CellGPU: cellListGPU Class Reference

Construct simple cell/bucket structures on the GPU, using kernels in cellListGPU Kernels. More...

#include <cellListGPU.h>

Public Member Functions
	cellListGPU ()
	Blank constructor.

	cellListGPU (vector< Dscalar > &points)
	construct with a given set of points More...

	cellListGPU (Dscalar a, vector< Dscalar > &points, gpubox &bx)
	constructor with points, a box, and a size for the underlying grid More...

void	setParticles (const vector< Dscalar > &points)
	Set the object's points to a given vector. More...

void	setParticles (const vector< Dscalar2 > &points)
	Set the object's points to a given vector of Dscalar2s. More...

void	setBox (gpubox &bx)
	Set the objects box object. More...

void	setBox (BoxPtr bx)
	Set the BoxPtr to point to an existing one.

void	setNp (int nn)
	Set the number of particles to put in the buckets. More...

void	setGridSize (Dscalar a)
	call setGridSize if the particles and box already set, as this doubles as a general initialization of data structures More...

int	getNmax ()
	Get am upper bound on the maximum number of particles in a given bucket.

int	getXsize ()
	The number of cells in the x-direction.

int	getYsize ()
	The number of cells in the y-direction.

Dscalar	getBoxsize ()
	Returns the length of the square that forms the base grid size.

int	positionToCellIndex (Dscalar x, Dscalar y)
	If the grid is already initialized, given a spatial position return the cell index. More...

void	getCellNeighbors (int cellIndex, int width, vector< int > &cellNeighbors)
	given a target cell and a width, get all cell indices that sit in the surrounding square More...

void	getCellShellNeighbors (int cellIndex, int width, vector< int > &cellNeighbors)
	given a target cell and a width, get all cell indices that sit on the requested shell More...

void	resetCellSizesCPU ()
	Initialization and helper without using the GPU. More...

void	resetCellSizes ()
	Initialization and helper. More...

const GPUArray< unsigned int > &	getCellSizeArray () const
	Return the array of particles per cell.

const GPUArray< int > &	getIdxArray () const
	Return the array of cell indices in the different cells.

void	compute ()
	Compute the cell list on the CPU, given the current particle positions in the GPUArray of particles. More...

void	computeGPU ()
	Compute the cell list for the class' GPUArray of particles on the GPU. More...

void	computeGPU (GPUArray< Dscalar2 > &points)
	compute the cell list of the gpuarry passed to it. GPU function More...

void	compute (GPUArray< Dscalar2 > &points)
	compute the cell list of the gpuarry passed to it. GPU function More...

void	repP (int i)
	A debugging function to report where a point is.

Public Attributes
Index2D	cell_indexer
	Indexes the cells in the grid themselves (so the bin corresponding to the (j,i) position of the grid is bin=cell_indexer(i,j))

Index2D	cell_list_indexer
	Indexes elements in the cell list.

GPUArray< Dscalar2 >	particles
	The particles that some methods act on.

GPUArray< unsigned int >	cell_sizes
	An array containing the number of elements in each cell.

GPUArray< int >	idxs
	An array containing the indices of particles in various cells. So, idx[cell_list_indexer(nn,bin)] gives the index of the nth particle in the bin "bin" of the cell list.

Protected Attributes
GPUArray< int >	assist
	first index is Nmax, second is whether to recompute

int	Np
	The number of particles to put in cells.

Dscalar	boxsize
	The linear size of each grid cell.

int	xsize
	The number of bins in the x-direction.

int	ysize
	the number of bins in the y-direction

int	totalCells
	xsize*ysize

int	Nmax
	the maximum number of particles found in any bin

BoxPtr	Box
	The Box used to compute periodic distances.

Detailed Description

Construct simple cell/bucket structures on the GPU, using kernels in cellListGPU Kernels.

A class that can sort points into a grid of buckets. This enables local searches for particle neighbors, etc. Note that at the moment this class (and some of the classes above it) can only handle square boxes. This is not a fundamental limitation, though.

Constructor & Destructor Documentation

◆ cellListGPU() [1/2]

cellListGPU::cellListGPU ( vector< Dscalar > & points )

construct with a given set of points

Parameters

points the positions of points to populate the cell list with

References Box, Nmax, and setParticles().

◆ cellListGPU() [2/2]

cellListGPU::cellListGPU	(	Dscalar	a,
		vector< Dscalar > &	points,
		gpubox &	bx
	)

constructor with points, a box, and a size for the underlying grid

Parameters

a	the approximate side length of the cells
points	the positions of points to populate the cell list with
bx	the period box for the system

Member Function Documentation

◆ setParticles() [1/2]

void cellListGPU::setParticles ( const vector< Dscalar > & points )

Set the object's points to a given vector.

Parameters

points set the list of points cellListGPU knows about to this vector

References ArrayHandle< T >::data, access_location::host, Np, access_mode::overwrite, particles, and GPUArray< T >::resize().

Referenced by cellListGPU(), and voronoiModelBase::updateCellList().

◆ setParticles() [2/2]

void cellListGPU::setParticles ( const vector< Dscalar2 > & points )

Set the object's points to a given vector of Dscalar2s.

Parameters

points set the list of points cellListGPU knows about to this vector of Dscalar2's

References ArrayHandle< T >::data, access_location::host, Np, access_mode::overwrite, particles, and GPUArray< T >::resize().

◆ setBox()

void cellListGPU::setBox ( gpubox & bx )

Set the objects box object.

Parameters

bx	the box defining the periodic unit cell

◆ setNp()

void cellListGPU::setNp ( int nn )

Set the number of particles to put in the buckets.

Parameters

nn	the number of particles to sort

References Np.

Referenced by voronoiModelBase::resizeAndReset(), and setBox().

◆ setGridSize()

void cellListGPU::setGridSize ( Dscalar a )

call setGridSize if the particles and box already set, as this doubles as a general initialization of data structures

Parameters

a	the approximate side length of all of the cells. This routine currently picks an even integer of cells, close to the desired size, that fit in the box.

Referenced by setBox().

◆ positionToCellIndex()

int cellListGPU::positionToCellIndex	(	Dscalar	x,
		Dscalar	y
	)

If the grid is already initialized, given a spatial position return the cell index.

Parameters

x	the x coordinate of the position
y	the y coordinate of the position returns the cell index that (x,y) would be contained in for the current cell list

◆ getCellNeighbors()

void cellListGPU::getCellNeighbors	(	int	cellIndex,
		int	width,
		vector< int > &	cellNeighbors
	)

given a target cell and a width, get all cell indices that sit in the surrounding square

Parameters

cellIndex	the base cell index to find the neighbors of
width	the distance (in cells) to search
cellNeighbors	a vector of all cell indices that are neighbors of cellIndex

References cell_indexer, xsize, and ysize.

◆ getCellShellNeighbors()

void cellListGPU::getCellShellNeighbors	(	int	cellIndex,
		int	width,
		vector< int > &	cellNeighbors
	)

given a target cell and a width, get all cell indices that sit on the requested shell

Parameters

cellIndex	the base cell index to find the neighbors of
width	the distance (in cells) to search
cellNeighbors	a vector of all cell indices that are neighbors of cellIndex This method returns a square outline of neighbors (the neighbor shell) rather than all neighbors within a set distance

References cell_indexer, xsize, and ysize.

◆ resetCellSizesCPU()

void cellListGPU::resetCellSizesCPU ( )

Initialization and helper without using the GPU.

Sets all cell sizes to zero, all cell indices to zero, and resets the "assist" utility structure, all on the CPU (so that no expensive copies are needed)

References assist, cell_list_indexer, cell_sizes, ArrayHandle< T >::data, Index2D::getNumElements(), GPUArray< T >::getNumElements(), access_location::host, idxs, Nmax, access_mode::overwrite, GPUArray< T >::resize(), totalCells, xsize, and ysize.

Referenced by compute().

◆ resetCellSizes()

void cellListGPU::resetCellSizes ( )

Initialization and helper.

Sets all cell sizes to zero, all cell indices to zero, and resets the "assist" utility structure, all on the GPU so that arrays don't need to be copied back to the host

References assist, cell_list_indexer, cell_sizes, ArrayHandle< T >::data, access_location::device, Index2D::getNumElements(), GPUArray< T >::getNumElements(), gpu_zero_array(), access_location::host, idxs, Nmax, access_mode::overwrite, GPUArray< T >::resize(), totalCells, xsize, and ysize.