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Merge pull request lammps#3974 from stanmoore1/skip_trim
Add trim option to skip neighbor list build styles
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| Original file line number | Diff line number | Diff line change |
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| // clang-format off | ||
| /* ---------------------------------------------------------------------- | ||
| LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator | ||
| https://www.lammps.org/, Sandia National Laboratories | ||
| LAMMPS development team: developers@lammps.org | ||
| 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: Stan Moore (SNL) | ||
| ------------------------------------------------------------------------- */ | ||
|
|
||
| #include "npair_skip_trim_intel.h" | ||
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| #include "atom.h" | ||
| #include "comm.h" | ||
| #include "error.h" | ||
| #include "modify.h" | ||
| #include "my_page.h" | ||
| #include "neigh_list.h" | ||
| #include "neigh_request.h" | ||
| #include "neighbor.h" | ||
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|
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| using namespace LAMMPS_NS; | ||
|
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| /* ---------------------------------------------------------------------- */ | ||
|
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| NPairSkipTrimIntel::NPairSkipTrimIntel(LAMMPS *lmp) : NPair(lmp) { | ||
| _fix = static_cast<FixIntel *>(modify->get_fix_by_id("package_intel")); | ||
| if (!_fix) error->all(FLERR, "The 'package intel' command is required for /intel styles"); | ||
| _inum_starts = new int[comm->nthreads]; | ||
| _inum_counts = new int[comm->nthreads]; | ||
| _full_props = nullptr; | ||
| } | ||
|
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| /* ---------------------------------------------------------------------- */ | ||
|
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| NPairSkipTrimIntel::~NPairSkipTrimIntel() { | ||
| delete []_inum_starts; | ||
| delete []_inum_counts; | ||
| delete[] _full_props; | ||
| } | ||
|
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| /* ---------------------------------------------------------------------- */ | ||
|
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| void NPairSkipTrimIntel::copy_neighbor_info() | ||
| { | ||
| NPair::copy_neighbor_info(); | ||
| // Only need to set _full_props once; npair object deleted for changes | ||
| if (_full_props) return; | ||
| _full_props = new int[neighbor->nrequest]; | ||
| for (int i = 0; i < neighbor->nrequest; i++) | ||
| _full_props[i] = neighbor->requests[i]->full; | ||
| } | ||
|
|
||
| /* ---------------------------------------------------------------------- | ||
| build skip list for subset of types from parent list | ||
| works for half and full lists | ||
| works for owned (non-ghost) list, also for ghost list | ||
| iskip and ijskip flag which atom types and type pairs to skip | ||
| if ghost, also store neighbors of ghost atoms & set inum,gnum correctly | ||
| ------------------------------------------------------------------------- */ | ||
|
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||
| template<class flt_t, class acc_t, int THREE> | ||
| void NPairSkipTrimIntel::build_t(NeighList *list, int *numhalf, int *cnumneigh, | ||
| int *numhalf_skip, IntelBuffers<flt_t,acc_t> *buffers) | ||
| { | ||
| const int nlocal = atom->nlocal; | ||
| const int e_nall = nlocal + atom->nghost; | ||
| const ATOM_T * _noalias const x = buffers->get_x(); | ||
| const int * _noalias const type = atom->type; | ||
| int * _noalias const ilist = list->ilist; | ||
| int * _noalias const numneigh = list->numneigh; | ||
| int ** _noalias const firstneigh = (int ** const)list->firstneigh; // NOLINT | ||
| const int * _noalias const ilist_skip = list->listskip->ilist; | ||
| const int * _noalias const numneigh_skip = list->listskip->numneigh; | ||
| const int ** _noalias const firstneigh_skip = (const int ** const)list->listskip->firstneigh; // NOLINT | ||
| const int * _noalias const iskip = list->iskip; | ||
| const int ** _noalias const ijskip = (const int ** const)list->ijskip; // NOLINT | ||
|
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| const flt_t cutsq_custom = cutoff_custom * cutoff_custom; | ||
| int num_skip = list->listskip->inum; | ||
| if (list->ghost) num_skip += list->listskip->gnum; | ||
|
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| int packthreads; | ||
| if (comm->nthreads > INTEL_HTHREADS && THREE==0) | ||
| packthreads = comm->nthreads; | ||
| else | ||
| packthreads = 1; | ||
|
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| #if defined(_OPENMP) | ||
| #pragma omp parallel if (packthreads > 1) | ||
| #endif | ||
| { | ||
| int tid, ifrom, ito; | ||
| IP_PRE_omp_range_id(ifrom, ito, tid, num_skip, packthreads); | ||
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| // each thread has its own page allocator | ||
| MyPage<int> &ipage = list->ipage[tid]; | ||
| ipage.reset(); | ||
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| int my_inum = ifrom; | ||
| _inum_starts[tid] = ifrom; | ||
|
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| // loop over parent full list | ||
| for (int ii = ifrom; ii < ito; ii++) { | ||
| const int i = ilist_skip[ii]; | ||
| const int itype = type[i]; | ||
| if (iskip[itype]) continue; | ||
|
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| const flt_t xtmp = x[i].x; | ||
| const flt_t ytmp = x[i].y; | ||
| const flt_t ztmp = x[i].z; | ||
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| int n = 0; | ||
| int *neighptr = ipage.vget(); | ||
|
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| // loop over parent non-skip list | ||
|
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| const int * _noalias const jlist = firstneigh_skip[i]; | ||
| const int jnum = numneigh_skip[i]; | ||
|
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| if (THREE) { | ||
| const int jnumhalf = numhalf_skip[ii]; | ||
| for (int jj = 0; jj < jnumhalf; jj++) { | ||
| const int joriginal = jlist[jj]; | ||
| const int j = joriginal & NEIGHMASK; | ||
|
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| int addme = 1; | ||
| if (ijskip[itype][type[j]]) addme = 0; | ||
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| // trim to shorter cutoff | ||
|
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| const flt_t delx = xtmp - x[j].x; | ||
| const flt_t dely = ytmp - x[j].y; | ||
| const flt_t delz = ztmp - x[j].z; | ||
| const flt_t rsq = delx * delx + dely * dely + delz * delz; | ||
| if (rsq > cutsq_custom) addme = 0; | ||
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| if (addme) | ||
| neighptr[n++] = joriginal; | ||
| } | ||
| numhalf[my_inum] = n; | ||
|
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| for (int jj = jnumhalf; jj < jnum; jj++) { | ||
| const int joriginal = jlist[jj]; | ||
| const int j = joriginal & NEIGHMASK; | ||
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| int addme = 1; | ||
| if (ijskip[itype][type[j]]) addme = 0; | ||
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| // trim to shorter cutoff | ||
|
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| const flt_t delx = xtmp - x[j].x; | ||
| const flt_t dely = ytmp - x[j].y; | ||
| const flt_t delz = ztmp - x[j].z; | ||
| const flt_t rsq = delx * delx + dely * dely + delz * delz; | ||
| if (rsq > cutsq_custom) addme = 0; | ||
|
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| if (addme) | ||
| neighptr[n++] = joriginal; | ||
| } | ||
| } else { | ||
| #if defined(LMP_SIMD_COMPILER) | ||
| #pragma vector aligned | ||
| #pragma ivdep | ||
| #endif | ||
| for (int jj = 0; jj < jnum; jj++) { | ||
| const int joriginal = jlist[jj]; | ||
| const int j = joriginal & NEIGHMASK; | ||
|
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| int addme = 1; | ||
| if (ijskip[itype][type[j]]) addme = 0; | ||
|
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| // trim to shorter cutoff | ||
|
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| const flt_t delx = xtmp - x[j].x; | ||
| const flt_t dely = ytmp - x[j].y; | ||
| const flt_t delz = ztmp - x[j].z; | ||
| const flt_t rsq = delx * delx + dely * dely + delz * delz; | ||
| if (rsq > cutsq_custom) addme = 0; | ||
|
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| if (addme) | ||
| neighptr[n++] = joriginal; | ||
| } | ||
| } | ||
|
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| ilist[my_inum++] = i; | ||
| firstneigh[i] = neighptr; | ||
| numneigh[i] = n; | ||
|
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| int pad_end = n; | ||
| IP_PRE_neighbor_pad(pad_end, 0); | ||
| #if defined(LMP_SIMD_COMPILER) | ||
| #pragma vector aligned | ||
| #pragma loop_count min=1, max=INTEL_COMPILE_WIDTH-1, \ | ||
| avg=INTEL_COMPILE_WIDTH/2 | ||
| #endif | ||
| for ( ; n < pad_end; n++) | ||
| neighptr[n] = e_nall; | ||
|
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| ipage.vgot(n); | ||
| if (ipage.status()) | ||
| error->one(FLERR,"Neighbor list overflow, boost neigh_modify one"); | ||
| } | ||
|
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| int last_inum = 0, loop_end; | ||
| _inum_counts[tid] = my_inum; | ||
| } | ||
| int inum = _inum_counts[0]; | ||
| for (int tid = 1; tid < packthreads; tid++) { | ||
| for (int i = _inum_starts[tid]; i < _inum_counts[tid]; i++) { | ||
| if (THREE) numhalf[inum] = numhalf[i]; | ||
| ilist[inum++] = ilist[i]; | ||
| } | ||
| } | ||
| list->inum = inum; | ||
|
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| if (THREE && num_skip > 0) { | ||
| int * const list_start = firstneigh[ilist[0]]; | ||
| for (int ii = 0; ii < inum; ii++) { | ||
| int i = ilist[ii]; | ||
| cnumneigh[ii] = static_cast<int>(firstneigh[i] - list_start); | ||
| } | ||
| } | ||
| if (list->ghost) { | ||
| int num = 0; | ||
| int my_inum = list->inum; | ||
| for (int i = 0; i < my_inum; i++) | ||
| if (ilist[i] < nlocal) num++; | ||
| else break; | ||
| list->inum = num; | ||
| list->gnum = my_inum - num; | ||
| } | ||
| } | ||
|
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| /* ---------------------------------------------------------------------- */ | ||
|
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| void NPairSkipTrimIntel::build(NeighList *list) | ||
| { | ||
| if (_fix->three_body_neighbor()==0 || | ||
| _full_props[list->listskip->index] == 0) { | ||
| if (_fix->precision() == FixIntel::PREC_MODE_MIXED) | ||
| build_t<float,double,0>(list, nullptr, nullptr, nullptr, _fix->get_mixed_buffers()); | ||
| else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) | ||
| build_t<double,double,0>(list, nullptr, nullptr, nullptr, _fix->get_double_buffers()); | ||
| else | ||
| build_t<float,float,0>(list, nullptr, nullptr, nullptr, _fix->get_single_buffers()); | ||
| } else { | ||
| int *nhalf, *cnumneigh, *nhalf_skip, *u; | ||
| if (_fix->precision() == FixIntel::PREC_MODE_MIXED) { | ||
| _fix->get_mixed_buffers()->get_list_data3(list->listskip,nhalf_skip,u); | ||
| _fix->get_mixed_buffers()->grow_data3(list, nhalf, cnumneigh); | ||
| build_t<float,double,1>(list, nhalf, cnumneigh, nhalf_skip, _fix->get_mixed_buffers()); | ||
| } else if (_fix->precision() == FixIntel::PREC_MODE_DOUBLE) { | ||
| _fix->get_double_buffers()->get_list_data3(list->listskip,nhalf_skip,u); | ||
| _fix->get_double_buffers()->grow_data3(list, nhalf, cnumneigh); | ||
| build_t<double,double,1>(list, nhalf, cnumneigh, nhalf_skip, _fix->get_double_buffers()); | ||
| } else { | ||
| _fix->get_single_buffers()->get_list_data3(list->listskip,nhalf_skip,u); | ||
| _fix->get_single_buffers()->grow_data3(list,nhalf,cnumneigh); | ||
| build_t<float,float,1>(list, nhalf, cnumneigh, nhalf_skip, _fix->get_single_buffers()); | ||
| } | ||
| } | ||
| } |
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