514 lines
16 KiB
C++
514 lines
16 KiB
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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/* ----------------------------------------------------------------------
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Contributing author: W. Michael Brown (Intel)
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------------------------------------------------------------------------- */
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#include "npair_half_bin_newton_tri_intel.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "atom.h"
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#include "comm.h"
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#include "group.h"
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using namespace LAMMPS_NS;
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/* ---------------------------------------------------------------------- */
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NPairHalfBinNewtonTriIntel::NPairHalfBinNewtonTriIntel(LAMMPS *lmp) :
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NPairIntel(lmp) {}
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/* ----------------------------------------------------------------------
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binned neighbor list construction with Newton's 3rd law for triclinic
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each owned atom i checks its own bin and other bins in triclinic stencil
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every pair stored exactly once by some processor
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------------------------------------------------------------------------- */
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void NPairHalfBinNewtonTriIntel::build(NeighList *list)
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{
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if (nstencil > INTEL_MAX_STENCIL)
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error->all(FLERR, "Too many neighbor bins for USER-INTEL package.");
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#ifdef _LMP_INTEL_OFFLOAD
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if (exclude)
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error->all(FLERR, "Exclusion lists not yet supported for Intel offload");
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#endif
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if (_fix->precision() == FixIntel::PREC_MODE_MIXED)
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hbnti(list, _fix->get_mixed_buffers());
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else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE)
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hbnti(list, _fix->get_double_buffers());
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else
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hbnti(list, _fix->get_single_buffers());
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_fix->stop_watch(TIME_HOST_NEIGHBOR);
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}
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template <class flt_t, class acc_t>
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void NPairHalfBinNewtonTriIntel::
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hbnti(NeighList *list, IntelBuffers<flt_t,acc_t> *buffers) {
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const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
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list->inum = nlocal;
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int host_start = _fix->host_start_neighbor();
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const int off_end = _fix->offload_end_neighbor();
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#ifdef _LMP_INTEL_OFFLOAD
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if (off_end) grow_stencil();
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if (_fix->full_host_list()) host_start = 0;
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int offload_noghost = _fix->offload_noghost();
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#endif
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buffers->grow_list(list, atom->nlocal, comm->nthreads, off_end);
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int need_ic = 0;
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if (atom->molecular)
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dminimum_image_check(need_ic, neighbor->cutneighmax, neighbor->cutneighmax,
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neighbor->cutneighmax);
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#ifdef _LMP_INTEL_OFFLOAD
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if (need_ic) {
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if (offload_noghost) {
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hbnti<flt_t,acc_t,1,1>(1, list, buffers, 0, off_end);
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hbnti<flt_t,acc_t,1,1>(0, list, buffers, host_start, nlocal, off_end);
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} else {
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hbnti<flt_t,acc_t,0,1>(1, list, buffers, 0, off_end);
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hbnti<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
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}
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} else {
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if (offload_noghost) {
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hbnti<flt_t,acc_t,1,0>(1, list, buffers, 0, off_end);
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hbnti<flt_t,acc_t,1,0>(0, list, buffers, host_start, nlocal, off_end);
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} else {
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hbnti<flt_t,acc_t,0,0>(1, list, buffers, 0, off_end);
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hbnti<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
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}
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}
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#else
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if (need_ic)
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hbnti<flt_t,acc_t,0,1>(0, list, buffers, host_start, nlocal);
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else
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hbnti<flt_t,acc_t,0,0>(0, list, buffers, host_start, nlocal);
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#endif
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}
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template <class flt_t, class acc_t, int offload_noghost, int need_ic>
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void NPairHalfBinNewtonTriIntel::
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hbnti(const int offload, NeighList *list, IntelBuffers<flt_t,acc_t> *buffers,
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const int astart, const int aend, const int offload_end) {
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if (aend-astart == 0) return;
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const int nall = atom->nlocal + atom->nghost;
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int pad = 1;
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int nall_t = nall;
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#ifdef _LMP_INTEL_OFFLOAD
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if (offload_noghost && offload) nall_t = atom->nlocal;
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if (offload) {
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if (INTEL_MIC_NBOR_PAD > 1)
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pad = INTEL_MIC_NBOR_PAD * sizeof(float) / sizeof(flt_t);
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} else
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#endif
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if (INTEL_NBOR_PAD > 1)
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pad = INTEL_NBOR_PAD * sizeof(float) / sizeof(flt_t);
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const int pad_width = pad;
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const ATOM_T * _noalias const x = buffers->get_x();
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int * _noalias const firstneigh = buffers->firstneigh(list);
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const int e_nall = nall_t;
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const int molecular = atom->molecular;
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int *ns = NULL;
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tagint *s = NULL;
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int tag_size = 0, special_size;
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if (buffers->need_tag()) tag_size = e_nall;
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if (molecular) {
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s = atom->special[0];
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ns = atom->nspecial[0];
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special_size = aend;
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} else {
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s = &buffers->_special_holder;
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ns = &buffers->_nspecial_holder;
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special_size = 0;
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}
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const tagint * _noalias const special = s;
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const int * _noalias const nspecial = ns;
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const int maxspecial = atom->maxspecial;
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const tagint * _noalias const tag = atom->tag;
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int * _noalias const ilist = list->ilist;
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int * _noalias numneigh = list->numneigh;
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int * _noalias const cnumneigh = buffers->cnumneigh(list);
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const int nstencil = this->nstencil;
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const int * _noalias const stencil = this->stencil;
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const flt_t * _noalias const cutneighsq = buffers->get_cutneighsq()[0];
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const int ntypes = atom->ntypes + 1;
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const int nlocal = atom->nlocal;
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#ifndef _LMP_INTEL_OFFLOAD
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int * const mask = atom->mask;
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tagint * const molecule = atom->molecule;
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#endif
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int tnum;
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int *overflow;
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double *timer_compute;
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#ifdef _LMP_INTEL_OFFLOAD
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if (offload) {
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timer_compute = _fix->off_watch_neighbor();
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tnum = buffers->get_off_threads();
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overflow = _fix->get_off_overflow_flag();
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_fix->stop_watch(TIME_HOST_NEIGHBOR);
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_fix->start_watch(TIME_OFFLOAD_LATENCY);
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} else
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#endif
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{
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tnum = comm->nthreads;
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overflow = _fix->get_overflow_flag();
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}
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const int nthreads = tnum;
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const int maxnbors = buffers->get_max_nbors();
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int * _noalias const atombin = buffers->get_atombin();
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const int * _noalias const binpacked = buffers->get_binpacked();
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const int xperiodic = domain->xperiodic;
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const int yperiodic = domain->yperiodic;
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const int zperiodic = domain->zperiodic;
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const flt_t xprd_half = domain->xprd_half;
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const flt_t yprd_half = domain->yprd_half;
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const flt_t zprd_half = domain->zprd_half;
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#ifdef _LMP_INTEL_OFFLOAD
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const int * _noalias const binhead = this->binhead;
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const int * _noalias const bins = this->bins;
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const int cop = _fix->coprocessor_number();
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const int separate_buffers = _fix->separate_buffers();
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#pragma offload target(mic:cop) if(offload) \
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in(x:length(e_nall+1) alloc_if(0) free_if(0)) \
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in(tag:length(tag_size) alloc_if(0) free_if(0)) \
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in(special:length(special_size*maxspecial) alloc_if(0) free_if(0)) \
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in(nspecial:length(special_size*3) alloc_if(0) free_if(0)) \
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in(bins,binpacked:length(nall) alloc_if(0) free_if(0)) \
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in(binhead:length(mbins+1) alloc_if(0) free_if(0)) \
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in(cutneighsq:length(0) alloc_if(0) free_if(0)) \
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in(firstneigh:length(0) alloc_if(0) free_if(0)) \
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in(cnumneigh:length(0) alloc_if(0) free_if(0)) \
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out(numneigh:length(0) alloc_if(0) free_if(0)) \
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in(ilist:length(0) alloc_if(0) free_if(0)) \
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in(atombin:length(aend) alloc_if(0) free_if(0)) \
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in(stencil:length(nstencil) alloc_if(0) free_if(0)) \
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in(maxnbors,nthreads,maxspecial,nstencil,offload_end,pad_width,e_nall) \
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in(offload,separate_buffers, astart, aend, nlocal, molecular, ntypes) \
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in(xperiodic, yperiodic, zperiodic, xprd_half, yprd_half, zprd_half) \
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out(overflow:length(5) alloc_if(0) free_if(0)) \
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out(timer_compute:length(1) alloc_if(0) free_if(0)) \
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signal(tag)
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#endif
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{
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#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
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*timer_compute = MIC_Wtime();
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#endif
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#ifdef _LMP_INTEL_OFFLOAD
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overflow[LMP_LOCAL_MIN] = astart;
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overflow[LMP_LOCAL_MAX] = aend - 1;
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overflow[LMP_GHOST_MIN] = e_nall;
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overflow[LMP_GHOST_MAX] = -1;
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#endif
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int nstencilp = 0;
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int binstart[INTEL_MAX_STENCIL], binend[INTEL_MAX_STENCIL];
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for (int k = 0; k < nstencil; k++) {
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binstart[nstencilp] = stencil[k];
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int end = stencil[k] + 1;
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for (int kk = k + 1; kk < nstencil; kk++) {
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if (stencil[kk-1]+1 == stencil[kk]) {
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end++;
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k++;
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} else break;
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}
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binend[nstencilp] = end;
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nstencilp++;
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}
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#if defined(_OPENMP)
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#pragma omp parallel default(none) \
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shared(numneigh, overflow, nstencilp, binstart, binend)
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#endif
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{
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#ifdef _LMP_INTEL_OFFLOAD
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int lmin = e_nall, lmax = -1, gmin = e_nall, gmax = -1;
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#endif
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const int num = aend - astart;
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int tid, ifrom, ito;
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IP_PRE_omp_range_id(ifrom, ito, tid, num, nthreads);
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ifrom += astart;
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ito += astart;
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int which;
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const int list_size = (ito + tid * 2 + 2) * maxnbors;
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int ct = (ifrom + tid * 2) * maxnbors;
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int *neighptr = firstneigh + ct;
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const int obound = maxnbors * 3;
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for (int i = ifrom; i < ito; i++) {
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const flt_t xtmp = x[i].x;
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const flt_t ytmp = x[i].y;
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const flt_t ztmp = x[i].z;
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const int itype = x[i].w;
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const int ioffset = ntypes * itype;
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// loop over all atoms in bins in stencil
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// pairs for atoms j "below" i are excluded
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// below = lower z or (equal z and lower y) or (equal zy and lower x)
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// (equal zyx and j <= i)
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// latter excludes self-self interaction but allows superposed atoms
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const int ibin = atombin[i];
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int raw_count = maxnbors;
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for (int k = 0; k < nstencilp; k++) {
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const int bstart = binhead[ibin + binstart[k]];
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const int bend = binhead[ibin + binend[k]];
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for (int jj = bstart; jj < bend; jj++) {
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const int j = binpacked[jj];
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#ifdef _LMP_INTEL_OFFLOAD
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if (offload_noghost) {
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if (j < nlocal) {
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if (i < offload_end) continue;
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} else if (offload) continue;
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}
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#endif
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if (x[j].z < ztmp) continue;
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if (x[j].z == ztmp) {
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if (x[j].y < ytmp) continue;
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if (x[j].y == ytmp) {
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if (x[j].x < xtmp) continue;
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if (x[j].x == xtmp && j <= i) continue;
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}
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}
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#ifndef _LMP_INTEL_OFFLOAD
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if (exclude) {
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const int jtype = x[j].w;
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if (exclusion(i,j,itype,jtype,mask,molecule)) continue;
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}
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#endif
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neighptr[raw_count++] = j;
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}
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}
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if (raw_count > obound)
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*overflow = 1;
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#if defined(LMP_SIMD_COMPILER)
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#ifdef _LMP_INTEL_OFFLOAD
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int vlmin = lmin, vlmax = lmax, vgmin = gmin, vgmax = gmax;
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#if __INTEL_COMPILER+0 > 1499
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#pragma vector aligned
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#pragma simd reduction(max:vlmax,vgmax) reduction(min:vlmin, vgmin)
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#endif
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#else
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#pragma vector aligned
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#pragma simd
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#endif
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#endif
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for (int u = maxnbors; u < raw_count; u++) {
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int j = neighptr[u];
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const flt_t delx = xtmp - x[j].x;
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const flt_t dely = ytmp - x[j].y;
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const flt_t delz = ztmp - x[j].z;
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const int jtype = x[j].w;
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const flt_t rsq = delx * delx + dely * dely + delz * delz;
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if (rsq > cutneighsq[ioffset + jtype])
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neighptr[u] = e_nall;
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else {
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if (need_ic) {
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int no_special;
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ominimum_image_check(no_special, delx, dely, delz);
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if (no_special)
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neighptr[u] = -j - 1;
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}
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#ifdef _LMP_INTEL_OFFLOAD
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if (j < nlocal) {
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if (j < vlmin) vlmin = j;
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if (j > vlmax) vlmax = j;
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} else {
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if (j < vgmin) vgmin = j;
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if (j > vgmax) vgmax = j;
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}
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#endif
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}
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}
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int n = 0, n2 = maxnbors;
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for (int u = maxnbors; u < raw_count; u++) {
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const int j = neighptr[u];
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int pj = j;
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if (pj < e_nall) {
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if (need_ic)
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if (pj < 0) pj = -pj - 1;
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if (pj < nlocal)
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neighptr[n++] = j;
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else
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neighptr[n2++] = j;
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}
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}
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int ns = n;
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for (int u = maxnbors; u < n2; u++)
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neighptr[n++] = neighptr[u];
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ilist[i] = i;
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cnumneigh[i] = ct;
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ns += n2 - maxnbors;
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int edge = (ns % pad_width);
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if (edge) {
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const int pad_end = ns + (pad_width - edge);
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#if defined(LMP_SIMD_COMPILER)
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#pragma loop_count min=1, max=15, avg=8
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#endif
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for ( ; ns < pad_end; ns++)
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neighptr[ns] = e_nall;
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}
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numneigh[i] = ns;
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ct += ns;
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const int alignb = (INTEL_DATA_ALIGN / sizeof(int));
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edge = (ct % alignb);
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if (edge) ct += alignb - edge;
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neighptr = firstneigh + ct;
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if (ct + obound > list_size) {
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if (i < ito - 1) {
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*overflow = 1;
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ct = (ifrom + tid * 2) * maxnbors;
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}
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}
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}
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if (*overflow == 1)
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for (int i = ifrom; i < ito; i++)
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numneigh[i] = 0;
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#ifdef _LMP_INTEL_OFFLOAD
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if (separate_buffers) {
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#if defined(_OPENMP)
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#pragma omp critical
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#endif
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{
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if (lmin < overflow[LMP_LOCAL_MIN]) overflow[LMP_LOCAL_MIN] = lmin;
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if (lmax > overflow[LMP_LOCAL_MAX]) overflow[LMP_LOCAL_MAX] = lmax;
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if (gmin < overflow[LMP_GHOST_MIN]) overflow[LMP_GHOST_MIN] = gmin;
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if (gmax > overflow[LMP_GHOST_MAX]) overflow[LMP_GHOST_MAX] = gmax;
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}
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#pragma omp barrier
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}
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int ghost_offset = 0, nall_offset = e_nall;
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if (separate_buffers) {
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int nghost = overflow[LMP_GHOST_MAX] + 1 - overflow[LMP_GHOST_MIN];
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if (nghost < 0) nghost = 0;
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if (offload) {
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ghost_offset = overflow[LMP_GHOST_MIN] - overflow[LMP_LOCAL_MAX] - 1;
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nall_offset = overflow[LMP_LOCAL_MAX] + 1 + nghost;
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} else {
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ghost_offset = overflow[LMP_GHOST_MIN] - nlocal;
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nall_offset = nlocal + nghost;
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}
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}
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#endif
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if (molecular) {
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for (int i = ifrom; i < ito; ++i) {
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int * _noalias jlist = firstneigh + cnumneigh[i];
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const int jnum = numneigh[i];
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#if defined(LMP_SIMD_COMPILER)
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#pragma vector aligned
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#pragma simd
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#endif
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for (int jj = 0; jj < jnum; jj++) {
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const int j = jlist[jj];
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if (need_ic && j < 0) {
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which = 0;
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jlist[jj] = -j - 1;
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} else
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ofind_special(which, special, nspecial, i, tag[j]);
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#ifdef _LMP_INTEL_OFFLOAD
|
|
if (j >= nlocal) {
|
|
if (j == e_nall)
|
|
jlist[jj] = nall_offset;
|
|
else if (which)
|
|
jlist[jj] = (j-ghost_offset) ^ (which << SBBITS);
|
|
else jlist[jj]-=ghost_offset;
|
|
} else
|
|
#endif
|
|
if (which) 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
|
|
#if defined(__MIC__) && defined(_LMP_INTEL_OFFLOAD)
|
|
*timer_compute = MIC_Wtime() - *timer_compute;
|
|
#endif
|
|
} // end offload
|
|
|
|
#ifdef _LMP_INTEL_OFFLOAD
|
|
if (offload) {
|
|
_fix->stop_watch(TIME_OFFLOAD_LATENCY);
|
|
_fix->start_watch(TIME_HOST_NEIGHBOR);
|
|
for (int n = 0; n < aend; n++) {
|
|
ilist[n] = n;
|
|
numneigh[n] = 0;
|
|
}
|
|
} else {
|
|
for (int i = astart; i < aend; i++)
|
|
list->firstneigh[i] = firstneigh + cnumneigh[i];
|
|
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);
|
|
}
|
|
}
|
|
#else
|
|
for (int i = astart; i < aend; i++)
|
|
list->firstneigh[i] = firstneigh + cnumneigh[i];
|
|
#endif
|
|
}
|