392 lines
11 KiB
C++
392 lines
11 KiB
C++
/* ----------------------------------------------------------------------
|
|
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 "math_special.h"
|
|
|
|
#include "suffix.h"
|
|
using namespace LAMMPS_NS;
|
|
using namespace MathConst;
|
|
using namespace MathSpecial;
|
|
|
|
#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*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);
|
|
}
|
|
}
|
|
|
|
|
|
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);
|
|
thr->timer(Timer::START);
|
|
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);
|
|
}
|
|
|
|
thr->timer(Timer::PAIR);
|
|
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/cube(beta1)*log(1.0/h_sep);
|
|
a_sq += (1.0+18.0*beta0-29.0*beta0*beta0+18.0*cube(beta0) +
|
|
powint(beta0,4))/21.0/powint(beta1,4)*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/cube(beta1) *
|
|
log(1.0/h_sep);
|
|
a_sh += 4.0*(16.0-45.0*beta0+58.0*beta0*beta0-45.0*cube(beta0) +
|
|
16.0*powint(beta0,4))/375.0/powint(beta1,4) *
|
|
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 *
|
|
cube(beta0))/250.0/cube(beta1)*h_sep*log(1.0/h_sep);
|
|
a_pu *= 8.0*MY_PI*mu*cube(radi);
|
|
|
|
} 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;
|
|
}
|