forked from lijiext/lammps
Add Kokkos halffull neighbor list capability
This commit is contained in:
Stan Moore
parent
45674e6cd3
commit
1ec54827d6
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@ -151,6 +151,8 @@ action neighbor_kokkos.cpp
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action neighbor_kokkos.h
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action npair_copy_kokkos.cpp
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action npair_copy_kokkos.h
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action npair_halffull_kokkos.cpp
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action npair_halffull_kokkos.h
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action npair_skip_kokkos.cpp
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action npair_skip_kokkos.h
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action npair_kokkos.cpp
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@ -0,0 +1,125 @@
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/* ----------------------------------------------------------------------
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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_halffull_kokkos.h"
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#include "neighbor.h"
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#include "neigh_list_kokkos.h"
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#include "atom_kokkos.h"
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#include "atom_vec.h"
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#include "molecule.h"
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#include "domain.h"
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#include "my_page.h"
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#include "error.h"
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#include "atom_masks.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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template<class DeviceType, int NEWTON>
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NPairHalffullKokkos<DeviceType,NEWTON>::NPairHalffullKokkos(LAMMPS *lmp) : NPair(lmp) {
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atomKK = (AtomKokkos *) atom;
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execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
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}
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/* ----------------------------------------------------------------------
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build half list from full list
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pair stored once if i,j are both owned and i < j
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pair stored by me if j is ghost (also stored by proc owning j)
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works if full list is a skip list
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works for owned (non-ghost) list, also for ghost list
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if ghost, also store neighbors of ghost atoms & set inum,gnum correctly
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------------------------------------------------------------------------- */
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template<class DeviceType, int NEWTON>
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void NPairHalffullKokkos<DeviceType,NEWTON>::build(NeighList *list)
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{
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if (NEWTON) {
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x = atomKK->k_x.view<DeviceType>();
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atomKK->sync(execution_space,X_MASK);
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}
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nlocal = atom->nlocal;
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NeighListKokkos<DeviceType>* k_list_full = static_cast<NeighListKokkos<DeviceType>*>(list->listfull);
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d_ilist_full = k_list_full->d_ilist;
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d_numneigh_full = k_list_full->d_numneigh;
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d_neighbors_full = k_list_full->d_neighbors;
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int inum_full = list->listfull->inum;
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if (list->ghost) inum_full += list->listfull->gnum;
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NeighListKokkos<DeviceType>* k_list = static_cast<NeighListKokkos<DeviceType>*>(list);
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k_list->maxneighs = k_list_full->maxneighs; // simple, but could be made more memory efficient
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k_list->grow(inum_full);
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d_ilist = k_list->d_ilist;
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d_numneigh = k_list->d_numneigh;
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d_neighbors = k_list->d_neighbors;
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// loop over parent full list
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Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagNPairHalffullCompute>(0,inum_full),*this);
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list->inum = k_list_full->inum;
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list->gnum = k_list_full->gnum;
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k_list->k_ilist.template modify<DeviceType>();
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}
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template<class DeviceType, int NEWTON>
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KOKKOS_INLINE_FUNCTION
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void NPairHalffullKokkos<DeviceType,NEWTON>::operator()(TagNPairHalffullCompute, const int &ii) const {
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int n = 0;
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const int i = d_ilist_full(ii);
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F_FLOAT xtmp,ytmp,ztmp;
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if (NEWTON) {
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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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}
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// loop over full neighbor list
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const int jnum = d_numneigh_full(i);
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const AtomNeighbors neighbors_i = AtomNeighbors(&d_neighbors(i,0),d_numneigh(i),
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&d_neighbors(i,1)-&d_neighbors(i,0));
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for (int jj = 0; jj < jnum; jj++) {
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const int joriginal = d_neighbors_full(i,jj);
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const int j = joriginal & NEIGHMASK;
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if (NEWTON) {
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if (j < nlocal) {
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if (i > j) continue;
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} else {
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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 && x(j,0) < xtmp) continue;
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}
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}
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neighbors_i(n++) = joriginal;
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} else {
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if (j > i) neighbors_i(n++) = joriginal;
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}
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}
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d_numneigh(i) = n;
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d_ilist(ii) = i;
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}
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namespace LAMMPS_NS {
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template class NPairHalffullKokkos<LMPDeviceType,0>;
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template class NPairHalffullKokkos<LMPDeviceType,1>;
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#ifdef KOKKOS_HAVE_CUDA
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template class NPairHalffullKokkos<LMPHostType,0>;
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template class NPairHalffullKokkos<LMPHostType,1>;
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#endif
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}
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@ -0,0 +1,170 @@
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/* -*- 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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#ifdef NPAIR_CLASS
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// Newton
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typedef NPairHalffullKokkos<LMPDeviceType,1> NPairKokkosHalffullNewtonDevice;
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NPairStyle(halffull/newton/kk/device,
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NPairKokkosHalffullNewtonDevice,
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NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_KOKKOS_DEVICE)
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typedef NPairHalffullKokkos<LMPHostType,1> NPairKokkosHalffullNewtonHost;
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NPairStyle(halffull/newton/kk/host,
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NPairKokkosHalffullNewtonHost,
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NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_KOKKOS_HOST)
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typedef NPairHalffullKokkos<LMPDeviceType,1> NPairKokkosHalffullNewtonDevice;
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NPairStyle(halffull/newton/skip/kk/device,
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NPairKokkosHalffullNewtonDevice,
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NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_SKIP | NP_KOKKOS_DEVICE)
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typedef NPairHalffullKokkos<LMPHostType,1> NPairKokkosHalffullNewtonHost;
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NPairStyle(halffull/newton/skip/kk/host,
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NPairKokkosHalffullNewtonHost,
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NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_SKIP | NP_KOKKOS_HOST)
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// Newtoff
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typedef NPairHalffullKokkos<LMPDeviceType,0> NPairKokkosHalffullNewtoffDevice;
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NPairStyle(halffull/newtoff/kk/device,
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NPairKokkosHalffullNewtoffDevice,
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NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_KOKKOS_DEVICE)
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typedef NPairHalffullKokkos<LMPHostType,0> NPairKokkosHalffullNewtoffHost;
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NPairStyle(halffull/newtoff/kk/host,
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NPairKokkosHalffullNewtoffHost,
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NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_KOKKOS_HOST)
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typedef NPairHalffullKokkos<LMPDeviceType,0> NPairKokkosHalffullNewtoffDevice;
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NPairStyle(halffull/newtoff/skip/kk/device,
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NPairKokkosHalffullNewtoffDevice,
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NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_SKIP | NP_KOKKOS_DEVICE)
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typedef NPairHalffullKokkos<LMPHostType,0> NPairKokkosHalffullNewtoffHost;
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NPairStyle(halffull/newtoff/skip/kk/host,
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NPairKokkosHalffullNewtoffHost,
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NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_SKIP | NP_KOKKOS_HOST)
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//************ Ghost **************
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// Newton
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typedef NPairHalffullKokkos<LMPDeviceType,1> NPairKokkosHalffullNewtonGhostDevice;
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NPairStyle(halffull/newton/ghost/kk/device,
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NPairKokkosHalffullNewtonGhostDevice,
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NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_DEVICE)
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typedef NPairHalffullKokkos<LMPHostType,1> NPairKokkosHalffullNewtonHost;
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NPairStyle(halffull/newton/ghost/kk/host,
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NPairKokkosHalffullNewtonHost,
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NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_HOST)
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typedef NPairHalffullKokkos<LMPDeviceType,1> NPairKokkosHalffullNewtonGhostDevice;
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NPairStyle(halffull/newton/skip/ghost/kk/device,
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NPairKokkosHalffullNewtonGhostDevice,
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NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_KOKKOS_DEVICE)
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typedef NPairHalffullKokkos<LMPHostType,1> NPairKokkosHalffullNewtonHost;
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NPairStyle(halffull/newton/skip/ghost/kk/host,
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NPairKokkosHalffullNewtonHost,
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NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_KOKKOS_HOST)
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// Newtoff
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typedef NPairHalffullKokkos<LMPDeviceType,0> NPairKokkosHalffullNewtoffGhostDevice;
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NPairStyle(halffull/newtoff/ghost/kk/device,
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NPairKokkosHalffullNewtoffGhostDevice,
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NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_DEVICE)
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typedef NPairHalffullKokkos<LMPHostType,0> NPairKokkosHalffullNewtoffHost;
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NPairStyle(halffull/newtoff/ghost/kk/host,
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NPairKokkosHalffullNewtoffHost,
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NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_GHOST | NP_KOKKOS_HOST)
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typedef NPairHalffullKokkos<LMPDeviceType,0> NPairKokkosHalffullNewtoffGhostDevice;
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NPairStyle(halffull/newtoff/skip/ghost/kk/device,
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NPairKokkosHalffullNewtoffGhostDevice,
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NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_KOKKOS_DEVICE)
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typedef NPairHalffullKokkos<LMPHostType,0> NPairKokkosHalffullNewtoffHost;
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NPairStyle(halffull/newtoff/skip/ghost/kk/host,
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NPairKokkosHalffullNewtoffHost,
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NP_HALF_FULL | NP_NEWTOFF | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
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NP_ORTHO | NP_TRI | NP_GHOST | NP_SKIP | NP_KOKKOS_HOST)
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#else
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#ifndef LMP_NPAIR_HALFFULL_KOKKOS_H
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#define LMP_NPAIR_HALFFULL_KOKKOS_H
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#include "npair.h"
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#include "kokkos_type.h"
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namespace LAMMPS_NS {
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struct TagNPairHalffullCompute{};
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template<class DeviceType, int NEWTON>
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class NPairHalffullKokkos : public NPair {
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public:
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typedef DeviceType device_type;
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typedef ArrayTypes<DeviceType> AT;
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NPairHalffullKokkos(class LAMMPS *);
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~NPairHalffullKokkos() {}
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void build(class NeighList *);
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KOKKOS_INLINE_FUNCTION
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void operator()(TagNPairHalffullCompute, const int&) const;
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private:
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int nlocal;
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typename AT::t_x_array_randomread x;
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typename AT::t_neighbors_2d_const d_neighbors_full;
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typename AT::t_int_1d_const d_ilist_full;
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typename AT::t_int_1d_const d_numneigh_full;
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typename AT::t_neighbors_2d d_neighbors;
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typename AT::t_int_1d d_ilist;
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typename AT::t_int_1d d_numneigh;
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ExecutionSpace execution_space;
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};
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}
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#endif
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#endif
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/* ERROR/WARNING messages:
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*/
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