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lammps/src/COLLOID/pair_lubricateU.cpp
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pair_lubricateU.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 authors: Amit Kumar and Michael Bybee (UIUC)
------------------------------------------------------------------------- */
#include <mpi.h>
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "pair_lubricateU.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 "math_const.h"
#include "modify.h"
#include "fix.h"
#include "fix_deform.h"
#include "fix_wall.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define TOL 1E-4 // tolerance for conjugate gradient
// same as fix_wall.cpp
enum{EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
PairLubricateU::PairLubricateU(LAMMPS *lmp) : Pair(lmp)
{
single_enable = 0;
// pair lubricateU cannot compute virial as F dot r
// due to how drag forces are applied to atoms
// correct method is how per-atom virial does it
no_virial_fdotr_compute = 1;
nmax = 0;
fl = Tl = xl = NULL;
cgmax = 0;
bcg = xcg = rcg = rcg1 = pcg = RU = NULL;
// set comm size needed by this Pair
comm_forward = 6;
}
/* ---------------------------------------------------------------------- */
PairLubricateU::~PairLubricateU()
{
memory->destroy(fl);
memory->destroy(Tl);
memory->destroy(xl);
memory->destroy(bcg);
memory->destroy(xcg);
memory->destroy(rcg);
memory->destroy(rcg1);
memory->destroy(pcg);
memory->destroy(RU);
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(cut);
memory->destroy(cut_inner);
}
}
/* ----------------------------------------------------------------------
It first has to solve for the velocity of the particles such that
the net force on the particles is zero. NOTE: it has to be the last
type of pair interaction specified in the input file. Also, it
assumes that no other types of interactions, like k-space, is
present. As already mentioned, the net force on the particles after
this pair interaction would be identically zero.
---------------------------------------------------------------------- */
void PairLubricateU::compute(int eflag, int vflag)
{
int i,j;
double **x = atom->x;
double **f = atom->f;
double **torque = atom->torque;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int nall = nlocal + nghost;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
// skip compute() if called from integrate::setup()
// this is b/c do not want compute() to update velocities twice on a restart
// when restarting, call compute on step N (last step of prev run),
// again on step N (setup of restart run),
// then on step N+1 (first step of restart)
// so this is one extra time which leads to bad dynamics
if (update->setupflag) return;
// grow per-atom arrays if necessary
// need to be atom->nmax in length
if (atom->nmax > nmax) {
memory->destroy(fl);
memory->destroy(Tl);
memory->destroy(xl);
nmax = atom->nmax;
memory->create(fl,nmax,3,"pair:fl");
memory->create(Tl,nmax,3,"pair:Tl");
memory->create(xl,nmax,3,"pair:xl");
}
// Added to implement midpoint integration scheme
// Save force, torque found so far. Also save the positions
for (i=0;i<nlocal+nghost;i++) {
for (j=0;j<3;j++) {
fl[i][j] = f[i][j];
Tl[i][j] = torque[i][j];
xl[i][j] = x[i][j];
}
}
// Stage one of Midpoint method
// Solve for velocities based on intial positions
stage_one();
// find positions at half the timestep and store in xl
intermediates(nall,xl);
// store back the saved forces and torques in original arrays
for(i=0;i<nlocal+nghost;i++) {
for(j=0;j<3;j++) {
f[i][j] = fl[i][j];
torque[i][j] = Tl[i][j];
}
}
// stage two: this will give the final velocities
stage_two(xl);
}
/* ------------------------------------------------------------------------
Stage one of midpoint method
------------------------------------------------------------------------- */
void PairLubricateU::stage_one()
{
int i,j,ii,inum;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
int newton_pair = force->newton_pair;
int *ilist;
inum = list->inum;
ilist = list->ilist;
if (6*inum > cgmax) {
memory->destroy(bcg);
memory->destroy(xcg);
memory->destroy(rcg);
memory->destroy(rcg1);
memory->destroy(pcg);
memory->destroy(RU);
cgmax = 6*inum;
memory->create(bcg,cgmax,"pair:bcg");
memory->create(xcg,cgmax,"pair:bcg");
memory->create(rcg,cgmax,"pair:bcg");
memory->create(rcg1,cgmax,"pair:bcg");
memory->create(pcg,cgmax,"pair:bcg");
memory->create(RU,cgmax,"pair:bcg");
}
double alpha,beta;
double normi,error,normig;
double send[2],recv[2],rcg_dot_rcg;
// First compute R_FE*E
compute_RE();
// Reverse communication of forces and torques to
// accumulate the net force on each of the particles
if (newton_pair) comm->reverse_comm();
// CONJUGATE GRADIENT
// Find the right hand side= -ve of all forces/torques
// b = 6*Npart in overall size
for(ii = 0; ii < inum; ii++) {
i = ilist[ii];
for (j = 0; j < 3; j++) {
bcg[6*ii+j] = -f[i][j];
bcg[6*ii+j+3] = -torque[i][j];
}
}
// Start solving the equation : F^H = -F^P -F^B - F^H_{Ef}
// Store initial guess for velocity and angular-velocities/angular momentum
// NOTE velocities and angular velocities are assumed relative to the fluid
for (ii=0;ii<inum;ii++)
for (j=0;j<3;j++) {
xcg[6*ii+j] = 0.0;
xcg[6*ii+j+3] = 0.0;
}
// Copy initial guess to the global arrays to be acted upon by R_{FU}
// and returned by f and torque arrays
copy_vec_uo(inum,xcg,v,omega);
// set velocities for ghost particles
comm->forward_comm_pair(this);
// Find initial residual
compute_RU();
// reverse communication of forces and torques
if (newton_pair) comm->reverse_comm();
copy_uo_vec(inum,f,torque,RU);
for (i=0;i<6*inum;i++)
rcg[i] = bcg[i] - RU[i];
// Set initial conjugate direction
for (i=0;i<6*inum;i++)
pcg[i] = rcg[i];
// Find initial norm of the residual or norm of the RHS (either is fine)
normi = dot_vec_vec(6*inum,bcg,bcg);
MPI_Allreduce(&normi,&normig,1,MPI_DOUBLE,MPI_SUM,world);
// Loop until convergence
do {
// find R*p
copy_vec_uo(inum,pcg,v,omega);
// set velocities for ghost particles
comm->forward_comm_pair(this);
compute_RU();
// reverse communication of forces and torques
if (newton_pair) comm->reverse_comm();
copy_uo_vec(inum,f,torque,RU);
// Find alpha
send[0] = dot_vec_vec(6*inum,rcg,rcg);
send[1] = dot_vec_vec(6*inum,RU,pcg);
MPI_Allreduce(send,recv,2,MPI_DOUBLE,MPI_SUM,world);
alpha = recv[0]/recv[1];
rcg_dot_rcg = recv[0];
// Find new x
for (i=0;i<6*inum;i++)
xcg[i] = xcg[i] + alpha*pcg[i];
// find new residual
for (i=0;i<6*inum;i++)
rcg1[i] = rcg[i] - alpha*RU[i];
// find beta
send[0] = dot_vec_vec(6*inum,rcg1,rcg1);
MPI_Allreduce(send,recv,1,MPI_DOUBLE,MPI_SUM,world);
beta = recv[0]/rcg_dot_rcg;
// Find new conjugate direction
for (i=0;i<6*inum;i++)
pcg[i] = rcg1[i] + beta*pcg[i];
for (i=0;i<6*inum;i++)
rcg[i] = rcg1[i];
// Find relative error
error = sqrt(recv[0]/normig);
} while (error > TOL);
// update the final converged velocities in respective arrays
copy_vec_uo(inum,xcg,v,omega);
// set velocities for ghost particles
comm->forward_comm_pair(this);
// Find actual particle's velocities from relative velocities
// Only non-zero component of fluid's vel : vx=gdot*y and wz=-gdot/2
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
v[i][0] = v[i][0] + gdot*x[i][1];
omega[i][2] = omega[i][2] - gdot/2.0;
}
}
/*---------------------------------------------------------------
Finds the position of the particles at half the time step
----------------------------------------------------------------*/
void PairLubricateU::intermediates(int nall, double **xl)
{
int i;
double **x = atom->x;
double **v = atom->v;
double dtv = update->dt;
for (i=0;i<nall;i++) {
xl[i][0] = x[i][0] + 0.5*dtv*v[i][0];
xl[i][1] = x[i][1] + 0.5*dtv*v[i][1];
xl[i][2] = x[i][2] + 0.5*dtv*v[i][2];
}
}
/* ------------------------------------------------------------------------
Stage one of midpoint method
------------------------------------------------------------------------- */
void PairLubricateU::stage_two(double **x)
{
int i,j,ii,inum;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
int newton_pair = force->newton_pair;
int *ilist;
inum = list->inum;
ilist = list->ilist;
double alpha,beta;
double normi,error,normig;
double send[2],recv[2],rcg_dot_rcg;
// First compute R_FE*E
compute_RE(x);
// Reverse communication of forces and torques to
// accumulate the net force on each of the particles
if (newton_pair) comm->reverse_comm();
// CONJUGATE GRADIENT
// Find the right hand side= -ve of all forces/torques
// b = 6*Npart in overall size
for(ii = 0; ii < inum; ii++) {
i = ilist[ii];
for (j = 0; j < 3; j++) {
bcg[6*ii+j] = -f[i][j];
bcg[6*ii+j+3] = -torque[i][j];
}
}
// Start solving the equation : F^H = -F^P -F^B - F^H_{Ef}
// Store initial guess for velocity and angular-velocities/angular momentum
// NOTE velocities and angular velocities are assumed relative to the fluid
for (ii=0;ii<inum;ii++)
for (j=0;j<3;j++) {
xcg[6*ii+j] = 0.0;
xcg[6*ii+j+3] = 0.0;
}
// Copy initial guess to the global arrays to be acted upon by R_{FU}
// and returned by f and torque arrays
copy_vec_uo(inum,xcg,v,omega);
// set velocities for ghost particles
comm->forward_comm_pair(this);
// Find initial residual
compute_RU(x);
// reverse communication of forces and torques
if (newton_pair) comm->reverse_comm();
copy_uo_vec(inum,f,torque,RU);
for (i=0;i<6*inum;i++)
rcg[i] = bcg[i] - RU[i];
// Set initial conjugate direction
for (i=0;i<6*inum;i++)
pcg[i] = rcg[i];
// Find initial norm of the residual or norm of the RHS (either is fine)
normi = dot_vec_vec(6*inum,bcg,bcg);
MPI_Allreduce(&normi,&normig,1,MPI_DOUBLE,MPI_SUM,world);
// Loop until convergence
do {
// find R*p
copy_vec_uo(inum,pcg,v,omega);
// set velocities for ghost particles
comm->forward_comm_pair(this);
compute_RU(x);
// reverse communication of forces and torques
if (newton_pair) comm->reverse_comm();
copy_uo_vec(inum,f,torque,RU);
// Find alpha
send[0] = dot_vec_vec(6*inum,rcg,rcg);
send[1] = dot_vec_vec(6*inum,RU,pcg);
MPI_Allreduce(send,recv,2,MPI_DOUBLE,MPI_SUM,world);
alpha = recv[0]/recv[1];
rcg_dot_rcg = recv[0];
// Find new x
for (i=0;i<6*inum;i++)
xcg[i] = xcg[i] + alpha*pcg[i];
// find new residual
for (i=0;i<6*inum;i++)
rcg1[i] = rcg[i] - alpha*RU[i];
// find beta
send[0] = dot_vec_vec(6*inum,rcg1,rcg1);
MPI_Allreduce(send,recv,1,MPI_DOUBLE,MPI_SUM,world);
beta = recv[0]/rcg_dot_rcg;
// Find new conjugate direction
for (i=0;i<6*inum;i++)
pcg[i] = rcg1[i] + beta*pcg[i];
for (i=0;i<6*inum;i++)
rcg[i] = rcg1[i];
// Find relative error
error = sqrt(recv[0]/normig);
} while (error > TOL);
// update the final converged velocities in respective arrays
copy_vec_uo(inum,xcg,v,omega);
// set velocities for ghost particles
comm->forward_comm_pair(this);
// Compute the viscosity/pressure
if (evflag) compute_Fh(x);
// Find actual particle's velocities from relative velocities
// Only non-zero component of fluid's vel : vx=gdot*y and wz=-gdot/2
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
v[i][0] = v[i][0] + gdot*x[i][1];
omega[i][2] = omega[i][2] - gdot/2.0;
}
}
/* ------------------------------------------------------------------------
This function computes the final hydrodynamic force once the
velocities have converged.
------------------------------------------------------------------------- */
void PairLubricateU::compute_Fh(double **x)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,fx,fy,fz;
double rsq,r,h_sep;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3;
int *ilist,*jlist,*numneigh,**firstneigh;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int newton_pair = force->newton_pair;
double radi;
double vxmu2f = force->vxmu2f;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// 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*pow(rad,3);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
(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*pow(rad,3)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*
(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
// end of R0 adjustment code
// Set force to zero which is the final value after this pair interaction
for (i=0;i<nlocal+nghost;i++)
for (j=0;j<3;j++) {
f[i][j] = 0.0;
torque[i][j] = 0.0;
}
// reverse communication of forces and torques
if (newton_pair) comm->reverse_comm(); // not really needed
// Find additional contribution from the stresslets
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];
// Find the contribution to stress from isotropic RS0
// Set psuedo force to obtain the required contribution
// need to set delx and fy only
fx = 0.0; delx = radi;
fy = vxmu2f*RS0*gdot/2.0/radi; dely = 0.0;
fz = 0.0; delz = 0.0;
if (evflag)
ev_tally_xyz(i,i,nlocal,newton_pair,0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
// Find angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
wi[2] = omega[i][2];
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);
// Use omega directly if it exists, else angmom
// angular momentum = I*omega = 2/5 * M*R^2 * omega
wj[0] = omega[j][0];
wj[1] = omega[j][1];
wj[2] = omega[j][2];
// loc of the point of closest approach on particle i from its cente
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl
// particle i
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0]);
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1]);
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2]);
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0]);
// Relative velocity at the point of closest approach
// include contribution from Einf of the fluid
vr1 = vi[0] - vj[0] -
2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vr2 = vi[1] - vj[1] -
2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
vr3 = vi[2] - vj[2] -
2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
// Normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
// Tangential component vr - (vr.n)n
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// Find the scalar resistances a_sq, a_sh and a_pu
h_sep = r - 2.0*radi;
// If less than the minimum gap use the 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));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
// Find force due to squeeze type motion
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
fz = fz + a_sh*vt3;
}
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
}
/* ----------------------------------------------------------------------
computes R_FU * U
---------------------------------------------------------------------- */
void PairLubricateU::compute_RU()
{
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;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
int *ilist,*jlist,*numneigh,**firstneigh;
double **x = atom->x;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int newton_pair = force->newton_pair;
double vxmu2f = force->vxmu2f;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// 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*pow(rad,3.0);
// 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*pow(rad,3.0)*(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);
}
}
// end of R0 adjustment code
// Initialize f to zero
for (i=0;i<nlocal+nghost;i++)
for (j=0;j<3;j++) {
f[i][j] = 0.0;
torque[i][j] = 0.0;
}
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];
// Find angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
wi[2] = omega[i][2];
// Contribution due to the isotropic terms
f[i][0] += -vxmu2f*R0*v[i][0];
f[i][1] += -vxmu2f*R0*v[i][1];
f[i][2] += -vxmu2f*R0*v[i][2];
torque[i][0] += -vxmu2f*RT0*wi[0];
torque[i][1] += -vxmu2f*RT0*wi[1];
torque[i][2] += -vxmu2f*RT0*wi[2];
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);
// Use omega directly if it exists, else angmom
// angular momentum = I*omega = 2/5 * M*R^2 * omega
wj[0] = omega[j][0];
wj[1] = omega[j][1];
wj[2] = omega[j][2];
// loc of the point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl
// particle i
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0]);
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1]);
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2]);
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0]);
// Find the scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
// If less than the minimum gap use the 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*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
// Relative velocity at the point of closest approach
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
// Normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
// Tangential component vr - (vr.n)n
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// Find force due to squeeze type motion
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
fz = fz + a_sh*vt3;
}
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
// Add to the total forc
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
f[j][2] += fz;
}
// Find torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
// Why a scale factor ?
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
if(newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
// Torque due to a_pu
wdotn = ((wi[0]-wj[0])*delx +
(wi[1]-wj[1])*dely + (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
// add to total
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
if (newton_pair || j < nlocal) {
torque[j][0] += vxmu2f*tx;
torque[j][1] += vxmu2f*ty;
torque[j][2] += vxmu2f*tz;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
computes R_FU * U
---------------------------------------------------------------------- */
void PairLubricateU::compute_RU(double **x)
{
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;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3,wdotn,wt1,wt2,wt3;
int *ilist,*jlist,*numneigh,**firstneigh;
double **v = atom->v;
double **f = atom->f;
double **omega = atom->omega;
double **torque = atom->torque;
double *radius = atom->radius;
int *type = atom->type;
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int newton_pair = force->newton_pair;
double vxmu2f = force->vxmu2f;
double vi[3],vj[3],wi[3],wj[3],xl[3],a_sq,a_sh,a_pu;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// 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*pow(rad,3.0);
// 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*pow(rad,3.0)*(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);
}
}
// end of R0 adjustment code
// Initialize f to zero
for (i=0;i<nlocal+nghost;i++)
for (j=0;j<3;j++) {
f[i][j] = 0.0;
torque[i][j] = 0.0;
}
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];
// Find angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
wi[2] = omega[i][2];
// Contribution due to the isotropic terms
f[i][0] += -vxmu2f*R0*v[i][0];
f[i][1] += -vxmu2f*R0*v[i][1];
f[i][2] += -vxmu2f*R0*v[i][2];
torque[i][0] += -vxmu2f*RT0*wi[0];
torque[i][1] += -vxmu2f*RT0*wi[1];
torque[i][2] += -vxmu2f*RT0*wi[2];
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);
// Use omega directly if it exists, else angmom
// angular momentum = I*omega = 2/5 * M*R^2 * omega
wj[0] = omega[j][0];
wj[1] = omega[j][1];
wj[2] = omega[j][2];
// loc of the point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// velocity at the point of closest approach on both particles
// v = v + omega_cross_xl
// particle i
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0]);
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1]);
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2]);
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0]);
// Find the scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
// If less than the minimum gap use the 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*pow(radi,3.0)*(3.0/160.0*log(1.0/h_sep));
} else
a_sq = 6.0*MY_PI*mu*radi*(1.0/4.0/h_sep);
// Relative velocity at the point of closest approach
vr1 = vi[0] - vj[0];
vr2 = vi[1] - vj[1];
vr3 = vi[2] - vj[2];
// Normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
// Tangential component vr - (vr.n)n
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// Find force due to squeeze type motion
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
fz = fz + a_sh*vt3;
}
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
// Add to the total force
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
f[j][2] += fz;
}
// Find torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
// Why a scale factor ?
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
if(newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
// Torque due to a_pu
wdotn = ((wi[0]-wj[0])*delx +
(wi[1]-wj[1])*dely + (wi[2]-wj[2])*delz)/r;
wt1 = (wi[0]-wj[0]) - wdotn*delx/r;
wt2 = (wi[1]-wj[1]) - wdotn*dely/r;
wt3 = (wi[2]-wj[2]) - wdotn*delz/r;
tx = a_pu*wt1;
ty = a_pu*wt2;
tz = a_pu*wt3;
// add to total
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
if (newton_pair || j < nlocal) {
torque[j][0] += vxmu2f*tx;
torque[j][1] += vxmu2f*ty;
torque[j][2] += vxmu2f*tz;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
This computes R_{FE}*E , where E is the rate of strain of tensor which is
known apriori, as it depends only on the known fluid velocity.
So, this part of the hydrodynamic interaction can be pre computed and
transferred to the RHS
---------------------------------------------------------------------- */
void PairLubricateU::compute_RE()
{
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;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3;
int *ilist,*jlist,*numneigh,**firstneigh;
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 xl[3],a_sq,a_sh;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
if (!flagHI) return;
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];
// No contribution from isotropic terms due to E
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);
// loc of the point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// Find the scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
// If less than the minimum gap use the 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 resistance for Squeeze type motions
if (flaglog)
a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1/h_sep));
else
a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep);
// Scalar resistance for Shear type motions
if (flaglog) {
a_sh = 6*MY_PI*mu*radi*(1.0/6.0*log(1/h_sep));
}
// Relative velocity at the point of closest approach due to Ef only
vr1 = -2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vr2 = -2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
vr3 = -2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
// Normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
// Tangential component vr - (vr.n)n
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// Find force due to squeeze type motion
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
fz = fz + a_sh*vt3;
}
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
// Add to the total forc
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
f[j][2] += fz;
}
// Find torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
// Why a scale factor ?
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
if (newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
This computes R_{FE}*E , where E is the rate of strain of tensor which is
known apriori, as it depends only on the known fluid velocity.
So, this part of the hydrodynamic interaction can be pre computed and
transferred to the RHS
---------------------------------------------------------------------- */
void PairLubricateU::compute_RE(double **x)
{
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;
double vr1,vr2,vr3,vnnr,vn1,vn2,vn3;
double vt1,vt2,vt3;
int *ilist,*jlist,*numneigh,**firstneigh;
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 xl[3],a_sq,a_sh;
if (!flagHI) return;
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];
// No contribution from isotropic terms due to E
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);
// loc of the point of closest approach on particle i from its center
xl[0] = -delx/r*radi;
xl[1] = -dely/r*radi;
xl[2] = -delz/r*radi;
// Find the scalar resistances a_sq and a_sh
h_sep = r - 2.0*radi;
// If less than the minimum gap use the 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 resistance for Squeeze type motions
if (flaglog)
a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep + 9.0/40.0*log(1/h_sep));
else
a_sq = 6*MY_PI*mu*radi*(1.0/4.0/h_sep);
// Scalar resistance for Shear type motions
if (flaglog) {
a_sh = 6*MY_PI*mu*radi*(1.0/6.0*log(1/h_sep));
}
// Relative velocity at the point of closest approach due to Ef only
vr1 = -2.0*(Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vr2 = -2.0*(Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
vr3 = -2.0*(Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
// Normal component (vr.n)n
vnnr = (vr1*delx + vr2*dely + vr3*delz)/r;
vn1 = vnnr*delx/r;
vn2 = vnnr*dely/r;
vn3 = vnnr*delz/r;
// Tangential component vr - (vr.n)n
vt1 = vr1 - vn1;
vt2 = vr2 - vn2;
vt3 = vr3 - vn3;
// Find force due to squeeze type motion
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
// Find force due to all shear kind of motions
if (flaglog) {
fx = fx + a_sh*vt1;
fy = fy + a_sh*vt2;
fz = fz + a_sh*vt3;
}
// Scale forces to obtain in appropriate units
fx = vxmu2f*fx;
fy = vxmu2f*fy;
fz = vxmu2f*fz;
// Add to the total forc
f[i][0] -= fx;
f[i][1] -= fy;
f[i][2] -= fz;
if (newton_pair || j < nlocal) {
f[j][0] += fx;
f[j][1] += fy;
f[j][2] += fz;
}
// Find torque due to this force
if (flaglog) {
tx = xl[1]*fz - xl[2]*fy;
ty = xl[2]*fx - xl[0]*fz;
tz = xl[0]*fy - xl[1]*fx;
// Why a scale factor ?
torque[i][0] -= vxmu2f*tx;
torque[i][1] -= vxmu2f*ty;
torque[i][2] -= vxmu2f*tz;
if (newton_pair || j < nlocal) {
torque[j][0] -= vxmu2f*tx;
torque[j][1] -= vxmu2f*ty;
torque[j][2] -= vxmu2f*tz;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLubricateU::allocate()
{
allocated = 1;
int n = atom->ntypes;
setflag = 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;
cutsq = 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 PairLubricateU::settings(int narg, char **arg)
{
if (narg != 5 && narg != 7) error->all(FLERR,"Illegal pair_style command");
mu = force->numeric(FLERR,arg[0]);
flaglog = force->inumeric(FLERR,arg[1]);
cut_inner_global = force->numeric(FLERR,arg[2]);
cut_global = force->numeric(FLERR,arg[3]);
gdot = force->numeric(FLERR,arg[4]);
flagHI = flagVF = 1;
if (narg == 7) {
flagHI = force->inumeric(FLERR,arg[5]);
flagVF = force->inumeric(FLERR,arg[6]);
}
if (flaglog == 1 && flagHI == 0) {
error->warning(FLERR,"Cannot include log terms without 1/r terms; "
"setting flagHI to 1.");
flagHI = 1;
}
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
cut_inner[i][j] = cut_inner_global;
cut[i][j] = cut_global;
}
}
// store the rate of strain tensor
Ef[0][0] = 0.0;
Ef[0][1] = 0.5*gdot;
Ef[0][2] = 0.0;
Ef[1][0] = 0.5*gdot;
Ef[1][1] = 0.0;
Ef[1][2] = 0.0;
Ef[2][0] = 0.0;
Ef[2][1] = 0.0;
Ef[2][2] = 0.0;
}
/*-----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLubricateU::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 PairLubricateU::init_style()
{
if (!atom->sphere_flag)
error->all(FLERR,"Pair lubricateU requires atom style sphere");
if (comm->ghost_velocity == 0)
error->all(FLERR,"Pair lubricateU requires ghost atoms store velocity");
neighbor->request(this,instance_me);
// require that atom radii are identical within each type
// 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 lubricateU requires monodisperse particles");
if (i > 1 && radtype != rad)
error->all(FLERR,"Pair lubricateU requires monodisperse particles");
}
// 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 lubricateU");
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]);
}
// assuming monodisperse spheres, vol_P = volume of the particles
double tmp = 0.0;
if (atom->radius) tmp = atom->radius[0];
MPI_Allreduce(&tmp,&rad,1,MPI_DOUBLE,MPI_MAX,world);
vol_P = atom->natoms * (4.0/3.0)*MY_PI*pow(rad,3.0);
// vol_f = volume fraction
double vol_f = vol_P/vol_T;
if (!flagVF) vol_f = 0;
// set the isotropic constant
if (flaglog == 0) {
R0 = 6*MY_PI*mu*rad*(1.0 + 2.16*vol_f);
RT0 = 8*MY_PI*mu*pow(rad,3.0); // not actually needed
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*(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*pow(rad,3.0)*(1.0 + 0.749*vol_f - 2.469*vol_f*vol_f);
RS0 = 20.0/3.0*MY_PI*mu*pow(rad,3.0)*(1.0 + 3.64*vol_f - 6.95*vol_f*vol_f);
}
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLubricateU::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 PairLubricateU::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 PairLubricateU::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 PairLubricateU::write_restart_settings(FILE *fp)
{
fwrite(&mu,sizeof(double),1,fp);
fwrite(&flaglog,sizeof(int),1,fp);
fwrite(&cut_inner_global,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),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 PairLubricateU::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(&cut_inner_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),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(&cut_inner_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,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);
}
/*---------------------------------------------------------------------------*/
void PairLubricateU::copy_vec_uo(int inum, double *xcg,
double **v, double **omega)
{
int i,j,ii;
int *ilist = list->ilist;
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
for (j=0;j<3;j++) {
v[i][j] = xcg[6*ii+j];
omega[i][j] = xcg[6*ii+j+3];
}
}
}
/*---------------------------------------------------------------------------*/
void PairLubricateU::copy_uo_vec(int inum, double **f, double **torque,
double *RU)
{
int i,j,ii;
int *ilist;
ilist = list->ilist;
for (ii=0;ii<inum;ii++) {
i = ilist[ii];
for (j=0;j<3;j++) {
RU[6*ii+j] = f[i][j];
RU[6*ii+j+3] = torque[i][j];
}
}
}
/* ---------------------------------------------------------------------- */
int PairLubricateU::pack_forward_comm(int n, int *list, double *buf,
int pbc_flag, int *pbc)
{
int i,j,m;
double **v = atom->v;
double **omega = atom->omega;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = v[j][0];
buf[m++] = v[j][1];
buf[m++] = v[j][2];
buf[m++] = omega[j][0];
buf[m++] = omega[j][1];
buf[m++] = omega[j][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void PairLubricateU::unpack_forward_comm(int n, int first, double *buf)
{
int i,m,last;
double **v = atom->v;
double **omega = atom->omega;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
v[i][0] = buf[m++];
v[i][1] = buf[m++];
v[i][2] = buf[m++];
omega[i][0] = buf[m++];
omega[i][1] = buf[m++];
omega[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
double PairLubricateU::dot_vec_vec(int N, double *x, double *y)
{
double dotp=0.0;
for (int i = 0; i < N; i++) dotp += x[i]*y[i];
return dotp;
}
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