Unverified Commit 13d56f3c authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

Merge branch 'master' into test-updates

parents ab421230 5e118783

src/KOKKOS/pair_snap_kokkos.h

+51 −12
Original line number Diff line number Diff line
@@ -30,19 +30,31 @@ PairStyle(snap/kk/host,PairSNAPKokkos<LMPHostType>) 


namespace LAMMPS_NS {



// Routines for both the CPU and GPU backend

template<int NEIGHFLAG, int EVFLAG>

struct TagPairSNAPComputeForce{};



struct TagPairSNAPBeta{};

struct TagPairSNAPComputeNeigh{};



// GPU backend only

struct TagPairSNAPPreUi{};

struct TagPairSNAPComputeUi{};

struct TagPairSNAPComputeUiCPU{};

struct TagPairSNAPTransformUi{}; // re-order ulisttot from SoA to AoSoA, zero ylist

struct TagPairSNAPComputeZi{};

struct TagPairSNAPBeta{};

struct TagPairSNAPComputeBi{};

struct TagPairSNAPZeroYi{};

struct TagPairSNAPTransformBi{}; // re-order blist from AoSoA to AoS

struct TagPairSNAPComputeYi{};

struct TagPairSNAPTransformYi{}; // re-order ylist from AoSoA to AoS

struct TagPairSNAPComputeFusedDeidrj{};



// CPU backend only

struct TagPairSNAPPreUiCPU{};

struct TagPairSNAPComputeUiCPU{};

struct TagPairSNAPComputeZiCPU{};

struct TagPairSNAPBetaCPU{};

struct TagPairSNAPComputeBiCPU{};

struct TagPairSNAPZeroYiCPU{};

struct TagPairSNAPComputeYiCPU{};

struct TagPairSNAPComputeDuidrjCPU{};

struct TagPairSNAPComputeDeidrjCPU{};
@@ -81,6 +93,10 @@ public: 
  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeNeigh,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeNeigh>::member_type& team) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPBetaCPU,const int& ii) const;



  // GPU backend only

  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPPreUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPPreUi>::member_type& team) const;
@@ -88,31 +104,53 @@ public: 
  void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi>::member_type& team) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeUiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiCPU>::member_type& team) const;

  void operator() (TagPairSNAPTransformUi,const int iatom_mod, const int idxu, const int iatom_div) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeZi,const int iatom_mod, const int idxz, const int iatom_div) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeZi,const int& ii) const;

  void operator() (TagPairSNAPBeta, const int& ii) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeBi,const int iatom_mod, const int idxb, const int iatom_div) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeBi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeBi>::member_type& team) const;

  void operator() (TagPairSNAPTransformBi,const int iatom_mod, const int idxb, const int iatom_div) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPZeroYi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPZeroYi>::member_type& team) const;

  void operator() (TagPairSNAPComputeYi,const int iatom_mod, const int idxz, const int iatom_div) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeYi,const int& ii) const;

  void operator() (TagPairSNAPTransformYi,const int iatom_mod, const int idxu, const int iatom_div) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeFusedDeidrj,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeFusedDeidrj>::member_type& team) const;



  // CPU backend only

  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeDuidrjCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrjCPU>::member_type& team) const;

  void operator() (TagPairSNAPPreUiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPPreUiCPU>::member_type& team) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeDeidrjCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrjCPU>::member_type& team) const;

  void operator() (TagPairSNAPComputeUiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiCPU>::member_type& team) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPBeta,const int& ii) const;

  void operator() (TagPairSNAPComputeZiCPU,const int& ii) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeBiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeBiCPU>::member_type& team) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPZeroYiCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPZeroYiCPU>::member_type& team) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeYiCPU,const int& ii) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeDuidrjCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDuidrjCPU>::member_type& team) const;



  KOKKOS_INLINE_FUNCTION

  void operator() (TagPairSNAPComputeDeidrjCPU,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeDeidrjCPU>::member_type& team) const;



  template<int NEIGHFLAG>

  KOKKOS_INLINE_FUNCTION
@@ -175,6 +213,7 @@ inline double dist2(double* x,double* y); 
  Kokkos::View<T_INT*, DeviceType> d_map;                    // mapping from atom types to elements

  Kokkos::View<T_INT*, DeviceType> d_ninside;                // ninside for all atoms in list

  Kokkos::View<F_FLOAT**, DeviceType> d_beta;                // betas for all atoms in list

  Kokkos::View<F_FLOAT***, Kokkos::LayoutLeft, DeviceType> d_beta_pack;          // betas for all atoms in list, GPU

  Kokkos::View<F_FLOAT**, DeviceType> d_bispectrum;          // bispectrum components for all atoms in list



  typedef Kokkos::DualView<F_FLOAT**, DeviceType> tdual_fparams;

src/KOKKOS/pair_snap_kokkos_impl.h

+391 −131

File changed.

Preview size limit exceeded, changes collapsed.

src/KOKKOS/sna_kokkos.h

+45 −19
Original line number Diff line number Diff line
@@ -36,7 +36,9 @@ public: 
  typedef Kokkos::View<double**, DeviceType> t_sna_2d;

  typedef Kokkos::View<double**, Kokkos::LayoutLeft, DeviceType> t_sna_2d_ll;

  typedef Kokkos::View<double***, DeviceType> t_sna_3d;

  typedef Kokkos::View<double***, Kokkos::LayoutLeft, DeviceType> t_sna_3d_ll;

  typedef Kokkos::View<double***[3], DeviceType> t_sna_4d;

  typedef Kokkos::View<double****, Kokkos::LayoutLeft, DeviceType> t_sna_4d_ll;

  typedef Kokkos::View<double**[3], DeviceType> t_sna_3d3;

  typedef Kokkos::View<double*****, DeviceType> t_sna_5d;
@@ -48,7 +50,8 @@ public: 
  typedef Kokkos::View<SNAcomplex***, DeviceType> t_sna_3c;

  typedef Kokkos::View<SNAcomplex***, Kokkos::LayoutLeft, DeviceType> t_sna_3c_ll;

  typedef Kokkos::View<SNAcomplex***[3], DeviceType> t_sna_4c;

  typedef Kokkos::View<SNAcomplex***[3], Kokkos::LayoutLeft, DeviceType> t_sna_4c_ll;

  typedef Kokkos::View<SNAcomplex***[3], Kokkos::LayoutLeft, DeviceType> t_sna_4c3_ll;

  typedef Kokkos::View<SNAcomplex****, Kokkos::LayoutLeft, DeviceType> t_sna_4c_ll;

  typedef Kokkos::View<SNAcomplex**[3], DeviceType> t_sna_3c3;

  typedef Kokkos::View<SNAcomplex*****, DeviceType> t_sna_5c;
@@ -73,27 +76,39 @@ inline 


  int ncoeff;



  // functions for bispectrum coefficients

  // functions for bispectrum coefficients, GPU only

  KOKKOS_INLINE_FUNCTION

  void pre_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team,const int&, int); // ForceSNAP

  void pre_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team,const int&,const int&); // ForceSNAP

  KOKKOS_INLINE_FUNCTION

  void compute_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int); // ForceSNAP

  KOKKOS_INLINE_FUNCTION

  void compute_zi(const int&, const int&, const int&);    // ForceSNAP

  KOKKOS_INLINE_FUNCTION

  void compute_yi(int,int,int,

   const Kokkos::View<F_FLOAT***, Kokkos::LayoutLeft, DeviceType> &beta_pack); // ForceSNAP

  KOKKOS_INLINE_FUNCTION

  void compute_bi(const int&, const int&, const int&);    // ForceSNAP



  // functions for bispectrum coefficients, CPU only

  KOKKOS_INLINE_FUNCTION

  void pre_ui_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team,const int&,const int&); // ForceSNAP

  KOKKOS_INLINE_FUNCTION

  void compute_ui_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); // ForceSNAP

  KOKKOS_INLINE_FUNCTION

  void compute_zi(const int&);    // ForceSNAP

  void compute_zi_cpu(const int&);    // ForceSNAP

  KOKKOS_INLINE_FUNCTION

  void zero_yi(const int&, const int&, int); // ForceSNAP

  void zero_yi_cpu(const int&,const int&,const int&); // ForceSNAP

  KOKKOS_INLINE_FUNCTION

  void compute_yi(int,

  void compute_yi_cpu(int,

   const Kokkos::View<F_FLOAT**, DeviceType> &beta); // ForceSNAP

    KOKKOS_INLINE_FUNCTION

  void compute_bi(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int);    // ForceSNAP



  // functions for derivatives

  void compute_bi_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int);    // ForceSNAP



  // functions for derivatives, GPU only

  KOKKOS_INLINE_FUNCTION

  void compute_fused_deidrj(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int); //ForceSNAP



  // functions for derivatives, CPU only

  KOKKOS_INLINE_FUNCTION

  void compute_duidrj_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); //ForceSNAP

  KOKKOS_INLINE_FUNCTION
@@ -139,18 +154,32 @@ inline 


  int twojmax, diagonalstyle;



  t_sna_2d_ll blist;

  t_sna_2c_ll ulisttot;

  t_sna_2c_ll zlist;

  t_sna_3d_ll blist;

  t_sna_3c_ll ulisttot;

  t_sna_3c_ll zlist;



  t_sna_3c_ll ulist;

  t_sna_2c_ll ylist;

  t_sna_3c_ll ylist;

  

  // derivatives of data

  t_sna_4c_ll dulist;

  t_sna_4c3_ll dulist;

  

  // Modified structures for GPU backend

  t_sna_3d_ll ulisttot_re; // split real,

  t_sna_3d_ll ulisttot_im; // imag

  t_sna_4c_ll ulisttot_pack; // AoSoA layout

  t_sna_4c_ll zlist_pack; // AoSoA layout

  t_sna_4d_ll blist_pack;

  t_sna_4d_ll ylist_pack_re; // split real, 

  t_sna_4d_ll ylist_pack_im; // imag AoSoA layout



  int idxcg_max, idxu_max, idxz_max, idxb_max;



  // Chem snap counts

  int nelements;

  int ndoubles;

  int ntriples;



private:

  double rmin0, rfac0;
@@ -212,9 +241,6 @@ inline 
  // Chem snap flags

  int chem_flag;

  int bnorm_flag;

  int nelements;

  int ndoubles;

  int ntriples;



  // Self-weight

  double wself;

src/KOKKOS/sna_kokkos_impl.h

+665 −331

File changed.

Preview size limit exceeded, changes collapsed.

src/KSPACE/msm.cpp

+31 −26
Original line number Diff line number Diff line
@@ -362,6 +362,7 @@ void MSM::setup() 


  nmax_direct = 8*(nxhi_direct+1)*(nyhi_direct+1)*(nzhi_direct+1);



  deallocate();

  if (peratom_allocate_flag) deallocate_peratom();



  // compute direct sum interaction weights
@@ -612,8 +613,6 @@ void MSM::compute(int eflag, int vflag) 


void MSM::allocate()

{

  deallocate();



  // interpolation coeffs



  order_allocated = order;
@@ -635,9 +634,9 @@ void MSM::allocate() 
  // allocate memory for each grid level



  for (int n=0; n<levels; n++) {



    memory->create3d_offset(qgrid[n],nzlo_out[n],nzhi_out[n],

            nylo_out[n],nyhi_out[n],nxlo_out[n],nxhi_out[n],"msm:qgrid");



    memory->create3d_offset(egrid[n],nzlo_out[n],nzhi_out[n],

            nylo_out[n],nyhi_out[n],nxlo_out[n],nxhi_out[n],"msm:egrid");
@@ -660,25 +659,31 @@ void MSM::allocate() 


void MSM::deallocate()

{

  delete cg_all;

  cg_all = nullptr;



  memory->destroy2d_offset(phi1d,-order_allocated);

  memory->destroy2d_offset(dphi1d,-order_allocated);



  if (cg_all) delete cg_all;

  cg_all = nullptr;



  for (int n=0; n<levels; n++) {

    if (qgrid[n])

      memory->destroy3d_offset(qgrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);



    if (egrid[n])

      memory->destroy3d_offset(egrid[n],nzlo_out[n],nylo_out[n],nxlo_out[n]);



    if (world_levels)

      if (world_levels[n] != MPI_COMM_NULL)

          MPI_Comm_free(&world_levels[n]);

    world_levels[n] = MPI_COMM_NULL;

    active_flag[n] = 0;



    if (cg) {

      if (cg[n]) {

        delete cg[n];

        cg[n] = nullptr;

      }

    }

  }

}



/* ----------------------------------------------------------------------

   allocate per-atom virial memory that depends on # of grid points
@@ -765,7 +770,6 @@ void MSM::deallocate_peratom() 


void MSM::allocate_levels()

{

  deallocate_levels();

  ngrid = new int[levels];



  cg = new GridComm*[levels];
@@ -815,21 +819,21 @@ void MSM::allocate_levels() 
  v5grid = new double***[levels];



  for (int n=0; n<levels; n++) {

    cg[n] = nullptr;

    cg[n] = NULL;

    world_levels[n] = MPI_COMM_NULL;

    active_flag[n] = 0;

    cg_peratom[n] = nullptr;

    cg_peratom[n] = NULL;



    qgrid[n] = nullptr;

    egrid[n] = nullptr;

    qgrid[n] = NULL;

    egrid[n] = NULL;



    v0grid[n] = nullptr;

    v1grid[n] = nullptr;

    v2grid[n] = nullptr;

    v3grid[n] = nullptr;

    v4grid[n] = nullptr;

    v5grid[n] = nullptr;

    v0grid[n] = NULL;

    v1grid[n] = NULL;

    v2grid[n] = NULL;

    v3grid[n] = NULL;

    v4grid[n] = NULL;

    v5grid[n] = NULL;

  }



}



/* ----------------------------------------------------------------------
@@ -1105,6 +1109,7 @@ void MSM::set_grid_global() 


  if (!domain->nonperiodic) levels -= 1;



  deallocate_levels();

  allocate_levels();



  // find number of grid levels in each direction

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