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lammps/src/USER-INTEL/neigh_half_bin_intel.cpp
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neigh_half_bin_intel.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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: W. Michael Brown (Intel)
------------------------------------------------------------------------- */
#include "neighbor.h"
#include "neigh_list.h"
#include "atom.h"
#include "comm.h"
#include "group.h"
#include "fix_intel.h"
#if defined(_OPENMP)
#include <omp.h>
#endif
using namespace LAMMPS_NS;
#ifdef _LMP_INTEL_OFFLOAD
#pragma offload_attribute(push,target(mic))
#endif
template <class flt_t>
inline int mcoord2bin(const flt_t x0, const flt_t x1, const flt_t x2,
const flt_t bboxlo0, const flt_t bboxlo1,
const flt_t bboxlo2, const flt_t bboxhi0,
const flt_t bboxhi1, const flt_t bboxhi2,
const flt_t bininvx, const flt_t bininvy,
const flt_t bininvz, const int nbinx, const int nbiny,
const int nbinz, const int mbinx, const int mbiny,
const int mbinz, const int mbinxlo, const int mbinylo,
const int mbinzlo)
{
int ix, iy, iz;
if (x0 >= bboxhi0)
ix = static_cast<int> ((x0 - bboxhi0) * bininvx) + nbinx;
else if (x0 >= bboxlo0) {
ix = static_cast<int> ((x0 - bboxlo0) * bininvx);
ix = MIN(ix, nbinx-1);
} else
ix = static_cast<int> ((x0 - bboxlo0) * bininvx) - 1;
if (x1 >= bboxhi1)
iy = static_cast<int> ((x1 - bboxhi1) * bininvy) + nbiny;
else if (x1 >= bboxlo1) {
iy = static_cast<int> ((x1 - bboxlo1) * bininvy);
iy = MIN(iy, nbiny-1);
} else
iy = static_cast<int> ((x1 - bboxlo1) * bininvy) - 1;
if (x2 >= bboxhi2)
iz = static_cast<int> ((x2 - bboxhi2) * bininvz) + nbinz;
else if (x2 >= bboxlo2) {
iz = static_cast<int> ((x2 - bboxlo2) * bininvz);
iz = MIN(iz, nbinz - 1);
} else
iz = static_cast<int> ((x2 - bboxlo2) * bininvz) - 1;
return (iz - mbinzlo) * mbiny * mbinx + (iy - mbinylo) * mbinx +
(ix - mbinxlo);
}
#define ofind_special(which, special, nspecial, i, tag, special_flag) \
{ \
which = 0; \
const int n1 = nspecial[i * 3]; \
const int n2 = nspecial[i * 3 + 1]; \
const int n3 = nspecial[i * 3 + 2]; \
const tagint *sptr = special + i * maxspecial; \
for (int s = 0; s < n3; s++) { \
if (sptr[s] == tag) { \
if (s < n1) { \
if (special_flag[1] == 0) which = -1; \
else if (special_flag[1] == 1) which = 0; \
else which = 1; \
} else if (s < n2) { \
if (special_flag[2] == 0) which = -1; \
else if (special_flag[2] == 1) which = 0; \
else which = 2; \
} else { \
if (special_flag[3] == 0) which = -1; \
else if (special_flag[3] == 1) which = 0; \
else which = 3; \
} \
} \
} \
}
#ifdef _LMP_INTEL_OFFLOAD
#pragma offload_attribute(pop)
#endif
template <class flt_t, class acc_t>
void Neighbor::bin_atoms(void * xin) {
const ATOM_T * _noalias const x = (const ATOM_T * _noalias const)xin;
int nlocal = atom->nlocal;
const int nall = nlocal + atom->nghost;
const flt_t bininvx = this->bininvx;
const flt_t bininvy = this->bininvy;
const flt_t bininvz = this->bininvz;
const flt_t bboxlo0 = this->bboxlo[0];
const flt_t bboxlo1 = this->bboxlo[1];
const flt_t bboxlo2 = this->bboxlo[2];
const flt_t bboxhi0 = this->bboxhi[0];
const flt_t bboxhi1 = this->bboxhi[1];
const flt_t bboxhi2 = this->bboxhi[2];
int i, ibin;
for (i = 0; i < mbins; i++) binhead[i] = -1;
int *mask = atom->mask;
if (includegroup) {
int bitmask = group->bitmask[includegroup];
for (i = nall-1; i >= nlocal; i--) {
if (mask[i] & bitmask) {
ibin = mcoord2bin(x[i].x, x[i].y, x[i].z, bboxlo0, bboxlo1, bboxlo2,
bboxhi0, bboxhi1, bboxhi2, bininvx, bininvy, bininvz, nbinx, nbiny,
nbinz, mbinx, mbiny, mbinz, mbinxlo, mbinylo, mbinzlo);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
for (i = atom->nfirst-1; i >= 0; i--) {
ibin = mcoord2bin(x[i].x, x[i].y, x[i].z, bboxlo0, bboxlo1, bboxlo2,
bboxhi0, bboxhi1, bboxhi2, bininvx, bininvy, bininvz, nbinx, nbiny,
nbinz, mbinx, mbiny, mbinz, mbinxlo, mbinylo, mbinzlo);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
} else {
for (i = nall-1; i >= 0; i--) {
ibin = mcoord2bin(x[i].x, x[i].y, x[i].z, bboxlo0, bboxlo1, bboxlo2,
bboxhi0, bboxhi1, bboxhi2, bininvx, bininvy, bininvz, nbinx, nbiny,
nbinz, mbinx, mbiny, mbinz, mbinxlo, mbinylo, mbinzlo);
bins[i] = binhead[ibin];
binhead[ibin] = i;
}
}
}
/* ----------------------------------------------------------------------
binned neighbor list construction with partial Newton's 3rd law
each owned atom i checks own bin and other bins in stencil
pair stored once if i,j are both owned and i < j
pair stored by me if j is ghost (also stored by proc owning j)
------------------------------------------------------------------------- */
void Neighbor::half_bin_no_newton_intel(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
list->inum = nlocal;
// Get fix for intel stuff
FixIntel *fix = static_cast<FixIntel *>(fix_intel);
const int off_end = fix->offload_end_neighbor();
int host_start = off_end;;
#ifdef _LMP_INTEL_OFFLOAD
if (fix->full_host_list()) host_start = 0;
if (exclude)
error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
#endif
if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
hbnni<float,double>(1, list, fix->get_mixed_buffers(),
0, off_end, fix);
hbnni<float,double>(0, list, fix->get_mixed_buffers(),
host_start, nlocal,fix);
} else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
hbnni<double,double>(1, list, fix->get_double_buffers(),
0, off_end, fix);
hbnni<double,double>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix);
} else {
hbnni<float,float>(1, list, fix->get_single_buffers(),
0, off_end, fix);
hbnni<float,float>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix);
}
}
template <class flt_t, class acc_t>
void Neighbor::hbnni(const int offload, NeighList *list, void *buffers_in,
const int astart, const int aend, void *fix_in) {
IntelBuffers<flt_t,acc_t> *buffers = (IntelBuffers<flt_t,acc_t> *)buffers_in;
FixIntel *fix = (FixIntel *)fix_in;
const int nall = atom->nlocal + atom->nghost;
int pad = 1;
if (offload) {
fix->start_watch(TIME_PACK);
buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
buffers->grow_nbor(list, atom->nlocal, aend);
ATOM_T biga;
biga.x = INTEL_BIGP;
biga.y = INTEL_BIGP;
biga.z = INTEL_BIGP;
biga.w = 1;
buffers->get_x()[nall] = biga;
const int nthreads = comm->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(buffers)
#endif
{
int ifrom, ito, tid;
IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
buffers->thr_pack(ifrom, ito, 0);
}
fix->stop_watch(TIME_PACK);
fix->start_watch(TIME_HOST_NEIGHBOR);
bin_atoms<flt_t,acc_t>(buffers->get_x());
if (INTEL_MIC_NBOR_PAD > 1)
pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
} else {
fix->start_watch(TIME_HOST_NEIGHBOR);
if (INTEL_NBOR_PAD > 1)
pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
}
const int pad_width = pad;
if (aend-astart == 0) {
fix->stop_watch(TIME_HOST_NEIGHBOR);
return;
}
const ATOM_T * _noalias const x = buffers->get_x();
int * _noalias const firstneigh = buffers->firstneigh(list);
const int molecular = atom->molecular;
int *ns = NULL;
tagint *s = NULL;
int tag_size, special_size;
if (molecular) {
s = atom->special[0];
ns = atom->nspecial[0];
tag_size = nall;
special_size = aend;
} else {
s = &buffers->_special_holder;
ns = &buffers->_nspecial_holder;
tag_size = 0;
special_size = 0;
}
const tagint * _noalias const special = s;
const int * _noalias const nspecial = ns;
const int maxspecial = atom->maxspecial;
const tagint * _noalias const tag = atom->tag;
int * _noalias const ilist = list->ilist;
int * _noalias numneigh = list->numneigh;
int * _noalias const cnumneigh = buffers->cnumneigh(list);
const int nstencil = list->nstencil;
const int * _noalias const stencil = list->stencil;
const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
const int ntypes = atom->ntypes + 1;
const int nlocal = atom->nlocal;
#ifndef _LMP_INTEL_OFFLOAD
int * const mask = atom->mask;
tagint * const molecule = atom->molecule;
#endif
int tnum;
int *overflow;
double *timer_compute;
if (offload) {
timer_compute = fix->off_watch_neighbor();
tnum = buffers->get_off_threads();
overflow = fix->get_off_overflow_flag();
fix->stop_watch(TIME_HOST_NEIGHBOR);
fix->start_watch(TIME_OFFLOAD_LATENCY);
} else {
tnum = comm->nthreads;
overflow = fix->get_overflow_flag();
}
const int nthreads = tnum;
const int maxnbors = buffers->get_max_nbors();
const flt_t bboxlo0 = this->bboxlo[0];
const flt_t bboxlo1 = this->bboxlo[1];
const flt_t bboxlo2 = this->bboxlo[2];
const flt_t bboxhi0 = this->bboxhi[0];
const flt_t bboxhi1 = this->bboxhi[1];
const flt_t bboxhi2 = this->bboxhi[2];
const flt_t bininvx = this->bininvx;
const flt_t bininvy = this->bininvy;
const flt_t bininvz = this->bininvz;
// Make sure dummy coordinates to eliminate loop remainder not within cutoff
{
const flt_t dx = (INTEL_BIGP - bboxhi0);
const flt_t dy = (INTEL_BIGP - bboxhi1);
const flt_t dz = (INTEL_BIGP - bboxhi2);
if (dx * dx + dy * dy + dz * dz < static_cast<flt_t>(cutneighmaxsq))
error->one(FLERR,
"Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
}
#ifdef _LMP_INTEL_OFFLOAD
const int * _noalias const binhead = this->binhead;
const int * _noalias const special_flag = this->special_flag;
const int nbinx = this->nbinx;
const int nbiny = this->nbiny;
const int nbinz = this->nbinz;
const int mbinxlo = this->mbinxlo;
const int mbinylo = this->mbinylo;
const int mbinzlo = this->mbinzlo;
const int mbinx = this->mbinx;
const int mbiny = this->mbiny;
const int mbinz = this->mbinz;
const int * _noalias const bins = this->bins;
const int cop = fix->coprocessor_number();
const int separate_buffers = fix->separate_buffers();
#pragma offload target(mic:cop) if(offload) \
in(x:length(nall+1) alloc_if(0) free_if(0)) \
in(tag:length(tag_size) alloc_if(0) free_if(0)) \
in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
in(bins:length(nall) alloc_if(0) free_if(0)) \
in(binhead:length(mbins) alloc_if(0) free_if(0)) \
in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
in(firstneigh:length(0) alloc_if(0) free_if(0)) \
in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
out(numneigh:length(0) alloc_if(0) free_if(0)) \
in(ilist:length(0) alloc_if(0) free_if(0)) \
in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
in(special_flag:length(0) alloc_if(0) free_if(0)) \
in(maxnbors,nthreads,maxspecial,nstencil,nbinx,nbiny,nbinz) \
in(mbinxlo,mbinylo,mbinzlo,mbinx,mbiny,mbinz,pad_width,offload) \
in(bininvx,bininvy,bininvz,bboxlo0,bboxlo1,bboxlo2,separate_buffers) \
in(bboxhi0, bboxhi1, bboxhi2, astart, aend, nlocal, molecular, ntypes) \
out(overflow:length(5) alloc_if(0) free_if(0)) \
out(timer_compute:length(1) alloc_if(0) free_if(0)) \
signal(numneigh)
#endif
{
#ifdef __MIC__
*timer_compute = MIC_Wtime();
#endif
#ifdef _LMP_INTEL_OFFLOAD
overflow[LMP_LOCAL_MIN] = astart;
overflow[LMP_LOCAL_MAX] = aend - 1;
overflow[LMP_GHOST_MIN] = nall;
overflow[LMP_GHOST_MAX] = -1;
#endif
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(numneigh,overflow)
#endif
{
#ifdef _LMP_INTEL_OFFLOAD
int lmin = nall, lmax = -1, gmin = nall, gmax = -1;
#endif
const int num = aend - astart;
int tid, ifrom, ito;
IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
ifrom += astart;
ito += astart;
int which;
const int list_size = (ito + tid + 1) * maxnbors;
int ct = (ifrom + tid) * maxnbors;
int *neighptr = firstneigh + ct;
for (int i = ifrom; i < ito; i++) {
int j, k, n, n2, itype, jtype, ibin;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
n = 0;
n2 = maxnbors;
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = x[i].w;
const int ioffset = ntypes*itype;
// loop over all atoms in other bins in stencil including self
// only store pair if i < j
// stores own/own pairs only once
// stores own/ghost pairs on both procs
ibin = mcoord2bin(x[i].x, x[i].y, x[i].z, bboxlo0, bboxlo1, bboxlo2,
bboxhi0, bboxhi1, bboxhi2, bininvx, bininvy, bininvz,
nbinx, nbiny, nbinz, mbinx, mbiny, mbinz,
mbinxlo, mbinylo, mbinzlo);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin + stencil[k]]; j >= 0; j = bins[j]) {
if (j <= i) continue;
jtype = x[j].w;
#ifndef _LMP_INTEL_OFFLOAD
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
#endif
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq <= cutneighsq[ioffset + jtype]) {
if (j < nlocal) {
neighptr[n++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < lmin) lmin = j;
if (j > lmax) lmax = j;
#endif
} else {
neighptr[n2++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < gmin) gmin = j;
if (j > gmax) gmax = j;
#endif
}
}
}
}
ilist[i] = i;
cnumneigh[i] = ct;
if (n > maxnbors) *overflow = 1;
for (k = maxnbors; k < n2; k++) neighptr[n++] = neighptr[k];
while( (n % pad_width) != 0 ) neighptr[n++] = nall;
numneigh[i] = n;
while((n % (INTEL_DATA_ALIGN / sizeof(int))) != 0) n++;
ct += n;
neighptr += n;
if (ct + n + maxnbors > list_size) {
*overflow = 1;
ct = (ifrom + tid) * maxnbors;
}
}
if (*overflow == 1)
for (int i = ifrom; i < ito; i++)
numneigh[i] = 0;
#ifdef _LMP_INTEL_OFFLOAD
if (separate_buffers) {
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
}
#pragma omp barrier
}
int ghost_offset = 0, nall_offset = nall;
if (separate_buffers) {
int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
if (nghost < 0) nghost = 0;
if (offload) {
ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
} else {
ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
nall_offset = nlocal + nghost;
}
}
#endif
if (molecular) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++) {
const int j = jlist[jj];
ofind_special(which, special, nspecial, i, tag[j], special_flag);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
if (j == nall)
jlist[jj] = nall_offset;
else if (which > 0)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
#endif
if (which > 0) jlist[jj] = j ^ (which << SBBITS);
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
else if (separate_buffers) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
}
#endif
} // end omp
#ifdef __MIC__
*timer_compute = MIC_Wtime() - *timer_compute;
#endif
} // end offload
if (offload) {
fix->stop_watch(TIME_OFFLOAD_LATENCY);
#ifdef _LMP_INTEL_OFFLOAD
for (int n = 0; n < aend; n++) {
ilist[n] = n;
numneigh[n] = 0;
}
#endif
} else {
for (int i = astart; i < aend; i++)
list->firstneigh[i] = firstneigh + cnumneigh[i];
fix->stop_watch(TIME_HOST_NEIGHBOR);
#ifdef _LMP_INTEL_OFFLOAD
if (separate_buffers) {
fix->start_watch(TIME_PACK);
fix->set_neighbor_host_sizes();
buffers->pack_sep_from_single(fix->host_min_local(),
fix->host_used_local(),
fix->host_min_ghost(),
fix->host_used_ghost());
fix->stop_watch(TIME_PACK);
}
#endif
}
}
/* ----------------------------------------------------------------------
binned neighbor list construction with full Newton's 3rd law
each owned atom i checks its own bin and other bins in Newton stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::half_bin_newton_intel(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
list->inum = nlocal;
// Get fix for intel stuff
FixIntel *fix = static_cast<FixIntel *>(fix_intel);
const int off_end = fix->offload_end_neighbor();
int host_start = fix->host_start_neighbor();;
int offload_noghost = 0;
#ifdef _LMP_INTEL_OFFLOAD
if (fix->full_host_list()) host_start = 0;
offload_noghost = fix->offload_noghost();
if (exclude)
error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
#endif
if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
if (offload_noghost) {
hbni<float,double,1>(1, list, fix->get_mixed_buffers(),
0, off_end, fix);
hbni<float,double,1>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix, off_end);
} else {
hbni<float,double,0>(1, list, fix->get_mixed_buffers(),
0, off_end, fix);
hbni<float,double,0>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix);
}
} else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
if (offload_noghost) {
hbni<double,double,1>(1, list, fix->get_double_buffers(),
0, off_end, fix);
hbni<double,double,1>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix, off_end);
} else {
hbni<double,double,0>(1, list, fix->get_double_buffers(),
0, off_end, fix);
hbni<double,double,0>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix);
}
} else {
if (offload_noghost) {
hbni<float,float,1>(1, list, fix->get_single_buffers(), 0, off_end, fix);
hbni<float,float,1>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix, off_end);
} else {
hbni<float,float,0>(1, list, fix->get_single_buffers(), 0, off_end, fix);
hbni<float,float,0>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix);
}
}
}
template <class flt_t, class acc_t, int offload_noghost>
void Neighbor::hbni(const int offload, NeighList *list, void *buffers_in,
const int astart, const int aend, void *fix_in,
const int offload_end) {
IntelBuffers<flt_t,acc_t> *buffers = (IntelBuffers<flt_t,acc_t> *)buffers_in;
FixIntel *fix = (FixIntel *)fix_in;
const int nall = atom->nlocal + atom->nghost;
int pad = 1;
if (offload) {
fix->start_watch(TIME_PACK);
buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
buffers->grow_nbor(list, atom->nlocal, aend);
ATOM_T biga;
biga.x = INTEL_BIGP;
biga.y = INTEL_BIGP;
biga.z = INTEL_BIGP;
biga.w = 1;
buffers->get_x()[nall]=biga;
const int nthreads = comm->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(buffers)
#endif
{
int ifrom, ito, tid;
IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
buffers->thr_pack(ifrom, ito, 0);
}
fix->stop_watch(TIME_PACK);
fix->start_watch(TIME_HOST_NEIGHBOR);
bin_atoms<flt_t,acc_t>(buffers->get_x());
if (INTEL_MIC_NBOR_PAD > 1)
pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
} else {
fix->start_watch(TIME_HOST_NEIGHBOR);
if (INTEL_NBOR_PAD > 1)
pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
}
const int pad_width = pad;
if (aend-astart == 0) {
fix->stop_watch(TIME_HOST_NEIGHBOR);
return;
}
const ATOM_T * _noalias const x = buffers->get_x();
int * _noalias const firstneigh = buffers->firstneigh(list);
int nall_t = nall;
if (offload_noghost && offload) nall_t = atom->nlocal;
const int e_nall = nall_t;
const int molecular = atom->molecular;
int *ns = NULL;
tagint *s = NULL;
int tag_size, special_size;
if (molecular) {
s = atom->special[0];
ns = atom->nspecial[0];
tag_size = e_nall;
special_size = aend;
} else {
s = &buffers->_special_holder;
ns = &buffers->_nspecial_holder;
tag_size = 0;
special_size = 0;
}
const tagint * _noalias const special = s;
const int * _noalias const nspecial = ns;
const int maxspecial = atom->maxspecial;
const tagint * _noalias const tag = atom->tag;
int * _noalias const ilist = list->ilist;
int * _noalias numneigh = list->numneigh;
int * _noalias const cnumneigh = buffers->cnumneigh(list);
const int nstencil = list->nstencil;
const int * _noalias const stencil = list->stencil;
const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
const int ntypes = atom->ntypes + 1;
const int nlocal = atom->nlocal;
#ifndef _LMP_INTEL_OFFLOAD
int * const mask = atom->mask;
tagint * const molecule = atom->molecule;
#endif
int tnum;
int *overflow;
double *timer_compute;
if (offload) {
timer_compute = fix->off_watch_neighbor();
tnum = buffers->get_off_threads();
overflow = fix->get_off_overflow_flag();
fix->stop_watch(TIME_HOST_NEIGHBOR);
fix->start_watch(TIME_OFFLOAD_LATENCY);
} else {
tnum = comm->nthreads;
overflow = fix->get_overflow_flag();
}
const int nthreads = tnum;
const int maxnbors = buffers->get_max_nbors();
const flt_t bboxlo0 = this->bboxlo[0];
const flt_t bboxlo1 = this->bboxlo[1];
const flt_t bboxlo2 = this->bboxlo[2];
const flt_t bboxhi0 = this->bboxhi[0];
const flt_t bboxhi1 = this->bboxhi[1];
const flt_t bboxhi2 = this->bboxhi[2];
const flt_t bininvx = this->bininvx;
const flt_t bininvy = this->bininvy;
const flt_t bininvz = this->bininvz;
// Make sure dummy coordinates to eliminate loop remainder not within cutoff
{
const flt_t dx = (INTEL_BIGP - bboxhi0);
const flt_t dy = (INTEL_BIGP - bboxhi1);
const flt_t dz = (INTEL_BIGP - bboxhi2);
if (dx * dx + dy * dy + dz * dz < static_cast<flt_t>(cutneighmaxsq))
error->one(FLERR,
"Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
}
#ifdef _LMP_INTEL_OFFLOAD
const int * _noalias const binhead = this->binhead;
const int * _noalias const special_flag = this->special_flag;
const int nbinx = this->nbinx;
const int nbiny = this->nbiny;
const int nbinz = this->nbinz;
const int mbinxlo = this->mbinxlo;
const int mbinylo = this->mbinylo;
const int mbinzlo = this->mbinzlo;
const int mbinx = this->mbinx;
const int mbiny = this->mbiny;
const int mbinz = this->mbinz;
const int * _noalias const bins = this->bins;
const int cop = fix->coprocessor_number();
const int separate_buffers = fix->separate_buffers();
#pragma offload target(mic:cop) if(offload) \
in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
in(tag:length(tag_size) alloc_if(0) free_if(0)) \
in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
in(bins:length(nall) alloc_if(0) free_if(0)) \
in(binhead:length(mbins) alloc_if(0) free_if(0)) \
in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
in(firstneigh:length(0) alloc_if(0) free_if(0)) \
in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
out(numneigh:length(0) alloc_if(0) free_if(0)) \
in(ilist:length(0) alloc_if(0) free_if(0)) \
in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
in(special_flag:length(0) alloc_if(0) free_if(0)) \
in(maxnbors,nthreads,maxspecial,nstencil,nbinx,nbiny,nbinz,e_nall,offload)\
in(mbinxlo,mbinylo,mbinzlo,mbinx,mbiny,mbinz,pad_width,offload_end) \
in(bininvx,bininvy,bininvz,bboxlo0,bboxlo1,bboxlo2,separate_buffers) \
in(bboxhi0, bboxhi1, bboxhi2, astart, aend, nlocal, molecular, ntypes) \
out(overflow:length(5) alloc_if(0) free_if(0)) \
out(timer_compute:length(1) alloc_if(0) free_if(0)) \
signal(numneigh)
#endif
{
#ifdef __MIC__
*timer_compute = MIC_Wtime();
#endif
#ifdef _LMP_INTEL_OFFLOAD
overflow[LMP_LOCAL_MIN] = astart;
overflow[LMP_LOCAL_MAX] = aend - 1;
overflow[LMP_GHOST_MIN] = e_nall;
overflow[LMP_GHOST_MAX] = -1;
#endif
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(numneigh, overflow)
#endif
{
#ifdef _LMP_INTEL_OFFLOAD
int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
#endif
const int num = aend - astart;
int tid, ifrom, ito;
IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
ifrom += astart;
ito += astart;
int which;
const int list_size = (ito + tid + 1) * maxnbors;
int ct = (ifrom + tid) * maxnbors;
int *neighptr = firstneigh + ct;
for (int i = ifrom; i < ito; i++) {
int j, k, n, n2, itype, jtype, ibin;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
n = 0;
n2 = maxnbors;
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = x[i].w;
const int ioffset = ntypes * itype;
// loop over rest of atoms in i's bin, ghosts are at end of linked list
// if j is owned atom, store it, since j is beyond i in linked list
// if j is ghost, only store if j coords are "above/to the right" of i
for (j = bins[i]; j >= 0; j = bins[j]) {
if (j >= nlocal) {
if (offload_noghost && offload) continue;
if (x[j].z < ztmp) continue;
if (x[j].z == ztmp) {
if (x[j].y < ytmp) continue;
if (x[j].y == ytmp && x[j].x < xtmp) continue;
}
} else if (offload_noghost && i < offload_end) continue;
jtype = x[j].w;
#ifndef _LMP_INTEL_OFFLOAD
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
#endif
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq <= cutneighsq[ioffset + jtype]) {
if (j < nlocal) {
neighptr[n++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < lmin) lmin = j;
if (j > lmax) lmax = j;
#endif
} else {
neighptr[n2++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < gmin) gmin = j;
if (j > gmax) gmax = j;
#endif
}
}
}
// loop over all atoms in other bins in stencil, store every pair
ibin = mcoord2bin(x[i].x, x[i].y, x[i].z, bboxlo0, bboxlo1, bboxlo2,
bboxhi0, bboxhi1, bboxhi2, bininvx, bininvy, bininvz,
nbinx, nbiny, nbinz, mbinx, mbiny, mbinz,
mbinxlo, mbinylo, mbinzlo);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin + stencil[k]]; j >= 0; j = bins[j]) {
if (offload_noghost) {
if (j < nlocal) {
if (i < offload_end) continue;
} else if (offload) continue;
}
jtype = x[j].w;
#ifndef _LMP_INTEL_OFFLOAD
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
#endif
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq <= cutneighsq[ioffset + jtype]) {
if (j < nlocal) {
neighptr[n++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < lmin) lmin = j;
if (j > lmax) lmax = j;
#endif
} else {
neighptr[n2++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < gmin) gmin = j;
if (j > gmax) gmax = j;
#endif
}
}
}
}
ilist[i] = i;
cnumneigh[i] = ct;
if (n > maxnbors) *overflow = 1;
for (k = maxnbors; k < n2; k++) neighptr[n++] = neighptr[k];
while( (n % pad_width) != 0 ) neighptr[n++] = e_nall;
numneigh[i] = n;
while((n % (INTEL_DATA_ALIGN / sizeof(int))) != 0) n++;
ct += n;
neighptr += n;
if (ct + n + maxnbors > list_size) {
*overflow = 1;
ct = (ifrom + tid) * maxnbors;
}
}
if (*overflow == 1)
for (int i = ifrom; i < ito; i++)
numneigh[i] = 0;
#ifdef _LMP_INTEL_OFFLOAD
if (separate_buffers) {
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
}
#pragma omp barrier
}
int ghost_offset = 0, nall_offset = e_nall;
if (separate_buffers) {
int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
if (nghost < 0) nghost = 0;
if (offload) {
ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
} else {
ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
nall_offset = nlocal + nghost;
}
}
#endif
if (molecular) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++) {
const int j = jlist[jj];
ofind_special(which, special, nspecial, i, tag[j],
special_flag);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
if (j == e_nall)
jlist[jj] = nall_offset;
else if (which > 0)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
#endif
if (which > 0) jlist[jj] = j ^ (which << SBBITS);
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
else if (separate_buffers) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
}
#endif
} // end omp
#ifdef __MIC__
*timer_compute = MIC_Wtime() - *timer_compute;
#endif
} // end offload
if (offload) {
fix->stop_watch(TIME_OFFLOAD_LATENCY);
#ifdef _LMP_INTEL_OFFLOAD
for (int n = 0; n < aend; n++) {
ilist[n] = n;
numneigh[n] = 0;
}
#endif
} else {
for (int i = astart; i < aend; i++)
list->firstneigh[i] = firstneigh + cnumneigh[i];
fix->stop_watch(TIME_HOST_NEIGHBOR);
#ifdef _LMP_INTEL_OFFLOAD
if (separate_buffers) {
fix->start_watch(TIME_PACK);
fix->set_neighbor_host_sizes();
buffers->pack_sep_from_single(fix->host_min_local(),
fix->host_used_local(),
fix->host_min_ghost(),
fix->host_used_ghost());
fix->stop_watch(TIME_PACK);
}
#endif
}
}
/* ----------------------------------------------------------------------
binned neighbor list construction with Newton's 3rd law for triclinic
each owned atom i checks its own bin and other bins in triclinic stencil
every pair stored exactly once by some processor
------------------------------------------------------------------------- */
void Neighbor::half_bin_newton_tri_intel(NeighList *list)
{
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
list->inum = nlocal;
// Get fix for intel stuff
FixIntel *fix = static_cast<FixIntel *>(fix_intel);
const int off_end = fix->offload_end_neighbor();
int host_start = fix->host_start_neighbor();
int offload_noghost = 0;
#ifdef _LMP_INTEL_OFFLOAD
if (fix->full_host_list()) host_start = 0;
offload_noghost = fix->offload_noghost();
if (exclude)
error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
#endif
if (fix->precision() == FixIntel::PREC_MODE_MIXED) {
if (offload_noghost) {
hbnti<float,double,1>(1, list, fix->get_mixed_buffers(),
0, off_end, fix);
hbnti<float,double,1>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix, off_end);
} else {
hbnti<float,double,0>(1, list, fix->get_mixed_buffers(),
0, off_end, fix);
hbnti<float,double,0>(0, list, fix->get_mixed_buffers(),
host_start, nlocal, fix);
}
} else if (fix->precision() == FixIntel::PREC_MODE_DOUBLE) {
if (offload_noghost) {
hbnti<double,double,1>(1, list, fix->get_double_buffers(),
0, off_end, fix);
hbnti<double,double,1>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix, off_end);
} else {
hbnti<double,double,0>(1, list, fix->get_double_buffers(),
0, off_end, fix);
hbnti<double,double,0>(0, list, fix->get_double_buffers(),
host_start, nlocal, fix);
}
} else {
if (offload_noghost) {
hbnti<float,float,1>(1, list, fix->get_single_buffers(),
0, off_end, fix);
hbnti<float,float,1>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix, off_end);
} else {
hbnti<float,float,0>(1, list, fix->get_single_buffers(),
0, off_end, fix);
hbnti<float,float,0>(0, list, fix->get_single_buffers(),
host_start, nlocal, fix);
}
}
}
template <class flt_t, class acc_t, int offload_noghost>
void Neighbor::hbnti(const int offload, NeighList *list, void *buffers_in,
const int astart, const int aend, void *fix_in,
const int offload_end) {
IntelBuffers<flt_t,acc_t> *buffers = (IntelBuffers<flt_t,acc_t> *)buffers_in;
FixIntel *fix = (FixIntel *)fix_in;
const int nall = atom->nlocal + atom->nghost;
int pad = 1;
if (offload) {
fix->start_watch(TIME_PACK);
buffers->grow(nall, atom->nlocal, comm->nthreads, aend);
buffers->grow_nbor(list, atom->nlocal, aend);
ATOM_T biga;
biga.x = INTEL_BIGP;
biga.y = INTEL_BIGP;
biga.z = INTEL_BIGP;
biga.w = 1;
buffers->get_x()[nall]=biga;
const int nthreads = comm->nthreads;
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(buffers)
#endif
{
int ifrom, ito, tid;
IP_PRE_omp_range_id_align(ifrom, ito, tid, nall, nthreads,
sizeof(ATOM_T));
buffers->thr_pack(ifrom, ito, 0);
}
fix->stop_watch(TIME_PACK);
fix->start_watch(TIME_HOST_NEIGHBOR);
bin_atoms<flt_t,acc_t>(buffers->get_x());
if (INTEL_MIC_NBOR_PAD > 1)
pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
} else {
fix->start_watch(TIME_HOST_NEIGHBOR);
if (INTEL_NBOR_PAD > 1)
pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
}
const int pad_width = pad;
if (aend-astart == 0) {
fix->stop_watch(TIME_HOST_NEIGHBOR);
return;
}
const ATOM_T * _noalias const x = buffers->get_x();
int * _noalias const firstneigh = buffers->firstneigh(list);
int nall_t = nall;
if (offload_noghost && offload) nall_t = atom->nlocal;
const int e_nall = nall_t;
const int molecular = atom->molecular;
int *ns = NULL;
tagint *s = NULL;
int tag_size, special_size;
if (molecular) {
s = atom->special[0];
ns = atom->nspecial[0];
tag_size = e_nall;
special_size = aend;
} else {
s = &buffers->_special_holder;
ns = &buffers->_nspecial_holder;
tag_size = 0;
special_size = 0;
}
const tagint * _noalias const special = s;
const int * _noalias const nspecial = ns;
const int maxspecial = atom->maxspecial;
const tagint * _noalias const tag = atom->tag;
int * _noalias const ilist = list->ilist;
int * _noalias numneigh = list->numneigh;
int * _noalias const cnumneigh = buffers->cnumneigh(list);
const int nstencil = list->nstencil;
const int * _noalias const stencil = list->stencil;
const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
const int ntypes = atom->ntypes + 1;
const int nlocal = atom->nlocal;
#ifndef _LMP_INTEL_OFFLOAD
int * const mask = atom->mask;
tagint * const molecule = atom->molecule;
#endif
int tnum;
int *overflow;
double *timer_compute;
if (offload) {
timer_compute = fix->off_watch_neighbor();
tnum = buffers->get_off_threads();
overflow = fix->get_off_overflow_flag();
fix->stop_watch(TIME_HOST_NEIGHBOR);
fix->start_watch(TIME_OFFLOAD_LATENCY);
} else {
tnum = comm->nthreads;
overflow = fix->get_overflow_flag();
}
const int nthreads = tnum;
const int maxnbors = buffers->get_max_nbors();
const flt_t bboxlo0 = this->bboxlo[0];
const flt_t bboxlo1 = this->bboxlo[1];
const flt_t bboxlo2 = this->bboxlo[2];
const flt_t bboxhi0 = this->bboxhi[0];
const flt_t bboxhi1 = this->bboxhi[1];
const flt_t bboxhi2 = this->bboxhi[2];
const flt_t bininvx = this->bininvx;
const flt_t bininvy = this->bininvy;
const flt_t bininvz = this->bininvz;
// Make sure dummy coordinates to eliminate loop remainder not within cutoff
{
const flt_t dx = (INTEL_BIGP - bboxhi0);
const flt_t dy = (INTEL_BIGP - bboxhi1);
const flt_t dz = (INTEL_BIGP - bboxhi2);
if (dx * dx + dy * dy + dz * dz < static_cast<flt_t>(cutneighmaxsq))
error->one(FLERR,
"Intel package expects no atoms within cutoff of {1e15,1e15,1e15}.");
}
#ifdef _LMP_INTEL_OFFLOAD
const int * _noalias const binhead = this->binhead;
const int * _noalias const special_flag = this->special_flag;
const int nbinx = this->nbinx;
const int nbiny = this->nbiny;
const int nbinz = this->nbinz;
const int mbinxlo = this->mbinxlo;
const int mbinylo = this->mbinylo;
const int mbinzlo = this->mbinzlo;
const int mbinx = this->mbinx;
const int mbiny = this->mbiny;
const int mbinz = this->mbinz;
const int * _noalias const bins = this->bins;
const int cop = fix->coprocessor_number();
const int separate_buffers = fix->separate_buffers();
#pragma offload target(mic:cop) if(offload) \
in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
in(tag:length(tag_size) alloc_if(0) free_if(0)) \
in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
in(bins:length(nall) alloc_if(0) free_if(0)) \
in(binhead:length(mbins) alloc_if(0) free_if(0)) \
in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
in(firstneigh:length(0) alloc_if(0) free_if(0)) \
in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
out(numneigh:length(0) alloc_if(0) free_if(0)) \
in(ilist:length(0) alloc_if(0) free_if(0)) \
in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
in(special_flag:length(0) alloc_if(0) free_if(0)) \
in(maxnbors,nthreads,maxspecial,nstencil,nbinx,nbiny,nbinz,offload_end) \
in(mbinxlo,mbinylo,mbinzlo,mbinx,mbiny,mbinz,pad_width,e_nall,offload) \
in(bininvx,bininvy,bininvz,bboxlo0,bboxlo1,bboxlo2,separate_buffers) \
in(bboxhi0, bboxhi1, bboxhi2, astart, aend, nlocal, molecular, ntypes) \
out(overflow:length(5) alloc_if(0) free_if(0)) \
out(timer_compute:length(1) alloc_if(0) free_if(0)) \
signal(numneigh)
#endif
{
#ifdef __MIC__
*timer_compute = MIC_Wtime();
#endif
#ifdef _LMP_INTEL_OFFLOAD
overflow[LMP_LOCAL_MIN] = astart;
overflow[LMP_LOCAL_MAX] = aend - 1;
overflow[LMP_GHOST_MIN] = e_nall;
overflow[LMP_GHOST_MAX] = -1;
#endif
#if defined(_OPENMP)
#pragma omp parallel default(none) shared(numneigh, overflow)
#endif
{
#ifdef _LMP_INTEL_OFFLOAD
int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
#endif
const int num = aend-astart;
int tid, ifrom, ito;
IP_PRE_omp_range_id(ifrom,ito,tid,num,nthreads);
ifrom += astart;
ito += astart;
int which;
const int list_size = (ito + tid + 1) * maxnbors;
int ct = (ifrom + tid) * maxnbors;
int *neighptr = firstneigh + ct;
for (int i = ifrom; i < ito; i++) {
int j, k, n, n2, itype, jtype, ibin;
double xtmp, ytmp, ztmp, delx, dely, delz, rsq;
n = 0;
n2 = maxnbors;
xtmp = x[i].x;
ytmp = x[i].y;
ztmp = x[i].z;
itype = x[i].w;
const int ioffset = ntypes * itype;
// loop over all atoms in bins in stencil
// pairs for atoms j "below" i are excluded
// below = lower z or (equal z and lower y) or (equal zy and lower x)
// (equal zyx and j <= i)
// latter excludes self-self interaction but allows superposed atoms
ibin = mcoord2bin(x[i].x, x[i].y, x[i].z, bboxlo0, bboxlo1, bboxlo2,
bboxhi0, bboxhi1, bboxhi2, bininvx, bininvy, bininvz,
nbinx, nbiny, nbinz, mbinx, mbiny, mbinz,
mbinxlo, mbinylo, mbinzlo);
for (k = 0; k < nstencil; k++) {
for (j = binhead[ibin + stencil[k]]; j >= 0; j = bins[j]) {
if (offload_noghost) {
if (j < nlocal) {
if (i < offload_end) continue;
} else if (offload) continue;
}
if (x[j].z < ztmp) continue;
if (x[j].z == ztmp) {
if (x[j].y < ytmp) continue;
if (x[j].y == ytmp) {
if (x[j].x < xtmp) continue;
if (x[j].x == xtmp && j <= i) continue;
}
}
jtype = x[j].w;
#ifndef _LMP_INTEL_OFFLOAD
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
#endif
delx = xtmp - x[j].x;
dely = ytmp - x[j].y;
delz = ztmp - x[j].z;
rsq = delx * delx + dely * dely + delz * delz;
if (rsq <= cutneighsq[ioffset + jtype]) {
if (j < nlocal) {
neighptr[n++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < lmin) lmin = j;
if (j > lmax) lmax = j;
#endif
} else {
neighptr[n2++] = j;
#ifdef _LMP_INTEL_OFFLOAD
if (j < gmin) gmin = j;
if (j > gmax) gmax = j;
#endif
}
}
}
}
ilist[i] = i;
cnumneigh[i] = ct;
if (n > maxnbors) *overflow = 1;
for (k = maxnbors; k < n2; k++) neighptr[n++] = neighptr[k];
while( (n % pad_width) != 0 ) neighptr[n++] = e_nall;
numneigh[i] = n;
while((n % (INTEL_DATA_ALIGN / sizeof(int))) != 0) n++;
ct += n;
neighptr += n;
if (ct + n + maxnbors > list_size) {
*overflow = 1;
ct = (ifrom + tid) * maxnbors;
}
}
if (*overflow == 1)
for (int i = ifrom; i < ito; i++)
numneigh[i] = 0;
#ifdef _LMP_INTEL_OFFLOAD
if (separate_buffers) {
#if defined(_OPENMP)
#pragma omp critical
#endif
{
if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
}
#pragma omp barrier
}
int ghost_offset = 0, nall_offset = e_nall;
if (separate_buffers) {
int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
if (nghost < 0) nghost = 0;
if (offload) {
ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
} else {
ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
nall_offset = nlocal + nghost;
}
}
#endif
if (molecular) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
for (int jj = 0; jj < jnum; jj++) {
const int j = jlist[jj];
ofind_special(which, special, nspecial, i, tag[j], special_flag);
#ifdef _LMP_INTEL_OFFLOAD
if (j >= nlocal) {
if (j == e_nall)
jlist[jj] = nall_offset;
else if (which > 0)
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
else jlist[jj]-=ghost_offset;
} else
#endif
if (which > 0) jlist[jj] = j ^ (which << SBBITS);
}
}
}
#ifdef _LMP_INTEL_OFFLOAD
else if (separate_buffers) {
for (int i = ifrom; i < ito; ++i) {
int * _noalias jlist = firstneigh + cnumneigh[i];
const int jnum = numneigh[i];
int jj = 0;
for (jj = 0; jj < jnum; jj++)
if (jlist[jj] >= nlocal) break;
while (jj < jnum) {
if (jlist[jj] == e_nall) jlist[jj] = nall_offset;
else jlist[jj] -= ghost_offset;
jj++;
}
}
}
#endif
} // end omp
#ifdef __MIC__
*timer_compute = MIC_Wtime() - *timer_compute;
#endif
} // end offload
if (offload) {
fix->stop_watch(TIME_OFFLOAD_LATENCY);
#ifdef _LMP_INTEL_OFFLOAD
for (int n = 0; n < aend; n++) {
ilist[n] = n;
numneigh[n] = 0;
}
#endif
} else {
for (int i = astart; i < aend; i++)
list->firstneigh[i] = firstneigh + cnumneigh[i];
fix->stop_watch(TIME_HOST_NEIGHBOR);
#ifdef _LMP_INTEL_OFFLOAD
if (separate_buffers) {
fix->start_watch(TIME_PACK);
fix->set_neighbor_host_sizes();
buffers->pack_sep_from_single(fix->host_min_local(),
fix->host_used_local(),
fix->host_min_ghost(),
fix->host_used_ghost());
fix->stop_watch(TIME_PACK);
}
#endif
}
}
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