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CUDASpatialSearch.cu File Reference

CUDA kernels that build data structures for spatial sorting, hashing, and searching, used by QuickSurf, MDFF, etc. More...

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <cuda.h>
#include "Inform.h"
#include "utilities.h"
#include "WKFThreads.h"
#include "WKFUtils.h"
#include "CUDAKernels.h"
#include "CUDASpatialSearch.h"
#include "CUDASort.h"
#include "AtomSel.h"
#include "VMDApp.h"
#include "MoleculeList.h"
#include "VolumetricData.h"
#include "VolMapCreate.h"
#include <tcl.h>
#include "TclCommands.h"

Go to the source code of this file.

Defines

#define CUERR
#define RESTRICT
#define MAXTHRSORTHASH   512
#define MINBLOCKSORTHASH   1
#define GRID_CELL_EMPTY   0xffffffff

Functions

__global__ void hashAtoms (unsigned int natoms, const float4 *RESTRICT xyzr, int3 numcells, float invgridspacing, unsigned int *RESTRICT atomIndex, unsigned int *RESTRICT atomHash)
__global__ void sortAtomsColorsGenCellLists (unsigned int natoms, const float4 *RESTRICT xyzr_d, const float4 *RESTRICT color_d, const unsigned int *atomIndex_d, const unsigned int *atomHash_d, float4 *RESTRICT sorted_xyzr_d, float4 *RESTRICT sorted_color_d, uint2 *RESTRICT cellStartEnd_d)
__global__ void sortAtomsGenCellLists (unsigned int natoms, const float4 *RESTRICT xyzr_d, const unsigned int *atomIndex_d, const unsigned int *atomHash_d, float4 *RESTRICT sorted_xyzr_d, uint2 *RESTRICT cellStartEnd_d)
int vmd_cuda_build_density_atom_grid (int natoms, const float4 *xyzr_d, const float4 *color_d, float4 *sorted_xyzr_d, float4 *sorted_color_d, unsigned int *atomIndex_d, unsigned int *atomHash_d, uint2 *cellStartEnd_d, int3 volsz, float invgridspacing)
int vmd_cuda_build_density_atom_grid (int natoms, const float4 *xyzr_d, float4 *&sorted_xyzr_d, uint2 *&cellStartEnd_d, int3 volsz, float invgridspacing)

Detailed Description

CUDA kernels that build data structures for spatial sorting, hashing, and searching, used by QuickSurf, MDFF, etc.

Definition in file CUDASpatialSearch.cu.

Define Documentation

#define CUERR
 

Value:

{ cudaError_t err; \
  if ((err = cudaGetLastError()) != cudaSuccess) { \
  printf("CUDA error: %s, %s line %d\n", cudaGetErrorString(err), __FILE__, __LINE__); \
  printf("Thread aborting...\n"); \
  return NULL; }}

Definition at line 49 of file CUDASpatialSearch.cu.

#define GRID_CELL_EMPTY   0xffffffff
 

Definition at line 86 of file CUDASpatialSearch.cu.

Referenced by vmd_cuda_build_density_atom_grid.

#define MAXTHRSORTHASH   512
 

Definition at line 75 of file CUDASpatialSearch.cu.

#define MINBLOCKSORTHASH   1
 

Definition at line 76 of file CUDASpatialSearch.cu.

#define RESTRICT
 

Definition at line 65 of file CUDASpatialSearch.cu.

Referenced by hashAtoms, sortAtomsColorsGenCellLists, and sortAtomsGenCellLists.

Function Documentation

__global__ void hashAtoms (  unsigned int    natoms,
const float4 *RESTRICT    xyzr,
int3    numcells,
float    invgridspacing,
unsigned int *RESTRICT    atomIndex,
unsigned int *RESTRICT    atomHash
)  [static]
 

Definition at line 91 of file CUDASpatialSearch.cu.

References RESTRICT.

__global__ void sortAtomsColorsGenCellLists (  unsigned int    natoms,
const float4 *RESTRICT    xyzr_d,
const float4 *RESTRICT    color_d,
const unsigned int *    atomIndex_d,
const unsigned int *    atomHash_d,
float4 *RESTRICT    sorted_xyzr_d,
float4 *RESTRICT    sorted_color_d,
uint2 *RESTRICT    cellStartEnd_d
)  [static]
 

Definition at line 120 of file CUDASpatialSearch.cu.

References NULL, and RESTRICT.

__global__ void sortAtomsGenCellLists (  unsigned int    natoms,
const float4 *RESTRICT    xyzr_d,
const unsigned int *    atomIndex_d,
const unsigned int *    atomHash_d,
float4 *RESTRICT    sorted_xyzr_d,
uint2 *RESTRICT    cellStartEnd_d
)  [static]
 

Definition at line 175 of file CUDASpatialSearch.cu.

References RESTRICT.

int vmd_cuda_build_density_atom_grid (  int    natoms,
const float4 *    xyzr_d,
float4 *&    sorted_xyzr_d,
uint2 *&    cellStartEnd_d,
int3    volsz,
float    invgridspacing
) 
 

Definition at line 290 of file CUDASpatialSearch.cu.

References dev_radix_sort_by_key, GRID_CELL_EMPTY, NULL, and volsz.

int vmd_cuda_build_density_atom_grid (  int    natoms,
const float4 *    xyzr_d,
const float4 *    color_d,
float4 *    sorted_xyzr_d,
float4 *    sorted_color_d,
unsigned int *    atomIndex_d,
unsigned int *    atomHash_d,
uint2 *    cellStartEnd_d,
int3    volsz,
float    invgridspacing
) 
 

Definition at line 219 of file CUDASpatialSearch.cu.

References dev_radix_sort_by_key, GRID_CELL_EMPTY, NULL, and volsz.

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