Merge pull request lammps#4167 from stanmoore1/kk_hybrid_topo

Port hybrid bond topology styles to Kokkos

doc/src/Commands_bond.rst

@@ -72,7 +72,7 @@ OPT.
 
    * :doc:`none <angle_none>`
    * :doc:`zero <angle_zero>`
-   * :doc:`hybrid <angle_hybrid>`
+   * :doc:`hybrid (k) <angle_hybrid>`
    *
    *
    *

doc/src/bond_hybrid.rst

@@ -1,8 +1,11 @@
 .. index:: bond_style hybrid
+.. index:: bond_style hybrid/kk
 
 bond_style hybrid command
 =========================
 
+Accelerator Variants: *hybrid/kk*
+
 Syntax
 """"""
 
@@ -15,7 +18,7 @@ Syntax
 Examples
 """"""""
 
-.. code-block: LAMMPS
+.. code-block:: LAMMPS
 
    bond_style hybrid harmonic fene
    bond_coeff 1 harmonic 80.0 1.2
@@ -60,6 +63,10 @@ bond types.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Restrictions
 """"""""""""
 

src/KOKKOS/Install.sh

@@ -86,6 +86,8 @@ action bond_fene_kokkos.cpp bond_fene.cpp
 action bond_fene_kokkos.h bond_fene.h
 action bond_harmonic_kokkos.cpp bond_harmonic.cpp
 action bond_harmonic_kokkos.h bond_harmonic.h
+action bond_hybrid_kokkos.cpp bond_hybrid.cpp
+action bond_hybrid_kokkos.h bond_hybrid.h
 action comm_kokkos.cpp
 action comm_kokkos.h
 action comm_tiled_kokkos.cpp

src/KOKKOS/bond_class2_kokkos.cpp

@@ -34,6 +34,8 @@ using namespace LAMMPS_NS;
 template<class DeviceType>
 BondClass2Kokkos<DeviceType>::BondClass2Kokkos(LAMMPS *lmp) : BondClass2(lmp)
 {
+  kokkosable = 1;
+
   atomKK = (AtomKokkos *) atom;
   neighborKK = (NeighborKokkos *) neighbor;
   execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
@@ -122,12 +124,12 @@ void BondClass2Kokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
   if (eflag_atom) {
     k_eatom.template modify<DeviceType>();
-    k_eatom.template sync<LMPHostType>();
+    k_eatom.sync_host();
   }
 
   if (vflag_atom) {
     k_vatom.template modify<DeviceType>();
-    k_vatom.template sync<LMPHostType>();
+    k_vatom.sync_host();
   }
 
   copymode = 0;
@@ -227,13 +229,13 @@ void BondClass2Kokkos<DeviceType>::coeff(int narg, char **arg)
     k_r0.h_view[i] = r0[i];
   }
 
-  k_k2.template modify<LMPHostType>();
+  k_k2.modify_host();
   k_k2.template sync<DeviceType>();
-  k_k3.template modify<LMPHostType>();
+  k_k3.modify_host();
   k_k3.template sync<DeviceType>();
-  k_k4.template modify<LMPHostType>();
+  k_k4.modify_host();
   k_k4.template sync<DeviceType>();
-  k_r0.template modify<LMPHostType>();
+  k_r0.modify_host();
   k_r0.template sync<DeviceType>();
 }
 
@@ -264,13 +266,13 @@ void BondClass2Kokkos<DeviceType>::read_restart(FILE *fp)
     k_r0.h_view[i] = r0[i];
   }
 
-  k_k2.template modify<LMPHostType>();
+  k_k2.modify_host();
   k_k2.template sync<DeviceType>();
-  k_k3.template modify<LMPHostType>();
+  k_k3.modify_host();
   k_k3.template sync<DeviceType>();
-  k_k4.template modify<LMPHostType>();
+  k_k4.modify_host();
   k_k4.template sync<DeviceType>();
-  k_r0.template modify<LMPHostType>();
+  k_r0.modify_host();
   k_r0.template sync<DeviceType>();
 }
 

src/KOKKOS/bond_class2_kokkos.h

@@ -59,6 +59,10 @@ class BondClass2Kokkos : public BondClass2 {
       const F_FLOAT &ebond, const F_FLOAT &fbond, const F_FLOAT &delx,
                   const F_FLOAT &dely, const F_FLOAT &delz) const;
 
+  typedef typename KKDevice<DeviceType>::value KKDeviceType;
+  Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType> k_eatom;
+  Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType> k_vatom;
+
  protected:
 
   class NeighborKokkos *neighborKK;
@@ -67,9 +71,6 @@ class BondClass2Kokkos : public BondClass2 {
   typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
   typename AT::t_int_2d bondlist;
 
-  typedef typename KKDevice<DeviceType>::value KKDeviceType;
-  Kokkos::DualView<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType> k_eatom;
-  Kokkos::DualView<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType> k_vatom;
   Kokkos::View<E_FLOAT*,Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_eatom;
   Kokkos::View<F_FLOAT*[6],Kokkos::LayoutRight,KKDeviceType,Kokkos::MemoryTraits<Kokkos::Atomic> > d_vatom;
 

src/KOKKOS/bond_fene_kokkos.cpp

@@ -37,6 +37,8 @@ using MathConst::MY_CUBEROOT2;
 template<class DeviceType>
 BondFENEKokkos<DeviceType>::BondFENEKokkos(LAMMPS *lmp) : BondFENE(lmp)
 {
+  kokkosable = 1;
+
   atomKK = (AtomKokkos *) atom;
   neighborKK = (NeighborKokkos *) neighbor;
   execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
@@ -135,12 +137,12 @@ void BondFENEKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
   if (eflag_atom) {
     k_eatom.template modify<DeviceType>();
-    k_eatom.template sync<LMPHostType>();
+    k_eatom.sync_host();
   }
 
   if (vflag_atom) {
     k_vatom.template modify<DeviceType>();
-    k_vatom.template sync<LMPHostType>();
+    k_vatom.sync_host();
   }
 
   copymode = 0;
@@ -267,10 +269,10 @@ void BondFENEKokkos<DeviceType>::coeff(int narg, char **arg)
     k_sigma.h_view[i] = sigma[i];
   }
 
-  k_k.template modify<LMPHostType>();
-  k_r0.template modify<LMPHostType>();
-  k_epsilon.template modify<LMPHostType>();
-  k_sigma.template modify<LMPHostType>();
+  k_k.modify_host();
+  k_r0.modify_host();
+  k_epsilon.modify_host();
+  k_sigma.modify_host();
 }
 
 
@@ -291,10 +293,10 @@ void BondFENEKokkos<DeviceType>::read_restart(FILE *fp)
     k_sigma.h_view[i] = sigma[i];
   }
 
-  k_k.template modify<LMPHostType>();
-  k_r0.template modify<LMPHostType>();
-  k_epsilon.template modify<LMPHostType>();
-  k_sigma.template modify<LMPHostType>();
+  k_k.modify_host();
+  k_r0.modify_host();
+  k_epsilon.modify_host();
+  k_sigma.modify_host();
 }
 
 /* ----------------------------------------------------------------------

src/KOKKOS/bond_fene_kokkos.h

@@ -58,6 +58,9 @@ class BondFENEKokkos : public BondFENE {
       const F_FLOAT &ebond, const F_FLOAT &fbond, const F_FLOAT &delx,
                   const F_FLOAT &dely, const F_FLOAT &delz) const;
 
+  DAT::tdual_efloat_1d k_eatom;
+  DAT::tdual_virial_array k_vatom;
+
  protected:
 
   class NeighborKokkos *neighborKK;
@@ -66,8 +69,6 @@ class BondFENEKokkos : public BondFENE {
   typename ArrayTypes<DeviceType>::t_f_array f;
   typename ArrayTypes<DeviceType>::t_int_2d bondlist;
 
-  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;
 

src/KOKKOS/bond_harmonic_kokkos.cpp

@@ -34,6 +34,8 @@ using namespace LAMMPS_NS;
 template<class DeviceType>
 BondHarmonicKokkos<DeviceType>::BondHarmonicKokkos(LAMMPS *lmp) : BondHarmonic(lmp)
 {
+  kokkosable = 1;
+
   atomKK = (AtomKokkos *) atom;
   neighborKK = (NeighborKokkos *) neighbor;
   execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
@@ -65,23 +67,20 @@ void BondHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
   // reallocate per-atom arrays if necessary
 
   if (eflag_atom) {
-    //if(k_eatom.extent(0)<maxeatom) { // won't work without adding zero functor
+    if (k_eatom.extent(0) < maxeatom) {
       memoryKK->destroy_kokkos(k_eatom,eatom);
       memoryKK->create_kokkos(k_eatom,eatom,maxeatom,"improper:eatom");
       d_eatom = k_eatom.template view<KKDeviceType>();
-    //}
+    } else Kokkos::deep_copy(d_eatom,0.0);
   }
   if (vflag_atom) {
-    //if(k_vatom.extent(0)<maxvatom) { // won't work without adding zero functor
+    if (k_vatom.extent(0) < maxvatom) {
       memoryKK->destroy_kokkos(k_vatom,vatom);
       memoryKK->create_kokkos(k_vatom,vatom,maxvatom,"improper:vatom");
       d_vatom = k_vatom.template view<KKDeviceType>();
-    //}
+    } else Kokkos::deep_copy(d_vatom,0.0);
   }
 
-//  if (eflag || vflag) atomKK->modified(execution_space,datamask_modify);
-//  else atomKK->modified(execution_space,F_MASK);
-
   x = atomKK->k_x.template view<DeviceType>();
   f = atomKK->k_f.template view<DeviceType>();
   neighborKK->k_bondlist.template sync<DeviceType>();
@@ -122,12 +121,12 @@ void BondHarmonicKokkos<DeviceType>::compute(int eflag_in, int vflag_in)
 
   if (eflag_atom) {
     k_eatom.template modify<DeviceType>();
-    k_eatom.template sync<LMPHostType>();
+    k_eatom.sync_host();
   }
 
   if (vflag_atom) {
     k_vatom.template modify<DeviceType>();
-    k_vatom.template sync<LMPHostType>();
+    k_vatom.sync_host();
   }
 
   copymode = 0;
@@ -214,8 +213,8 @@ void BondHarmonicKokkos<DeviceType>::coeff(int narg, char **arg)
     k_r0.h_view[i] = r0[i];
   }
 
-  k_k.template modify<LMPHostType>();
-  k_r0.template modify<LMPHostType>();
+  k_k.modify_host();
+  k_r0.modify_host();
   k_k.template sync<DeviceType>();
   k_r0.template sync<DeviceType>();
 }
@@ -241,8 +240,8 @@ void BondHarmonicKokkos<DeviceType>::read_restart(FILE *fp)
     k_r0.h_view[i] = r0[i];
   }
 
-  k_k.template modify<LMPHostType>();
-  k_r0.template modify<LMPHostType>();
+  k_k.modify_host();
+  k_r0.modify_host();
   k_k.template sync<DeviceType>();
   k_r0.template sync<DeviceType>();
 }

src/KOKKOS/bond_harmonic_kokkos.h

@@ -37,6 +37,7 @@ class BondHarmonicKokkos : public BondHarmonic {
  public:
   typedef DeviceType device_type;
   typedef EV_FLOAT value_type;
+  typedef ArrayTypes<DeviceType> AT;
 
   BondHarmonicKokkos(class LAMMPS *);
   ~BondHarmonicKokkos() override;
@@ -62,7 +63,6 @@ class BondHarmonicKokkos : public BondHarmonic {
 
   class NeighborKokkos *neighborKK;
 
-  typedef ArrayTypes<DeviceType> AT;
   typename AT::t_x_array_randomread x;
   typename Kokkos::View<double*[3],typename AT::t_f_array::array_layout,typename KKDevice<DeviceType>::value,Kokkos::MemoryTraits<Kokkos::Atomic> > f;
   typename AT::t_int_2d bondlist;