Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/src/USER-LB/fix_lb_pc.cpp
323e3075c413lammm-master-deprecated

Last Change
Raw File

fix_lb_pc.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: Frances Mackay, Santtu Ollila, Colin Denniston (UWO)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "string.h"
#include "fix_lb_pc.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "respa.h"
#include "error.h"
#include "memory.h"
#include "comm.h"
#include "domain.h"
#include "fix_lb_fluid.h"
#include "modify.h"
#include "mpi.h"
#include "group.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
FixLbPC::FixLbPC(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 3)
error->all(FLERR,"Illegal fix lb/pc command");
time_integrate = 1;
// perform initial allocation of atom-based array
// register with Atom class
force_old = NULL;
up = NULL;
up_old = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
Gamma_MD = new double[atom->ntypes+1];
int groupbit_lb_fluid = 0;
for(int ifix=0; ifix<modify->nfix; ifix++)
if(strcmp(modify->fix[ifix]->style,"lb/fluid")==0){
fix_lb_fluid = (FixLbFluid *)modify->fix[ifix];
groupbit_lb_fluid = group->bitmask[modify->fix[ifix]->igroup];
}
if(groupbit_lb_fluid == 0)
error->all(FLERR,"the lb/fluid fix must also be used if using the lb/pc fix");
int *mask = atom->mask;
int nlocal = atom->nlocal;
for(int j=0; j<nlocal; j++){
if((mask[j] & groupbit) && !(mask[j] & groupbit_lb_fluid))
error->one(FLERR,"can only use the lb/pc fix for an atom if also using the lb/fluid fix for that atom");
}
}
/* ---------------------------------------------------------------------- */
FixLbPC::~FixLbPC() {
atom->delete_callback(id,0);
memory->destroy(force_old);
memory->destroy(up);
memory->destroy(up_old);
delete [] Gamma_MD;
}
/* ---------------------------------------------------------------------- */
int FixLbPC::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixLbPC::init()
{
double *Gamma = fix_lb_fluid->Gamma;
double dm_lb = fix_lb_fluid->dm_lb;
double dt_lb = fix_lb_fluid->dt_lb;
MPI_Comm_rank(world,&me);
dtv = update->dt;
dtf = update->dt * force->ftm2v;
for(int i=0; i<=atom->ntypes; i++)
Gamma_MD[i] = Gamma[i]*dm_lb/dt_lb;
}
/* ---------------------------------------------------------------------- */
void FixLbPC::initial_integrate(int vflag) {
double dtfm;
double **x = atom->x;
double dx[3];
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
compute_up();
for(int i=0; i<nlocal; i++){
up_old[i][0] = up[i][0];
up_old[i][1] = up[i][1];
up_old[i][2] = up[i][2];
force_old[i][0] = f[i][0];
force_old[i][1] = f[i][1];
force_old[i][2] = f[i][2];
}
if(rmass){
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/rmass[i];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/rmass[i]);
dx[0] = dtv*v[i][0] + 0.5*(f[i][0]*force->ftm2v - Gamma_MD[type[i]]*(v[i][0]-up[i][0]))*dtv*dtv/rmass[i];
dx[1] = dtv*v[i][1] + 0.5*(f[i][1]*force->ftm2v - Gamma_MD[type[i]]*(v[i][1]-up[i][1]))*dtv*dtv/rmass[i];
dx[2] = dtv*v[i][2] + 0.5*(f[i][2]*force->ftm2v - Gamma_MD[type[i]]*(v[i][2]-up[i][2]))*dtv*dtv/rmass[i];
x[i][0] += dx[0];
x[i][1] += dx[1];
x[i][2] += dx[2];
// Approximation for v
if(Gamma_MD[type[i]] == 0.0){
v[i][0] += f[i][0]*dtfm;
v[i][1] += f[i][1]*dtfm;
v[i][2] += f[i][2]*dtfm;
}else{
v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][0]*force->ftm2v/Gamma_MD[type[i]] + up[i][0];
v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][1]*force->ftm2v/Gamma_MD[type[i]] + up[i][1];
v[i][2] = (v[i][2]-up[i][2]-f[i][2]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
}
}
}
} else {
// this does NOT take varying masses into account
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/mass[type[i]];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/mass[type[i]]);
dx[0] = dtv*v[i][0] + 0.5*(f[i][0]*force->ftm2v - Gamma_MD[type[i]]*(v[i][0]-up[i][0]))*dtv*dtv/mass[type[i]];
dx[1] = dtv*v[i][1] + 0.5*(f[i][1]*force->ftm2v - Gamma_MD[type[i]]*(v[i][1]-up[i][1]))*dtv*dtv/mass[type[i]];
dx[2] = dtv*v[i][2] + 0.5*(f[i][2]*force->ftm2v - Gamma_MD[type[i]]*(v[i][2]-up[i][2]))*dtv*dtv/mass[type[i]];
x[i][0] += dx[0];
x[i][1] += dx[1];
x[i][2] += dx[2];
// Approximation for v
if(Gamma_MD[type[i]] == 0.0){
v[i][0] += f[i][0]*dtfm;
v[i][1] += f[i][1]*dtfm;
v[i][2] += f[i][2]*dtfm;
}else{
v[i][0] = (v[i][0]-up[i][0]-f[i][0]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][0]*force->ftm2v/Gamma_MD[type[i]] + up[i][0];
v[i][1] = (v[i][1]-up[i][1]-f[i][1]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][1]*force->ftm2v/Gamma_MD[type[i]] + up[i][1];
v[i][2] = (v[i][2]-up[i][2]-f[i][2]*force->ftm2v/Gamma_MD[type[i]])*expminusdttimesgamma +
f[i][2]*force->ftm2v/Gamma_MD[type[i]] + up[i][2];
}
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixLbPC::final_integrate()
{
double dtfm;
double **v = atom->v;
double **f = atom->f;
double *mass = atom->mass;
double *rmass = atom->rmass;
int *type = atom->type;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
compute_up();
if(rmass){
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/rmass[i];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/rmass[i]);
DMDcoeff = (dtv - rmass[i]*(1.0-expminusdttimesgamma)/Gamma_MD[type[i]]);
if(Gamma_MD[type[i]] == 0.0){
v[i][0] += 0.5*(f[i][0] - force_old[i][0])*dtfm;
v[i][1] += 0.5*(f[i][1] - force_old[i][1])*dtfm;
v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm;
}else{
v[i][0] += DMDcoeff*((f[i][0] - force_old[i][0])*force->ftm2v/Gamma_MD[type[i]] + up[i][0] - up_old[i][0])/dtv;
v[i][1] += DMDcoeff*((f[i][1] - force_old[i][1])*force->ftm2v/Gamma_MD[type[i]] + up[i][1] - up_old[i][1])/dtv;
v[i][2] += DMDcoeff*((f[i][2] - force_old[i][2])*force->ftm2v/Gamma_MD[type[i]] + up[i][2] - up_old[i][2])/dtv;
}
}
}
} else {
// this does NOT take varying masses into account
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) {
dtfm = dtf/mass[type[i]];
expminusdttimesgamma = exp(-dtv*Gamma_MD[type[i]]/mass[type[i]]);
DMDcoeff = (dtv - mass[type[i]]*(1.0-expminusdttimesgamma)/Gamma_MD[type[i]]);
if(Gamma_MD[type[i]] == 0.0){
v[i][0] += 0.5*(f[i][0] - force_old[i][0])*dtfm;
v[i][1] += 0.5*(f[i][1] - force_old[i][1])*dtfm;
v[i][2] += 0.5*(f[i][2] - force_old[i][2])*dtfm;
}else{
v[i][0] += DMDcoeff*((f[i][0] - force_old[i][0])*force->ftm2v/Gamma_MD[type[i]] + up[i][0] - up_old[i][0])/dtv;
v[i][1] += DMDcoeff*((f[i][1] - force_old[i][1])*force->ftm2v/Gamma_MD[type[i]] + up[i][1] - up_old[i][1])/dtv;
v[i][2] += DMDcoeff*((f[i][2] - force_old[i][2])*force->ftm2v/Gamma_MD[type[i]] + up[i][2] - up_old[i][2])/dtv;
}
}
}
}
}
/* ----------------------------------------------------------------------
allocate atom-based array
------------------------------------------------------------------------- */
void FixLbPC::grow_arrays(int nmax)
{
memory->grow(force_old,nmax,3,"FixLbPC:force_old");
memory->grow(up_old,nmax,3,"FixLbPC:up_old");
memory->grow(up,nmax,3,"FixLbPC:up");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixLbPC::copy_arrays(int i, int j, int delflag)
{
force_old[j][0] = force_old[i][0];
force_old[j][1] = force_old[i][1];
force_old[j][2] = force_old[i][2];
up_old[j][0] = up_old[i][0];
up_old[j][1] = up_old[i][1];
up_old[j][2] = up_old[i][2];
up[j][0] = up[i][0];
up[j][1] = up[i][1];
up[j][2] = up[i][2];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixLbPC::pack_exchange(int i, double *buf)
{
buf[0] = force_old[i][0];
buf[1] = force_old[i][1];
buf[2] = force_old[i][2];
buf[3] = up_old[i][0];
buf[4] = up_old[i][1];
buf[5] = up_old[i][2];
buf[6] = up[i][0];
buf[7] = up[i][1];
buf[8] = up[i][2];
return 9;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixLbPC::unpack_exchange(int nlocal, double *buf)
{
force_old[nlocal][0] = buf[0];
force_old[nlocal][1] = buf[1];
force_old[nlocal][2] = buf[2];
up_old[nlocal][0] = buf[3];
up_old[nlocal][1] = buf[4];
up_old[nlocal][2] = buf[5];
up[nlocal][0] = buf[6];
up[nlocal][1] = buf[7];
up[nlocal][2] = buf[8];
return 9;
}
/* ---------------------------------------------------------------------- */
void FixLbPC::compute_up(void)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
double **x = atom->x;
int i,k;
int ix,iy,iz;
int ixp,iyp,izp;
double dx1,dy1,dz1;
int isten,ii,jj,kk;
double r,rsq,weightx,weighty,weightz;
double ****u_lb = fix_lb_fluid->u_lb;
int subNbx = fix_lb_fluid->subNbx;
int subNby = fix_lb_fluid->subNby;
int subNbz = fix_lb_fluid->subNbz;
double dx_lb = fix_lb_fluid->dx_lb;
double dt_lb = fix_lb_fluid->dt_lb;
double FfP[64];
int trilinear_stencil = fix_lb_fluid->trilinear_stencil;
for(i=0; i<nlocal; i++){
if(mask[i] & groupbit){
//Calculate nearest leftmost grid point.
//Since array indices from 1 to subNb-2 correspond to the
// local subprocessor domain (not indices from 0), use the
// ceiling value.
ix = (int)ceil((x[i][0]-domain->sublo[0])/dx_lb);
iy = (int)ceil((x[i][1]-domain->sublo[1])/dx_lb);
iz = (int)ceil((x[i][2]-domain->sublo[2])/dx_lb);
//Calculate distances to the nearest points.
dx1 = x[i][0] - (domain->sublo[0] + (ix-1)*dx_lb);
dy1 = x[i][1] - (domain->sublo[1] + (iy-1)*dx_lb);
dz1 = x[i][2] - (domain->sublo[2] + (iz-1)*dx_lb);
// Need to convert these to lattice units:
dx1 = dx1/dx_lb;
dy1 = dy1/dx_lb;
dz1 = dz1/dx_lb;
up[i][0]=0.0; up[i][1]=0.0; up[i][2]=0.0;
if(trilinear_stencil==0){
isten=0;
for(ii=-1; ii<3; ii++){
rsq=(-dx1+ii)*(-dx1+ii);
if(rsq>=4)
weightx=0.0;
else{
r=sqrt(rsq);
if(rsq>1){
weightx=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
} else{
weightx=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
}
}
for(jj=-1; jj<3; jj++){
rsq=(-dy1+jj)*(-dy1+jj);
if(rsq>=4)
weighty=0.0;
else{
r=sqrt(rsq);
if(rsq>1){
weighty=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
} else{
weighty=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
}
}
for(kk=-1; kk<3; kk++){
rsq=(-dz1+kk)*(-dz1+kk);
if(rsq>=4)
weightz=0.0;
else{
r=sqrt(rsq);
if(rsq>1){
weightz=(5.0-2.0*r-sqrt(-7.0+12.0*r-4.0*rsq))/8.;
} else{
weightz=(3.0-2.0*r+sqrt(1.0+4.0*r-4.0*rsq))/8.;
}
}
ixp = ix+ii;
iyp = iy+jj;
izp = iz+kk;
if(ixp==-1) ixp=subNbx+2;
if(iyp==-1) iyp=subNby+2;
if(izp==-1) izp=subNbz+2;
FfP[isten] = weightx*weighty*weightz;
// interpolated velocity based on delta function.
for(k=0; k<3; k++){
up[i][k] += u_lb[ixp][iyp][izp][k]*FfP[isten];
}
}
}
}
}else{
FfP[0] = (1.-dx1)*(1.-dy1)*(1.-dz1);
FfP[1] = (1.-dx1)*(1.-dy1)*dz1;
FfP[2] = (1.-dx1)*dy1*(1.-dz1);
FfP[3] = (1.-dx1)*dy1*dz1;
FfP[4] = dx1*(1.-dy1)*(1.-dz1);
FfP[5] = dx1*(1.-dy1)*dz1;
FfP[6] = dx1*dy1*(1.-dz1);
FfP[7] = dx1*dy1*dz1;
ixp = (ix+1);
iyp = (iy+1);
izp = (iz+1);
for (k=0; k<3; k++) { // tri-linearly interpolated velocity at node
up[i][k] = u_lb[ix][iy][iz][k]*FfP[0]
+ u_lb[ix][iy][izp][k]*FfP[1]
+ u_lb[ix][iyp][iz][k]*FfP[2]
+ u_lb[ix][iyp][izp][k]*FfP[3]
+ u_lb[ixp][iy][iz][k]*FfP[4]
+ u_lb[ixp][iy][izp][k]*FfP[5]
+ u_lb[ixp][iyp][iz][k]*FfP[6]
+ u_lb[ixp][iyp][izp][k]*FfP[7];
}
}
for(k=0; k<3; k++)
up[i][k] = up[i][k]*dx_lb/dt_lb;
}
}
}
c4science · Help