Homec4science
Diffusion lammps (lammm-master) Browse

lammps/src/COLLOID/pair_brownian.cpp
f5a9a0b3a196lammm-master

Last Change
Raw File

pair_brownian.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)
------------------------------------------------------------------------- */
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_brownian.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 "modify.h"
#include "fix.h"
#include "fix_deform.h"
#include "fix_wall.h"
#include "input.h"
#include "variable.h"
#include "random_mars.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
using namespace MathSpecial;
// same as fix_wall.cpp
enum{EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
PairBrownian::PairBrownian(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
random = NULL;
}
/* ---------------------------------------------------------------------- */
PairBrownian::~PairBrownian()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(cut_inner);
}
delete random;
}
/* ---------------------------------------------------------------------- */
void PairBrownian::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,radi;
int *ilist,*jlist,*numneigh,**firstneigh;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double **torque = atom->torque;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
double vxmu2f = force->vxmu2f;
double randr;
double prethermostat;
double xl[3],a_sq,a_sh,a_pu,Fbmag;
double p1[3],p2[3],p3[3];
int overlaps = 0;
// This section of code adjusts R0/RT0/RS0 if necessary due to changes
// in the volume fraction as a result of fix deform or moving walls
double dims[3], wallcoord;
if (flagVF) // Flag for volume fraction corrections
if (flagdeform || flagwall == 2){ // Possible changes in volume fraction
if (flagdeform && !flagwall)
for (j = 0; j < 3; j++)
dims[j] = domain->prd[j];
else if (flagwall == 2 || (flagdeform && flagwall == 1)){
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
for (int j = 0; j < 3; j++)
dims[j] = wallhi[j] - walllo[j];
}
double vol_T = dims[0]*dims[1]*dims[2];
double vol_f = vol_P/vol_T;
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*cube(rad);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.33*vol_f + 2.80*vol_f*vol_f);
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*cube(rad)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
//RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// 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)*(random->uniform()-0.5);
f[i][1] += prethermostat*sqrt(R0)*(random->uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0)*(random->uniform()-0.5);
if (flaglog) {
torque[i][0] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
torque[i][1] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
torque[i][2] += prethermostat*sqrt(RT0)*(random->uniform()-0.5);
}
}
if (!flagHI) continue;
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];
if (rsq < cutsq[itype][jtype]) {
r = sqrt(rsq);
// scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
// 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] - 2.0*radi;
// scale h_sep by radi
h_sep = h_sep/radi;
// scalar resistances
if (flaglog) {
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1.0/h_sep));
a_sh = 6.0*MY_PI*mu*radi*(1.0/6.0*log(1.0/h_sep));
a_pu = 8.0*MY_PI*mu*cube(radi)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/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;
if (newton_pair || j < nlocal) {
//randr = random->uniform()-0.5;
//fx = Fbmag*randr*delx/r;
//fy = Fbmag*randr*dely/r;
//fz = Fbmag*randr*delz/r;
f[j][0] += fx;
f[j][1] += fy;
f[j][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;
if (newton_pair || j < nlocal) {
torque[j][0] -= tx;
torque[j][1] -= ty;
torque[j][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;
if (newton_pair || j < nlocal) {
torque[j][0] += tx;
torque[j][1] += ty;
torque[j][2] += tz;
}
}
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
int print_overlaps = 0;
if (print_overlaps && overlaps)
printf("Number of overlaps=%d\n",overlaps);
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairBrownian::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(cut_inner,n+1,n+1,"pair:cut_inner");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairBrownian::settings(int narg, char **arg)
{
if (narg != 7 && narg != 9) error->all(FLERR,"Illegal pair_style command");
mu = force->numeric(FLERR,arg[0]);
flaglog = force->inumeric(FLERR,arg[1]);
flagfld = force->inumeric(FLERR,arg[2]);
cut_inner_global = force->numeric(FLERR,arg[3]);
cut_global = force->numeric(FLERR,arg[4]);
t_target = force->numeric(FLERR,arg[5]);
seed = force->inumeric(FLERR,arg[6]);
flagHI = flagVF = 1;
if (narg == 9) {
flagHI = force->inumeric(FLERR,arg[7]);
flagVF = force->inumeric(FLERR,arg[8]);
}
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "
"setting flagHI to 1");
flagHI = 1;
}
// initialize Marsaglia RNG with processor-unique seed
delete random;
random = new RanMars(lmp,seed + comm->me);
// reset cutoffs that have been explicitly set
if (allocated) {
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
cut_inner[i][j] = cut_inner_global;
cut[i][j] = cut_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairBrownian::coeff(int narg, char **arg)
{
if (narg != 2 && narg != 4)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double cut_inner_one = cut_inner_global;
double cut_one = cut_global;
if (narg == 4) {
cut_inner_one = force->numeric(FLERR,arg[2]);
cut_one = force->numeric(FLERR,arg[3]);
}
int count = 0;
for (int i = ilo; i <= ihi; i++)
for (int j = MAX(jlo,i); j <= jhi; j++) {
cut_inner[i][j] = cut_inner_one;
cut[i][j] = cut_one;
setflag[i][j] = 1;
count++;
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairBrownian::init_style()
{
if (!atom->sphere_flag)
error->all(FLERR,"Pair brownian requires atom style sphere");
// if newton off, forces between atoms ij will be double computed
// using different random numbers
if (force->newton_pair == 0 && comm->me == 0)
error->warning(FLERR,
"Pair brownian needs newton pair on for "
"momentum conservation");
neighbor->request(this,instance_me);
// insure all particles are finite-size
// for pair hybrid, should limit test to types using the pair style
double *radius = atom->radius;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (radius[i] == 0.0)
error->one(FLERR,"Pair brownian requires extended particles");
// require monodisperse system with same radii for all types
double radtype;
for (int i = 1; i <= atom->ntypes; i++) {
if (!atom->radius_consistency(i,radtype))
error->all(FLERR,"Pair brownian requires monodisperse particles");
if (i > 1 && radtype != rad)
error->all(FLERR,"Pair brownian requires monodisperse particles");
rad = radtype;
}
// set the isotropic constants that depend on the volume fraction
// vol_T = total volume
// check for fix deform, if exists it must use "remap v"
// If box will change volume, set appropriate flag so that volume
// and v.f. corrections are re-calculated at every step.
//
// If available volume is different from box volume
// due to walls, set volume appropriately; if walls will
// move, set appropriate flag so that volume and v.f. corrections
// are re-calculated at every step.
flagdeform = flagwall = 0;
for (int i = 0; i < modify->nfix; i++){
if (strcmp(modify->fix[i]->style,"deform") == 0)
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL) {
if (flagwall)
error->all(FLERR,
"Cannot use multiple fix wall commands with pair brownian");
flagwall = 1; // Walls exist
wallfix = (FixWall *) modify->fix[i];
if (wallfix->xflag) flagwall = 2; // Moving walls exist
}
}
// set the isotropic constants depending on the volume fraction
// vol_T = total volumeshearing = flagdeform = flagwall = 0;
double vol_T, wallcoord;
if (!flagwall) vol_T = domain->xprd*domain->yprd*domain->zprd;
else {
double wallhi[3], walllo[3];
for (int j = 0; j < 3; j++){
wallhi[j] = domain->prd[j];
walllo[j] = 0;
}
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->xstyle[m] == VARIABLE){
wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]);
// Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
else wallhi[dim] = wallcoord;
}
vol_T = (wallhi[0] - walllo[0]) * (wallhi[1] - walllo[1]) *
(wallhi[2] - walllo[2]);
}
// vol_P = volume of particles, assuming mono-dispersity
// vol_f = volume fraction
vol_P = atom->natoms*(4.0/3.0)*MY_PI*cube(rad);
double vol_f = vol_P/vol_T;
// set isotropic constants
if (!flagVF) vol_f = 0;
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*cube(rad); // not actually needed
} else {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.725*vol_f - 6.583*vol_f*vol_f);
RT0 = 8*MY_PI*mu*cube(rad)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairBrownian::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];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBrownian::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&cut_inner[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBrownian::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&cut_inner[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&cut_inner[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairBrownian::write_restart_settings(FILE *fp)
{
fwrite(&mu,sizeof(double),1,fp);
fwrite(&flaglog,sizeof(int),1,fp);
fwrite(&flagfld,sizeof(int),1,fp);
fwrite(&cut_inner_global,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&t_target,sizeof(double),1,fp);
fwrite(&seed,sizeof(int),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&flagHI,sizeof(int),1,fp);
fwrite(&flagVF,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairBrownian::read_restart_settings(FILE *fp)
{
int me = comm->me;
if (me == 0) {
fread(&mu,sizeof(double),1,fp);
fread(&flaglog,sizeof(int),1,fp);
fread(&flagfld,sizeof(int),1,fp);
fread(&cut_inner_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&t_target, sizeof(double),1,fp);
fread(&seed, sizeof(int),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&flagHI,sizeof(int),1,fp);
fread(&flagVF,sizeof(int),1,fp);
}
MPI_Bcast(&mu,1,MPI_DOUBLE,0,world);
MPI_Bcast(&flaglog,1,MPI_INT,0,world);
MPI_Bcast(&flagfld,1,MPI_INT,0,world);
MPI_Bcast(&cut_inner_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&t_target,1,MPI_DOUBLE,0,world);
MPI_Bcast(&seed,1,MPI_INT,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&flagHI,1,MPI_INT,0,world);
MPI_Bcast(&flagVF,1,MPI_INT,0,world);
// additional setup based on restart parameters
delete random;
random = new RanMars(lmp,seed + comm->me);
}
/* ----------------------------------------------------------------------*/
void PairBrownian::set_3_orthogonal_vectors(double p1[3],
double p2[3], double p3[3])
{
double norm;
int ix,iy,iz;
// find the index of maximum magnitude and store it in iz
if (fabs(p1[0]) > fabs(p1[1])) {
iz=0;
ix=1;
iy=2;
} else {
iz=1;
ix=2;
iy=0;
}
if (iz==0) {
if (fabs(p1[0]) < fabs(p1[2])) {
iz = 2;
ix = 0;
iy = 1;
}
} else {
if (fabs(p1[1]) < fabs(p1[2])) {
iz = 2;
ix = 0;
iy = 1;
}
}
// set p2 arbitrarily such that it's orthogonal to p1
p2[ix]=1.0;
p2[iy]=1.0;
p2[iz] = -(p1[ix]*p2[ix] + p1[iy]*p2[iy])/p1[iz];
// normalize p2
norm = sqrt(p2[0]*p2[0] + p2[1]*p2[1] + p2[2]*p2[2]);
p2[0] = p2[0]/norm;
p2[1] = p2[1]/norm;
p2[2] = p2[2]/norm;
// Set p3 by taking the cross product p3=p2xp1
p3[0] = p1[1]*p2[2] - p1[2]*p2[1];
p3[1] = p1[2]*p2[0] - p1[0]*p2[2];
p3[2] = p1[0]*p2[1] - p1[1]*p2[0];
}
c4science · Help