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lammps/src/KOKKOS/neigh_full_kokkos.h
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/* -*- c++ -*- ----------------------------------------------------------
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 "atom_kokkos.h"
#include "atom_masks.h"
#include "domain_kokkos.h"
namespace LAMMPS_NS {
/* ---------------------------------------------------------------------- */
template<class DeviceType, int HALF_NEIGH, int GHOST>
void NeighborKokkos::full_bin_kokkos(NeighListKokkos<DeviceType> *list)
{
const int nlocal = includegroup?atom->nfirst:atom->nlocal;
int nall = nlocal;
if (GHOST)
nall += atom->nghost;
list->grow(nall);
NeighborKokkosExecute<DeviceType>
data(*list,
k_cutneighsq.view<DeviceType>(),
k_bincount.view<DeviceType>(),
k_bins.view<DeviceType>(),nlocal,
atomKK->k_x.view<DeviceType>(),
atomKK->k_type.view<DeviceType>(),
atomKK->k_mask.view<DeviceType>(),
atomKK->k_molecule.view<DeviceType>(),
atomKK->k_tag.view<DeviceType>(),
atomKK->k_special.view<DeviceType>(),
atomKK->k_nspecial.view<DeviceType>(),
atomKK->molecular,
nbinx,nbiny,nbinz,mbinx,mbiny,mbinz,mbinxlo,mbinylo,mbinzlo,
bininvx,bininvy,bininvz,
exclude, nex_type,maxex_type,
k_ex1_type.view<DeviceType>(),
k_ex2_type.view<DeviceType>(),
k_ex_type.view<DeviceType>(),
nex_group,maxex_group,
k_ex1_group.view<DeviceType>(),
k_ex2_group.view<DeviceType>(),
k_ex1_bit.view<DeviceType>(),
k_ex2_bit.view<DeviceType>(),
nex_mol, maxex_mol,
k_ex_mol_group.view<DeviceType>(),
k_ex_mol_bit.view<DeviceType>(),
bboxhi,bboxlo,
domain->xperiodic,domain->yperiodic,domain->zperiodic,
domain->xprd_half,domain->yprd_half,domain->zprd_half);
k_cutneighsq.sync<DeviceType>();
k_ex1_type.sync<DeviceType>();
k_ex2_type.sync<DeviceType>();
k_ex_type.sync<DeviceType>();
k_ex1_group.sync<DeviceType>();
k_ex2_group.sync<DeviceType>();
k_ex1_bit.sync<DeviceType>();
k_ex2_bit.sync<DeviceType>();
k_ex_mol_group.sync<DeviceType>();
k_ex_mol_bit.sync<DeviceType>();
atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
Kokkos::deep_copy(list->d_stencil,list->h_stencil);
if (GHOST)
Kokkos::deep_copy(list->d_stencilxyz,list->h_stencilxyz);
data.special_flag[0] = special_flag[0];
data.special_flag[1] = special_flag[1];
data.special_flag[2] = special_flag[2];
data.special_flag[3] = special_flag[3];
while(data.h_resize() > 0) {
data.h_resize() = 0;
deep_copy(data.resize, data.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();
NeighborKokkosBinAtomsFunctor<DeviceType> f(data);
Kokkos::parallel_for(atom->nlocal+atom->nghost, f);
DeviceType::fence();
deep_copy(data.h_resize, data.resize);
if(data.h_resize()) {
atoms_per_bin += 16;
k_bins = DAT::tdual_int_2d("bins", mbins, atoms_per_bin);
data.bins = k_bins.view<DeviceType>();
data.c_bins = data.bins;
}
}
if(list->d_neighbors.dimension_0()<nall) {
list->d_neighbors = typename ArrayTypes<DeviceType>::t_neighbors_2d("neighbors", nall*1.1, list->maxneighs);
list->d_numneigh = typename ArrayTypes<DeviceType>::t_int_1d("numneigh", nall*1.1);
data.neigh_list.d_neighbors = list->d_neighbors;
data.neigh_list.d_numneigh = list->d_numneigh;
}
data.h_resize()=1;
while(data.h_resize()) {
data.h_new_maxneighs() = list->maxneighs;
data.h_resize() = 0;
Kokkos::deep_copy(data.resize, data.h_resize);
Kokkos::deep_copy(data.new_maxneighs, data.h_new_maxneighs);
#ifdef KOKKOS_HAVE_CUDA
#define BINS_PER_BLOCK 2
const int factor = atoms_per_bin<64?2:1;
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,atoms_per_bin*factor);
#else
const int factor = 1;
#endif
if (GHOST && !HALF_NEIGH) {
NeighborKokkosBuildFunctorFullGhost<DeviceType> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
Kokkos::parallel_for(nall, f);
} else {
if(newton_pair) {
NeighborKokkosBuildFunctor<DeviceType,HALF_NEIGH,1> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
#ifdef KOKKOS_HAVE_CUDA
Kokkos::parallel_for(config, f);
#else
Kokkos::parallel_for(nall, f);
#endif
} else {
NeighborKokkosBuildFunctor<DeviceType,HALF_NEIGH,0> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
#ifdef KOKKOS_HAVE_CUDA
Kokkos::parallel_for(config, f);
#else
Kokkos::parallel_for(nall, f);
#endif
}
}
DeviceType::fence();
deep_copy(data.h_resize, data.resize);
if(data.h_resize()) {
deep_copy(data.h_new_maxneighs, data.new_maxneighs);
list->maxneighs = data.h_new_maxneighs() * 1.2;
list->d_neighbors = typename ArrayTypes<DeviceType>::t_neighbors_2d("neighbors", list->d_neighbors.dimension_0(), list->maxneighs);
data.neigh_list.d_neighbors = list->d_neighbors;
data.neigh_list.maxneighs = list->maxneighs;
}
}
if (GHOST) {
list->inum = atom->nlocal;
list->gnum = nall - atom->nlocal;
} else {
list->inum = nall;
list->gnum = 0;
}
}
/* ---------------------------------------------------------------------- */
template<class Device>
KOKKOS_INLINE_FUNCTION
void NeighborKokkosExecute<Device>::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 {
resize() = 1;
}
}
/* ---------------------------------------------------------------------- */
template<class Device>
KOKKOS_INLINE_FUNCTION
int NeighborKokkosExecute<Device>::find_special(const int &i, const int &j) const
{
const int n1 = nspecial(i,0);
const int n2 = nspecial(i,1);
const int n3 = nspecial(i,2);
for (int k = 0; k < n3; k++) {
if (special(i,k) == tag(j)) {
if (k < n1) {
if (special_flag[1] == 0) return -1;
else if (special_flag[1] == 1) return 0;
else return 1;
} else if (k < n2) {
if (special_flag[2] == 0) return -1;
else if (special_flag[2] == 1) return 0;
else return 2;
} else {
if (special_flag[3] == 0) return -1;
else if (special_flag[3] == 1) return 0;
else return 3;
}
}
}
return 0;
};
/* ---------------------------------------------------------------------- */
template<class Device>
KOKKOS_INLINE_FUNCTION
int NeighborKokkosExecute<Device>::exclusion(const int &i,const int &j,
const int &itype,const int &jtype) const
{
int m;
if (nex_type && ex_type(itype,jtype)) return 1;
if (nex_group) {
for (m = 0; m < nex_group; m++) {
if (mask(i) & ex1_bit(m) && mask(j) & ex2_bit(m)) return 1;
if (mask(i) & ex2_bit(m) && mask(j) & ex1_bit(m)) return 1;
}
}
if (nex_mol) {
for (m = 0; m < nex_mol; m++)
if (mask(i) & ex_mol_bit(m) && mask(j) & ex_mol_bit(m) &&
molecule(i) == molecule(j)) return 1;
}
return 0;
}
/* ---------------------------------------------------------------------- */
template<class Device> template<int HalfNeigh,int GhostNewton>
void NeighborKokkosExecute<Device>::
build_Item(const int &i) const
{
/* if necessary, goto next page and add pages */
int n = 0;
int which = 0;
int moltemplate;
if (molecular == 2) moltemplate = 1;
else moltemplate = 0;
// get subview of neighbors of i
const AtomNeighbors neighbors_i = neigh_list.get_neighbors(i);
const X_FLOAT xtmp = x(i, 0);
const X_FLOAT ytmp = x(i, 1);
const X_FLOAT ztmp = x(i, 2);
const int itype = type(i);
const int ibin = coord2bin(xtmp, ytmp, ztmp);
const int nstencil = neigh_list.nstencil;
const typename ArrayTypes<Device>::t_int_1d_const_um stencil
= neigh_list.d_stencil;
// loop over all bins in neighborhood (includes ibin)
if(HalfNeigh)
for(int m = 0; m < c_bincount(ibin); m++) {
const int j = c_bins(ibin,m);
const int jtype = type(j);
//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using HalfNeighborlists
if((j == i) || (HalfNeigh && !GhostNewton && (j < i)) ||
(HalfNeigh && GhostNewton && ((j < i) || ((j >= nlocal) &&
((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) ||
(x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp)))))
) continue;
if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - x(j, 0);
const X_FLOAT dely = ytmp - x(j, 1);
const X_FLOAT delz = ztmp - x(j, 2);
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq <= cutneighsq(itype,jtype)) {
if (molecular) {
if (!moltemplate)
which = find_special(i,j);
/* else if (imol >= 0) */
/* which = find_special(onemols[imol]->special[iatom], */
/* onemols[imol]->nspecial[iatom], */
/* tag[j]-tagprev); */
/* else which = 0; */
if (which == 0){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}else if (minimum_image_check(delx,dely,delz)){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
else if (which > 0) {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
}
} else {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
}
}
for(int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
// get subview of jbin
if(HalfNeigh&&(ibin==jbin)) continue;
//const ArrayTypes<Device>::t_int_1d_const_um =Kokkos::subview<t_int_1d_const_um>(bins,jbin,ALL);
for(int m = 0; m < c_bincount(jbin); m++) {
const int j = c_bins(jbin,m);
const int jtype = type(j);
if(HalfNeigh && !GhostNewton && (j < i)) continue;
if(!HalfNeigh && j==i) continue;
if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - x(j, 0);
const X_FLOAT dely = ytmp - x(j, 1);
const X_FLOAT delz = ztmp - x(j, 2);
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq <= cutneighsq(itype,jtype)) {
if (molecular) {
if (!moltemplate)
which = find_special(i,j);
/* else if (imol >= 0) */
/* which = find_special(onemols[imol]->special[iatom], */
/* onemols[imol]->nspecial[iatom], */
/* tag[j]-tagprev); */
/* else which = 0; */
if (which == 0){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}else if (minimum_image_check(delx,dely,delz)){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
else if (which > 0) {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
}
} else {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
}
}
}
neigh_list.d_numneigh(i) = n;
if(n >= neigh_list.maxneighs) {
resize() = 1;
if(n >= new_maxneighs()) new_maxneighs() = n;
}
neigh_list.d_ilist(i) = i;
}
#ifdef KOKKOS_HAVE_CUDA
extern __shared__ X_FLOAT sharedmem[];
/* ---------------------------------------------------------------------- */
template<class DeviceType> template<int HalfNeigh,int GhostNewton>
__device__ inline
void NeighborKokkosExecute<DeviceType>::build_ItemCuda(typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const
{
/* loop over atoms in i's bin,
*/
const int atoms_per_bin = c_bins.dimension_1();
const int BINS_PER_TEAM = dev.team_size()/atoms_per_bin<1?1:dev.team_size()/atoms_per_bin;
const int TEAMS_PER_BIN = atoms_per_bin/dev.team_size()<1?1:atoms_per_bin/dev.team_size();
const int MY_BIN = dev.team_rank()/atoms_per_bin;
const int ibin = dev.league_rank()*BINS_PER_TEAM+MY_BIN;
if(ibin >=c_bincount.dimension_0()) return;
X_FLOAT* other_x = sharedmem;
other_x = other_x + 5*atoms_per_bin*MY_BIN;
int* other_id = (int*) &other_x[4 * atoms_per_bin];
int bincount_current = c_bincount[ibin];
for(int kk = 0; kk < TEAMS_PER_BIN; kk++) {
const int MY_II = dev.team_rank()%atoms_per_bin+kk*dev.team_size();
const int i = MY_II < bincount_current ? c_bins(ibin, MY_II) : -1;
/* if necessary, goto next page and add pages */
int n = 0;
X_FLOAT xtmp;
X_FLOAT ytmp;
X_FLOAT ztmp;
int itype;
const AtomNeighbors neighbors_i = neigh_list.get_neighbors((i>=0&&i<nlocal)?i:0);
if(i >= 0) {
xtmp = x(i, 0);
ytmp = x(i, 1);
ztmp = x(i, 2);
itype = type(i);
other_x[MY_II] = xtmp;
other_x[MY_II + atoms_per_bin] = ytmp;
other_x[MY_II + 2 * atoms_per_bin] = ztmp;
other_x[MY_II + 3 * atoms_per_bin] = itype;
}
other_id[MY_II] = i;
int test = (__syncthreads_count(i >= 0 && i <= nlocal) == 0);
if(test) return;
if(i >= 0 && i < nlocal) {
#pragma unroll 4
for(int m = 0; m < bincount_current; m++) {
int j = other_id[m];
const int jtype = other_x[m + 3 * atoms_per_bin];
//for same bin as atom i skip j if i==j and skip atoms "below and to the left" if using halfneighborlists
if((j == i) ||
(HalfNeigh && !GhostNewton && (j < i)) ||
(HalfNeigh && GhostNewton &&
((j < i) ||
((j >= nlocal) && ((x(j, 2) < ztmp) || (x(j, 2) == ztmp && x(j, 1) < ytmp) ||
(x(j, 2) == ztmp && x(j, 1) == ytmp && x(j, 0) < xtmp)))))
) continue;
if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - other_x[m];
const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq <= cutneighsq(itype,jtype)) {
if (molecular) {
int which = 0;
if (!moltemplate)
which = find_special(i,j);
/* else if (imol >= 0) */
/* which = find_special(onemols[imol]->special[iatom], */
/* onemols[imol]->nspecial[iatom], */
/* tag[j]-tagprev); */
/* else which = 0; */
if (which == 0){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}else if (minimum_image_check(delx,dely,delz)){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
else if (which > 0) {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
}
} else {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
}
}
}
__syncthreads();
const int nstencil = neigh_list.nstencil;
const typename ArrayTypes<DeviceType>::t_int_1d_const_um stencil
= neigh_list.d_stencil;
for(int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
if(ibin == jbin) continue;
bincount_current = c_bincount[jbin];
int j = MY_II < bincount_current ? c_bins(jbin, MY_II) : -1;
if(j >= 0) {
other_x[MY_II] = x(j, 0);
other_x[MY_II + atoms_per_bin] = x(j, 1);
other_x[MY_II + 2 * atoms_per_bin] = x(j, 2);
other_x[MY_II + 3 * atoms_per_bin] = type(j);
}
other_id[MY_II] = j;
__syncthreads();
if(i >= 0 && i < nlocal) {
#pragma unroll 8
for(int m = 0; m < bincount_current; m++) {
const int j = other_id[m];
const int jtype = other_x[m + 3 * atoms_per_bin];
//if(HalfNeigh && (j < i)) continue;
if(HalfNeigh && !GhostNewton && (j < i)) continue;
if(!HalfNeigh && j==i) continue;
if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - other_x[m];
const X_FLOAT dely = ytmp - other_x[m + atoms_per_bin];
const X_FLOAT delz = ztmp - other_x[m + 2 * atoms_per_bin];
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq <= cutneighsq(itype,jtype)) {
if (molecular) {
int which = 0;
if (!moltemplate)
which = find_special(i,j);
/* else if (imol >= 0) */
/* which = find_special(onemols[imol]->special[iatom], */
/* onemols[imol]->nspecial[iatom], */
/* tag[j]-tagprev); */
/* else which = 0; */
if (which == 0){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}else if (minimum_image_check(delx,dely,delz)){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
else if (which > 0) {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
}
} else {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
}
}
}
__syncthreads();
}
if(i >= 0 && i < nlocal) {
neigh_list.d_numneigh(i) = n;
neigh_list.d_ilist(i) = i;
}
if(n >= neigh_list.maxneighs) {
resize() = 1;
if(n >= new_maxneighs()) new_maxneighs() = n;
}
}
}
#endif
/* ---------------------------------------------------------------------- */
template<class Device>
void NeighborKokkosExecute<Device>::
build_Item_Full_Ghost(const int &i) const
{
/* if necessary, goto next page and add pages */
int n = 0;
int which = 0;
int moltemplate;
if (molecular == 2) moltemplate = 1;
else moltemplate = 0;
// get subview of neighbors of i
const AtomNeighbors neighbors_i = neigh_list.get_neighbors(i);
const X_FLOAT xtmp = x(i, 0);
const X_FLOAT ytmp = x(i, 1);
const X_FLOAT ztmp = x(i, 2);
const int itype = type(i);
const int nstencil = neigh_list.nstencil;
const typename ArrayTypes<Device>::t_int_1d_const_um stencil
= neigh_list.d_stencil;
const typename ArrayTypes<Device>::t_int_1d_3_const_um stencilxyz
= neigh_list.d_stencilxyz;
// loop over all atoms in surrounding bins in stencil including self
// when i is a ghost atom, must check if stencil bin is out of bounds
// skip i = j
// no molecular test when i = ghost atom
if (i < nlocal) {
const int ibin = coord2bin(xtmp, ytmp, ztmp);
for (int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
for(int m = 0; m < c_bincount(jbin); m++) {
const int j = c_bins(jbin,m);
if (i == j) continue;
const int jtype = type[j];
if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
const X_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq(itype,jtype)) {
if (molecular) {
if (!moltemplate)
which = find_special(i,j);
/* else if (imol >= 0) */
/* which = find_special(onemols[imol]->special[iatom], */
/* onemols[imol]->nspecial[iatom], */
/* tag[j]-tagprev); */
/* else which = 0; */
if (which == 0){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}else if (minimum_image_check(delx,dely,delz)){
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
else if (which > 0) {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j ^ (which << SBBITS);
}
} else {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
}
}
}
} else {
int binxyz[3];
const int ibin = coord2bin(xtmp, ytmp, ztmp, binxyz);
const int xbin = binxyz[0];
const int ybin = binxyz[1];
const int zbin = binxyz[2];
for (int k = 0; k < nstencil; k++) {
const X_FLOAT xbin2 = xbin + stencilxyz(k,0);
const X_FLOAT ybin2 = ybin + stencilxyz(k,1);
const X_FLOAT zbin2 = zbin + stencilxyz(k,2);
if (xbin2 < 0 || xbin2 >= mbinx ||
ybin2 < 0 || ybin2 >= mbiny ||
zbin2 < 0 || zbin2 >= mbinz) continue;
const int jbin = ibin + stencil[k];
for(int m = 0; m < c_bincount(jbin); m++) {
const int j = c_bins(jbin,m);
if (i == j) continue;
const int jtype = type[j];
if(exclude && exclusion(i,j,itype,jtype)) continue;
const X_FLOAT delx = xtmp - x(j,0);
const X_FLOAT dely = ytmp - x(j,1);
const X_FLOAT delz = ztmp - x(j,2);
const X_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq <= cutneighsq(itype,jtype)) {
if(n<neigh_list.maxneighs) neighbors_i(n++) = j;
}
}
}
}
neigh_list.d_numneigh(i) = n;
if(n >= neigh_list.maxneighs) {
resize() = 1;
if(n >= new_maxneighs()) new_maxneighs() = n;
}
neigh_list.d_ilist(i) = i;
}
template<class DeviceType>
void NeighborKokkos::full_bin_cluster_kokkos(NeighListKokkos<DeviceType> *list)
{
const int nall = includegroup?atom->nfirst:atom->nlocal;
list->grow(nall);
NeighborKokkosExecute<DeviceType>
data(*list,
k_cutneighsq.view<DeviceType>(),
k_bincount.view<DeviceType>(),
k_bins.view<DeviceType>(),nall,
atomKK->k_x.view<DeviceType>(),
atomKK->k_type.view<DeviceType>(),
atomKK->k_mask.view<DeviceType>(),
atomKK->k_molecule.view<DeviceType>(),
atomKK->k_tag.view<DeviceType>(),
atomKK->k_special.view<DeviceType>(),
atomKK->k_nspecial.view<DeviceType>(),
atomKK->molecular,
nbinx,nbiny,nbinz,mbinx,mbiny,mbinz,mbinxlo,mbinylo,mbinzlo,
bininvx,bininvy,bininvz,
exclude, nex_type,maxex_type,
k_ex1_type.view<DeviceType>(),
k_ex2_type.view<DeviceType>(),
k_ex_type.view<DeviceType>(),
nex_group,maxex_group,
k_ex1_group.view<DeviceType>(),
k_ex2_group.view<DeviceType>(),
k_ex1_bit.view<DeviceType>(),
k_ex2_bit.view<DeviceType>(),
nex_mol, maxex_mol,
k_ex_mol_group.view<DeviceType>(),
k_ex_mol_bit.view<DeviceType>(),
bboxhi,bboxlo,
domain->xperiodic,domain->yperiodic,domain->zperiodic,
domain->xprd_half,domain->yprd_half,domain->zprd_half);
k_cutneighsq.sync<DeviceType>();
k_ex1_type.sync<DeviceType>();
k_ex2_type.sync<DeviceType>();
k_ex_type.sync<DeviceType>();
k_ex1_group.sync<DeviceType>();
k_ex2_group.sync<DeviceType>();
k_ex1_bit.sync<DeviceType>();
k_ex2_bit.sync<DeviceType>();
k_ex_mol_group.sync<DeviceType>();
k_ex_mol_bit.sync<DeviceType>();
data.special_flag[0] = special_flag[0];
data.special_flag[1] = special_flag[1];
data.special_flag[2] = special_flag[2];
data.special_flag[3] = special_flag[3];
atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
Kokkos::deep_copy(list->d_stencil,list->h_stencil);
DeviceType::fence();
while(data.h_resize() > 0) {
data.h_resize() = 0;
deep_copy(data.resize, data.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();
NeighborKokkosBinAtomsFunctor<DeviceType> f(data);
Kokkos::parallel_for(atom->nlocal+atom->nghost, f);
DeviceType::fence();
deep_copy(data.h_resize, data.resize);
if(data.h_resize()) {
atoms_per_bin += 16;
k_bins = DAT::tdual_int_2d("bins", mbins, atoms_per_bin);
data.bins = k_bins.view<DeviceType>();
data.c_bins = data.bins;
}
}
if(list->d_neighbors.dimension_0()<nall) {
list->d_neighbors = typename ArrayTypes<DeviceType>::t_neighbors_2d("neighbors", nall*1.1, list->maxneighs);
list->d_numneigh = typename ArrayTypes<DeviceType>::t_int_1d("numneigh", nall*1.1);
data.neigh_list.d_neighbors = list->d_neighbors;
data.neigh_list.d_numneigh = list->d_numneigh;
}
data.h_resize()=1;
while(data.h_resize()) {
data.h_new_maxneighs() = list->maxneighs;
data.h_resize() = 0;
Kokkos::deep_copy(data.resize, data.h_resize);
Kokkos::deep_copy(data.new_maxneighs, data.h_new_maxneighs);
#ifdef KOKKOS_HAVE_CUDA
#define BINS_PER_BLOCK 2
const int factor = atoms_per_bin<64?2:1;
Kokkos::TeamPolicy<DeviceType> config((mbins+factor-1)/factor,atoms_per_bin*factor);
#else
const int factor = 1;
#endif
if(newton_pair) {
NeighborClusterKokkosBuildFunctor<DeviceType,NeighClusterSize> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
//#ifdef KOKKOS_HAVE_CUDA
// Kokkos::parallel_for(config, f);
//#else
Kokkos::parallel_for(nall, f);
//#endif
} else {
NeighborClusterKokkosBuildFunctor<DeviceType,NeighClusterSize> f(data,atoms_per_bin * 5 * sizeof(X_FLOAT) * factor);
//#ifdef KOKKOS_HAVE_CUDA
// Kokkos::parallel_for(config, f);
//#else
Kokkos::parallel_for(nall, f);
//#endif
}
DeviceType::fence();
deep_copy(data.h_resize, data.resize);
if(data.h_resize()) {
deep_copy(data.h_new_maxneighs, data.new_maxneighs);
list->maxneighs = data.h_new_maxneighs() * 1.2;
list->d_neighbors = typename ArrayTypes<DeviceType>::t_neighbors_2d("neighbors", list->d_neighbors.dimension_0(), list->maxneighs);
data.neigh_list.d_neighbors = list->d_neighbors;
data.neigh_list.maxneighs = list->maxneighs;
}
}
list->inum = nall;
list->gnum = 0;
}
/* ---------------------------------------------------------------------- */
template<class Device> template<int ClusterSize>
void NeighborKokkosExecute<Device>::
build_cluster_Item(const int &i) const
{
/* if necessary, goto next page and add pages */
int n = 0;
// get subview of neighbors of i
const AtomNeighbors neighbors_i = neigh_list.get_neighbors(i);
const X_FLOAT xtmp = x(i, 0);
const X_FLOAT ytmp = x(i, 1);
const X_FLOAT ztmp = x(i, 2);
const int itype = type(i);
const int ibin = coord2bin(xtmp, ytmp, ztmp);
const int nstencil = neigh_list.nstencil;
const typename ArrayTypes<Device>::t_int_1d_const_um stencil
= neigh_list.d_stencil;
for(int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
for(int m = 0; m < c_bincount(jbin); m++) {
const int j = c_bins(jbin,m);
bool skip = i == j;
for(int k = 0; k< (n<neigh_list.maxneighs?n:neigh_list.maxneighs); k++)
if((j-(j%ClusterSize)) == neighbors_i(k)) {skip=true;};//{m += ClusterSize - j&(ClusterSize-1)-1; skip=true;}
if(!skip) {
const int jtype = type(j);
const X_FLOAT delx = xtmp - x(j, 0);
const X_FLOAT dely = ytmp - x(j, 1);
const X_FLOAT delz = ztmp - x(j, 2);
const X_FLOAT rsq = delx * delx + dely * dely + delz * delz;
if(rsq <= cutneighsq(itype,jtype)) {
if(n<neigh_list.maxneighs) neighbors_i(n) = (j-(j%ClusterSize));
n++;
//m += ClusterSize - j&(ClusterSize-1)-1;
}
}
}
}
neigh_list.d_numneigh(i) = n;
if(n >= neigh_list.maxneighs) {
resize() = 1;
if(n >= new_maxneighs()) new_maxneighs() = n;
}
neigh_list.d_ilist(i) = i;
}
}
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