
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];
// FLD contribution to force and torque due to isotropic terms
if (flagfld) {
f[i][0] += prethermostat*sqrt(R0*radi)*(random->uniform()-0.5);
f[i][1] += prethermostat*sqrt(R0*radi)*(random->uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0*radi)*(random->uniform()-0.5);
if (flaglog) {
torque[i][0] += prethermostat*sqrt(RT0*pow(radi,3)) *
(random->uniform()-0.5);
torque[i][1] += prethermostat*sqrt(RT0*pow(radi,3)) *
(random->uniform()-0.5);
torque[i][2] += prethermostat*sqrt(RT0*pow(radi,3)) *
(random->uniform()-0.5);
}
}
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
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);
// scalar resistances a_sq and a_sh
h_sep = r - radi-radj;
// check for overlaps
if (h_sep < 0.0) overlaps++;
// if less than minimum gap, use minimum gap instead
if (r < cut_inner[itype][jtype])
h_sep = cut_inner[itype][jtype] - radi-radj;
// scale h_sep by radi
h_sep = h_sep/radi;
beta0 = radj/radi;
beta1 = 1.0 + beta0;
// scalar resistances
if (flaglog) {
a_sq = beta0*beta0/beta1/beta1/h_sep +
(1.0+7.0*beta0+beta0*beta0)/5.0/pow(beta1,3)*log(1.0/h_sep);
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3) +
pow(beta0,4))/21.0/pow(beta1,4)*h_sep*log(1.0/h_sep);
a_sq *= 6.0*MY_PI*mu*radi;
a_sh = 4.0*beta0*(2.0+beta0+2.0*beta0*beta0)/15.0/pow(beta1,3) *
log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3) +
16.0*pow(beta0,4))/375.0/pow(beta1,4) *
h_sep*log(1.0/h_sep);
a_sh *= 6.0*MY_PI*mu*radi;
a_pu = beta0*(4.0+beta0)/10.0/beta1/beta1*log(1.0/h_sep);
a_pu += (32.0-33.0*beta0+83.0*beta0*beta0+43.0 *
pow(beta0,3))/250.0/pow(beta1,3)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3);
} else a_sq = 6.0*MY_PI*mu*radi*(beta0*beta0/beta1/beta1/h_sep);
// generate the Pairwise Brownian Force: a_sq
Fbmag = prethermostat*sqrt(a_sq);
// generate a random number
randr = random->uniform()-0.5;
// contribution due to Brownian motion
fx = Fbmag*randr*delx/r;
fy = Fbmag*randr*dely/r;
fz = Fbmag*randr*delz/r;
// add terms due to a_sh
if (flaglog) {
// generate two orthogonal vectors to the line of centers
p1[0] = delx/r; p1[1] = dely/r; p1[2] = delz/r;
set_3_orthogonal_vectors(p1,p2,p3);
// magnitude
Fbmag = prethermostat*sqrt(a_sh);
// force in each of the two directions
randr = random->uniform()-0.5;
fx += Fbmag*randr*p2[0];
fy += Fbmag*randr*p2[1];
fz += Fbmag*randr*p2[2];
randr = random->uniform()-0.5;
fx += Fbmag*randr*p3[0];
fy += Fbmag*randr*p3[1];
fz += Fbmag*randr*p3[2];
}
// scale forces to appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
// sum to total Force
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
// torque due to the Brownian Force
if (flaglog) {
// location of the point of closest approach on I from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// torque = xl_cross_F
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
// torque is same on both particles
torque[i][0] -= tx;
torque[i][1] -= ty;
torque[i][2] -= tz;
// torque due to a_pu
Fbmag = prethermostat*sqrt(a_pu);
// force in each direction
randr = random->uniform()-0.5;
tx = Fbmag*randr*p2[0];
ty = Fbmag*randr*p2[1];
tz = Fbmag*randr*p2[2];
randr = random->uniform()-0.5;
tx += Fbmag*randr*p3[0];
ty += Fbmag*randr*p3[1];
tz += Fbmag*randr*p3[2];
// torque has opposite sign on two particles
torque[i][0] -= tx;
torque[i][1] -= ty;
torque[i][2] -= tz;
}
// set j = nlocal so that only I gets tallied
if (evflag) ev_tally_xyz(i,nlocal,nlocal,0,
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBrownianPoly::init_style()
{
if (force->newton_pair == 1)
error->all(FLERR,"Pair brownian/poly requires newton pair off");
if (!atom->sphere_flag)
error->all(FLERR,"Pair brownian/poly requires atom style sphere");
// insure all particles are finite-size
// for pair hybrid, should limit test to types using the pair style
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (radius[i] == 0.0)
error->one(FLERR,"Pair brownian/poly requires extended particles");
int irequest = neighbor->request(this);
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
// set the isotropic constants that depend on the volume fraction
// vol_T = total volume
double vol_T = domain->xprd*domain->yprd*domain->zprd;
// vol_P = volume of particles, assuming mono-dispersity
// vol_f = volume fraction
double volP = 0.0;
for (int i = 0; i < nlocal; i++)
volP += (4.0/3.0)*MY_PI*pow(atom->radius[i],3);
double vol_P;
MPI_Allreduce(&volP,&vol_P,1,MPI_DOUBLE,MPI_SUM,world);
double vol_f = vol_P/vol_T;
// set isotropic constants
if (flaglog == 0) {
R0 = 6*MY_PI*mu*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu;
} else {
R0 = 6*MY_PI*mu*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBrownianPoly::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
cut_inner[i][j] = mix_distance(cut_inner[i][i],cut_inner[j][j]);
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
}
cut_inner[j][i] = cut_inner[i][j];
return cut[i][j];
}
c4science · Help