update pod

src/KOKKOS/pair_pod_kokkos.h

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+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: [email protected]
+
+   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
+// clang-format off
+PairStyle(pod/kk,PairPODKokkos<LMPDeviceType>);
+PairStyle(pod/kk/device,PairPODKokkos<LMPDeviceType>);
+PairStyle(pod/kk/host,PairPODKokkos<LMPHostType>);
+// clang-format on
+#else
+
+// clang-format off
+#ifndef LMP_PAIR_POD_KOKKOS_H
+#define LMP_PAIR_POD_KOKKOS_H
+
+#include "eapod.h"
+#include "pair_pod.h"
+#include "kokkos_type.h"
+#include "pair_kokkos.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class PairPODKokkos : public PairPOD {
+ public:   
+  typedef DeviceType device_type;
+  typedef ArrayTypes<DeviceType> AT;
+
+  PairPODKokkos(class LAMMPS *);
+  ~PairPODKokkos() override;
+
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  void init_style() override;
+  double init_one(int, int) override;
+
+ //protected:
+  int inum, maxneigh;
+  int host_flag;
+
+  int eflag, vflag;
+  int neighflag;
+
+  typename AT::t_neighbors_2d d_neighbors;
+  typename AT::t_int_1d d_ilist;
+  typename AT::t_int_1d d_numneigh;  
+//   typename AT::t_int_1d_randomread d_ilist;
+//   typename AT::t_int_1d_randomread d_numneigh;
+
+  DAT::tdual_efloat_1d k_eatom;
+  DAT::tdual_virial_array k_vatom;
+  typename AT::t_efloat_1d d_eatom;
+  typename AT::t_virial_array d_vatom;
+
+  typename AT::t_x_array_randomread x;
+  typename AT::t_f_array f;
+  typename AT::t_int_1d_randomread type;
+
+  typedef Kokkos::DualView<F_FLOAT**, DeviceType> tdual_fparams;
+  tdual_fparams k_cutsq, k_scale;
+  typedef Kokkos::View<F_FLOAT**, DeviceType> t_fparams;
+  t_fparams d_cutsq, d_scale;
+  typename AT::t_int_1d d_map;
+
+  friend void pair_virial_fdotr_compute<PairPODKokkos>(PairPODKokkos*);
+
+  void grow(int, int);  
+  void copy_from_pod_class(EAPOD *podptr);
+  void divideInterval(int *intervals, int N, int M);
+  int calculateNumberOfIntervals(int N, int intervalSize);     
+  void grow_atoms(int Ni);
+  void grow_pairs(int Nij);
+
+  void allocate() override;
+  double memory_usage() override;
+
+  typedef Kokkos::View<int*, DeviceType> t_pod_1i;
+  typedef Kokkos::View<int**, DeviceType> t_pod_2i;
+  typedef Kokkos::View<double*, DeviceType> t_pod_1d;
+  typedef Kokkos::View<double**, DeviceType> t_pod_2d;
+  typedef Kokkos::View<double**[3], DeviceType> t_pod_3d3;
+
+
+  int atomBlockSize;        // size of each atom block
+  int nAtomBlocks;          // number of atoms blocks
+  int atomBlocks[101];      // atom blocks
+  double comptime[100];
+  int timing;
+
+  int ni;            // number of atoms i in the current atom block 
+  int nij;           // number of pairs (i,j) in the current atom block 
+  int nimax;         // maximum number of atoms i
+  int nijmax;        // maximum number of pairs (i,j) 
+
+  int nelements; // number of elements 
+  int onebody;   // one-body descriptors
+  int besseldegree; // degree of Bessel functions
+  int inversedegree; // degree of inverse functions
+  int nbesselpars;  // number of Bessel parameters
+  int nCoeffPerElement; // number of coefficients per element = (nl1 + Mdesc*nClusters)
+  int ns;      // number of snapshots for radial basis functions
+  int nl1, nl2, nl3, nl4, nl23, nl33, nl34, nl44, n23, n32, nl;   // number of local descriptors
+  int nrbf2, nrbf3, nrbf4, nrbfmax;            // number of radial basis functions
+  int nabf3, nabf4;                            // number of angular basis functions  
+  int K3, K4, Q4;                                  // number of monomials
+
+  // environmental variables
+  int nClusters; // number of environment clusters
+  int nComponents; // number of principal components
+  int Mdesc; // number of base descriptors 
+
+  double rin;  // inner cut-off radius
+  double rcut; // outer cut-off radius
+  double rmax; // rcut - rin  
+  double rcutsq;
+
+  t_pod_1d rij;         // (xj - xi) for all pairs (I, J)
+  t_pod_1d fij;         // force for all pairs (I, J)
+  t_pod_1d ei;          // energy for each atom I
+  t_pod_1i typeai;         // types of atoms I only
+  t_pod_1i numij;          // number of pairs (I, J) for each atom I   
+  t_pod_1i idxi;           // storing linear indices of atom I for all pairs (I, J)
+  t_pod_1i ai;             // IDs of atoms I for all pairs (I, J)
+  t_pod_1i aj;             // IDs of atoms J for all pairs (I, J)
+  t_pod_1i ti;             // types of atoms I for all pairs (I, J)
+  t_pod_1i tj;             // types of atoms J for all pairs (I, J)  
+
+  t_pod_1d besselparams;
+  t_pod_1d Phi;  // eigenvectors matrix ns x ns
+  t_pod_1d rbf;  // radial basis functions nij x nrbfmax  
+  t_pod_1d rbfx; // x-derivatives of radial basis functions nij x nrbfmax 
+  t_pod_1d rbfy; // y-derivatives of radial basis functions nij x nrbfmax
+  t_pod_1d rbfz; // z-derivatives of radial basis functions nij x nrbfmax   
+  t_pod_1d abf;  // angular basis functions nij x K3
+  t_pod_1d abfx; // x-derivatives of angular basis functions nij x K3
+  t_pod_1d abfy; // y-derivatives of angular basis functions nij x K3  
+  t_pod_1d abfz; // z-derivatives of angular basis functions nij x K3
+  t_pod_1d sumU; // sum of radial basis functions ni x K3 x nrbfmax x nelements
+  t_pod_1d Proj; // PCA Projection matrix
+  t_pod_1d Centroids; // centroids of the clusters  
+  t_pod_1d bd;   // base descriptors ni x Mdesc
+  t_pod_1d bdd;  // base descriptors derivatives 3 x nij x Mdesc 
+  t_pod_1d coefficients; // coefficients nCoeffPerElement x nelements
+  t_pod_1i pq3, pn3, pc3; // arrays to compute 3-body angular basis functions
+  t_pod_1i pa4, pb4, pc4; // arrays to compute 4-body angular basis functions  
+  t_pod_1i ind23; // n23 
+  t_pod_1i ind32; // n32
+  t_pod_1i ind33l, ind33r; // nl33
+  t_pod_1i ind34l, ind34r; // nl34
+  t_pod_1i ind44l, ind44r; // nl44
+  t_pod_1i elemindex;  
+
+  void set_array_to_zero(t_pod_1d a, int N);
+
+  int NeighborCount(t_pod_1i, double, int, int);
+  int NeighborCount(t_pod_1i, int);
+
+  void NeighborList(t_pod_1d l_rij, t_pod_1i l_numij,  t_pod_1i l_typeai, t_pod_1i l_idxi, 
+    t_pod_1i l_ai, t_pod_1i l_aj, t_pod_1i l_ti, t_pod_1i l_tj, double l_rcutsq, int gi1, int Ni);
+
+  void radialbasis(t_pod_1d rbft, t_pod_1d rbftx, t_pod_1d rbfty, t_pod_1d rbftz, 
+    t_pod_1d rij, t_pod_1d l_besselparams, double l_rin, double l_rmax, int l_besseldegree, 
+    int l_inversedegree, int l_nbesselpars, int l_ns,  int Nij); 
+
+  void matrixMultiply(t_pod_1d a, t_pod_1d b, t_pod_1d c, int r1, int c1, int c2); 
+
+  void angularbasis(t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz,
+        t_pod_1d l_rij, t_pod_1i l_pq3, int l_K3, int N);  
+
+  void radialangularsum(t_pod_1d l_sumU, t_pod_1d l_rbf, t_pod_1d l_abf, t_pod_1i l_tj, 
+    t_pod_1i l_numij, const int l_nelements, const int l_nrbf3, const int l_K3, const int Ni, const int Nij);
+
+  void twobodydescderiv(t_pod_1d d2, t_pod_1d dd2, t_pod_1d l_rbf, t_pod_1d l_rbfx, t_pod_1d l_rbfy, 
+    t_pod_1d l_rbfz, t_pod_1i l_idxi, t_pod_1i l_tj, int l_nrbfmax, int l_nrbf2, const int Ni, const int Nij); 
+
+  void threebodydesc(t_pod_1d d3, t_pod_1d l_sumU, t_pod_1i l_pc3, t_pod_1i l_pn3, 
+        int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, const int Ni);
+
+  void threebodydescderiv(t_pod_1d dd3, t_pod_1d l_rbf, t_pod_1d l_rbfx, 
+    t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, 
+    t_pod_1d l_sumU, t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pc3, t_pod_1i l_pn3, t_pod_1i l_elemindex, 
+    int l_nelements, int l_nrbfmax, int l_nrbf3, int l_nabf3, int l_K3, int Ni, int Nij);
+
+  void fourbodydesc(t_pod_1d d4,  t_pod_1d l_sumU, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, 
+      int l_nelements, int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni);
+
+  void fourbodydescderiv(t_pod_1d dd4, t_pod_1d l_rbf, t_pod_1d l_rbfx, t_pod_1d l_rbfy, t_pod_1d l_rbfz, 
+    t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, t_pod_1d l_sumU, t_pod_1i l_idxi, 
+    t_pod_1i l_tj, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, t_pod_1i l_elemindex, int l_nelements, 
+    int l_nrbfmax,  int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni, int Nij);
+
+  void fourbodydesc23(t_pod_1d d23, t_pod_1d d2, t_pod_1d d3, t_pod_1i l_ind23,
+    t_pod_1i l_ind32, int l_n23, int l_n32, int Ni);
+
+  void fourbodydescderiv23(t_pod_1d dd23, t_pod_1d d2, t_pod_1d d3, t_pod_1d dd2, 
+    t_pod_1d dd3,  t_pod_1i l_idxi, t_pod_1i l_ind23, t_pod_1i l_ind32, int l_n23, int l_n32, int Ni, int N);
+
+  void crossdesc(t_pod_1d d12, t_pod_1d d1, t_pod_1d d2, t_pod_1i ind1, t_pod_1i ind2, int n12, int Ni);
+
+  void crossdescderiv(t_pod_1d dd12, t_pod_1d d1, t_pod_1d d2, t_pod_1d dd1, t_pod_1d dd2,
+        t_pod_1i l_idxi, t_pod_1i ind1, t_pod_1i ind2, int n12, int Ni, int Nij);
+
+  void blockatom_base_descriptors(t_pod_1d bd, t_pod_1d bdd, int Ni, int Nij);
+  void blockatomenv_descriptors(t_pod_1d ei, t_pod_1d cb, t_pod_1d B, int Ni);
+
+  void blockatomenergyforce(int Ni, int Nij);
+
+  void tallyforce(int Nij);
+
+  void tallyenergy(int istart, int Ni);
+
+  void tallystress(int Nij);  
+
+  void savematrix2binfile(std::string filename, t_pod_1d d_A, int nrows, int ncols);
+  void saveintmatrix2binfile(std::string filename, t_pod_1i d_A, int nrows, int ncols);
+  void savedatafordebugging();
+};
+}    // namespace LAMMPS_NS
+
+#endif
+#endif