forked from lijiext/lammps
Merge pull request #731 from Pakketeretet2/pair-yukawa-kk
Added a KOKKOS-enabled Yukawa pair style.
This commit is contained in:
Steve Plimpton
GitHub
commit
fa0c28b717
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@ -9,6 +9,7 @@
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pair_style yukawa command :h3
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pair_style yukawa/gpu command :h3
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pair_style yukawa/omp command :h3
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pair_style yukawa/kk command :h3
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[Syntax:]
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@ -229,6 +229,8 @@ action pair_tersoff_mod_kokkos.cpp pair_tersoff_mod.cpp
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action pair_tersoff_mod_kokkos.h pair_tersoff_mod.h
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action pair_tersoff_zbl_kokkos.cpp pair_tersoff_zbl.cpp
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action pair_tersoff_zbl_kokkos.h pair_tersoff_zbl.h
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action pair_yukawa_kokkos.cpp
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action pair_yukawa_kokkos.h
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action pppm_kokkos.cpp pppm.cpp
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action pppm_kokkos.h pppm.h
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action rand_pool_wrap_kokkos.cpp
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@ -0,0 +1,301 @@
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/* ----------------------------------------------------------------------
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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 authors: Stefan Paquay (Brandeis University)
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------------------------------------------------------------------------- */
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#include <math.h>
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#include <stdlib.h>
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#include "pair_yukawa_kokkos.h"
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#include "kokkos.h"
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#include "atom_kokkos.h"
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#include "comm.h"
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#include "force.h"
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#include "neighbor.h"
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#include "neigh_list.h"
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#include "neigh_request.h"
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#include "update.h"
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#include "integrate.h"
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#include "respa.h"
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#include "math_const.h"
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#include "memory.h"
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#include "error.h"
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#include "atom_masks.h"
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using namespace LAMMPS_NS;
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using namespace MathConst;
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#define KOKKOS_CUDA_MAX_THREADS 256
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#define KOKKOS_CUDA_MIN_BLOCKS 8
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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PairYukawaKokkos<DeviceType>::PairYukawaKokkos(LAMMPS *lmp) : PairYukawa(lmp)
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{
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respa_enable = 0;
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atomKK = (AtomKokkos *) atom;
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execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
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datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK;
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datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
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cutsq = NULL;
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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PairYukawaKokkos<DeviceType>::~PairYukawaKokkos()
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{
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if (allocated) {
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memory->destroy_kokkos(k_eatom,eatom);
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memory->destroy_kokkos(k_vatom,vatom);
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k_cutsq = DAT::tdual_ffloat_2d();
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memory->sfree(cutsq);
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eatom = NULL;
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vatom = NULL;
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cutsq = NULL;
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}
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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void PairYukawaKokkos<DeviceType>::cleanup_copy() {
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// WHY needed: this prevents parent copy from deallocating any arrays
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allocated = 0;
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cutsq = NULL;
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eatom = NULL;
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vatom = NULL;
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}
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/* ----------------------------------------------------------------------
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allocate all arrays
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------------------------------------------------------------------------- */
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template<class DeviceType>
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void PairYukawaKokkos<DeviceType>::allocate()
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{
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PairYukawa::allocate();
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int n = atom->ntypes;
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memory->destroy(cutsq);
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memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
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d_cutsq = k_cutsq.template view<DeviceType>();
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k_params = Kokkos::DualView<params_yukawa**,
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Kokkos::LayoutRight,DeviceType>(
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"PairYukawa::params",n+1,n+1);
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params = k_params.template view<DeviceType>();
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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template<class DeviceType>
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void PairYukawaKokkos<DeviceType>::init_style()
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{
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PairYukawa::init_style();
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// error if rRESPA with inner levels
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if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
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int respa = 0;
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if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
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if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
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if (respa)
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error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
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}
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// irequest = neigh request made by parent class
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neighflag = lmp->kokkos->neighflag;
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int irequest = neighbor->nrequest - 1;
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neighbor->requests[irequest]->
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kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
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!Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
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neighbor->requests[irequest]->
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kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
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if (neighflag == FULL) {
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neighbor->requests[irequest]->full = 1;
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neighbor->requests[irequest]->half = 0;
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} else if (neighflag == HALF || neighflag == HALFTHREAD) {
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neighbor->requests[irequest]->full = 0;
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neighbor->requests[irequest]->half = 1;
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} else {
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error->all(FLERR,"Cannot use chosen neighbor list style with yukawa/kk");
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}
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}
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/* ----------------------------------------------------------------------
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init for one type pair i,j and corresponding j,i
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------------------------------------------------------------------------- */
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// Rewrite this.
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template<class DeviceType>
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double PairYukawaKokkos<DeviceType>::init_one(int i, int j)
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{
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double cutone = PairYukawa::init_one(i,j);
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k_params.h_view(i,j).a = a[i][j];
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k_params.h_view(i,j).offset = offset[i][j];
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k_params.h_view(i,j).cutsq = cutone*cutone;
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k_params.h_view(j,i) = k_params.h_view(i,j);
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if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
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m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
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m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
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}
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k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone;
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k_cutsq.template modify<LMPHostType>();
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k_params.template modify<LMPHostType>();
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return cutone;
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}
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/* ---------------------------------------------------------------------- */
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template<class DeviceType>
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void PairYukawaKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
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{
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eflag = eflag_in;
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vflag = vflag_in;
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if (neighflag == FULL) no_virial_fdotr_compute = 1;
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if (eflag || vflag) ev_setup(eflag,vflag,0);
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else evflag = vflag_fdotr = 0;
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// reallocate per-atom arrays if necessary
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if (eflag_atom) {
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memory->destroy_kokkos(k_eatom,eatom);
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memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
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d_eatom = k_eatom.view<DeviceType>();
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}
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if (vflag_atom) {
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memory->destroy_kokkos(k_vatom,vatom);
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memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
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d_vatom = k_vatom.view<DeviceType>();
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}
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atomKK->sync(execution_space,datamask_read);
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k_cutsq.template sync<DeviceType>();
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k_params.template sync<DeviceType>();
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if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
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else atomKK->modified(execution_space,F_MASK);
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x = atomKK->k_x.view<DeviceType>();
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c_x = atomKK->k_x.view<DeviceType>();
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f = atomKK->k_f.view<DeviceType>();
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type = atomKK->k_type.view<DeviceType>();
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tag = atomKK->k_tag.view<DeviceType>();
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nlocal = atom->nlocal;
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nall = atom->nlocal + atom->nghost;
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newton_pair = force->newton_pair;
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special_lj[0] = force->special_lj[0];
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special_lj[1] = force->special_lj[1];
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special_lj[2] = force->special_lj[2];
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special_lj[3] = force->special_lj[3];
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// loop over neighbors of my atoms
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EV_FLOAT ev = pair_compute<PairYukawaKokkos<DeviceType>,void >(
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this,(NeighListKokkos<DeviceType>*)list);
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if (eflag_global) eng_vdwl += ev.evdwl;
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if (vflag_global) {
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virial[0] += ev.v[0];
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virial[1] += ev.v[1];
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virial[2] += ev.v[2];
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virial[3] += ev.v[3];
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virial[4] += ev.v[4];
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virial[5] += ev.v[5];
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}
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if (vflag_fdotr) pair_virial_fdotr_compute(this);
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if (eflag_atom) {
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k_eatom.template modify<DeviceType>();
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k_eatom.template sync<LMPHostType>();
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}
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if (vflag_atom) {
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k_vatom.template modify<DeviceType>();
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k_vatom.template sync<LMPHostType>();
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}
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}
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template<class DeviceType>
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template<bool STACKPARAMS, class Specialisation>
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KOKKOS_INLINE_FUNCTION
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F_FLOAT PairYukawaKokkos<DeviceType>::
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compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
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const int& itype, const int& jtype) const {
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(void) i;
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(void) j;
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const F_FLOAT rr = sqrt(rsq);
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// Fetch the params either off the stack or from some mapped memory?
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const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].a
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: params(itype,jtype).a;
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// U = a * exp(-kappa*r) / r
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// f = (kappa * a * exp(-kappa*r) / r + a*exp(-kappa*r)/r^2)*grad(r)
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// = (kappa + 1/r) * (a * exp(-kappa*r) / r)
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// f/r = (kappa + 1/r) * (a * exp(-kappa*r) / r^2)
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const F_FLOAT rinv = 1.0 / rr;
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const F_FLOAT rinv2 = rinv*rinv;
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const F_FLOAT screening = exp(-kappa*rr);
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const F_FLOAT forceyukawa = aa * screening * (kappa + rinv);
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const F_FLOAT fpair = forceyukawa * rinv2;
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return fpair;
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}
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template<class DeviceType>
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template<bool STACKPARAMS, class Specialisation>
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KOKKOS_INLINE_FUNCTION
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F_FLOAT PairYukawaKokkos<DeviceType>::
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compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
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const int& itype, const int& jtype) const {
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(void) i;
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(void) j;
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const F_FLOAT rr = sqrt(rsq);
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const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].a
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: params(itype,jtype).a;
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const F_FLOAT offset = STACKPARAMS ? m_params[itype][jtype].offset
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: params(itype,jtype).offset;
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// U = a * exp(-kappa*r) / r
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// f = (kappa * a * exp(-kappa*r) / r + a*exp(-kappa*r)/r^2)*grad(r)
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// = (kappa + 1/r) * (a * exp(-kappa*r) / r)
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// f/r = (kappa + 1/r) * (a * exp(-kappa*r) / r^2)
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const F_FLOAT rinv = 1.0 / rr;
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const F_FLOAT screening = exp(-kappa*rr);
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return aa * screening * rinv - offset;
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}
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namespace LAMMPS_NS {
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template class PairYukawaKokkos<LMPDeviceType>;
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#ifdef KOKKOS_HAVE_CUDA
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template class PairYukawaKokkos<LMPHostType>;
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#endif
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}
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@ -0,0 +1,146 @@
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/* -*- 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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|
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(yukawa/kk,PairYukawaKokkos<LMPDeviceType>)
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PairStyle(yukawa/kk/device,PairYukawaKokkos<LMPDeviceType>)
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PairStyle(yukawa/kk/host,PairYukawaKokkos<LMPHostType>)
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#else
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#ifndef LMP_PAIR_YUKAWA_KOKKOS_H
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#define LMP_PAIR_YUKAWA_KOKKOS_H
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#include "pair_kokkos.h"
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#include "pair_yukawa.h"
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#include "neigh_list_kokkos.h"
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namespace LAMMPS_NS {
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template<class DeviceType>
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class PairYukawaKokkos : public PairYukawa {
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public:
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enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF};
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enum {COUL_FLAG=0};
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typedef DeviceType device_type;
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typedef ArrayTypes<DeviceType> AT;
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PairYukawaKokkos(class LAMMPS *);
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virtual ~PairYukawaKokkos();
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void compute(int, int);
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void init_style();
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double init_one(int,int);
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struct params_yukawa {
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KOKKOS_INLINE_FUNCTION
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params_yukawa(){ cutsq=0, a = 0; offset = 0; }
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KOKKOS_INLINE_FUNCTION
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params_yukawa(int i){ cutsq=0, a = 0; offset = 0; }
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F_FLOAT cutsq, a, offset;
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};
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protected:
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void cleanup_copy();
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template<bool STACKPARAMS, class Specialisation>
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KOKKOS_INLINE_FUNCTION
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F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j,
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const int& itype, const int& jtype) const;
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template<bool STACKPARAMS, class Specialisation>
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KOKKOS_INLINE_FUNCTION
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F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j,
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const int& itype, const int& jtype) const;
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template<bool STACKPARAMS, class Specialisation>
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KOKKOS_INLINE_FUNCTION
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F_FLOAT compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j,
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const int& itype, const int& jtype) const
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{
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return 0;
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}
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Kokkos::DualView<params_yukawa**,Kokkos::LayoutRight,DeviceType> k_params;
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typename Kokkos::DualView<params_yukawa**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
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params_yukawa m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
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F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
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typename AT::t_x_array_randomread x;
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typename AT::t_x_array c_x;
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typename AT::t_f_array f;
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typename AT::t_int_1d_randomread type;
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DAT::tdual_efloat_1d k_eatom;
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DAT::tdual_virial_array k_vatom;
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typename AT::t_efloat_1d d_eatom;
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typename AT::t_virial_array d_vatom;
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typename AT::t_tagint_1d tag;
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int newton_pair;
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double special_lj[4];
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typename AT::tdual_ffloat_2d k_cutsq;
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typename AT::t_ffloat_2d d_cutsq;
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int neighflag;
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int nlocal,nall,eflag,vflag;
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void allocate();
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friend class PairComputeFunctor<PairYukawaKokkos,FULL,true>;
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friend class PairComputeFunctor<PairYukawaKokkos,HALF,true>;
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friend class PairComputeFunctor<PairYukawaKokkos,HALFTHREAD,true>;
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friend class PairComputeFunctor<PairYukawaKokkos,N2,true>;
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friend class PairComputeFunctor<PairYukawaKokkos,FULL,false>;
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friend class PairComputeFunctor<PairYukawaKokkos,HALF,false>;
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friend class PairComputeFunctor<PairYukawaKokkos,HALFTHREAD,false>;
|
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friend class PairComputeFunctor<PairYukawaKokkos,N2,false>;
|
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friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,FULL,void>(
|
||||
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
|
||||
friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,HALF,void>(
|
||||
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
|
||||
friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,HALFTHREAD,void>(
|
||||
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
|
||||
friend EV_FLOAT pair_compute_neighlist<PairYukawaKokkos,N2,void>(
|
||||
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
|
||||
friend EV_FLOAT pair_compute<PairYukawaKokkos,void>(
|
||||
PairYukawaKokkos*,NeighListKokkos<DeviceType>*);
|
||||
friend void pair_virial_fdotr_compute<PairYukawaKokkos>(PairYukawaKokkos*);
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#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: Incorrect args for pair coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Cannot use chosen neighbor list style with yukawa/kk
|
||||
|
||||
That style is not supported by Kokkos.
|
||||
|
||||
*/
|
||||
|
|
@ -139,7 +139,6 @@ void PairYukawa::allocate()
|
|||
setflag[i][j] = 0;
|
||||
|
||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||
|
||||
memory->create(rad,n+1,"pair:rad");
|
||||
memory->create(cut,n+1,n+1,"pair:cut");
|
||||
memory->create(a,n+1,n+1,"pair:a");
|
||||
|
|
|
|||
|
|
@ -46,7 +46,7 @@ class PairYukawa : public Pair {
|
|||
double *rad;
|
||||
double **cut,**a,**offset;
|
||||
|
||||
void allocate();
|
||||
virtual void allocate();
|
||||
};
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue