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Fri, May 24, 17:25

neighbor_kokkos.cpp
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;/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "neighbor_kokkos.h"
#include "atom.h"
#include "pair.h"
#include "neigh_request.h"
#include "memory.h"
#include "update.h"
#include "atom_masks.h"
#include "error.h"
#include "kokkos.h"
using namespace LAMMPS_NS;
enum{NSQ,BIN,MULTI}; // also in neigh_list.cpp
/* ---------------------------------------------------------------------- */
NeighborKokkos::NeighborKokkos(LAMMPS *lmp) : Neighbor(lmp),
neighbond_host(lmp),neighbond_device(lmp)
{
atoms_per_bin = 16;
nlist_host = 0;
lists_host = NULL;
pair_build_host = NULL;
stencil_create_host = NULL;
nlist_device = 0;
lists_device = NULL;
pair_build_device = NULL;
stencil_create_device = NULL;
device_flag = 0;
}
/* ---------------------------------------------------------------------- */
NeighborKokkos::~NeighborKokkos()
{
if (!copymode) {
memory->destroy_kokkos(k_cutneighsq,cutneighsq);
cutneighsq = NULL;
for (int i = 0; i < nlist_host; i++) delete lists_host[i];
delete [] lists_host;
for (int i = 0; i < nlist_device; i++) delete lists_device[i];
delete [] lists_device;
delete [] pair_build_device;
delete [] pair_build_host;
memory->destroy_kokkos(k_ex_type,ex_type);
memory->destroy_kokkos(k_ex1_type,ex1_type);
memory->destroy_kokkos(k_ex2_type,ex2_type);
memory->destroy_kokkos(k_ex1_group,ex1_group);
memory->destroy_kokkos(k_ex2_group,ex2_group);
memory->destroy_kokkos(k_ex_mol_group,ex_mol_group);
memory->destroy_kokkos(k_ex1_bit,ex1_bit);
memory->destroy_kokkos(k_ex2_bit,ex2_bit);
memory->destroy_kokkos(k_ex_mol_bit,ex_mol_bit);
memory->destroy_kokkos(k_bondlist,bondlist);
memory->destroy_kokkos(k_anglelist,anglelist);
memory->destroy_kokkos(k_dihedrallist,dihedrallist);
memory->destroy_kokkos(k_improperlist,improperlist);
}
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init()
{
atomKK = (AtomKokkos *) atom;
Neighbor::init();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_cutneighsq_kokkos(int n)
{
memory->create_kokkos(k_cutneighsq,cutneighsq,n+1,n+1,"neigh:cutneighsq");
k_cutneighsq.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
int NeighborKokkos::init_lists_kokkos()
{
int i;
for (i = 0; i < nlist_host; i++) delete lists_host[i];
delete [] lists_host;
delete [] pair_build_host;
delete [] stencil_create_host;
nlist_host = 0;
for (i = 0; i < nlist_device; i++) delete lists_device[i];
delete [] lists_device;
delete [] pair_build_device;
delete [] stencil_create_device;
nlist_device = 0;
nlist = 0;
for (i = 0; i < nrequest; i++) {
if (requests[i]->kokkos_device) nlist_device++;
else if (requests[i]->kokkos_host) nlist_host++;
else nlist++;
}
lists_host = new NeighListKokkos<LMPHostType>*[nrequest];
pair_build_host = new PairPtrHost[nrequest];
stencil_create_host = new StencilPtrHost[nrequest];
for (i = 0; i < nrequest; i++) {
lists_host[i] = NULL;
pair_build_host[i] = NULL;
stencil_create_host[i] = NULL;
}
for (i = 0; i < nrequest; i++) {
if (!requests[i]->kokkos_host) continue;
lists_host[i] = new NeighListKokkos<LMPHostType>(lmp);
lists_host[i]->index = i;
lists_host[i]->dnum = requests[i]->dnum;
if (requests[i]->pair) {
Pair *pair = (Pair *) requests[i]->requestor;
pair->init_list(requests[i]->id,lists_host[i]);
}
}
lists_device = new NeighListKokkos<LMPDeviceType>*[nrequest];
pair_build_device = new PairPtrDevice[nrequest];
stencil_create_device = new StencilPtrDevice[nrequest];
for (i = 0; i < nrequest; i++) {
lists_device[i] = NULL;
pair_build_device[i] = NULL;
stencil_create_device[i] = NULL;
}
for (i = 0; i < nrequest; i++) {
if (!requests[i]->kokkos_device) continue;
lists_device[i] = new NeighListKokkos<LMPDeviceType>(lmp);
lists_device[i]->index = i;
lists_device[i]->dnum = requests[i]->dnum;
if (requests[i]->pair) {
Pair *pair = (Pair *) requests[i]->requestor;
pair->init_list(requests[i]->id,lists_device[i]);
}
}
// 1st time allocation of xhold
if (dist_check)
xhold = DAT::tdual_x_array("neigh:xhold",maxhold);
// return # of non-Kokkos lists
return nlist;
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_list_flags1_kokkos(int i)
{
if (lists_host[i]) {
lists_host[i]->buildflag = 1;
if (pair_build_host[i] == NULL) lists_host[i]->buildflag = 0;
if (requests[i]->occasional) lists_host[i]->buildflag = 0;
lists_host[i]->growflag = 1;
if (requests[i]->copy) lists_host[i]->growflag = 0;
lists_host[i]->stencilflag = 1;
if (style == NSQ) lists_host[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists_host[i]->stencilflag = 0;
lists_host[i]->ghostflag = 0;
if (requests[i]->ghost) lists_host[i]->ghostflag = 1;
if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
}
if (lists_device[i]) {
lists_device[i]->buildflag = 1;
if (pair_build_device[i] == NULL) lists_device[i]->buildflag = 0;
if (requests[i]->occasional) lists_device[i]->buildflag = 0;
lists_device[i]->growflag = 1;
if (requests[i]->copy) lists_device[i]->growflag = 0;
lists_device[i]->stencilflag = 1;
if (style == NSQ) lists_device[i]->stencilflag = 0;
if (stencil_create[i] == NULL) lists_device[i]->stencilflag = 0;
lists_device[i]->ghostflag = 0;
if (requests[i]->ghost) lists_device[i]->ghostflag = 1;
if (requests[i]->ghost && !requests[i]->occasional) anyghostlist = 1;
}
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_list_flags2_kokkos(int i)
{
if (lists_host[i]) {
if (lists_host[i]->buildflag) blist[nblist++] = i;
if (lists_host[i]->growflag && requests[i]->occasional == 0)
glist[nglist++] = i;
if (lists_host[i]->stencilflag && requests[i]->occasional == 0)
slist[nslist++] = i;
}
if (lists_device[i]) {
if (lists_device[i]->buildflag) blist[nblist++] = i;
if (lists_device[i]->growflag && requests[i]->occasional == 0)
glist[nglist++] = i;
if (lists_device[i]->stencilflag && requests[i]->occasional == 0)
slist[nslist++] = i;
}
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_list_grow_kokkos(int i)
{
if (lists_host[i]!=NULL && lists_host[i]->growflag)
lists_host[i]->grow(maxatom);
if (lists_device[i]!=NULL && lists_device[i]->growflag)
lists_device[i]->grow(maxatom);
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_ex_type_kokkos(int n)
{
memory->create_kokkos(k_ex_type,ex_type,n+1,n+1,"neigh:ex_type");
k_ex_type.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_ex_bit_kokkos()
{
memory->create_kokkos(k_ex1_bit, ex1_bit, nex_group, "neigh:ex1_bit");
k_ex1_bit.modify<LMPHostType>();
memory->create_kokkos(k_ex2_bit, ex2_bit, nex_group, "neigh:ex2_bit");
k_ex2_bit.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_ex_mol_bit_kokkos()
{
memory->create_kokkos(k_ex_mol_bit, ex_mol_bit, nex_mol, "neigh:ex_mol_bit");
k_ex_mol_bit.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::choose_build(int index, NeighRequest *rq)
{
if (rq->kokkos_host != 0) {
PairPtrHost pb = NULL;
if (rq->ghost) {
if (rq->full) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,1>;
else if (rq->half) error->one(FLERR,"Cannot (yet) request ghost atoms with Kokkos half neighbor list");
pair_build_host[index] = pb;
} else {
if (rq->full) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,0,0>;
else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPHostType,1,0>;
pair_build_host[index] = pb;
}
return;
}
if (rq->kokkos_device != 0) {
PairPtrDevice pb = NULL;
if (rq->ghost) {
if (rq->full) {
if (rq->full_cluster) pb = &NeighborKokkos::full_bin_cluster_kokkos<LMPDeviceType>;
else pb = &NeighborKokkos::full_bin_kokkos<LMPDeviceType,0,1>;
}
else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPDeviceType,1,1>;
} else {
if (rq->full) {
if (rq->full_cluster) pb = &NeighborKokkos::full_bin_cluster_kokkos<LMPDeviceType>;
else pb = &NeighborKokkos::full_bin_kokkos<LMPDeviceType,0,0>;
}
else if (rq->half) pb = &NeighborKokkos::full_bin_kokkos<LMPDeviceType,1,0>;
}
pair_build_device[index] = pb;
return;
}
Neighbor::choose_build(index,rq);
}
/* ----------------------------------------------------------------------
if any atom moved trigger distance (half of neighbor skin) return 1
shrink trigger distance if box size has changed
conservative shrink procedure:
compute distance each of 8 corners of box has moved since last reneighbor
reduce skin distance by sum of 2 largest of the 8 values
new trigger = 1/2 of reduced skin distance
for orthogonal box, only need 2 lo/hi corners
for triclinic, need all 8 corners since deformations can displace all 8
------------------------------------------------------------------------- */
int NeighborKokkos::check_distance()
{
if (nlist_device)
check_distance_kokkos<LMPDeviceType>();
else
check_distance_kokkos<LMPHostType>();
}
template<class DeviceType>
int NeighborKokkos::check_distance_kokkos()
{
typedef DeviceType device_type;
double delx,dely,delz,rsq;
double delta,delta1,delta2;
if (boxcheck) {
if (triclinic == 0) {
delx = bboxlo[0] - boxlo_hold[0];
dely = bboxlo[1] - boxlo_hold[1];
delz = bboxlo[2] - boxlo_hold[2];
delta1 = sqrt(delx*delx + dely*dely + delz*delz);
delx = bboxhi[0] - boxhi_hold[0];
dely = bboxhi[1] - boxhi_hold[1];
delz = bboxhi[2] - boxhi_hold[2];
delta2 = sqrt(delx*delx + dely*dely + delz*delz);
delta = 0.5 * (skin - (delta1+delta2));
deltasq = delta*delta;
} else {
domain->box_corners();
delta1 = delta2 = 0.0;
for (int i = 0; i < 8; i++) {
delx = corners[i][0] - corners_hold[i][0];
dely = corners[i][1] - corners_hold[i][1];
delz = corners[i][2] - corners_hold[i][2];
delta = sqrt(delx*delx + dely*dely + delz*delz);
if (delta > delta1) delta1 = delta;
else if (delta > delta2) delta2 = delta;
}
delta = 0.5 * (skin - (delta1+delta2));
deltasq = delta*delta;
}
} else deltasq = triggersq;
atomKK->sync(ExecutionSpaceFromDevice<DeviceType>::space,X_MASK);
x = atomKK->k_x;
xhold.sync<DeviceType>();
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int flag = 0;
copymode = 1;
Kokkos::parallel_reduce(Kokkos::RangePolicy<DeviceType, TagNeighborCheckDistance<DeviceType> >(0,nlocal),*this,flag);
DeviceType::fence();
copymode = 0;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_MAX,world);
if (flagall && ago == MAX(every,delay)) ndanger++;
return flagall;
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void NeighborKokkos::operator()(TagNeighborCheckDistance<DeviceType>, const int &i, int &flag) const {
typedef DeviceType device_type;
const X_FLOAT delx = x.view<DeviceType>()(i,0) - xhold.view<DeviceType>()(i,0);
const X_FLOAT dely = x.view<DeviceType>()(i,1) - xhold.view<DeviceType>()(i,1);
const X_FLOAT delz = x.view<DeviceType>()(i,2) - xhold.view<DeviceType>()(i,2);
const X_FLOAT rsq = delx*delx + dely*dely + delz*delz;
if (rsq > deltasq) flag = 1;
}
/* ----------------------------------------------------------------------
build perpetuals neighbor lists
called at setup and every few timesteps during run or minimization
topology lists also built if topoflag = 1, USER-CUDA calls with topoflag = 0
------------------------------------------------------------------------- */
void NeighborKokkos::build(int topoflag)
{
if (nlist_device)
build_kokkos<LMPDeviceType>(topoflag);
else
build_kokkos<LMPHostType>(topoflag);
}
template<class DeviceType>
void NeighborKokkos::build_kokkos(int topoflag)
{
typedef DeviceType device_type;
int i;
ago = 0;
ncalls++;
lastcall = update->ntimestep;
// store current atom positions and box size if needed
if (dist_check) {
atomKK->sync(ExecutionSpaceFromDevice<DeviceType>::space,X_MASK);
x = atomKK->k_x;
int nlocal = atom->nlocal;
if (includegroup) nlocal = atom->nfirst;
int maxhold_kokkos = xhold.view<DeviceType>().dimension_0();
if (nlocal > maxhold || maxhold_kokkos < maxhold) {
maxhold = atom->nmax;
xhold = DAT::tdual_x_array("neigh:xhold",maxhold);
}
copymode = 1;
Kokkos::parallel_for(Kokkos::RangePolicy<DeviceType, TagNeighborXhold<DeviceType> >(0,nlocal),*this);
DeviceType::fence();
copymode = 0;
xhold.modify<DeviceType>();
if (boxcheck) {
if (triclinic == 0) {
boxlo_hold[0] = bboxlo[0];
boxlo_hold[1] = bboxlo[1];
boxlo_hold[2] = bboxlo[2];
boxhi_hold[0] = bboxhi[0];
boxhi_hold[1] = bboxhi[1];
boxhi_hold[2] = bboxhi[2];
} else {
domain->box_corners();
corners = domain->corners;
for (i = 0; i < 8; i++) {
corners_hold[i][0] = corners[i][0];
corners_hold[i][1] = corners[i][1];
corners_hold[i][2] = corners[i][2];
}
}
}
}
// if any lists store neighbors of ghosts:
// invoke grow() if nlocal+nghost exceeds previous list size
// else only invoke grow() if nlocal exceeds previous list size
// only for lists with growflag set and which are perpetual (glist)
if (anyghostlist && atom->nlocal+atom->nghost > maxatom) {
maxatom = atom->nmax;
for (i = 0; i < nglist; i++)
if (lists[glist[i]]) lists[glist[i]]->grow(maxatom);
else init_list_grow_kokkos(glist[i]);
} else if (atom->nlocal > maxatom) {
maxatom = atom->nmax;
for (i = 0; i < nglist; i++)
if (lists[glist[i]]) lists[glist[i]]->grow(maxatom);
else init_list_grow_kokkos(glist[i]);
}
// extend atom bin list if necessary
if (style != NSQ && atom->nmax > maxbin) {
maxbin = atom->nmax;
memory->destroy(bins);
memory->create(bins,maxbin,"bins");
}
// check that using special bond flags will not overflow neigh lists
if (atom->nlocal+atom->nghost > NEIGHMASK)
error->one(FLERR,"Too many local+ghost atoms for neighbor list");
// invoke building of pair and molecular topology neighbor lists
// only for pairwise lists with buildflag set
// blist is for standard neigh lists, otherwise is a Kokkos list
for (i = 0; i < nblist; i++) {
if (lists[blist[i]])
(this->*pair_build[blist[i]])(lists[blist[i]]);
else {
if (lists_host[blist[i]])
(this->*pair_build_host[blist[i]])(lists_host[blist[i]]);
else if (lists_device[blist[i]])
(this->*pair_build_device[blist[i]])(lists_device[blist[i]]);
}
}
if (atom->molecular && topoflag)
build_topology_kokkos();
}
template<class DeviceType>
KOKKOS_INLINE_FUNCTION
void NeighborKokkos::operator()(TagNeighborXhold<DeviceType>, const int &i) const {
typedef DeviceType device_type;
xhold.view<DeviceType>()(i,0) = x.view<DeviceType>()(i,0);
xhold.view<DeviceType>()(i,1) = x.view<DeviceType>()(i,1);
xhold.view<DeviceType>()(i,2) = x.view<DeviceType>()(i,2);
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::setup_bins_kokkos(int i)
{
if (lists_host[slist[i]]) {
lists_host[slist[i]]->stencil_allocate(smax,style);
(this->*stencil_create[slist[i]])(lists_host[slist[i]],sx,sy,sz);
} else if (lists_device[slist[i]]) {
lists_device[slist[i]]->stencil_allocate(smax,style);
(this->*stencil_create[slist[i]])(lists_device[slist[i]],sx,sy,sz);
}
//if (i < nslist-1) return; // this won't work if a non-kokkos neighbor list is last
if (maxhead > k_bins.d_view.dimension_0()) {
k_bins = DAT::tdual_int_2d("Neighbor::d_bins",maxhead,atoms_per_bin);
k_bincount = DAT::tdual_int_1d("Neighbor::d_bincount",maxhead);
}
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::modify_ex_type_grow_kokkos(){
memory->grow_kokkos(k_ex1_type,ex1_type,maxex_type,"neigh:ex1_type");
k_ex1_type.modify<LMPHostType>();
memory->grow_kokkos(k_ex2_type,ex2_type,maxex_type,"neigh:ex2_type");
k_ex2_type.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::modify_ex_group_grow_kokkos(){
memory->grow_kokkos(k_ex1_group,ex1_group,maxex_group,"neigh:ex1_group");
k_ex1_group.modify<LMPHostType>();
memory->grow_kokkos(k_ex2_group,ex2_group,maxex_group,"neigh:ex2_group");
k_ex2_group.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::modify_mol_group_grow_kokkos(){
memory->grow_kokkos(k_ex_mol_group,ex_mol_group,maxex_mol,"neigh:ex_mol_group");
k_ex_mol_group.modify<LMPHostType>();
}
/* ---------------------------------------------------------------------- */
void NeighborKokkos::init_topology_kokkos() {
if (nlist_device) {
neighbond_device.init_topology_kk();
} else {
neighbond_host.init_topology_kk();
}
}
/* ----------------------------------------------------------------------
build all topology neighbor lists every few timesteps
normally built with pair lists, but USER-CUDA separates them
------------------------------------------------------------------------- */
void NeighborKokkos::build_topology_kokkos() {
if (nlist_device) {
neighbond_device.build_topology_kk();
k_bondlist = neighbond_device.k_bondlist;
k_anglelist = neighbond_device.k_anglelist;
k_dihedrallist = neighbond_device.k_dihedrallist;
k_improperlist = neighbond_device.k_improperlist;
k_bondlist.modify<LMPDeviceType>();
k_anglelist.modify<LMPDeviceType>();
k_dihedrallist.modify<LMPDeviceType>();
k_improperlist.modify<LMPDeviceType>();
} else {
neighbond_host.build_topology_kk();
k_bondlist = neighbond_host.k_bondlist;
k_anglelist = neighbond_host.k_anglelist;
k_dihedrallist = neighbond_host.k_dihedrallist;
k_improperlist = neighbond_host.k_improperlist;
k_bondlist.modify<LMPHostType>();
k_anglelist.modify<LMPHostType>();
k_dihedrallist.modify<LMPHostType>();
k_improperlist.modify<LMPHostType>();
}
}
// include to trigger instantiation of templated functions
#include "neigh_full_kokkos.h"

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