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nbin_kokkos.cpp
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Thu, Jun 6, 13:00

nbin_kokkos.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.
------------------------------------------------------------------------- */
#include "nbin_kokkos.h"
#include "neighbor.h"
#include "atom_kokkos.h"
#include "group.h"
#include "domain.h"
#include "comm.h"
#include "update.h"
#include "error.h"
#include "atom_masks.h"
using namespace LAMMPS_NS;
enum{NSQ,BIN,MULTI}; // also in Neighbor
#define SMALL 1.0e-6
#define CUT2BIN_RATIO 100
/* ---------------------------------------------------------------------- */
template<class DeviceType>
NBinKokkos<DeviceType>::NBinKokkos(LAMMPS *lmp) : NBinStandard(lmp) {
atoms_per_bin = 16;
d_resize = typename AT::t_int_scalar("NeighborKokkosFunctor::resize");
#ifndef KOKKOS_USE_CUDA_UVM
h_resize = Kokkos::create_mirror_view(d_resize);
#else
h_resize = d_resize;
#endif
h_resize() = 1;
}
/* ----------------------------------------------------------------------
setup neighbor binning geometry
bin numbering in each dimension is global:
0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc
nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc
-1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc
code will work for any binsize
since next(xyz) and stencil extend as far as necessary
binsize = 1/2 of cutoff is roughly optimal
for orthogonal boxes:
a dim must be filled exactly by integer # of bins
in periodic, procs on both sides of PBC must see same bin boundary
in non-periodic, coord2bin() still assumes this by use of nbin xyz
for triclinic boxes:
tilted simulation box cannot contain integer # of bins
stencil & neigh list built differently to account for this
mbinlo = lowest global bin any of my ghost atoms could fall into
mbinhi = highest global bin any of my ghost atoms could fall into
mbin = number of bins I need in a dimension
------------------------------------------------------------------------- */
template<class DeviceType>
void NBinKokkos<DeviceType>::bin_atoms_setup(int nall)
{
if (mbins > k_bins.d_view.dimension_0()) {
k_bins = DAT::tdual_int_2d("Neighbor::d_bins",mbins,atoms_per_bin);
bins = k_bins.view<DeviceType>();
k_bincount = DAT::tdual_int_1d("Neighbor::d_bincount",mbins);
bincount = k_bincount.view<DeviceType>();
}
}
/* ----------------------------------------------------------------------
bin owned and ghost atoms
------------------------------------------------------------------------- */
template<class DeviceType>
void NBinKokkos<DeviceType>::bin_atoms()
{
last_bin = update->ntimestep;
h_resize() = 1;
while(h_resize() > 0) {
h_resize() = 0;
deep_copy(d_resize, h_resize);
MemsetZeroFunctor<DeviceType> f_zero;
f_zero.ptr = (void*) k_bincount.view<DeviceType>().ptr_on_device();
Kokkos::parallel_for(mbins, f_zero);
DeviceType::fence();
atomKK->sync(ExecutionSpaceFromDevice<DeviceType>::space,X_MASK);
x = atomKK->k_x.view<DeviceType>();
bboxlo_[0] = bboxlo[0]; bboxlo_[1] = bboxlo[1]; bboxlo_[2] = bboxlo[2];
bboxhi_[0] = bboxhi[0]; bboxhi_[1] = bboxhi[1]; bboxhi_[2] = bboxhi[2];
NPairKokkosBinAtomsFunctor<DeviceType> f(*this);
Kokkos::parallel_for(atom->nlocal+atom->nghost, f);
DeviceType::fence();
deep_copy(h_resize, d_resize);
if(h_resize()) {
atoms_per_bin += 16;
k_bins = DAT::tdual_int_2d("bins", mbins, atoms_per_bin);
bins = k_bins.view<DeviceType>();
c_bins = bins;
}
}
}
/* ---------------------------------------------------------------------- */
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void NBinKokkos<DeviceType>::binatomsItem(const int &i) const
{
const int ibin = coord2bin(x(i, 0), x(i, 1), x(i, 2));
const int ac = Kokkos::atomic_fetch_add(&bincount[ibin], (int)1);
if(ac < bins.dimension_1()) {
bins(ibin, ac) = i;
} else {
d_resize() = 1;
}
}
namespace LAMMPS_NS {
template class NBinKokkos<LMPDeviceType>;
#ifdef KOKKOS_HAVE_CUDA
template class NBinKokkos<LMPHostType>;
#endif
}

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