Loading src/.gitignore +2 −0 Original line number Diff line number Diff line Loading @@ -18,6 +18,8 @@ /*_tally.cpp /*_rx.h /*_rx.cpp /*_ssa.h /*_ssa.cpp /kokkos.cpp /kokkos.h Loading src/USER-DPD/nbin_ssa.cpp 0 → 100644 +129 −0 Original line number Diff line number Diff line /* ---------------------------------------------------------------------- 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 authors: James Larentzos (ARL) and Timothy I. Mattox (Engility Corporation) ------------------------------------------------------------------------- */ #include "nbin_ssa.h" #include "atom.h" #include "group.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ NBinSSA::NBinSSA(LAMMPS *lmp) : NBinStandard(lmp) { maxbin_ssa = 0; bins_ssa = NULL; maxhead_ssa = 0; binhead_ssa = NULL; gbinhead_ssa = NULL; } NBinSSA::~NBinSSA() { memory->destroy(bins_ssa); memory->destroy(binhead_ssa); memory->destroy(gbinhead_ssa); } /* ---------------------------------------------------------------------- bin owned and ghost atoms for the Shardlow Splitting Algorithm (SSA) local atoms are in distinct bins (binhead_ssa) from the ghosts ghost atoms are in distinct bins (gbinhead_ssa) from the locals ghosts which are not in an Active Interaction Region (AIR) are skipped ------------------------------------------------------------------------- */ void NBinSSA::bin_atoms() { int i,ibin; int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; if (includegroup) nlocal = atom->nfirst; double **x = atom->x; int *mask = atom->mask; int *ssaAIR = atom->ssaAIR; for (i = 0; i < mbins; i++) { gbinhead_ssa[i] = -1; binhead_ssa[i] = -1; } // bin in reverse order so linked list will be in forward order if (includegroup) { int bitmask = group->bitmask[includegroup]; int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above for (i = nall-1; i >= nowned; i--) { if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR if (mask[i] & bitmask) { ibin = coord2bin(x[i]); bins_ssa[i] = gbinhead_ssa[ibin]; gbinhead_ssa[ibin] = i; } } } else { for (i = nall-1; i >= nlocal; i--) { if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR ibin = coord2bin(x[i]); bins_ssa[i] = gbinhead_ssa[ibin]; gbinhead_ssa[ibin] = i; } } for (i = nlocal-1; i >= 0; i--) { ibin = coord2bin(x[i]); bins_ssa[i] = binhead_ssa[ibin]; binhead_ssa[ibin] = i; } } /* ---------------------------------------------------------------------- */ void NBinSSA::bin_atoms_setup(int nall) { NBinStandard::bin_atoms_setup(nall); // Setup the parent class's data too if (mbins > maxhead_ssa) { maxhead_ssa = mbins; memory->destroy(gbinhead_ssa); memory->destroy(binhead_ssa); memory->create(binhead_ssa,maxhead_ssa,"binhead_ssa"); memory->create(gbinhead_ssa,maxhead_ssa,"gbinhead_ssa"); } if (nall > maxbin_ssa) { maxbin_ssa = nall; memory->destroy(bins_ssa); memory->create(bins_ssa,maxbin_ssa,"bins_ssa"); } } /* ---------------------------------------------------------------------- */ bigint NBinSSA::memory_usage() { bigint bytes = NBinStandard::memory_usage(); // Count the parent's usage too if (maxbin_ssa) bytes += memory->usage(bins_ssa,maxbin_ssa); if (maxhead_ssa) { bytes += memory->usage(binhead_ssa,maxhead_ssa); bytes += memory->usage(gbinhead_ssa,maxhead_ssa); } return bytes; } src/USER-DPD/nbin_ssa.h 0 → 100644 +54 −0 Original line number Diff line number Diff line /* -*- c++ -*- ---------------------------------------------------------- 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. ------------------------------------------------------------------------- */ #ifdef NBIN_CLASS NBinStyle(ssa, NBinSSA, NB_SSA) #else #ifndef LMP_NBIN_SSA_H #define LMP_NBIN_SSA_H #include "nbin_standard.h" namespace LAMMPS_NS { class NBinSSA : public NBinStandard { public: int *bins_ssa; // index of next atom in each bin int maxbin_ssa; // size of bins_ssa array int *binhead_ssa; // index of 1st local atom in each bin int *gbinhead_ssa; // index of 1st ghost atom in each bin int maxhead_ssa; // size of binhead_ssa and gbinhead_ssa arrays NBinSSA(class LAMMPS *); ~NBinSSA(); void bin_atoms_setup(int); void bin_atoms(); bigint memory_usage(); }; } #endif #endif /* ERROR/WARNING messages: */ src/USER-DPD/npair_half_bin_newton_ssa.cpp +19 −70 Original line number Diff line number Diff line Loading @@ -18,6 +18,8 @@ #include "npair_half_bin_newton_ssa.h" #include "neighbor.h" #include "nstencil_ssa.h" #include "nbin_ssa.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" Loading Loading @@ -78,71 +80,18 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) int **firstneigh = list->firstneigh; MyPage<int> *ipage = list->ipage; int inum = 0; // bin owned and ghost atoms for use by Shardlow Splitting Algorithm // exclude ghost atoms that are not in the Active Interaction Regions (AIR) // NOTE to Tim: this binatomflag no longer exists // the logic up higher assures that binning has been done // before this build() method is called // maybe this code below needs to be in a new NBinShardlow class? // this class also inherits NPair::nb from its parent // which points to the NBin class that did the binning // there are last_step variables stored there which indicate // the last time binning was done // the basic question is what data is created/stored by SSA binning // and in what class should it live? // if it is created by the binning operation, then I think // it should be in a new NBinShardlow class if (true /* binatomflag */) { // only false in Neighbor::build_one if (mbins > list->maxhead_ssa) { list->maxhead_ssa = mbins; memory->destroy(list->gbinhead_ssa); memory->destroy(list->binhead_ssa); memory->create(list->binhead_ssa,list->maxhead_ssa,"binhead_ssa"); memory->create(list->gbinhead_ssa,list->maxhead_ssa,"gbinhead_ssa"); } for (i = 0; i < mbins; i++) { list->gbinhead_ssa[i] = -1; list->binhead_ssa[i] = -1; } NStencilSSA *ns_ssa = dynamic_cast<NStencilSSA*>(ns); if (!ns_ssa) error->one(FLERR, "NStencil wasn't a NStencilSSA object"); int nstencil_half = ns_ssa->nstencil_half; int nstencil_full = ns_ssa->nstencil; if (nall > list->maxbin_ssa) { list->maxbin_ssa = nall; memory->destroy(list->bins_ssa); memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa"); } // bin in reverse order so linked list will be in forward order NBinSSA *nb_ssa = dynamic_cast<NBinSSA*>(nb); if (!nb_ssa) error->one(FLERR, "NBin wasn't a NBinSSA object"); int *bins_ssa = nb_ssa->bins_ssa; int *binhead_ssa = nb_ssa->binhead_ssa; int *gbinhead_ssa = nb_ssa->gbinhead_ssa; if (includegroup) { int bitmask = group->bitmask[includegroup]; int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above for (i = nall-1; i >= nowned; i--) { if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR if (mask[i] & bitmask) { ibin = coord2bin(x[i]); list->bins_ssa[i] = list->gbinhead_ssa[ibin]; list->gbinhead_ssa[ibin] = i; } } } else { for (i = nall-1; i >= nlocal; i--) { if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR ibin = coord2bin(x[i]); list->bins_ssa[i] = list->gbinhead_ssa[ibin]; list->gbinhead_ssa[ibin] = i; } } for (i = nlocal-1; i >= 0; i--) { ibin = coord2bin(x[i]); list->bins_ssa[i] = list->binhead_ssa[ibin]; list->binhead_ssa[ibin] = i; } } // else reuse previous binning. See Neighbor::build_one comment int inum = 0; ipage->reset(); Loading @@ -166,7 +115,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) // loop over rest of local atoms in i's bin // just store them, since j is beyond i in linked list for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[j]) { for (j = bins_ssa[i]; j >= 0; j = bins_ssa[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; Loading Loading @@ -197,9 +146,9 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) // loop over all local atoms in other bins in "half" stencil for (k = 0; k < nstencil; k++) { for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) { for (k = 0; k < nstencil_half; k++) { for (j = binhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; Loading Loading @@ -233,9 +182,9 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) // That is a significant time savings because of the "full" stencil // Note2: only non-pure locals can have ghosts as neighbors if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) { for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) { if (ssaAIR[i] == 1) for (k = 0; k < nstencil_full; k++) { for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; Loading src/USER-DPD/npair_half_bin_newton_ssa.h +1 −1 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ NPairStyle(half/bin/newton/ssa, NPairHalfBinNewtonSSA, NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA) NP_HALF | NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA) #else Loading Loading
src/.gitignore +2 −0 Original line number Diff line number Diff line Loading @@ -18,6 +18,8 @@ /*_tally.cpp /*_rx.h /*_rx.cpp /*_ssa.h /*_ssa.cpp /kokkos.cpp /kokkos.h Loading
src/USER-DPD/nbin_ssa.cpp 0 → 100644 +129 −0 Original line number Diff line number Diff line /* ---------------------------------------------------------------------- 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 authors: James Larentzos (ARL) and Timothy I. Mattox (Engility Corporation) ------------------------------------------------------------------------- */ #include "nbin_ssa.h" #include "atom.h" #include "group.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ NBinSSA::NBinSSA(LAMMPS *lmp) : NBinStandard(lmp) { maxbin_ssa = 0; bins_ssa = NULL; maxhead_ssa = 0; binhead_ssa = NULL; gbinhead_ssa = NULL; } NBinSSA::~NBinSSA() { memory->destroy(bins_ssa); memory->destroy(binhead_ssa); memory->destroy(gbinhead_ssa); } /* ---------------------------------------------------------------------- bin owned and ghost atoms for the Shardlow Splitting Algorithm (SSA) local atoms are in distinct bins (binhead_ssa) from the ghosts ghost atoms are in distinct bins (gbinhead_ssa) from the locals ghosts which are not in an Active Interaction Region (AIR) are skipped ------------------------------------------------------------------------- */ void NBinSSA::bin_atoms() { int i,ibin; int nlocal = atom->nlocal; int nall = nlocal + atom->nghost; if (includegroup) nlocal = atom->nfirst; double **x = atom->x; int *mask = atom->mask; int *ssaAIR = atom->ssaAIR; for (i = 0; i < mbins; i++) { gbinhead_ssa[i] = -1; binhead_ssa[i] = -1; } // bin in reverse order so linked list will be in forward order if (includegroup) { int bitmask = group->bitmask[includegroup]; int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above for (i = nall-1; i >= nowned; i--) { if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR if (mask[i] & bitmask) { ibin = coord2bin(x[i]); bins_ssa[i] = gbinhead_ssa[ibin]; gbinhead_ssa[ibin] = i; } } } else { for (i = nall-1; i >= nlocal; i--) { if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR ibin = coord2bin(x[i]); bins_ssa[i] = gbinhead_ssa[ibin]; gbinhead_ssa[ibin] = i; } } for (i = nlocal-1; i >= 0; i--) { ibin = coord2bin(x[i]); bins_ssa[i] = binhead_ssa[ibin]; binhead_ssa[ibin] = i; } } /* ---------------------------------------------------------------------- */ void NBinSSA::bin_atoms_setup(int nall) { NBinStandard::bin_atoms_setup(nall); // Setup the parent class's data too if (mbins > maxhead_ssa) { maxhead_ssa = mbins; memory->destroy(gbinhead_ssa); memory->destroy(binhead_ssa); memory->create(binhead_ssa,maxhead_ssa,"binhead_ssa"); memory->create(gbinhead_ssa,maxhead_ssa,"gbinhead_ssa"); } if (nall > maxbin_ssa) { maxbin_ssa = nall; memory->destroy(bins_ssa); memory->create(bins_ssa,maxbin_ssa,"bins_ssa"); } } /* ---------------------------------------------------------------------- */ bigint NBinSSA::memory_usage() { bigint bytes = NBinStandard::memory_usage(); // Count the parent's usage too if (maxbin_ssa) bytes += memory->usage(bins_ssa,maxbin_ssa); if (maxhead_ssa) { bytes += memory->usage(binhead_ssa,maxhead_ssa); bytes += memory->usage(gbinhead_ssa,maxhead_ssa); } return bytes; }
src/USER-DPD/nbin_ssa.h 0 → 100644 +54 −0 Original line number Diff line number Diff line /* -*- c++ -*- ---------------------------------------------------------- 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. ------------------------------------------------------------------------- */ #ifdef NBIN_CLASS NBinStyle(ssa, NBinSSA, NB_SSA) #else #ifndef LMP_NBIN_SSA_H #define LMP_NBIN_SSA_H #include "nbin_standard.h" namespace LAMMPS_NS { class NBinSSA : public NBinStandard { public: int *bins_ssa; // index of next atom in each bin int maxbin_ssa; // size of bins_ssa array int *binhead_ssa; // index of 1st local atom in each bin int *gbinhead_ssa; // index of 1st ghost atom in each bin int maxhead_ssa; // size of binhead_ssa and gbinhead_ssa arrays NBinSSA(class LAMMPS *); ~NBinSSA(); void bin_atoms_setup(int); void bin_atoms(); bigint memory_usage(); }; } #endif #endif /* ERROR/WARNING messages: */
src/USER-DPD/npair_half_bin_newton_ssa.cpp +19 −70 Original line number Diff line number Diff line Loading @@ -18,6 +18,8 @@ #include "npair_half_bin_newton_ssa.h" #include "neighbor.h" #include "nstencil_ssa.h" #include "nbin_ssa.h" #include "neigh_list.h" #include "atom.h" #include "atom_vec.h" Loading Loading @@ -78,71 +80,18 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) int **firstneigh = list->firstneigh; MyPage<int> *ipage = list->ipage; int inum = 0; // bin owned and ghost atoms for use by Shardlow Splitting Algorithm // exclude ghost atoms that are not in the Active Interaction Regions (AIR) // NOTE to Tim: this binatomflag no longer exists // the logic up higher assures that binning has been done // before this build() method is called // maybe this code below needs to be in a new NBinShardlow class? // this class also inherits NPair::nb from its parent // which points to the NBin class that did the binning // there are last_step variables stored there which indicate // the last time binning was done // the basic question is what data is created/stored by SSA binning // and in what class should it live? // if it is created by the binning operation, then I think // it should be in a new NBinShardlow class if (true /* binatomflag */) { // only false in Neighbor::build_one if (mbins > list->maxhead_ssa) { list->maxhead_ssa = mbins; memory->destroy(list->gbinhead_ssa); memory->destroy(list->binhead_ssa); memory->create(list->binhead_ssa,list->maxhead_ssa,"binhead_ssa"); memory->create(list->gbinhead_ssa,list->maxhead_ssa,"gbinhead_ssa"); } for (i = 0; i < mbins; i++) { list->gbinhead_ssa[i] = -1; list->binhead_ssa[i] = -1; } NStencilSSA *ns_ssa = dynamic_cast<NStencilSSA*>(ns); if (!ns_ssa) error->one(FLERR, "NStencil wasn't a NStencilSSA object"); int nstencil_half = ns_ssa->nstencil_half; int nstencil_full = ns_ssa->nstencil; if (nall > list->maxbin_ssa) { list->maxbin_ssa = nall; memory->destroy(list->bins_ssa); memory->create(list->bins_ssa,list->maxbin_ssa,"bins_ssa"); } // bin in reverse order so linked list will be in forward order NBinSSA *nb_ssa = dynamic_cast<NBinSSA*>(nb); if (!nb_ssa) error->one(FLERR, "NBin wasn't a NBinSSA object"); int *bins_ssa = nb_ssa->bins_ssa; int *binhead_ssa = nb_ssa->binhead_ssa; int *gbinhead_ssa = nb_ssa->gbinhead_ssa; if (includegroup) { int bitmask = group->bitmask[includegroup]; int nowned = atom->nlocal; // NOTE: nlocal was set to atom->nfirst above for (i = nall-1; i >= nowned; i--) { if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR if (mask[i] & bitmask) { ibin = coord2bin(x[i]); list->bins_ssa[i] = list->gbinhead_ssa[ibin]; list->gbinhead_ssa[ibin] = i; } } } else { for (i = nall-1; i >= nlocal; i--) { if (ssaAIR[i] < 2) continue; // skip ghost atoms not in AIR ibin = coord2bin(x[i]); list->bins_ssa[i] = list->gbinhead_ssa[ibin]; list->gbinhead_ssa[ibin] = i; } } for (i = nlocal-1; i >= 0; i--) { ibin = coord2bin(x[i]); list->bins_ssa[i] = list->binhead_ssa[ibin]; list->binhead_ssa[ibin] = i; } } // else reuse previous binning. See Neighbor::build_one comment int inum = 0; ipage->reset(); Loading @@ -166,7 +115,7 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) // loop over rest of local atoms in i's bin // just store them, since j is beyond i in linked list for (j = list->bins_ssa[i]; j >= 0; j = list->bins_ssa[j]) { for (j = bins_ssa[i]; j >= 0; j = bins_ssa[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; Loading Loading @@ -197,9 +146,9 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) // loop over all local atoms in other bins in "half" stencil for (k = 0; k < nstencil; k++) { for (j = list->binhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) { for (k = 0; k < nstencil_half; k++) { for (j = binhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; Loading Loading @@ -233,9 +182,9 @@ void NPairHalfBinNewtonSSA::build(NeighList *list) // That is a significant time savings because of the "full" stencil // Note2: only non-pure locals can have ghosts as neighbors if (ssaAIR[i] == 1) for (k = 0; k < nstencil_ssa; k++) { for (j = list->gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = list->bins_ssa[j]) { if (ssaAIR[i] == 1) for (k = 0; k < nstencil_full; k++) { for (j = gbinhead_ssa[ibin+stencil[k]]; j >= 0; j = bins_ssa[j]) { jtype = type[j]; if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue; Loading
src/USER-DPD/npair_half_bin_newton_ssa.h +1 −1 Original line number Diff line number Diff line Loading @@ -15,7 +15,7 @@ NPairStyle(half/bin/newton/ssa, NPairHalfBinNewtonSSA, NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA) NP_HALF | NP_BIN | NP_NEWTON | NP_ORTHO | NP_SSA) #else Loading
