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first pass at implementing atom2bin for KOKKOS neighbor lists

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This commit is contained in:
Tim Mattox
2017-09-22 15:10:53 -05:00
parent 789812ec3d
commit 32e0de7a67
4 changed files with 17 additions and 34 deletions
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5
src/KOKKOS/nbin_kokkos.cpp
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@ -75,6 +75,10 @@ void NBinKokkos<DeviceType>::bin_atoms_setup(int nall)
k_bincount = DAT::tdual_int_1d("Neighbor::d_bincount",mbins);
bincount = k_bincount.view<DeviceType>();
}
if (nall > k_atom2bin.d_view.dimension_0()) {
k_atom2bin = DAT::tdual_int_1d("Neighbor::d_atom2bin",nall);
atom2bin = k_atom2bin.view<DeviceType>();
}
}
/* ----------------------------------------------------------------------
@ -125,6 +129,7 @@ void NBinKokkos<DeviceType>::binatomsItem(const int &i) const
{
const int ibin = coord2bin(x(i, 0), x(i, 1), x(i, 2));
atom2bin(i) = ibin;
const int ac = Kokkos::atomic_fetch_add(&bincount[ibin], (int)1);
if(ac < bins.dimension_1()) {
bins(ibin, ac) = i;

2
src/KOKKOS/nbin_kokkos.h
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@ -44,11 +44,13 @@ class NBinKokkos : public NBinStandard {
int atoms_per_bin;
DAT::tdual_int_1d k_bincount;
DAT::tdual_int_2d k_bins;
DAT::tdual_int_1d k_atom2bin;
typename AT::t_int_1d bincount;
const typename AT::t_int_1d_const c_bincount;
typename AT::t_int_2d bins;
typename AT::t_int_2d_const c_bins;
typename AT::t_int_1d atom2bin;
typename AT::t_int_scalar d_resize;
typename ArrayTypes<LMPHostType>::t_int_scalar h_resize;
typename AT::t_x_array_randomread x;

7
src/KOKKOS/npair_kokkos.cpp
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@ -73,6 +73,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::copy_bin_info()
atoms_per_bin = nbKK->atoms_per_bin;
k_bincount = nbKK->k_bincount;
k_bins = nbKK->k_bins;
k_atom2bin = nbKK->k_atom2bin;
}
/* ----------------------------------------------------------------------
@ -122,6 +123,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::build(NeighList *list_)
k_cutneighsq.view<DeviceType>(),
k_bincount.view<DeviceType>(),
k_bins.view<DeviceType>(),
k_atom2bin.view<DeviceType>(),
nstencil,
k_stencil.view<DeviceType>(),
k_stencilxyz.view<DeviceType>(),
@ -166,6 +168,7 @@ void NPairKokkos<DeviceType,HALF_NEIGH,GHOST,TRI>::build(NeighList *list_)
k_ex_mol_intra.sync<DeviceType>();
k_bincount.sync<DeviceType>();
k_bins.sync<DeviceType>();
k_atom2bin.sync<DeviceType>();
atomKK->sync(Device,X_MASK|TYPE_MASK|MASK_MASK|MOLECULE_MASK|TAG_MASK|SPECIAL_MASK);
data.special_flag[0] = special_flag[0];
@ -317,7 +320,7 @@ void NeighborKokkosExecute<DeviceType>::
const X_FLOAT ztmp = x(i, 2);
const int itype = type(i);
const int ibin = coord2bin(xtmp, ytmp, ztmp);
const int ibin = c_atom2bin(i);
const typename ArrayTypes<DeviceType>::t_int_1d_const_um stencil
= d_stencil;
@ -678,7 +681,7 @@ void NeighborKokkosExecute<DeviceType>::
// no molecular test when i = ghost atom
if (i < nlocal) {
const int ibin = coord2bin(xtmp, ytmp, ztmp);
const int ibin = c_atom2bin(i);
for (int k = 0; k < nstencil; k++) {
const int jbin = ibin + stencil[k];
for(int m = 0; m < c_bincount(jbin); m++) {

37
src/KOKKOS/npair_kokkos.h
View File

@ -105,6 +105,7 @@ class NPairKokkos : public NPair {
int atoms_per_bin;
DAT::tdual_int_1d k_bincount;
DAT::tdual_int_2d k_bins;
DAT::tdual_int_1d k_atom2bin;
// data from NStencil class
@ -148,6 +149,8 @@ class NeighborKokkosExecute
const typename AT::t_int_1d_const c_bincount;
typename AT::t_int_2d bins;
typename AT::t_int_2d_const c_bins;
const typename AT::t_int_1d atom2bin;
const typename AT::t_int_1d_const c_atom2bin;
// data from NStencil class
@ -190,6 +193,7 @@ class NeighborKokkosExecute
const typename AT::t_xfloat_2d_randomread &_cutneighsq,
const typename AT::t_int_1d &_bincount,
const typename AT::t_int_2d &_bins,
const typename AT::t_int_1d &_atom2bin,
const int _nstencil,
const typename AT::t_int_1d &_d_stencil,
const typename AT::t_int_1d_3 &_d_stencilxyz,
@ -224,6 +228,7 @@ class NeighborKokkosExecute
const int & _xprd_half, const int & _yprd_half, const int & _zprd_half):
neigh_list(_neigh_list), cutneighsq(_cutneighsq),
bincount(_bincount),c_bincount(_bincount),bins(_bins),c_bins(_bins),
atom2bin(_atom2bin),c_atom2bin(_atom2bin),
nstencil(_nstencil),d_stencil(_d_stencil),d_stencilxyz(_d_stencilxyz),
nlocal(_nlocal),
x(_x),type(_type),mask(_mask),molecule(_molecule),
@ -281,38 +286,6 @@ class NeighborKokkosExecute
void build_ItemCuda(typename Kokkos::TeamPolicy<DeviceType>::member_type dev) const;
#endif
KOKKOS_INLINE_FUNCTION
int coord2bin(const X_FLOAT & x,const X_FLOAT & y,const X_FLOAT & z) const
{
int ix,iy,iz;
if (x >= bboxhi[0])
ix = static_cast<int> ((x-bboxhi[0])*bininvx) + nbinx;
else if (x >= bboxlo[0]) {
ix = static_cast<int> ((x-bboxlo[0])*bininvx);
ix = MIN(ix,nbinx-1);
} else
ix = static_cast<int> ((x-bboxlo[0])*bininvx) - 1;
if (y >= bboxhi[1])
iy = static_cast<int> ((y-bboxhi[1])*bininvy) + nbiny;
else if (y >= bboxlo[1]) {
iy = static_cast<int> ((y-bboxlo[1])*bininvy);
iy = MIN(iy,nbiny-1);
} else
iy = static_cast<int> ((y-bboxlo[1])*bininvy) - 1;
if (z >= bboxhi[2])
iz = static_cast<int> ((z-bboxhi[2])*bininvz) + nbinz;
else if (z >= bboxlo[2]) {
iz = static_cast<int> ((z-bboxlo[2])*bininvz);
iz = MIN(iz,nbinz-1);
} else
iz = static_cast<int> ((z-bboxlo[2])*bininvz) - 1;
return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
}
KOKKOS_INLINE_FUNCTION
int coord2bin(const X_FLOAT & x,const X_FLOAT & y,const X_FLOAT & z, int* i) const
{