Ported Morse to KOKKOS

src/KOKKOS/Install.sh

@@ -173,6 +173,8 @@ action pair_lj_gromacs_kokkos.cpp
 action pair_lj_gromacs_kokkos.h
 action pair_lj_sdk_kokkos.cpp pair_lj_sdk.cpp
 action pair_lj_sdk_kokkos.h pair_lj_sdk.h
+action pair_morse_kokkos.cpp
+action pair_morse_kokkos.h
 action pair_reax_c_kokkos.cpp pair_reax_c.cpp
 action pair_reax_c_kokkos.h pair_reax_c.h
 action pair_sw_kokkos.cpp pair_sw.cpp

src/KOKKOS/pair_morse_kokkos.cpp

+/* ----------------------------------------------------------------------
+   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 <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_morse_kokkos.h"
+#include "kokkos.h"
+#include "atom_kokkos.h"
+#include "comm.h"
+#include "force.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "update.h"
+#include "integrate.h"
+#include "respa.h"
+#include "math_const.h"
+#include "memory.h"
+#include "error.h"
+#include "atom_masks.h"
+
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define KOKKOS_CUDA_MAX_THREADS 256
+#define KOKKOS_CUDA_MIN_BLOCKS 8
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairMorseKokkos<DeviceType>::PairMorseKokkos(LAMMPS *lmp) : PairMorse(lmp)
+{
+  respa_enable = 0;
+
+  atomKK = (AtomKokkos *) atom;
+  execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+  datamask_read = X_MASK | F_MASK | TYPE_MASK | ENERGY_MASK | VIRIAL_MASK;
+  datamask_modify = F_MASK | ENERGY_MASK | VIRIAL_MASK;
+  cutsq = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+PairMorseKokkos<DeviceType>::~PairMorseKokkos()
+{
+  if (allocated) {
+    memory->destroy_kokkos(k_eatom,eatom);
+    memory->destroy_kokkos(k_vatom,vatom);
+    k_cutsq = DAT::tdual_ffloat_2d();
+    memory->sfree(cutsq);
+    eatom = NULL;
+    vatom = NULL;
+    cutsq = NULL;
+  }
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairMorseKokkos<DeviceType>::cleanup_copy() {
+  // WHY needed: this prevents parent copy from deallocating any arrays
+  allocated = 0;
+  cutsq = NULL;
+  eatom = NULL;
+  vatom = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairMorseKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
+{
+  eflag = eflag_in;
+  vflag = vflag_in;
+
+
+  if (neighflag == FULL) no_virial_fdotr_compute = 1;
+
+  if (eflag || vflag) ev_setup(eflag,vflag);
+  else evflag = vflag_fdotr = 0;
+
+  // reallocate per-atom arrays if necessary
+
+  if (eflag_atom) {
+    memory->destroy_kokkos(k_eatom,eatom);
+    memory->create_kokkos(k_eatom,eatom,maxeatom,"pair:eatom");
+    d_eatom = k_eatom.view<DeviceType>();
+  }
+  if (vflag_atom) {
+    memory->destroy_kokkos(k_vatom,vatom);
+    memory->create_kokkos(k_vatom,vatom,maxvatom,6,"pair:vatom");
+    d_vatom = k_vatom.view<DeviceType>();
+  }
+
+  atomKK->sync(execution_space,datamask_read);
+  k_cutsq.template sync<DeviceType>();
+  k_params.template sync<DeviceType>();
+  if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
+  else atomKK->modified(execution_space,F_MASK);
+
+  x = atomKK->k_x.view<DeviceType>();
+  c_x = atomKK->k_x.view<DeviceType>();
+  f = atomKK->k_f.view<DeviceType>();
+  type = atomKK->k_type.view<DeviceType>();
+  tag = atomKK->k_tag.view<DeviceType>();
+  nlocal = atom->nlocal;
+  nall = atom->nlocal + atom->nghost;
+  newton_pair = force->newton_pair;
+  special_lj[0] = force->special_lj[0];
+  special_lj[1] = force->special_lj[1];
+  special_lj[2] = force->special_lj[2];
+  special_lj[3] = force->special_lj[3];
+
+  // loop over neighbors of my atoms
+
+  EV_FLOAT ev = pair_compute<PairMorseKokkos<DeviceType>,void >(this,(NeighListKokkos<DeviceType>*)list);
+
+  if (eflag_global) eng_vdwl += ev.evdwl;
+  if (vflag_global) {
+    virial[0] += ev.v[0];
+    virial[1] += ev.v[1];
+    virial[2] += ev.v[2];
+    virial[3] += ev.v[3];
+    virial[4] += ev.v[4];
+    virial[5] += ev.v[5];
+  }
+
+  if (vflag_fdotr) pair_virial_fdotr_compute(this);
+
+  if (eflag_atom) {
+    k_eatom.template modify<DeviceType>();
+    k_eatom.template sync<LMPHostType>();
+  }
+
+  if (vflag_atom) {
+    k_vatom.template modify<DeviceType>();
+    k_vatom.template sync<LMPHostType>();
+  }
+}
+
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairMorseKokkos<DeviceType>::
+compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+  (void) i;
+  (void) j;
+  const F_FLOAT rr = sqrt(rsq);
+  const F_FLOAT r0 = STACKPARAMS ? m_params[itype][jtype].r0 : params(itype,jtype).r0;
+  const F_FLOAT d0 = STACKPARAMS ? m_params[itype][jtype].d0 : params(itype,jtype).d0;
+  const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].alpha : params(itype,jtype).alpha;
+  const F_FLOAT dr = rr - r0;
+  
+  // U  =  d0 * [ exp( -2*a*(x-r0)) - 2*exp(-a*(x-r0)) ]
+  // f  = -2*a*d0*[ -exp( -2*a*(x-r0) ) + exp( -a*(x-r0) ) ] * grad(r)
+  //    = +2*a*d0*[  exp( -2*a*(x-r0) ) - exp( -a*(x-r0) ) ] * grad(r)
+  const F_FLOAT dexp    = exp( -aa*dr );
+  const F_FLOAT forcelj = 2*aa*d0*dexp*(dexp-1.0);
+
+  return forcelj / rr;
+}
+
+template<class DeviceType>
+template<bool STACKPARAMS, class Specialisation>
+KOKKOS_INLINE_FUNCTION
+F_FLOAT PairMorseKokkos<DeviceType>::
+compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+  (void) i;
+  (void) j;
+  const F_FLOAT rr = sqrt(rsq);
+  const F_FLOAT r0 = STACKPARAMS ? m_params[itype][jtype].r0 : params(itype,jtype).r0;
+  const F_FLOAT d0 = STACKPARAMS ? m_params[itype][jtype].d0 : params(itype,jtype).d0;
+  const F_FLOAT aa = STACKPARAMS ? m_params[itype][jtype].alpha : params(itype,jtype).alpha;
+  const F_FLOAT dr = rr - r0;
+  
+  // U  =  d0 * [ exp( -2*a*(x-r0)) - 2*exp(-a*(x-r0)) ]
+  // f  = -2*a*d0*[ -exp( -2*a*(x-r0) ) + exp( -a*(x-r0) ) ] * grad(r)
+  //    = +2*a*d0*[  exp( -2*a*(x-r0) ) - exp( -a*(x-r0) ) ] * grad(r)
+  const F_FLOAT dexp    = exp( -aa*dr );
+
+  return d0 * dexp * ( dexp - 2.0 );
+}
+
+/* ----------------------------------------------------------------------
+   allocate all arrays
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairMorseKokkos<DeviceType>::allocate()
+{
+  PairMorse::allocate();
+
+  int n = atom->ntypes;
+  memory->destroy(cutsq);
+  memory->create_kokkos(k_cutsq,cutsq,n+1,n+1,"pair:cutsq");
+  d_cutsq = k_cutsq.template view<DeviceType>();
+  k_params = Kokkos::DualView<params_morse**,Kokkos::LayoutRight,DeviceType>("PairMorse::params",n+1,n+1);
+  params = k_params.d_view;
+}
+
+/* ----------------------------------------------------------------------
+   global settings
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairMorseKokkos<DeviceType>::settings(int narg, char **arg)
+{
+  if (narg > 2) error->all(FLERR,"Illegal pair_style command");
+
+  PairMorse::settings(1,arg);
+}
+
+/* ----------------------------------------------------------------------
+   init specific to this pair style
+------------------------------------------------------------------------- */
+
+template<class DeviceType>
+void PairMorseKokkos<DeviceType>::init_style()
+{
+  PairMorse::init_style();
+
+  // error if rRESPA with inner levels
+
+  if (update->whichflag == 1 && strstr(update->integrate_style,"respa")) {
+    int respa = 0;
+    if (((Respa *) update->integrate)->level_inner >= 0) respa = 1;
+    if (((Respa *) update->integrate)->level_middle >= 0) respa = 2;
+    if (respa)
+      error->all(FLERR,"Cannot use Kokkos pair style with rRESPA inner/middle");
+  }
+
+  // irequest = neigh request made by parent class
+
+  neighflag = lmp->kokkos->neighflag;
+  int irequest = neighbor->nrequest - 1;
+
+  neighbor->requests[irequest]->
+    kokkos_host = Kokkos::Impl::is_same<DeviceType,LMPHostType>::value &&
+    !Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+  neighbor->requests[irequest]->
+    kokkos_device = Kokkos::Impl::is_same<DeviceType,LMPDeviceType>::value;
+
+  if (neighflag == FULL) {
+    neighbor->requests[irequest]->full = 1;
+    neighbor->requests[irequest]->half = 0;
+  } else if (neighflag == HALF || neighflag == HALFTHREAD) {
+    neighbor->requests[irequest]->full = 0;
+    neighbor->requests[irequest]->half = 1;
+  } else if (neighflag == N2) {
+    neighbor->requests[irequest]->full = 0;
+    neighbor->requests[irequest]->half = 0;
+  } else {
+    error->all(FLERR,"Cannot use chosen neighbor list style with morse/kk");
+  }
+}
+
+/* ----------------------------------------------------------------------
+   init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+// Rewrite this.
+template<class DeviceType>
+double PairMorseKokkos<DeviceType>::init_one(int i, int j)
+{
+  double cutone = PairMorse::init_one(i,j);
+
+  k_params.h_view(i,j).d0     = d0[i][j];
+  k_params.h_view(i,j).alpha  = alpha[i][j];
+  k_params.h_view(i,j).r0     = r0[i][j];
+  k_params.h_view(i,j).offset = offset[i][j];
+  k_params.h_view(i,j).cutsq  = cutone*cutone;
+  k_params.h_view(j,i)        = k_params.h_view(i,j);
+  
+  if(i<MAX_TYPES_STACKPARAMS+1 && j<MAX_TYPES_STACKPARAMS+1) {
+    m_params[i][j] = m_params[j][i] = k_params.h_view(i,j);
+    m_cutsq[j][i] = m_cutsq[i][j] = cutone*cutone;
+  }
+
+  k_cutsq.h_view(i,j) = k_cutsq.h_view(j,i) = cutone*cutone;
+  k_cutsq.template modify<LMPHostType>();
+  k_params.template modify<LMPHostType>();
+
+  return cutone;
+}
+
+
+
+namespace LAMMPS_NS {
+template class PairMorseKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class PairMorseKokkos<LMPHostType>;
+#endif
+}
+

src/KOKKOS/pair_morse_kokkos.h

+/* -*- 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.
+-------------------------------------------------------------------------
+   Contributed by Stefan Paquay @ Eindhoven University of Technology
+   Based on pair lj/cut/kokkos.
+------------------------------------------------------------------------- */
+
+#ifdef PAIR_CLASS
+
+PairStyle(morse/kk,PairMorseKokkos<LMPDeviceType>)
+PairStyle(morse/kk/device,PairMorseKokkos<LMPDeviceType>)
+PairStyle(morse/kk/host,PairMorseKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_PAIR_MORSE_KOKKOS_H
+#define LMP_PAIR_MORSE_KOKKOS_H
+
+#include "pair_kokkos.h"
+#include "pair_morse.h"
+#include "neigh_list_kokkos.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class PairMorseKokkos : public PairMorse {
+ public:
+  enum {EnabledNeighFlags=FULL|HALFTHREAD|HALF|N2};
+  enum {COUL_FLAG=0};
+  typedef DeviceType device_type;
+  PairMorseKokkos(class LAMMPS *);
+  virtual ~PairMorseKokkos();
+
+  void compute(int, int);
+
+  void settings(int, char **);
+  void init_style();
+  double init_one(int, int);
+
+  struct params_morse{
+    KOKKOS_INLINE_FUNCTION
+    params_morse(){cutsq=0,d0=0;alpha=0;r0=0;offset=0;}
+    KOKKOS_INLINE_FUNCTION
+    params_morse(int i){cutsq=0,d0=0;alpha=0;r0=0;offset=0;}
+    F_FLOAT cutsq,d0,alpha,r0,offset;
+  };
+
+ protected:
+  void cleanup_copy();
+
+  template<bool STACKPARAMS, class Specialisation>
+  KOKKOS_INLINE_FUNCTION
+  F_FLOAT compute_fpair(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const;
+
+  template<bool STACKPARAMS, class Specialisation>
+  KOKKOS_INLINE_FUNCTION
+  F_FLOAT compute_evdwl(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const;
+
+  template<bool STACKPARAMS, class Specialisation>
+  KOKKOS_INLINE_FUNCTION
+  F_FLOAT compute_ecoul(const F_FLOAT& rsq, const int& i, const int&j, const int& itype, const int& jtype) const {
+    return 0;
+  }
+
+
+  Kokkos::DualView<params_morse**,Kokkos::LayoutRight,DeviceType> k_params;
+  typename Kokkos::DualView<params_morse**,Kokkos::LayoutRight,DeviceType>::t_dev_const_um params;
+  params_morse m_params[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1]; 
+  F_FLOAT m_cutsq[MAX_TYPES_STACKPARAMS+1][MAX_TYPES_STACKPARAMS+1];
+  typename ArrayTypes<DeviceType>::t_x_array_randomread x;
+  typename ArrayTypes<DeviceType>::t_x_array c_x;
+  typename ArrayTypes<DeviceType>::t_f_array f;
+  typename ArrayTypes<DeviceType>::t_int_1d_randomread type;
+
+  DAT::tdual_efloat_1d k_eatom;
+  DAT::tdual_virial_array k_vatom;
+  typename ArrayTypes<DeviceType>::t_efloat_1d d_eatom;
+  typename ArrayTypes<DeviceType>::t_virial_array d_vatom;
+  typename ArrayTypes<DeviceType>::t_tagint_1d tag;
+
+  int newton_pair;
+  double special_lj[4];
+
+  typename ArrayTypes<DeviceType>::tdual_ffloat_2d k_cutsq;
+  typename ArrayTypes<DeviceType>::t_ffloat_2d d_cutsq;
+
+
+  int neighflag;
+  int nlocal,nall,eflag,vflag;
+
+  void allocate();
+  friend class PairComputeFunctor<PairMorseKokkos,FULL,true>;
+  friend class PairComputeFunctor<PairMorseKokkos,HALF,true>;
+  friend class PairComputeFunctor<PairMorseKokkos,HALFTHREAD,true>;
+  friend class PairComputeFunctor<PairMorseKokkos,N2,true>;
+  friend class PairComputeFunctor<PairMorseKokkos,FULL,false>;
+  friend class PairComputeFunctor<PairMorseKokkos,HALF,false>;
+  friend class PairComputeFunctor<PairMorseKokkos,HALFTHREAD,false>;
+  friend class PairComputeFunctor<PairMorseKokkos,N2,false>;
+  friend EV_FLOAT pair_compute_neighlist<PairMorseKokkos,FULL,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
+  friend EV_FLOAT pair_compute_neighlist<PairMorseKokkos,HALF,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
+  friend EV_FLOAT pair_compute_neighlist<PairMorseKokkos,HALFTHREAD,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
+  friend EV_FLOAT pair_compute_neighlist<PairMorseKokkos,N2,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
+  friend EV_FLOAT pair_compute<PairMorseKokkos,void>(PairMorseKokkos*,NeighListKokkos<DeviceType>*);
+  friend void pair_virial_fdotr_compute<PairMorseKokkos>(PairMorseKokkos*);
+};
+
+}
+
+#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: Cannot use Kokkos pair style with rRESPA inner/middle
+
+Self-explanatory.
+
+E: Cannot use chosen neighbor list style with morse/kk
+
+That style is not supported by Kokkos.
+
+*/

src/pair_morse.h

@@ -28,8 +28,8 @@ class PairMorse : public Pair {
  public:
   PairMorse(class LAMMPS *);
   virtual ~PairMorse();
-
   virtual void compute(int, int);
+	
   void settings(int, char **);
   void coeff(int, char **);
   double init_one(int, int);
@@ -49,7 +49,7 @@ class PairMorse : public Pair {
   double **morse1;
   double **offset;
 
-  void allocate();
+  virtual void allocate();
 };
 
 }