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pair_lubricate_omp.cpp
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Sat, Jul 13, 22:43

pair_lubricate_omp.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
This software is distributed under the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include <math.h>
#include "pair_lubricate_omp.h"
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "force.h"
#include "input.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "update.h"
#include "variable.h"
#include "random_mars.h"
#include "fix_wall.h"
#include "fix_deform.h"
#include "math_const.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
// same as fix_deform.cpp
enum{NO_REMAP,X_REMAP,V_REMAP};
// same as fix_wall.cpp
enum{EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
PairLubricateOMP::PairLubricateOMP(LAMMPS *lmp) :
PairLubricate(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
}
/* ---------------------------------------------------------------------- */
PairLubricateOMP::~PairLubricateOMP()
{}
/* ---------------------------------------------------------------------- */
void PairLubricateOMP::compute(int eflag, int vflag)
{
if (eflag || vflag) {
ev_setup(eflag,vflag);
} else evflag = vflag_fdotr = 0;
const int nall = atom->nlocal + atom->nghost;
const int nthreads = comm->nthreads;
const int inum = list->inum;
// 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 (int 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,3.0)*
(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);
}
}
// end of R0 adjustment code
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(eflag,vflag)
#endif
{
int ifrom, ito, tid;
loop_setup_thr(ifrom, ito, tid, inum, nthreads);
ThrData *thr = fix->get_thr(tid);
thr->timer(Timer::START);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
if (flaglog) {
if (evflag) {
if (force->newton_pair) eval<1,1,1>(ifrom, ito, thr);
else eval<1,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<1,0,1>(ifrom, ito, thr);
else eval<1,0,0>(ifrom, ito, thr);
}
} else {
if (evflag) {
if (force->newton_pair) eval<0,1,1>(ifrom, ito, thr);
else eval<0,1,0>(ifrom, ito, thr);
} else {
if (force->newton_pair) eval<0,0,1>(ifrom, ito, thr);
else eval<0,0,0>(ifrom, ito, thr);
}
}
thr->timer(Timer::PAIR);
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int FLAGLOG, int EVFLAG, int NEWTON_PAIR>
void PairLubricateOMP::eval(int iifrom, int iito, ThrData * const thr)
{
int i,j,ii,jj,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,wt1,wt2,wt3,wdotn;
double vRS0;
double vi[3],vj[3],wi[3],wj[3],xl[3];
double a_sq,a_sh,a_pu;
int *ilist,*jlist,*numneigh,**firstneigh;
double lamda[3],vstream[3];
double vxmu2f = force->vxmu2f;
double * const * const x = atom->x;
double * const * const v = atom->v;
double * const * const f = thr->get_f();
double * const * const omega = atom->omega;
double * const * const torque = thr->get_torque();
const double * const radius = atom->radius;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
int overlaps = 0;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// subtract streaming component of velocity, omega, angmom
// assume fluid streaming velocity = box deformation rate
// vstream = (ux,uy,uz)
// ux = h_rate[0]*x + h_rate[5]*y + h_rate[4]*z
// uy = h_rate[1]*y + h_rate[3]*z
// uz = h_rate[2]*z
// omega_new = omega - curl(vstream)/2
// angmom_new = angmom - I*curl(vstream)/2
// Ef = (grad(vstream) + (grad(vstream))^T) / 2
if (shearing) {
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
itype = type[i];
radi = radius[i];
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vstream[0];
v[i][1] -= vstream[1];
v[i][2] -= vstream[2];
omega[i][0] += 0.5*h_rate[3];
omega[i][1] -= 0.5*h_rate[4];
omega[i][2] += 0.5*h_rate[5];
}
// set Ef from h_rate in strain units
Ef[0][0] = h_rate[0]/domain->xprd;
Ef[1][1] = h_rate[1]/domain->yprd;
Ef[2][2] = h_rate[2]/domain->zprd;
Ef[0][1] = Ef[1][0] = 0.5 * h_rate[5]/domain->yprd;
Ef[0][2] = Ef[2][0] = 0.5 * h_rate[4]/domain->zprd;
Ef[1][2] = Ef[2][1] = 0.5 * h_rate[3]/domain->zprd;
// copy updated velocity/omega/angmom to the ghost particles
// no need to do this if not shearing since comm->ghost_velocity is set
sync_threads();
// MPI communication only on master thread
#if defined(_OPENMP)
#pragma omp master
#endif
{ comm->forward_comm_pair(this); }
sync_threads();
}
// loop over neighbors of my atoms
for (ii = iifrom; ii < iito; ++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];
// angular velocity
wi[0] = omega[i][0];
wi[1] = omega[i][1];
wi[2] = omega[i][2];
// FLD contribution to force and torque due to isotropic terms
// FLD contribution to stress from isotropic RS0
if (flagfld) {
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 (shearing && vflag_either) {
vRS0 = -vxmu2f * RS0;
v_tally_tensor(i,i,nlocal,NEWTON_PAIR,
vRS0*Ef[0][0],vRS0*Ef[1][1],vRS0*Ef[2][2],
vRS0*Ef[0][1],vRS0*Ef[0][2],vRS0*Ef[1][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);
// 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];
// xl = 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 - Ef.xl
// particle i
vi[0] = v[i][0] + (wi[1]*xl[2] - wi[2]*xl[1])
- (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vi[1] = v[i][1] + (wi[2]*xl[0] - wi[0]*xl[2])
- (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
vi[2] = v[i][2] + (wi[0]*xl[1] - wi[1]*xl[0])
- (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
// particle j
vj[0] = v[j][0] - (wj[1]*xl[2] - wj[2]*xl[1])
+ (Ef[0][0]*xl[0] + Ef[0][1]*xl[1] + Ef[0][2]*xl[2]);
vj[1] = v[j][1] - (wj[2]*xl[0] - wj[0]*xl[2])
+ (Ef[1][0]*xl[0] + Ef[1][1]*xl[1] + Ef[1][2]*xl[2]);
vj[2] = v[j][2] - (wj[0]*xl[1] - wj[1]*xl[0])
+ (Ef[2][0]*xl[0] + Ef[2][1]*xl[1] + Ef[2][2]*xl[2]);
// scalar resistances XA and YA
h_sep = r - 2.0*radi;
// check for overlaps
if (h_sep < 0.0) overlaps++;
// 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
// includes fluid velocity
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;
// force due to squeeze type motion
fx = a_sq*vn1;
fy = a_sq*vn2;
fz = a_sq*vn3;
// 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 for appropriate units
fx *= vxmu2f;
fy *= vxmu2f;
fz *= vxmu2f;
// add to 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;
}
// 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;
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;
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;
}
}
if (EVFLAG) ev_tally_xyz_thr(this,i,j,nlocal,NEWTON_PAIR,0.0,0.0,
-fx,-fy,-fz,delx,dely,delz,thr);
}
}
}
// restore streaming component of velocity, omega, angmom
if (shearing) {
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
for (ii = iifrom; ii < iito; ii++) {
i = ilist[ii];
itype = type[i];
radi = radius[i];
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] += vstream[0];
v[i][1] += vstream[1];
v[i][2] += vstream[2];
omega[i][0] -= 0.5*h_rate[3];
omega[i][1] += 0.5*h_rate[4];
omega[i][2] -= 0.5*h_rate[5];
}
}
}
/* ---------------------------------------------------------------------- */
double PairLubricateOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairLubricate::memory_usage();
return bytes;
}

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