Homec4science
Diffusion lammps (master) Browse

lammps/src/USER-OMP/pair_brownian_poly_omp.cpp
a4bc5aa73a55master

Last Change
Raw File

pair_brownian_poly_omp.cpp
View Options

/* ----------------------------------------------------------------------
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_brownian_poly_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 "math_const.h"
#include "suffix.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EPSILON 1.0e-10
// same as fix_wall.cpp
enum{EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
PairBrownianPolyOMP::PairBrownianPolyOMP(LAMMPS *lmp) :
PairBrownianPoly(lmp), ThrOMP(lmp, THR_PAIR)
{
suffix_flag |= Suffix::OMP;
respa_enable = 0;
random_thr = NULL;
}
/* ---------------------------------------------------------------------- */
PairBrownianPolyOMP::~PairBrownianPolyOMP()
{
if (random_thr) {
for (int i=1; i < comm->nthreads; ++i)
delete random_thr[i];
delete[] random_thr;
random_thr = NULL;
}
}
/* ---------------------------------------------------------------------- */
void PairBrownianPolyOMP::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)*(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);
}
}
if (!random_thr)
random_thr = new RanMars*[nthreads];
// to ensure full compatibility with the serial BrownianPoly style
// we use is random number generator instance for thread 0
random_thr[0] = random;
#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);
ev_setup_thr(eflag, vflag, nall, eatom, vatom, thr);
// generate a random number generator instance for
// all threads != 0. make sure we use unique seeds.
if (random_thr && tid > 0)
random_thr[tid] = new RanMars(Pair::lmp, seed + comm->me
+ comm->nprocs*tid);
if (flaglog) {
if (evflag)
eval<1,1>(ifrom, ito, thr);
else
eval<1,0>(ifrom, ito, thr);
} else {
if (evflag)
eval<0,1>(ifrom, ito, thr);
else eval<0,0>(ifrom, ito, thr);
}
reduce_thr(this, eflag, vflag, thr);
} // end of omp parallel region
}
template <int FLAGLOG, int EVFLAG>
void PairBrownianPolyOMP::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,beta0,beta1,radi,radj;
int *ilist,*jlist,*numneigh,**firstneigh;
const double * const * const x = atom->x;
double * const * const f = thr->get_f();
double * const * const torque = thr->get_torque();
const double * const radius = atom->radius;
const int * const type = atom->type;
const int nlocal = atom->nlocal;
RanMars &rng = *random_thr[thr->get_tid()];
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);
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// 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];
// FLD contribution to force and torque due to isotropic terms
if (flagfld) {
f[i][0] += prethermostat*sqrt(R0*radi)*(rng.uniform()-0.5);
f[i][1] += prethermostat*sqrt(R0*radi)*(rng.uniform()-0.5);
f[i][2] += prethermostat*sqrt(R0*radi)*(rng.uniform()-0.5);
if (FLAGLOG) {
const double rad3 = radi*radi*radi;
torque[i][0] += prethermostat*sqrt(RT0*rad3)*(rng.uniform()-0.5);
torque[i][1] += prethermostat*sqrt(RT0*rad3)*(rng.uniform()-0.5);
torque[i][2] += prethermostat*sqrt(RT0*rad3)*(rng.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];
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(beta1,3.0)*log(1.0/h_sep);
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*pow(beta0,3.0) +
pow(beta0,4.0))/21.0/pow(beta1,4.0)*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(beta1,3.0) *
log(1.0/h_sep);
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*pow(beta0,3.0) +
16.0*pow(beta0,4.0))/375.0/pow(beta1,4.0) *
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(beta0,3.0))/250.0/pow(beta1,3.0)*h_sep*log(1.0/h_sep);
a_pu *= 8.0*MY_PI*mu*pow(radi,3.0);
} 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 = rng.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 = rng.uniform()-0.5;
fx += Fbmag*randr*p2[0];
fy += Fbmag*randr*p2[1];
fz += Fbmag*randr*p2[2];
randr = rng.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 = rng.uniform()-0.5;
tx = Fbmag*randr*p2[0];
ty = Fbmag*randr*p2[1];
tz = Fbmag*randr*p2[2];
randr = rng.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,/* newton_pair */ 0,
0.0,0.0,-fx,-fy,-fz,delx,dely,delz);
}
}
}
}
/* ---------------------------------------------------------------------- */
double PairBrownianPolyOMP::memory_usage()
{
double bytes = memory_usage_thr();
bytes += PairBrownianPoly::memory_usage();
bytes += comm->nthreads * sizeof(RanMars*);
bytes += comm->nthreads * sizeof(RanMars);
return bytes;
}
c4science · Help