From 2a35fa7a4e253facc698e834d47a0ccb2cd2cace Mon Sep 17 00:00:00 2001 From: Stan Moore Date: Fri, 13 Jan 2017 10:37:31 -0700 Subject: [PATCH] Adding initial versions of pair_hybrid_kokkos and pair_hybrid_overlay_kokkos --- src/KOKKOS/Install.sh | 4 + src/KOKKOS/pair_hybrid_kokkos.cpp | 147 ++++++++++++++++++++++ src/KOKKOS/pair_hybrid_kokkos.h | 109 ++++++++++++++++ src/KOKKOS/pair_hybrid_overlay_kokkos.cpp | 28 +++++ src/KOKKOS/pair_hybrid_overlay_kokkos.h | 48 +++++++ src/pair_hybrid.h | 6 +- src/pair_hybrid_overlay.h | 2 +- 7 files changed, 338 insertions(+), 6 deletions(-) create mode 100644 src/KOKKOS/pair_hybrid_kokkos.cpp create mode 100644 src/KOKKOS/pair_hybrid_kokkos.h create mode 100644 src/KOKKOS/pair_hybrid_overlay_kokkos.cpp create mode 100644 src/KOKKOS/pair_hybrid_overlay_kokkos.h diff --git a/src/KOKKOS/Install.sh b/src/KOKKOS/Install.sh index cf753ecee8..198946d9f0 100644 --- a/src/KOKKOS/Install.sh +++ b/src/KOKKOS/Install.sh @@ -154,6 +154,10 @@ action pair_eam_fs_kokkos.cpp pair_eam_fs.cpp action pair_eam_fs_kokkos.h pair_eam_fs.h action pair_exp6_rx_kokkos.cpp pair_exp6_rx.cpp action pair_exp6_rx_kokkos.h pair_exp6_rx.h +action pair_hybrid_kokkos.cpp +action pair_hybrid_kokkos.h +action pair_hybrid_overlay_kokkos.cpp +action pair_hybrid_overlay_kokkos.h action pair_kokkos.h action pair_lj_charmm_coul_charmm_implicit_kokkos.cpp pair_lj_charmm_coul_charmm_implicit.cpp action pair_lj_charmm_coul_charmm_implicit_kokkos.h pair_lj_charmm_coul_charmm_implicit.h diff --git a/src/KOKKOS/pair_hybrid_kokkos.cpp b/src/KOKKOS/pair_hybrid_kokkos.cpp new file mode 100644 index 0000000000..973d60348f --- /dev/null +++ b/src/KOKKOS/pair_hybrid_kokkos.cpp @@ -0,0 +1,147 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include +#include "pair_hybrid_kokkos.h" +#include "atom_kokkos.h" +#include "force.h" +#include "pair.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "update.h" +#include "comm.h" +#include "memory.h" +#include "error.h" +#include "respa.h" +#include "atom_masks.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairHybridKokkos::PairHybridKokkos(LAMMPS *lmp) : PairHybrid(lmp) +{ + atomKK = (AtomKokkos *) atom; + datamask_read = EMPTY_MASK; + datamask_modify = EMPTY_MASK; +} + +/* ---------------------------------------------------------------------- */ + +PairHybridKokkos::~PairHybridKokkos() +{ + +} + +/* ---------------------------------------------------------------------- + call each sub-style's compute() or compute_outer() function + accumulate sub-style global/peratom energy/virial in hybrid + for global vflag = 1: + each sub-style computes own virial[6] + sum sub-style virial[6] to hybrid's virial[6] + for global vflag = 2: + call sub-style with adjusted vflag to prevent it calling + virial_fdotr_compute() + hybrid calls virial_fdotr_compute() on final accumulated f +------------------------------------------------------------------------- */ + +void PairHybridKokkos::compute(int eflag, int vflag) +{ + int i,j,m,n; + + // if no_virial_fdotr_compute is set and global component of + // incoming vflag = 2, then + // reset vflag as if global component were 1 + // necessary since one or more sub-styles cannot compute virial as F dot r + + int neighflag = lmp->kokkos->neighflag; + if (neighflag == FULL) no_virial_fdotr_compute = 1; + + if (no_virial_fdotr_compute && vflag % 4 == 2) vflag = 1 + vflag/4 * 4; + + if (eflag || vflag) ev_setup(eflag,vflag); + else evflag = vflag_fdotr = eflag_global = vflag_global = + eflag_atom = vflag_atom = 0; + + // check if global component of incoming vflag = 2 + // if so, reset vflag passed to substyle as if it were 0 + // necessary so substyle will not invoke virial_fdotr_compute() + + int vflag_substyle; + if (vflag % 4 == 2) vflag_substyle = vflag/4 * 4; + else vflag_substyle = vflag; + + double *saved_special = save_special(); + + // check if we are running with r-RESPA using the hybrid keyword + + Respa *respa = NULL; + respaflag = 0; + if (strstr(update->integrate_style,"respa")) { + respa = (Respa *) update->integrate; + if (respa->nhybrid_styles > 0) respaflag = 1; + } + + for (m = 0; m < nstyles; m++) { + + set_special(m); + + if (!respaflag || (respaflag && respa->hybrid_compute[m])) { + + // invoke compute() unless compute flag is turned off or + // outerflag is set and sub-style has a compute_outer() method + + if (styles[m]->compute_flag == 0) continue; + atomKK->sync(styles[m]->execution_space,styles[m]->datamask_read); + if (outerflag && styles[m]->respa_enable) + styles[m]->compute_outer(eflag,vflag_substyle); + else styles[m]->compute(eflag,vflag_substyle); + atomKK->modified(styles[m]->execution_space,styles[m]->datamask_modify); + } + + restore_special(saved_special); + + // jump to next sub-style if r-RESPA does not want global accumulated data + + if (respaflag && !respa->tally_global) continue; + + if (eflag_global) { + eng_vdwl += styles[m]->eng_vdwl; + eng_coul += styles[m]->eng_coul; + } + if (vflag_global) { + for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n]; + } + if (eflag_atom) { + n = atom->nlocal; + if (force->newton_pair) n += atom->nghost; + double *eatom_substyle = styles[m]->eatom; + for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i]; + } + if (vflag_atom) { + n = atom->nlocal; + if (force->newton_pair) n += atom->nghost; + double **vatom_substyle = styles[m]->vatom; + for (i = 0; i < n; i++) + for (j = 0; j < 6; j++) + vatom[i][j] += vatom_substyle[i][j]; + } + } + + delete [] saved_special; + + if (vflag_fdotr) virial_fdotr_compute(); +} diff --git a/src/KOKKOS/pair_hybrid_kokkos.h b/src/KOKKOS/pair_hybrid_kokkos.h new file mode 100644 index 0000000000..cfcef7fb31 --- /dev/null +++ b/src/KOKKOS/pair_hybrid_kokkos.h @@ -0,0 +1,109 @@ +/* -*- 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 PAIR_CLASS + +PairStyle(hybrid/kk,PairHybridKokkos) + +#else + +#ifndef LMP_PAIR_HYBRID_KOKKOS_H +#define LMP_PAIR_HYBRID_KOKKOS_H + +#include +#include "pair_hybrid.h" + +namespace LAMMPS_NS { + +class PairHybridKokkos : public PairHybrid { + friend class FixGPU; + friend class FixIntel; + friend class FixOMP; + friend class Force; + friend class Respa; + friend class Info; + public: + PairHybridKokkos(class LAMMPS *); + virtual ~PairHybridKokkos(); + void compute(int, int); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Pair style hybrid cannot have hybrid as an argument + +Self-explanatory. + +E: Pair style hybrid cannot have none as an argument + +Self-explanatory. + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair coeff for hybrid has invalid style + +Style in pair coeff must have been listed in pair_style command. + +E: Pair hybrid sub-style is not used + +No pair_coeff command used a sub-style specified in the pair_style +command. + +E: Pair_modify special setting for pair hybrid incompatible with global special_bonds setting + +Cannot override a setting of 0.0 or 1.0 or change a setting between +0.0 and 1.0. + +E: All pair coeffs are not set + +All pair coefficients must be set in the data file or by the +pair_coeff command before running a simulation. + +E: Invoked pair single on pair style none + +A command (e.g. a dump) attempted to invoke the single() function on a +pair style none, which is illegal. You are probably attempting to +compute per-atom quantities with an undefined pair style. + +E: Pair hybrid sub-style does not support single call + +You are attempting to invoke a single() call on a pair style +that doesn't support it. + +E: Pair hybrid single calls do not support per sub-style special bond values + +Self-explanatory. + +E: Unknown pair_modify hybrid sub-style + +The choice of sub-style is unknown. + +E: Coulomb cutoffs of pair hybrid sub-styles do not match + +If using a Kspace solver, all Coulomb cutoffs of long pair styles must +be the same. + +*/ diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp new file mode 100644 index 0000000000..55fed33f96 --- /dev/null +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.cpp @@ -0,0 +1,28 @@ +/* ---------------------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "pair_hybrid_overlay_kokkos.h" +#include "atom.h" +#include "force.h" +#include "neighbor.h" +#include "neigh_request.h" +#include "error.h" + +using namespace LAMMPS_NS; + +/* ---------------------------------------------------------------------- */ + +PairHybridOverlayKokkos::PairHybridOverlayKokkos(LAMMPS *lmp) : PairHybridOverlay(lmp) {} diff --git a/src/KOKKOS/pair_hybrid_overlay_kokkos.h b/src/KOKKOS/pair_hybrid_overlay_kokkos.h new file mode 100644 index 0000000000..c9a50e3bb1 --- /dev/null +++ b/src/KOKKOS/pair_hybrid_overlay_kokkos.h @@ -0,0 +1,48 @@ +/* -*- 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 PAIR_CLASS + +PairStyle(hybrid/overlay/kk,PairHybridOverlayKokkos) + +#else + +#ifndef LMP_PAIR_HYBRID_OVERLAY_KOKKOS_H +#define LMP_PAIR_HYBRID_OVERLAY_KOKKOS_H + +#include "pair_hybrid_overlay.h" + +namespace LAMMPS_NS { + +class PairHybridOverlayKokkos : public PairHybridOverlay { + public: + PairHybridOverlayKokkos(class LAMMPS *); + virtual ~PairHybridOverlayKokkos() {} +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Incorrect args for pair coefficients + +Self-explanatory. Check the input script or data file. + +E: Pair coeff for hybrid has invalid style + +Style in pair coeff must have been listed in pair_style command. + +*/ diff --git a/src/pair_hybrid.h b/src/pair_hybrid.h index 4d224dafc3..a7a236d269 100644 --- a/src/pair_hybrid.h +++ b/src/pair_hybrid.h @@ -35,7 +35,7 @@ class PairHybrid : public Pair { public: PairHybrid(class LAMMPS *); virtual ~PairHybrid(); - void compute(int, int); + virtual void compute(int, int); void settings(int, char **); virtual void coeff(int, char **); void init_style(); @@ -88,10 +88,6 @@ class PairHybrid : public Pair { /* ERROR/WARNING messages: -E: Cannot yet use pair hybrid with Kokkos - -This feature is not yet supported. - E: Illegal ... command Self-explanatory. Check the input script syntax and compare to the diff --git a/src/pair_hybrid_overlay.h b/src/pair_hybrid_overlay.h index 60cff45508..169583a48b 100644 --- a/src/pair_hybrid_overlay.h +++ b/src/pair_hybrid_overlay.h @@ -27,7 +27,7 @@ namespace LAMMPS_NS { class PairHybridOverlay : public PairHybrid { public: PairHybridOverlay(class LAMMPS *); - ~PairHybridOverlay() {} + virtual ~PairHybridOverlay() {} void coeff(int, char **); private: