Open Qmin: hyperrectangularCellList Class Reference

Construct simple cell/bucket structures on the CPU or GPU given a hyper-rectangular domain with PBCs. More...

#include <hyperrectangularCellList.h>

Collaboration diagram for hyperrectangularCellList:

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Public Member Functions
	hyperrectangularCellList ()
	Blank constructor. More...

	hyperrectangularCellList (scalar a, BoxPtr _box)
	a box, and a size for the underlying grid More...

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

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

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

iVec	getBinsPerSide ()
	The number of cells in each direction. More...

dVec	getCellSize ()
	Returns the length of the square that forms the base grid size. More...

int	positionToCellIndex (const dVec &pos)
	Return the index of the cell that contains the given point. More...

iVec	indexToiVec (const int cellIndex)
	return the iVec corresponding to a 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	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. More...

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

void	computeCellList (GPUArray< dVec > &points)
	compute the cell list of the gpuarry passed to it. More...

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

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

virtual void	setGPU (bool _useGPU=true)
	Enforce GPU operation. More...

GPUArray< int > &	returnAdjacentCells ()
	return the list of adjacent cells More...

void	computeAdjacentCells (int width=1)
	compute the adjacent cells up to a scale More...

Public Attributes
IndexDD	cellIndexer
	Indexes the cells in the grid themselves (so the index of the bin corresponding to (iVec) is bin = cellIndexer(iVec) More...

Index2D	cellListIndexer
	Indexes elements in the cell list (i.e., the third element of cell index i is cellListIndexer(3,i) More...

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

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

GPUArray< dVec >	particlePositions
	An array containing the positions of particles in various cells. Aligned with the particleIndices array, so that derived methods can choose whatever is most convenient,so particlePositions[cellListIndexer(nn,bin)] gives the positionof the nth particle in the bin "bin" of the cell list. More...

int	computations
	A reporter index of how hard it was to compute the cell list. More...

int	adjacentCellsPerCell
	the number of cells in the adjacency list for each cell More...

Index2D	adjacentCellIndexer
	indexes the adjacent cells of each cell More...

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

GPUArray< int >	adjacentCells
	an array that stores the list cell adjacent to every cell More...

iVec	gridCellsPerSide
	The number of bins in each of the different dimensions. More...

dVec	gridCellSizes
	The size of each cell (e.g., each cell is a small hyperrectangle of these dimensions. More...

int	totalCells

int	Nmax
	the maximum number of particles found in any bin More...

BoxPtr	Box
	The Box used to compute periodic distances. More...

bool	useGPU
	whether the updater does its work on the GPU or not More...

bool	adjCellsComputed
	have we already computed the adjacent cell lists? More...

Detailed Description

Construct simple cell/bucket structures on the CPU or GPU given a hyper-rectangular domain with PBCs.

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 can only handle hyper-rectangular boxes.

Constructor & Destructor Documentation

◆ hyperrectangularCellList() [1/2]

hyperrectangularCellList::hyperrectangularCellList ( )

inline

Blank constructor.

References Box, and Nmax.

◆ hyperrectangularCellList() [2/2]

hyperrectangularCellList::hyperrectangularCellList	(	scalar	a,
		BoxPtr	_box
	)

a box, and a size for the underlying grid

Parameters

a	the approximate side length of the cells
_box	the period box for the system

References Box, Nmax, setGridSize(), and useGPU.

Member Function Documentation

◆ setBox()

void hyperrectangularCellList::setBox ( BoxPtr bx )

inline

Set the BoxPtr to point to an existing one.

References Box.

◆ setGridSize()

void hyperrectangularCellList::setGridSize ( scalar 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 in each dimension, close to the desired size, that fit in the box.

References adjCellsComputed, Box, cellIndexer, cellListIndexer, elementsPerCell, gridCellSizes, gridCellsPerSide, Nmax, resetCellSizesCPU(), GPUArray< T >::resize(), totalCells, and iVec::x.

Referenced by hyperrectangularCellList().

◆ getNmax()

int hyperrectangularCellList::getNmax ( )

inline

Get an upper bound on the maximum number of particles in a given bucket.

References Nmax.

◆ getBinsPerSide()

iVec hyperrectangularCellList::getBinsPerSide ( )

inline

The number of cells in each direction.

References gridCellsPerSide.

◆ getCellSize()

dVec hyperrectangularCellList::getCellSize ( )

inline

Returns the length of the square that forms the base grid size.

References gridCellSizes.

◆ positionToCellIndex()

int hyperrectangularCellList::positionToCellIndex ( const dVec & pos )

Return the index of the cell that contains the given point.

Parameters

pos	the dVec coordinate of the position returns the cell index that (pos) would be contained in for the current cell list

References cellIndexer, gridCellSizes, gridCellsPerSide, and iVec::x.

◆ indexToiVec()

iVec hyperrectangularCellList::indexToiVec ( const int cellIndex )

inline

return the iVec corresponding to a cell index

References cellIndexer, and IndexDD::inverseIndex().

◆ getCellNeighbors()

void hyperrectangularCellList::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 cellIndexer, gridCellsPerSide, idPow(), IndexDD::inverseIndex(), iVecIterate(), modularAddition(), and iVec::x.

◆ resetCellSizesCPU()

void hyperrectangularCellList::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, cellListIndexer, ArrayHandle< T >::data, elementsPerCell, Index2D::getNumElements(), GPUArray< T >::getNumElements(), access_location::host, Nmax, access_mode::overwrite, particleIndices, particlePositions, GPUArray< T >::resize(), and totalCells.

Referenced by computeCPU(), and setGridSize().

◆ resetCellSizes()

void hyperrectangularCellList::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, cellListIndexer, ArrayHandle< T >::data, access_location::device, elementsPerCell, Index2D::getNumElements(), GPUArray< T >::getNumElements(), gpu_set_array(), access_location::host, Nmax, NVTXPOP, NVTXPUSH, access_mode::overwrite, particleIndices, particlePositions, GPUArray< T >::resize(), and totalCells.

Referenced by computeGPU().

◆ getCellSizeArray()

const GPUArray<unsigned int>& hyperrectangularCellList::getCellSizeArray ( ) const

inline

Return the array of particles per cell.

References elementsPerCell.

◆ getIdxArray()

const GPUArray<int>& hyperrectangularCellList::getIdxArray ( ) const

inline

Return the array of cell indices in the different cells.

References particleIndices.

◆ computeCellList()

void hyperrectangularCellList::computeCellList ( GPUArray< dVec > & points )

inline

compute the cell list of the gpuarry passed to it.

References adjCellsComputed, computeAdjacentCells(), computeCPU(), computeGPU(), and useGPU.

◆ computeGPU()

void hyperrectangularCellList::computeGPU ( GPUArray< dVec > & points )

compute the cell list of the gpuarry passed to it. GPU function

Parameters

points the set of points to assign to cells...on the GPU

References assist, Box, cellIndexer, cellListIndexer, ArrayHandle< T >::data, access_location::device, elementsPerCell, GPUArray< T >::getNumElements(), gpu_compute_cell_list(), gridCellSizes, gridCellsPerSide, access_location::host, Nmax, NVTXPOP, NVTXPUSH, particleIndices, particlePositions, access_mode::read, access_mode::readwrite, resetCellSizes(), and totalCells.

Referenced by computeCellList().

◆ computeCPU()

void hyperrectangularCellList::computeCPU ( GPUArray< dVec > & points )

compute the cell list of the gpuarry passed to it. CPU function

Parameters

points the set of points to assign to cells

References cellIndexer, cellListIndexer, computations, ArrayHandle< T >::data, elementsPerCell, GPUArray< T >::getNumElements(), gridCellSizes, access_location::host, Nmax, particleIndices, particlePositions, access_mode::read, access_mode::readwrite, resetCellSizesCPU(), totalCells, and iVec::x.

Referenced by computeCellList().

◆ setGPU()

virtual void hyperrectangularCellList::setGPU ( bool _useGPU = true )

inlinevirtual

Enforce GPU operation.

References useGPU.

◆ returnAdjacentCells()

GPUArray<int>& hyperrectangularCellList::returnAdjacentCells ( )

inline

return the list of adjacent cells

References adjacentCells.

◆ computeAdjacentCells()

void hyperrectangularCellList::computeAdjacentCells ( int width = 1 )

compute the adjacent cells up to a scale

width*gridsize should be a cutoff scale in the problem... this will evaluate all cells that might containt a neighbor within gridsize*width; not all cells in a hypercube of sidelength width

References adjacentCellIndexer, adjacentCells, adjacentCellsPerCell, adjCellsComputed, cellIndexer, ArrayHandle< T >::data, GPUArray< T >::getNumElements(), gridCellSizes, gridCellsPerSide, IndexDD::inverseIndex(), iVecIterate(), modularAddition(), GPUArray< T >::resize(), scalar, totalCells, and iVec::x.

Referenced by computeCellList().

Member Data Documentation

◆ cellIndexer

IndexDD hyperrectangularCellList::cellIndexer

Indexes the cells in the grid themselves (so the index of the bin corresponding to (iVec) is bin = cellIndexer(iVec)

Referenced by computeAdjacentCells(), computeCPU(), computeGPU(), getCellNeighbors(), indexToiVec(), positionToCellIndex(), and setGridSize().

◆ cellListIndexer

Index2D hyperrectangularCellList::cellListIndexer

Indexes elements in the cell list (i.e., the third element of cell index i is cellListIndexer(3,i)

Referenced by computeCPU(), computeGPU(), resetCellSizes(), resetCellSizesCPU(), and setGridSize().

◆ elementsPerCell

GPUArray<unsigned int> hyperrectangularCellList::elementsPerCell

An array containing the number of elements in each cell.

Referenced by computeCPU(), computeGPU(), getCellSizeArray(), resetCellSizes(), resetCellSizesCPU(), and setGridSize().

◆ particleIndices

GPUArray<int> hyperrectangularCellList::particleIndices

An array containing the indices of particles in various cells. So, particleIndices[cellListIndexer(nn,bin)] gives the index of the nth particle in the bin "bin" of the cell list.

Referenced by computeCPU(), computeGPU(), getIdxArray(), resetCellSizes(), and resetCellSizesCPU().

◆ particlePositions

GPUArray<dVec> hyperrectangularCellList::particlePositions

An array containing the positions of particles in various cells. Aligned with the particleIndices array, so that derived methods can choose whatever is most convenient,so particlePositions[cellListIndexer(nn,bin)] gives the positionof the nth particle in the bin "bin" of the cell list.

Referenced by computeCPU(), computeGPU(), resetCellSizes(), and resetCellSizesCPU().

◆ computations

int hyperrectangularCellList::computations

A reporter index of how hard it was to compute the cell list.

Referenced by computeCPU().

◆ adjacentCellsPerCell

int hyperrectangularCellList::adjacentCellsPerCell

the number of cells in the adjacency list for each cell

Referenced by computeAdjacentCells().

◆ adjacentCellIndexer

Index2D hyperrectangularCellList::adjacentCellIndexer

indexes the adjacent cells of each cell

Referenced by computeAdjacentCells().

◆ assist

GPUArray<int> hyperrectangularCellList::assist

protected

first index is Nmax, second is whether to recompute

Referenced by computeGPU(), resetCellSizes(), and resetCellSizesCPU().

◆ adjacentCells

GPUArray<int> hyperrectangularCellList::adjacentCells

protected

an array that stores the list cell adjacent to every cell

Referenced by computeAdjacentCells(), and returnAdjacentCells().

◆ gridCellsPerSide

iVec hyperrectangularCellList::gridCellsPerSide

protected

The number of bins in each of the different dimensions.

Referenced by computeAdjacentCells(), computeGPU(), getBinsPerSide(), getCellNeighbors(), positionToCellIndex(), and setGridSize().

◆ gridCellSizes

dVec hyperrectangularCellList::gridCellSizes

protected

The size of each cell (e.g., each cell is a small hyperrectangle of these dimensions.

Referenced by computeAdjacentCells(), computeCPU(), computeGPU(), getCellSize(), positionToCellIndex(), and setGridSize().

◆ totalCells

int hyperrectangularCellList::totalCells

protected

Referenced by computeAdjacentCells(), computeCPU(), computeGPU(), resetCellSizes(), resetCellSizesCPU(), and setGridSize().

◆ Nmax

int hyperrectangularCellList::Nmax

protected

the maximum number of particles found in any bin

Referenced by computeCPU(), computeGPU(), getNmax(), hyperrectangularCellList(), resetCellSizes(), resetCellSizesCPU(), and setGridSize().

◆ Box

BoxPtr hyperrectangularCellList::Box

protected

The Box used to compute periodic distances.

Referenced by computeGPU(), hyperrectangularCellList(), setBox(), and setGridSize().

◆ useGPU

bool hyperrectangularCellList::useGPU

protected

whether the updater does its work on the GPU or not

Referenced by computeCellList(), hyperrectangularCellList(), and setGPU().

◆ adjCellsComputed

bool hyperrectangularCellList::adjCellsComputed

protected

have we already computed the adjacent cell lists?

Referenced by computeAdjacentCells(), computeCellList(), and setGridSize().

The documentation for this class was generated from the following files:

Public Member Functions

Public Attributes

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ hyperrectangularCellList() [1/2]

◆ hyperrectangularCellList() [2/2]

Member Function Documentation

◆ setBox()

◆ setGridSize()

◆ getNmax()

◆ getBinsPerSide()

◆ getCellSize()

◆ positionToCellIndex()

◆ indexToiVec()

◆ getCellNeighbors()

◆ resetCellSizesCPU()

◆ resetCellSizes()

◆ getCellSizeArray()

◆ getIdxArray()

◆ computeCellList()

◆ computeGPU()

◆ computeCPU()

◆ setGPU()

◆ returnAdjacentCells()

◆ computeAdjacentCells()

Member Data Documentation

◆ cellIndexer

◆ cellListIndexer

◆ elementsPerCell

◆ particleIndices

◆ particlePositions

◆ computations

◆ adjacentCellsPerCell

◆ adjacentCellIndexer

◆ assist

◆ adjacentCells

◆ gridCellsPerSide

◆ gridCellSizes

◆ totalCells

◆ Nmax

◆ Box

◆ useGPU

◆ adjCellsComputed