forked from lijiext/lammps
257 lines
9.6 KiB
C++
257 lines
9.6 KiB
C++
/***************************************************************************
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neighbor.h
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-------------------
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W. Michael Brown (ORNL)
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Peng Wang (Nvidia)
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Class for handling neighbor lists
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__________________________________________________________________________
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This file is part of the LAMMPS Accelerator Library (LAMMPS_AL)
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__________________________________________________________________________
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begin :
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email : brownw@ornl.gov, penwang@nvidia.com
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***************************************************************************/
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#ifndef LAL_NEIGHBOR_H
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#define LAL_NEIGHBOR_H
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#include "lal_atom.h"
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#include "lal_neighbor_shared.h"
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#define IJ_SIZE 131072
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namespace LAMMPS_AL {
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class Neighbor {
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public:
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Neighbor() : _allocated(false), _use_packing(false), _ncells(0) {}
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~Neighbor() { clear(); }
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/// Determine whether neighbor unpacking should be used
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/** If false, twice as much memory is reserved to allow unpacking neighbors by
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* atom for coalesced access. **/
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void packing(const bool use_packing) { _use_packing=use_packing; }
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/// Clear any old data and setup for new LAMMPS run
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/** \param inum Initial number of particles whose neighbors stored on device
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* \param host_inum Initial number of particles whose nbors copied to host
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* \param max_nbors Initial number of rows in the neighbor matrix
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* \param gpu_nbor 0 if neighboring will be performed on host
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* gpu_nbor 1 if neighboring will be performed on device
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* gpu_nbor 2 if binning on host and neighboring on device
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* \param gpu_host 0 if host will not perform force calculations,
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* 1 if gpu_nbor is true, and host needs a half nbor list,
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* 2 if gpu_nbor is true, and host needs a full nbor list
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* \param pre_cut True if cutoff test will be performed in separate kernel
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* than the force kernel
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* \param threads_per_atom Number of threads used per atom for force
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* calculation
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* \param compile_flags Flags for JIT compiling **/
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bool init(NeighborShared *shared, const int inum, const int host_inum,
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const int max_nbors, const int maxspecial, UCL_Device &dev,
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const int gpu_nbor, const int gpu_host, const bool pre_cut,
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const int block_cell_2d, const int block_cell_id,
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const int block_nbor_build, const int threads_per_atom,
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const int warp_size, const bool time_device,
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const std::string compile_flags);
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/// Set the size of the cutoff+skin
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inline void cell_size(const double size, const double cutoff) {
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_cell_size=size;
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_cutoff=cutoff;
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if (cutoff>size)
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_cells_in_cutoff=static_cast<int>(ceil(cutoff/size));
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else
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_cells_in_cutoff=1;
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}
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/// Get the size of the cutoff+skin
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inline double cell_size() const { return _cell_size; }
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/// Check if there is enough memory for neighbor data and realloc if not
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/** \param inum Number of particles whose nbors will be stored on device
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* \param max_nbor Current max number of neighbors for a particle
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* \param success False if insufficient memory **/
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inline void resize(const int inum, const int max_nbor, bool &success) {
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if (inum>_max_atoms || max_nbor>_max_nbors) {
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_max_atoms=static_cast<int>(static_cast<double>(inum)*1.10);
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if (max_nbor>_max_nbors)
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_max_nbors=static_cast<int>(static_cast<double>(max_nbor)*1.10);
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alloc(success);
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}
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}
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/// Check if there is enough memory for neighbor data and realloc if not
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/** \param inum Number of particles whose nbors will be stored on device
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* \param host_inum Number of particles whose nbors will be copied to host
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* \param max_nbor Current max number of neighbors for a particle
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* \param success False if insufficient memory **/
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inline void resize(const int inum, const int host_inum, const int max_nbor,
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bool &success) {
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if (inum>_max_atoms || max_nbor>_max_nbors || host_inum>_max_host) {
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_max_atoms=static_cast<int>(static_cast<double>(inum)*1.10);
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_max_host=static_cast<int>(static_cast<double>(host_inum)*1.10);
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if (max_nbor>_max_nbors)
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_max_nbors=static_cast<int>(static_cast<double>(max_nbor)*1.10);
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alloc(success);
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}
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}
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inline void acc_timers() {
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if (_nbor_time_avail) {
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if (_gpu_nbor==2) {
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int mn=0;
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for (int i=0; i<_total_atoms; i++)
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mn=std::max(mn,host_acc[i]);
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if (mn>_max_nbors)
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assert(0==1);
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}
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if (_time_device) {
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time_nbor.add_to_total();
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if (_use_packing==false) time_kernel.add_to_total();
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if (_gpu_nbor==2) {
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time_hybrid1.add_to_total();
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time_hybrid2.add_to_total();
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}
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if (_maxspecial>0)
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time_transpose.add_to_total();
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_nbor_time_avail=false;
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}
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}
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}
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/// Free all memory on host and device
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void clear();
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/// Bytes per atom used on device
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int bytes_per_atom(const int max_nbors) const;
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/// Total host memory used by class
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double host_memory_usage() const;
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/// Returns the type of neighboring:
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/** - 0 if neighboring will be performed on host
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* - 1 if neighboring will be performed on device
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* - 2 if binning on host and neighboring on device **/
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inline int gpu_nbor() const { return _gpu_nbor; }
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/// Make a copy of unpacked nbor lists in the packed storage area (for gb)
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inline void copy_unpacked(const int inum, const int maxj)
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{ ucl_copy(dev_packed,dev_nbor,inum*(maxj+2),true); }
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/// Copy neighbor list from host (first time or from a rebuild)
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void get_host(const int inum, int *ilist, int *numj,
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int **firstneigh, const int block_size);
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/// Copy neighbor list from host for 3-body (first time or from a rebuild)
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void get_host3(const int inum, const int nlist, int *ilist, int *numj,
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int **firstneigh, const int block_size);
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/// Return the stride in elements for each nbor row
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inline int nbor_pitch() const { return _nbor_pitch; }
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/// Return the maximum number of atoms that can currently be stored
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inline int max_atoms() const { return _max_atoms; }
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/// Return the maximum number of nbors for a particle based on current alloc
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inline int max_nbors() const { return _max_nbors; }
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/// Return the time spent binning on the CPU for hybrid neighbor builds
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inline double bin_time() const { return _bin_time; }
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/// Loop through neighbor count array and return maximum nbors for a particle
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inline int max_nbor_loop(const int inum, int *numj, int *ilist) const {
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int mn=0;
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for (int i=0; i<inum; i++)
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mn=std::max(mn,numj[ilist[i]]);
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return mn;
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}
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/// Build nbor list on the device
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template <class numtyp, class acctyp>
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void build_nbor_list(double **x, const int inum, const int host_inum,
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const int nall, Atom<numtyp,acctyp> &atom, double *sublo,
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double *subhi, tagint *tag, int **nspecial, tagint **special,
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bool &success, int &max_nbors);
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/// Return the number of bytes used on device
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inline double gpu_bytes() {
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double res = _gpu_bytes + _c_bytes + _cell_bytes;
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if (_gpu_nbor==0)
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res += 2*IJ_SIZE*sizeof(int);
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return res;
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}
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// ------------------------------- Data -------------------------------
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/// Device neighbor matrix
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/** - 1st row is i (index into atom data)
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* - 2nd row is numj (number of neighbors)
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* - 3rd row is starting location in packed nbors
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* - Remaining rows are the neighbors arranged for coalesced access **/
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UCL_D_Vec<int> dev_nbor;
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/// Packed storage for neighbor lists copied from host
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UCL_D_Vec<int> dev_packed;
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/// Host buffer for copying neighbor lists
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UCL_H_Vec<int> host_packed;
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/// Host storage for nbor counts (row 1) & accumulated neighbor counts (row2)
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UCL_H_Vec<int> host_acc;
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/// Device storage for accessing atom indices from the neighbor list (3-body)
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UCL_D_Vec<int> dev_ilist;
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// ----------------- Data for GPU Neighbor Calculation ---------------
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/// Host/Device storage for device calculated neighbor lists
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/** - 1st row is numj
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* - Remaining rows are by atom, columns are nbors **/
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UCL_Vector<int,int> nbor_host;
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UCL_D_Vec<int> dev_numj_host;
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UCL_H_Vec<int> host_ilist;
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UCL_H_Vec<int*> host_jlist;
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/// Device storage for special neighbor counts
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UCL_D_Vec<int> dev_nspecial;
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/// Device storage for special neighbors
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UCL_D_Vec<tagint> dev_special, dev_special_t;
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/// Host/Device storage for number of particles per cell
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UCL_Vector<int,int> cell_counts;
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int *cell_iter;
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/// Device timers
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UCL_Timer time_nbor, time_kernel, time_hybrid1, time_hybrid2, time_transpose;
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private:
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NeighborShared *_shared;
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UCL_Device *dev;
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bool _allocated, _use_packing, _nbor_time_avail, _time_device;
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int _gpu_nbor, _max_atoms, _max_nbors, _max_host, _nbor_pitch, _maxspecial;
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bool _gpu_host, _alloc_packed;
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double _cutoff, _cell_size, _bin_time;
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enum UCL_MEMOPT _packed_permissions;
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double _gpu_bytes, _c_bytes, _cell_bytes;
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void alloc(bool &success);
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int _block_cell_2d, _block_cell_id, _max_block_nbor_build, _block_nbor_build;
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int _ncells, _threads_per_atom, _total_atoms;
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int _cells_in_cutoff;
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template <class numtyp, class acctyp>
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inline void resize_max_neighbors(const int maxn, bool &success);
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int _warp_size;
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inline void set_nbor_block_size(const int mn) {
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int desired=mn/(2*_warp_size);
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desired*=_warp_size;
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if (desired<_warp_size) desired=_warp_size;
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else if (desired>_max_block_nbor_build) desired=_max_block_nbor_build;
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_block_nbor_build=desired;
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}
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};
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}
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#endif
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