789 lines
26 KiB
C++
789 lines
26 KiB
C++
/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "npair_kokkos.h"
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#include "atom_kokkos.h"
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#include "atom_masks.h"
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#include "domain_kokkos.h"
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#include "neighbor_kokkos.h"
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#include "nbin_kokkos.h"
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#include "nstencil.h"
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#include "force.h"
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namespace LAMMPS_NS {
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/* ---------------------------------------------------------------------- */
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template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI>
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NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::NPairKokkos(LAMMPS *lmp) : NPair(lmp) {
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}
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/* ----------------------------------------------------------------------
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copy needed info from Neighbor class to this build class
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------------------------------------------------------------------------- */
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template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI>
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void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::copy_neighbor_info()
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{
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NPair::copy_neighbor_info();
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NeighborKokkos* neighborKK = (NeighborKokkos*) neighbor;
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// general params
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newton_pair = force->newton_pair;
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k_cutneighsq = neighborKK->k_cutneighsq;
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// exclusion info
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k_ex1_type = neighborKK->k_ex1_type;
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k_ex2_type = neighborKK->k_ex2_type;
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k_ex_type = neighborKK->k_ex_type;
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k_ex1_group = neighborKK->k_ex1_group;
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k_ex2_group = neighborKK->k_ex2_group;
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k_ex1_bit = neighborKK->k_ex1_bit;
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k_ex2_bit = neighborKK->k_ex2_bit;
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k_ex_mol_group = neighborKK->k_ex_mol_group;
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k_ex_mol_bit = neighborKK->k_ex_mol_bit;
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k_ex_mol_intra = neighborKK->k_ex_mol_intra;
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}
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/* ----------------------------------------------------------------------
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copy per-atom and per-bin vectors from NBin class to this build class
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------------------------------------------------------------------------- */
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template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI>
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void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::copy_bin_info()
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{
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NPair::copy_bin_info();
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NBinKokkos<DeviceType>* nbKK = (NBinKokkos<DeviceType>*) nb;
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atoms_per_bin = nbKK->atoms_per_bin;
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k_bincount = nbKK->k_bincount;
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k_bins = nbKK->k_bins;
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}
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/* ----------------------------------------------------------------------
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copy needed info from NStencil class to this build class
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------------------------------------------------------------------------- */
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template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI>
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void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::copy_stencil_info()
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{
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NPair::copy_stencil_info();
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nstencil = ns->nstencil;
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int maxstencil = ns->get_maxstencil();
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k_stencil = DAT::tdual_int_1d("neighlist:stencil",maxstencil);
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for (int k = 0; k < maxstencil; k++)
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k_stencil.h_view(k) = ns->stencil[k];
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k_stencil.modify<LMPHostType>();
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k_stencil.sync<DeviceType>();
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if (GHOST) {
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k_stencilxyz = DAT::tdual_int_1d_3("neighlist:stencilxyz",maxstencil);
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for (int k = 0; k < maxstencil; k++) {
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k_stencilxyz.h_view(k,0) = ns->stencilxyz[k][0];
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k_stencilxyz.h_view(k,1) = ns->stencilxyz[k][1];
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k_stencilxyz.h_view(k,2) = ns->stencilxyz[k][2];
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}
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k_stencilxyz.modify<LMPHostType>();
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k_stencilxyz.sync<DeviceType>();
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}
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType, int HALF_NEIGH, int GHOST, int TRI>
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void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::build(NeighList *list_)
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{
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NeighListKokkos<DeviceType>* list = (NeighListKokkos<DeviceType>*) list_;
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const int nlocal = includegroup?atom->nfirst:atom->nlocal;
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int nall = nlocal;
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if (GHOST)
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nall += atom->nghost;
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list->grow(nall);
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NeighborKokkosExecute<DeviceType>
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data(*list,
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k_cutneighsq.view<DeviceType>(),
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k_bincount.view<DeviceType>(),
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k_bins.view<DeviceType>(),
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nstencil,
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k_stencil.view<DeviceType>(),
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k_stencilxyz.view<DeviceType>(),
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nlocal,
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atomKK->k_x.view<DeviceType>(),
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atomKK->k_type.view<DeviceType>(),
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atomKK->k_mask.view<DeviceType>(),
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atomKK->k_molecule.view<DeviceType>(),
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atomKK->k_tag.view<DeviceType>(),
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atomKK->k_special.view<DeviceType>(),
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atomKK->k_nspecial.view<DeviceType>(),
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atomKK->molecular,
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nbinx,nbiny,nbinz,mbinx,mbiny,mbinz,mbinxlo,mbinylo,mbinzlo,
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bininvx,bininvy,bininvz,
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exclude, nex_type,
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k_ex1_type.view<DeviceType>(),
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k_ex2_type.view<DeviceType>(),
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k_ex_type.view<DeviceType>(),
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nex_group,
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k_ex1_group.view<DeviceType>(),
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k_ex2_group.view<DeviceType>(),
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k_ex1_bit.view<DeviceType>(),
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k_ex2_bit.view<DeviceType>(),
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nex_mol,
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k_ex_mol_group.view<DeviceType>(),
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k_ex_mol_bit.view<DeviceType>(),
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k_ex_mol_intra.view<DeviceType>(),
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bboxhi,bboxlo,
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domain->xperiodic,domain->yperiodic,domain->zperiodic,
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domain->xprd_half,domain->yprd_half,domain->zprd_half);
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k_cutneighsq.sync<DeviceType>();
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k_ex1_type.sync<DeviceType>();
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k_ex2_type.sync<DeviceType>();
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k_ex_type.sync<DeviceType>();
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k_ex1_group.sync<DeviceType>();
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k_ex2_group.sync<DeviceType>();
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k_ex1_bit.sync<DeviceType>();
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k_ex2_bit.sync<DeviceType>();
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k_ex_mol_group.sync<DeviceType>();
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k_ex_mol_bit.sync<DeviceType>();
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k_ex_mol_intra.sync<DeviceType>();
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k_bincount.sync<DeviceType>(),
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k_bins.sync<DeviceType>(),
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atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
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data.special_flag[0] = special_flag[0];
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data.special_flag[1] = special_flag[1];
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data.special_flag[2] = special_flag[2];
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data.special_flag[3] = special_flag[3];
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if(list->d_neighbors.dimension_0()<nall) {
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list->d_neighbors = typename ArrayTypes<DeviceType>::t_neighbors_2d("neighbors", nall*1.1, list->maxneighs);
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list->d_numneigh = typename ArrayTypes<DeviceType>::t_int_1d("numneigh", nall*1.1);
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data.neigh_list.d_neighbors = list->d_neighbors;
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data.neigh_list.d_numneigh = list->d_numneigh;
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}
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data.h_resize()=1;
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while(data.h_resize()) {
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data.h_new_maxneighs() = list->maxneighs;
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data.h_resize() = 0;
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Kokkos::deep_copy(data.resize, data.h_resize);
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Kokkos::deep_copy(data.new_maxneighs, data.h_new_maxneighs);
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#ifdef KOKKOS_HAVE_CUDA
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#define BINS_PER_BLOCK 2
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const int factor = atoms_per_bin<64?2:1;
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Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,atoms_per_bin*factor);
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#else
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const int factor = 1;
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#endif
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if (GHOST) {
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NPairKokkosBuildFunctorGhost<DeviceType,HALF_NEIGH> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
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Kokkos::parallel_for(nall, f);
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} else {
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if (newton_pair) {
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NPairKokkosBuildFunctor<DeviceType,TRI?0:HALF_NEIGH,1,TRI> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
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#ifdef KOKKOS_HAVE_CUDA
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Kokkos::parallel_for(config, f);
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#else
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Kokkos::parallel_for(nall, f);
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#endif
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} else {
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NPairKokkosBuildFunctor<DeviceType,HALF_NEIGH,0,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
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#ifdef KOKKOS_HAVE_CUDA
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Kokkos::parallel_for(config, f);
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#else
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Kokkos::parallel_for(nall, f);
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#endif
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}
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}
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DeviceType::fence();
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deep_copy(data.h_resize, data.resize);
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if(data.h_resize()) {
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deep_copy(data.h_new_maxneighs, data.new_maxneighs);
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list->maxneighs = data.h_new_maxneighs() * 1.2;
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list->d_neighbors = typename ArrayTypes<DeviceType>::t_neighbors_2d("neighbors", list->d_neighbors.dimension_0(), list->maxneighs);
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data.neigh_list.d_neighbors = list->d_neighbors;
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data.neigh_list.maxneighs = list->maxneighs;
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}
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}
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if (GHOST) {
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list->inum = atom->nlocal;
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list->gnum = nall - atom->nlocal;
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} else {
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list->inum = nall;
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list->gnum = 0;
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}
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list->k_ilist.template modify<DeviceType>();
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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int NeighborKokkosExecute<DeviceType>::find_special(const int &i, const int &j) const
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{
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const int n1 = nspecial(i,0);
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const int n2 = nspecial(i,1);
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const int n3 = nspecial(i,2);
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for (int k = 0; k < n3; k++) {
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if (special(i,k) == tag(j)) {
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if (k < n1) {
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if (special_flag[1] == 0) return -1;
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else if (special_flag[1] == 1) return 0;
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else return 1;
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} else if (k < n2) {
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if (special_flag[2] == 0) return -1;
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else if (special_flag[2] == 1) return 0;
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else return 2;
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} else {
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if (special_flag[3] == 0) return -1;
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else if (special_flag[3] == 1) return 0;
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else return 3;
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}
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}
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}
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return 0;
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};
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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KOKKOS_INLINE_FUNCTION
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int NeighborKokkosExecute<DeviceType>::exclusion(const int &i,const int &j,
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const int &itype,const int &jtype) const
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{
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int m;
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if (nex_type && ex_type(itype,jtype)) return 1;
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if (nex_group) {
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for (m = 0; m < nex_group; m++) {
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if (mask(i) & ex1_bit(m) && mask(j) & ex2_bit(m)) return 1;
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if (mask(i) & ex2_bit(m) && mask(j) & ex1_bit(m)) return 1;
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}
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}
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if (nex_mol) {
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for (m = 0; m < nex_mol; m++)
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if (ex_mol_intra[m]) { // intra-chain: exclude i-j pair if on same molecule
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if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
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molecule[i] == molecule[j]) return 1;
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} else // exclude i-j pair if on different molecules
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if (mask[i] & ex_mol_bit[m] && mask[j] & ex_mol_bit[m] &&
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molecule[i] != molecule[j]) return 1;
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}
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return 0;
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType> template<int HalfNeigh,int Newton,int Tri>
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void NeighborKokkosExecute<DeviceType>::
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build_Item(const int &i) const
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{
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/* if necessary, goto next page and add pages */
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int n = 0;
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int which = 0;
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int moltemplate;
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if (molecular == 2) moltemplate = 1;
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else moltemplate = 0;
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// get subview of neighbors of i
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const AtomNeighbors neighbors_i = neigh_list.get_neighbors(i);
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const X_FLOAT xtmp = x(i, 0);
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const X_FLOAT ytmp = x(i, 1);
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const X_FLOAT ztmp = x(i, 2);
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const int itype = type(i);
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const int ibin = coord2bin(xtmp, ytmp, ztmp);
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const typename ArrayTypes<DeviceType>::t_int_1d_const_um stencil
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= d_stencil;
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// loop over all bins in neighborhood (includes ibin)
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if(HalfNeigh)
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for(int m = 0; m < c_bincount(ibin); m++) {
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const int j = c_bins(ibin,m);
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const int jtype = type(j);
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//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using HalfNeighborlists
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if((j == i) || (HalfNeigh && !Newton && (j < i)) ||
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(HalfNeigh && Newton && ((j < i) || ((j >= nlocal) &&
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((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) ||
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(x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp)))))
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) continue;
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if(exclude && exclusion(i,j,itype,jtype)) continue;
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const X_FLOAT delx = xtmp - x(j, 0);
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const X_FLOAT dely = ytmp - x(j, 1);
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const X_FLOAT delz = ztmp - x(j, 2);
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const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
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if(rsq <= cutneighsq(itype,jtype)) {
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if (molecular) {
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if (!moltemplate)
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which = find_special(i,j);
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/* else if (imol >= 0) */
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/* which = find_special(onemols[imol]->special[iatom], */
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/* onemols[imol]->nspecial[iatom], */
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/* tag[j]-tagprev); */
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/* else which = 0; */
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if (which == 0){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}else if (minimum_image_check(delx,dely,delz)){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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else if (which > 0) {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
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else n++;
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}
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} else {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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}
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}
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for(int k = 0; k < nstencil; k++) {
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const int jbin = ibin + stencil[k];
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// get subview of jbin
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if(HalfNeigh && (ibin==jbin)) continue;
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//const ArrayTypes<DeviceType>::t_int_1d_const_um =Kokkos::subview<t_int_1d_const_um>(bins,jbin,ALL);
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for(int m = 0; m < c_bincount(jbin); m++) {
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const int j = c_bins(jbin,m);
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const int jtype = type(j);
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if(HalfNeigh && !Newton && (j < i)) continue;
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if(!HalfNeigh && j==i) continue;
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if(Tri) {
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if (x(j,2) < ztmp) continue;
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if (x(j,2) == ztmp) {
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if (x(j,1) < ytmp) continue;
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if (x(j,1) == ytmp) {
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if (x(j,0) < xtmp) continue;
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if (x(j,0) == xtmp && j <= i) continue;
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}
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}
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}
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if(exclude && exclusion(i,j,itype,jtype)) continue;
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const X_FLOAT delx = xtmp - x(j, 0);
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const X_FLOAT dely = ytmp - x(j, 1);
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const X_FLOAT delz = ztmp - x(j, 2);
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const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
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if(rsq <= cutneighsq(itype,jtype)) {
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if (molecular) {
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if (!moltemplate)
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which = NeighborKokkosExecute<DeviceType>::find_special(i,j);
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/* else if (imol >= 0) */
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/* which = find_special(onemols[imol]->special[iatom], */
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/* onemols[imol]->nspecial[iatom], */
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/* tag[j]-tagprev); */
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/* else which = 0; */
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if (which == 0){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}else if (minimum_image_check(delx,dely,delz)){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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else if (which > 0) {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
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else n++;
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}
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} else {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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}
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}
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}
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neigh_list.d_numneigh(i) = n;
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if(n >= neigh_list.maxneighs) {
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resize() = 1;
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if(n >= new_maxneighs()) new_maxneighs() = n;
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}
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neigh_list.d_ilist(i) = i;
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}
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/* ---------------------------------------------------------------------- */
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#ifdef KOKKOS_HAVE_CUDA
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extern __shared__ X_FLOAT sharedmem[];
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/* ---------------------------------------------------------------------- */
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template<class DeviceType> template<int HalfNeigh,int Newton,int Tri>
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__device__ inline
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void NeighborKokkosExecute<DeviceType>::build_ItemCuda(typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const
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{
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/* loop over atoms in i's bin,
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*/
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const int atoms_per_bin = c_bins.dimension_1();
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const int BINS_PER_TEAM = dev.team_size()/atoms_per_bin<1?1:dev.team_size()/atoms_per_bin;
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const int TEAMS_PER_BIN = atoms_per_bin/dev.team_size()<1?1:atoms_per_bin/dev.team_size();
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const int MY_BIN = dev.team_rank()/atoms_per_bin;
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const int ibin = dev.league_rank()*BINS_PER_TEAM+MY_BIN;
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if(ibin >=c_bincount.dimension_0()) return;
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X_FLOAT* other_x = sharedmem;
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other_x = other_x + 5*atoms_per_bin*MY_BIN;
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int* other_id = (int*) &other_x[4 * atoms_per_bin];
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int bincount_current = c_bincount[ibin];
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for(int kk = 0; kk < TEAMS_PER_BIN; kk++) {
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const int MY_II = dev.team_rank()%atoms_per_bin+kk*dev.team_size();
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const int i = MY_II < bincount_current ? c_bins(ibin, MY_II) : -1;
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/* if necessary, goto next page and add pages */
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int n = 0;
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X_FLOAT xtmp;
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X_FLOAT ytmp;
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X_FLOAT ztmp;
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int itype;
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const AtomNeighbors neighbors_i = neigh_list.get_neighbors((i>=0&&i<nlocal)?i:0);
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if(i >= 0) {
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xtmp = x(i, 0);
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ytmp = x(i, 1);
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ztmp = x(i, 2);
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itype = type(i);
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other_x[MY_II] = xtmp;
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other_x[MY_II + atoms_per_bin] = ytmp;
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other_x[MY_II + 2 * atoms_per_bin] = ztmp;
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other_x[MY_II + 3 * atoms_per_bin] = itype;
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}
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other_id[MY_II] = i;
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int test = (__syncthreads_count(i >= 0 && i <= nlocal) == 0);
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if(test) return;
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if(i >= 0 && i < nlocal) {
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#pragma unroll 4
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for(int m = 0; m < bincount_current; m++) {
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int j = other_id[m];
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const int jtype = other_x[m + 3 * atoms_per_bin];
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//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists
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if((j == i) ||
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(HalfNeigh && !Newton && (j < i)) ||
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(HalfNeigh && Newton &&
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((j < i) ||
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((j >= nlocal) && ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) ||
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(x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp)))))
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) continue;
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if(Tri) {
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if (x(j,2) < ztmp) continue;
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if (x(j,2) == ztmp) {
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if (x(j,1) < ytmp) continue;
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if (x(j,1) == ytmp) {
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if (x(j,0) < xtmp) continue;
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if (x(j,0) == xtmp && j <= i) continue;
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}
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}
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}
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if(exclude && exclusion(i,j,itype,jtype)) continue;
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const X_FLOAT delx = xtmp - other_x[m];
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const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
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const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
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const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
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if(rsq <= cutneighsq(itype,jtype)) {
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if (molecular) {
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int which = 0;
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if (!moltemplate)
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which = NeighborKokkosExecute<DeviceType>::find_special(i,j);
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/* else if (imol >= 0) */
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/* which = find_special(onemols[imol]->special[iatom], */
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/* onemols[imol]->nspecial[iatom], */
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/* tag[j]-tagprev); */
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/* else which = 0; */
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if (which == 0){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}else if (minimum_image_check(delx,dely,delz)){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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else if (which > 0) {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
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else n++;
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}
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} else {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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}
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}
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}
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__syncthreads();
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const typename ArrayTypes<DeviceType>::t_int_1d_const_um stencil
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= d_stencil;
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for(int k = 0; k < nstencil; k++) {
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const int jbin = ibin + stencil[k];
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if(ibin == jbin) continue;
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bincount_current = c_bincount[jbin];
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int j = MY_II < bincount_current ? c_bins(jbin, MY_II) : -1;
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if(j >= 0) {
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other_x[MY_II] = x(j, 0);
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other_x[MY_II + atoms_per_bin] = x(j, 1);
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other_x[MY_II + 2 * atoms_per_bin] = x(j, 2);
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other_x[MY_II + 3 * atoms_per_bin] = type(j);
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}
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other_id[MY_II] = j;
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__syncthreads();
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if(i >= 0 && i < nlocal) {
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#pragma unroll 8
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for(int m = 0; m < bincount_current; m++) {
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const int j = other_id[m];
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const int jtype = other_x[m + 3 * atoms_per_bin];
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//if(HalfNeigh && (j < i)) continue;
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if(HalfNeigh && !Newton && (j < i)) continue;
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if(!HalfNeigh && j==i) continue;
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if(Tri) {
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if (x(j,2) < ztmp) continue;
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if (x(j,2) == ztmp) {
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if (x(j,1) < ytmp) continue;
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if (x(j,1) == ytmp) {
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if (x(j,0) < xtmp) continue;
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if (x(j,0) == xtmp && j <= i) continue;
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}
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}
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}
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if(exclude && exclusion(i,j,itype,jtype)) continue;
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const X_FLOAT delx = xtmp - other_x[m];
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const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
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const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
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const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
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if(rsq <= cutneighsq(itype,jtype)) {
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if (molecular) {
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int which = 0;
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if (!moltemplate)
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which = NeighborKokkosExecute<DeviceType>::find_special(i,j);
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/* else if (imol >= 0) */
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/* which = find_special(onemols[imol]->special[iatom], */
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/* onemols[imol]->nspecial[iatom], */
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/* tag[j]-tagprev); */
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/* else which = 0; */
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if (which == 0){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}else if (minimum_image_check(delx,dely,delz)){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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else if (which > 0) {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
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else n++;
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}
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} else {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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}
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}
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}
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__syncthreads();
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}
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if(i >= 0 && i < nlocal) {
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neigh_list.d_numneigh(i) = n;
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neigh_list.d_ilist(i) = i;
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}
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if(n >= neigh_list.maxneighs) {
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resize() = 1;
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if(n >= new_maxneighs()) new_maxneighs() = n;
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}
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}
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}
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#endif
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/* ---------------------------------------------------------------------- */
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template<class DeviceType> template<int HalfNeigh>
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void NeighborKokkosExecute<DeviceType>::
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build_Item_Ghost(const int &i) const
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{
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/* if necessary, goto next page and add pages */
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int n = 0;
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int which = 0;
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int moltemplate;
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if (molecular == 2) moltemplate = 1;
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else moltemplate = 0;
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// get subview of neighbors of i
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const AtomNeighbors neighbors_i = neigh_list.get_neighbors(i);
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const X_FLOAT xtmp = x(i, 0);
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const X_FLOAT ytmp = x(i, 1);
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const X_FLOAT ztmp = x(i, 2);
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const int itype = type(i);
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const typename ArrayTypes<DeviceType>::t_int_1d_const_um stencil
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= d_stencil;
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const typename ArrayTypes<DeviceType>::t_int_1d_3_const_um stencilxyz
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= d_stencilxyz;
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// loop over all atoms in surrounding bins in stencil including self
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// when i is a ghost atom, must check if stencil bin is out of bounds
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// skip i = j
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// no molecular test when i = ghost atom
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if (i < nlocal) {
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const int ibin = coord2bin(xtmp, ytmp, ztmp);
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for (int k = 0; k < nstencil; k++) {
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const int jbin = ibin + stencil[k];
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for(int m = 0; m < c_bincount(jbin); m++) {
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const int j = c_bins(jbin,m);
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if (HalfNeigh && j <= i) continue;
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else if (j == i) continue;
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const int jtype = type[j];
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if(exclude && exclusion(i,j,itype,jtype)) continue;
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const X_FLOAT delx = xtmp - x(j,0);
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const X_FLOAT dely = ytmp - x(j,1);
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const X_FLOAT delz = ztmp - x(j,2);
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const X_FLOAT rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq(itype,jtype)) {
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if (molecular) {
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if (!moltemplate)
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which = find_special(i,j);
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/* else if (imol >= 0) */
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/* which = find_special(onemols[imol]->special[iatom], */
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/* onemols[imol]->nspecial[iatom], */
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/* tag[j]-tagprev); */
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/* else which = 0; */
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if (which == 0){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}else if (minimum_image_check(delx,dely,delz)){
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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else if (which > 0) {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
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else n++;
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}
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} else {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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}
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}
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}
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} else {
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int binxyz[3];
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const int ibin = coord2bin(xtmp, ytmp, ztmp, binxyz);
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const int xbin = binxyz[0];
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const int ybin = binxyz[1];
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const int zbin = binxyz[2];
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for (int k = 0; k < nstencil; k++) {
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const X_FLOAT xbin2 = xbin + stencilxyz(k,0);
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const X_FLOAT ybin2 = ybin + stencilxyz(k,1);
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const X_FLOAT zbin2 = zbin + stencilxyz(k,2);
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if (xbin2 < 0 || xbin2 >= mbinx ||
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ybin2 < 0 || ybin2 >= mbiny ||
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zbin2 < 0 || zbin2 >= mbinz) continue;
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const int jbin = ibin + stencil[k];
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for(int m = 0; m < c_bincount(jbin); m++) {
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const int j = c_bins(jbin,m);
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if (HalfNeigh && j <= i) continue;
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else if (j == i) continue;
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const int jtype = type[j];
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if(exclude && exclusion(i,j,itype,jtype)) continue;
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const X_FLOAT delx = xtmp - x(j,0);
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const X_FLOAT dely = ytmp - x(j,1);
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const X_FLOAT delz = ztmp - x(j,2);
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const X_FLOAT rsq = delx*delx + dely*dely + delz*delz;
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if (rsq <= cutneighsq(itype,jtype)) {
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if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
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else n++;
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}
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}
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}
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}
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neigh_list.d_numneigh(i) = n;
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if(n >= neigh_list.maxneighs) {
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resize() = 1;
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if(n >= new_maxneighs()) new_maxneighs() = n;
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}
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neigh_list.d_ilist(i) = i;
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}
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}
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namespace LAMMPS_NS {
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template class NPairKokkos<LMPDeviceType,0,0,0>;
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template class NPairKokkos<LMPDeviceType,0,1,0>;
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template class NPairKokkos<LMPDeviceType,1,0,0>;
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template class NPairKokkos<LMPDeviceType,1,1,0>;
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template class NPairKokkos<LMPDeviceType,1,0,1>;
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#ifdef KOKKOS_HAVE_CUDA
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template class NPairKokkos<LMPHostType,0,0,0>;
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template class NPairKokkos<LMPHostType,0,1,0>;
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template class NPairKokkos<LMPHostType,1,0,0>;
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template class NPairKokkos<LMPHostType,1,1,0>;
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template class NPairKokkos<LMPHostType,1,0,1>;
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#endif
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}
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