Merge branch 'master' into prepare-clang-format
# Conflicts: # src/KOKKOS/nbin_kokkos.h # src/KOKKOS/nbin_ssa_kokkos.h # src/MOLECULE/bond_fene_expand.h # src/USER-DPD/nbin_ssa.h # src/USER-DPD/nstencil_half_bin_2d_ssa.h # src/USER-DPD/nstencil_half_bin_3d_ssa.h # src/USER-INTEL/nbin_intel.h # src/USER-MISC/fix_propel_self.cpp # src/USER-OMP/npair_full_multi_old_omp.h # src/USER-OMP/npair_half_multi_old_newton_omp.h # src/USER-OMP/npair_half_size_multi_newtoff_omp.h # src/USER-OMP/npair_halffull_newtoff_omp.h # src/USER-OMP/npair_halffull_newton_omp.h # src/USER-OMP/npair_skip_omp.h # src/main.cpp # src/nbin_standard.h # src/npair_full_multi_old.h # src/npair_halffull_newtoff.h # src/npair_halffull_newton.h # src/npair_skip.h # src/npair_skip_respa.h # src/npair_skip_size.h # src/npair_skip_size_off2on.h # src/npair_skip_size_off2on_oneside.h # src/nstencil_full_bin_2d.h # src/nstencil_full_bin_3d.h # src/nstencil_full_ghost_bin_2d.h # src/nstencil_full_ghost_bin_3d.h # src/nstencil_full_multi_2d.h # src/nstencil_full_multi_3d.h # src/nstencil_full_multi_old_2d.h # src/nstencil_full_multi_old_3d.h # src/nstencil_half_bin_2d_newtoff.cpp # src/nstencil_half_bin_3d_newtoff.cpp # src/nstencil_half_bin_3d_newton_tri.h # src/nstencil_half_ghost_bin_2d_newtoff.cpp # src/nstencil_half_ghost_bin_2d_newtoff.h # src/nstencil_half_ghost_bin_3d_newtoff.cpp # src/nstencil_half_ghost_bin_3d_newtoff.h # src/nstencil_half_multi_2d.h # src/nstencil_half_multi_2d_newtoff.h # src/nstencil_half_multi_2d_newton_tri.h # src/nstencil_half_multi_2d_tri.h # src/nstencil_half_multi_3d_newtoff.h # src/nstencil_half_multi_3d_newton_tri.h
This commit is contained in:
Axel Kohlmeyer
352
src/nstencil.cpp
352
src/nstencil.cpp
@ -32,26 +32,36 @@ using namespace LAMMPS_NS;
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sx,sy,sz = bin bounds = furthest the stencil could possibly extend
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calculated below in create_setup()
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3d creates xyz stencil, 2d creates xy stencil
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for half list with newton off:
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for full list or half list with newton off
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use a full stencil
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stencil is all surrounding bins including self
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regardless of triclinic
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for half list with newton on:
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for half list with newton on
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use a half stencil
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stencil is bins to the "upper right" of central bin
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stencil does not include self
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no versions that allow ghost on (no callers need it?)
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for half list with newton on and triclinic:
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use a half stencil
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stencil is all bins in z-plane of self and above, but not below
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in 2d is all bins in y-plane of self and above, but not below
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stencil includes self
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no versions that allow ghost on (no callers need it?)
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for full list:
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stencil is all surrounding bins including self
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regardless of newton on/off or triclinic
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for multi:
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for multi/old:
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create one stencil for each atom type
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stencil follows same rules for half/full, newton on/off, triclinic
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cutoff is not cutneighmaxsq, but max cutoff for that atom type
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no versions that allow ghost on (any need for it?)
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for multi:
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create one stencil for each icollection-jcollection pairing
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the full/half stencil label refers to the same-collection stencil
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a half list with newton on has a half same-collection stencil
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a full list or half list with newton off has a full same-collection stencil
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cross collection stencils are always full to allow small-to-large lookups
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for orthogonal boxes, a half stencil includes bins to the "upper right" of central bin
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for triclinic, a half stencil includes bins in the z (3D) or y (2D) plane of self and above
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cutoff is not cutneighmaxsq, but max cutoff for that atom collection
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no versions that allow ghost on (any need for it?)
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------------------------------------------------------------------------- */
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NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
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@ -59,12 +69,22 @@ NStencil::NStencil(LAMMPS *lmp) : Pointers(lmp)
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last_stencil = -1;
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xyzflag = 0;
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maxstencil = maxstencil_multi = 0;
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maxstencil = maxstencil_multi_old = 0;
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stencil = nullptr;
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stencilxyz = nullptr;
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nstencil_multi_old = nullptr;
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stencil_multi_old = nullptr;
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distsq_multi_old = nullptr;
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nstencil_multi = nullptr;
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stencil_multi = nullptr;
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distsq_multi = nullptr;
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maxstencil_multi = nullptr;
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flag_half_multi = nullptr;
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flag_skip_multi = nullptr;
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bin_collection_multi = nullptr;
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maxcollections = 0;
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dimension = domain->dimension;
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}
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@ -76,16 +96,44 @@ NStencil::~NStencil()
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memory->destroy(stencil);
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memory->destroy(stencilxyz);
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if (!stencil_multi) return;
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if (stencil_multi_old) {
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int n = atom->ntypes;
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for (int i = 1; i <= n; i++) {
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memory->destroy(stencil_multi[i]);
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memory->destroy(distsq_multi[i]);
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int n = atom->ntypes;
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for (int i = 1; i <= n; i++) {
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memory->destroy(stencil_multi_old[i]);
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memory->destroy(distsq_multi_old[i]);
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}
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delete [] nstencil_multi_old;
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delete [] stencil_multi_old;
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delete [] distsq_multi_old;
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}
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if (maxstencil_multi) {
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memory->destroy(nstencil_multi);
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for (int i = 0; i < maxcollections; i++) {
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for (int j = 0; j < maxcollections; j++)
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memory->destroy(stencil_multi[i][j]);
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delete [] stencil_multi[i];
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}
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delete [] stencil_multi;
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memory->destroy(maxstencil_multi);
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memory->destroy(flag_half_multi);
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memory->destroy(flag_skip_multi);
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memory->destroy(bin_collection_multi);
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memory->destroy(stencil_sx_multi);
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memory->destroy(stencil_sy_multi);
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memory->destroy(stencil_sz_multi);
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memory->destroy(stencil_mbinx_multi);
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memory->destroy(stencil_mbiny_multi);
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memory->destroy(stencil_mbinz_multi);
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memory->destroy(stencil_binsizex_multi);
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memory->destroy(stencil_binsizey_multi);
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memory->destroy(stencil_binsizez_multi);
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}
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delete [] nstencil_multi;
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delete [] stencil_multi;
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delete [] distsq_multi;
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}
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/* ---------------------------------------------------------------------- */
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@ -106,6 +154,11 @@ void NStencil::copy_neighbor_info()
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cutneighmax = neighbor->cutneighmax;
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cutneighmaxsq = neighbor->cutneighmaxsq;
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cuttypesq = neighbor->cuttypesq;
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cutneighsq = neighbor->cutneighsq;
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ncollections = neighbor->ncollections;
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collection = neighbor->collection;
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cutcollectionsq = neighbor->cutcollectionsq;
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// overwrite Neighbor cutoff with custom value set by requestor
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// only works for style = BIN (checked by Neighbor class)
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@ -133,6 +186,23 @@ void NStencil::copy_bin_info()
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bininvz = nb->bininvz;
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}
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/* ----------------------------------------------------------------------
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copy needed info for multi from NBin class to this stencil class
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------------------------------------------------------------------------- */
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void NStencil::copy_bin_info_multi()
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{
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mbinx_multi = nb->mbinx_multi;
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mbiny_multi = nb->mbiny_multi;
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mbinz_multi = nb->mbinz_multi;
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binsizex_multi = nb->binsizex_multi;
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binsizey_multi = nb->binsizey_multi;
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binsizez_multi = nb->binsizez_multi;
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bininvx_multi = nb->bininvx_multi;
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bininvy_multi = nb->bininvy_multi;
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bininvz_multi = nb->bininvz_multi;
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}
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/* ----------------------------------------------------------------------
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insure NBin data is current
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insure stencils are allocated large enough
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@ -140,59 +210,188 @@ void NStencil::copy_bin_info()
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void NStencil::create_setup()
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{
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if (nb) copy_bin_info();
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last_stencil = update->ntimestep;
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// sx,sy,sz = max range of stencil in each dim
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// smax = max possible size of entire 3d stencil
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// stencil will be empty if cutneighmax = 0.0
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if (neighstyle != Neighbor::MULTI) {
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if (nb) copy_bin_info();
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last_stencil = update->ntimestep;
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sx = static_cast<int> (cutneighmax*bininvx);
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if (sx*binsizex < cutneighmax) sx++;
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sy = static_cast<int> (cutneighmax*bininvy);
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if (sy*binsizey < cutneighmax) sy++;
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sz = static_cast<int> (cutneighmax*bininvz);
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if (sz*binsizez < cutneighmax) sz++;
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if (dimension == 2) sz = 0;
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// sx,sy,sz = max range of stencil in each dim
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// smax = max possible size of entire 3d stencil
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// stencil will be empty if cutneighmax = 0.0
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int smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
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sx = static_cast<int>(cutneighmax*bininvx);
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if (sx*binsizex < cutneighmax) sx++;
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sy = static_cast<int>(cutneighmax*bininvy);
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if (sy*binsizey < cutneighmax) sy++;
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sz = static_cast<int>(cutneighmax*bininvz);
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if (sz*binsizez < cutneighmax) sz++;
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if (dimension == 2) sz = 0;
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// reallocate stencil structs if necessary
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// for BIN and MULTI styles
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int smax = (2*sx+1) * (2*sy+1) * (2*sz+1);
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if (neighstyle == Neighbor::BIN) {
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if (smax > maxstencil) {
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maxstencil = smax;
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memory->destroy(stencil);
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memory->create(stencil,maxstencil,"neighstencil:stencil");
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if (xyzflag) {
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memory->destroy(stencilxyz);
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memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz");
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// reallocate stencil structs if necessary
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// for BIN and MULTI_OLD styles
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if (neighstyle == Neighbor::BIN) {
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if (smax > maxstencil) {
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maxstencil = smax;
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memory->destroy(stencil);
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memory->create(stencil,maxstencil,"neighstencil:stencil");
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if (xyzflag) {
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memory->destroy(stencilxyz);
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memory->create(stencilxyz,maxstencil,3,"neighstencil:stencilxyz");
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}
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}
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} else {
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int i;
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int n = atom->ntypes;
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if (maxstencil_multi_old == 0) {
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nstencil_multi_old = new int[n+1];
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stencil_multi_old = new int*[n+1];
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distsq_multi_old = new double*[n+1];
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for (i = 1; i <= n; i++) {
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nstencil_multi_old[i] = 0;
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stencil_multi_old[i] = nullptr;
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distsq_multi_old[i] = nullptr;
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}
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}
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if (smax > maxstencil_multi_old) {
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maxstencil_multi_old = smax;
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for (i = 1; i <= n; i++) {
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memory->destroy(stencil_multi_old[i]);
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memory->destroy(distsq_multi_old[i]);
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memory->create(stencil_multi_old[i],maxstencil_multi_old,
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"neighstencil:stencil_multi_old");
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memory->create(distsq_multi_old[i],maxstencil_multi_old,
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"neighstencil:distsq_multi_old");
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}
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}
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}
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} else {
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int i;
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int n = atom->ntypes;
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if (maxstencil_multi == 0) {
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nstencil_multi = new int[n+1];
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stencil_multi = new int*[n+1];
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distsq_multi = new double*[n+1];
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for (i = 1; i <= n; i++) {
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nstencil_multi[i] = 0;
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stencil_multi[i] = nullptr;
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distsq_multi[i] = nullptr;
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int i, j, bin_collection, smax;
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double stencil_range;
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int n = ncollections;
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if (nb) copy_bin_info_multi();
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// Deallocate arrays if previously allocated
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if((n > maxcollections) && stencil_multi){
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memory->destroy(nstencil_multi);
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for (i = 0; i < maxcollections; i++) {
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for (j = 0; j < maxcollections; j++)
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memory->destroy(stencil_multi[i][j]);
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delete [] stencil_multi[i];
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}
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delete [] stencil_multi;
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memory->destroy(maxstencil_multi);
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memory->destroy(flag_half_multi);
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memory->destroy(flag_skip_multi);
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memory->destroy(bin_collection_multi);
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memory->destroy(stencil_sx_multi);
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memory->destroy(stencil_sy_multi);
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memory->destroy(stencil_sz_multi);
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memory->destroy(stencil_binsizex_multi);
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memory->destroy(stencil_binsizey_multi);
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memory->destroy(stencil_binsizez_multi);
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memory->destroy(stencil_mbinx_multi);
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memory->destroy(stencil_mbiny_multi);
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memory->destroy(stencil_mbinz_multi);
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}
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// Allocate arrays
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if (!maxstencil_multi) {
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memory->create(flag_half_multi, n, n,
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"neighstencil:flag_half_multi");
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memory->create(flag_skip_multi, n, n,
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"neighstencil:flag_skip_multi");
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memory->create(bin_collection_multi, n, n,
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"neighstencil:bin_collection_multi");
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memory->create(stencil_sx_multi, n, n,
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"neighstencil:stencil_sx_multi");
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memory->create(stencil_sy_multi, n, n,
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"neighstencil:stencil_sy_multi");
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memory->create(stencil_sz_multi, n, n,
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"neighstencil:stencil_sz_multi");
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memory->create(stencil_binsizex_multi, n, n,
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"neighstencil:stencil_binsizex_multi");
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memory->create(stencil_binsizey_multi, n, n,
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"neighstencil:stencil_binsizey_multi");
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memory->create(stencil_binsizez_multi, n, n,
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"neighstencil:stencil_binsizez_multi");
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memory->create(stencil_mbinx_multi, n, n,
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"neighstencil:stencil_mbinx_multi");
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memory->create(stencil_mbiny_multi, n, n,
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"neighstencil:stencil_mbiny_multi");
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memory->create(stencil_mbinz_multi, n, n,
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"neighstencil:stencil_mbinz_multi");
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memory->create(maxstencil_multi, n, n, "neighstencil::maxstencil_multi");
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memory->create(nstencil_multi, n, n, "neighstencil::nstencil_multi");
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stencil_multi = new int**[n]();
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for (i = 0; i < n; ++i) {
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stencil_multi[i] = new int*[n]();
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for (j = 0; j < n; ++j) {
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maxstencil_multi[i][j] = 0;
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nstencil_multi[i][j] = 0;
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stencil_multi[i][j] = nullptr;
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}
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}
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maxcollections = n;
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}
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// Skip all stencils by default, initialize smax
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for (i = 0; i < n; i++) {
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for (j = 0; j < n; j++) {
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flag_skip_multi[i][j] = 1;
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}
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}
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if (smax > maxstencil_multi) {
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maxstencil_multi = smax;
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for (i = 1; i <= n; i++) {
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memory->destroy(stencil_multi[i]);
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memory->destroy(distsq_multi[i]);
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memory->create(stencil_multi[i],maxstencil_multi,
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"neighstencil:stencil_multi");
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memory->create(distsq_multi[i],maxstencil_multi,
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"neighstencil:distsq_multi");
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// Determine which stencils need to be built
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set_stencil_properties();
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for (i = 0; i < n; i++) {
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for (j = 0; j < n; j++) {
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// Skip creation of unused stencils
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if (flag_skip_multi[i][j]) continue;
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// Copy bin info for this pair of atom collections
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bin_collection = bin_collection_multi[i][j];
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stencil_binsizex_multi[i][j] = binsizex_multi[bin_collection];
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stencil_binsizey_multi[i][j] = binsizey_multi[bin_collection];
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stencil_binsizez_multi[i][j] = binsizez_multi[bin_collection];
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stencil_mbinx_multi[i][j] = mbinx_multi[bin_collection];
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stencil_mbiny_multi[i][j] = mbiny_multi[bin_collection];
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stencil_mbinz_multi[i][j] = mbinz_multi[bin_collection];
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stencil_range = sqrt(cutcollectionsq[i][j]);
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sx = static_cast<int> (stencil_range*bininvx_multi[bin_collection]);
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if (sx*binsizex_multi[bin_collection] < stencil_range) sx++;
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sy = static_cast<int> (stencil_range*bininvy_multi[bin_collection]);
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if (sy*binsizey_multi[bin_collection] < stencil_range) sy++;
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sz = static_cast<int> (stencil_range*bininvz_multi[bin_collection]);
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if (sz*binsizez_multi[bin_collection] < stencil_range) sz++;
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if (dimension == 2) sz = 0;
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stencil_sx_multi[i][j] = sx;
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stencil_sy_multi[i][j] = sy;
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stencil_sz_multi[i][j] = sz;
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smax = ((2*sx+1) * (2*sy+1) * (2*sz+1));
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if (smax > maxstencil_multi[i][j]) {
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maxstencil_multi[i][j] = smax;
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if(stencil_multi[i][j])
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memory->destroy(stencil_multi[i][j]);
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memory->create(stencil_multi[i][j], smax,
|
||||
"neighstencil::stencil_multi");
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
@ -221,6 +420,30 @@ double NStencil::bin_distance(int i, int j, int k)
|
||||
return (delx*delx + dely*dely + delz*delz);
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
compute closest distance for a given atom collection
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double NStencil::bin_distance_multi(int i, int j, int k, int ic)
|
||||
{
|
||||
double delx,dely,delz;
|
||||
|
||||
if (i > 0) delx = (i-1)*binsizex_multi[ic];
|
||||
else if (i == 0) delx = 0.0;
|
||||
else delx = (i+1)*binsizex_multi[ic];
|
||||
|
||||
if (j > 0) dely = (j-1)*binsizey_multi[ic];
|
||||
else if (j == 0) dely = 0.0;
|
||||
else dely = (j+1)*binsizey_multi[ic];
|
||||
|
||||
if (k > 0) delz = (k-1)*binsizez_multi[ic];
|
||||
else if (k == 0) delz = 0.0;
|
||||
else delz = (k+1)*binsizez_multi[ic];
|
||||
|
||||
return (delx*delx + dely*dely + delz*delz);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double NStencil::memory_usage()
|
||||
@ -229,9 +452,16 @@ double NStencil::memory_usage()
|
||||
if (neighstyle == Neighbor::BIN) {
|
||||
bytes += memory->usage(stencil,maxstencil);
|
||||
bytes += memory->usage(stencilxyz,maxstencil,3);
|
||||
} else if (neighstyle == Neighbor::MULTI_OLD) {
|
||||
bytes += (double)atom->ntypes*maxstencil_multi_old * sizeof(int);
|
||||
bytes += (double)atom->ntypes*maxstencil_multi_old * sizeof(double);
|
||||
} else if (neighstyle == Neighbor::MULTI) {
|
||||
bytes += (double)atom->ntypes*maxstencil_multi * sizeof(int);
|
||||
bytes += (double)atom->ntypes*maxstencil_multi * sizeof(double);
|
||||
int n = ncollections;
|
||||
for (int i = 0; i < n; i++) {
|
||||
for (int j = 0; j < n; j++) {
|
||||
bytes += (double)maxstencil_multi[i][j] * sizeof(int);
|
||||
}
|
||||
}
|
||||
}
|
||||
return bytes;
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user