Cell encapsulation class for implementing the linked cell method. More...

#include <CellContainer.h>

Classes
class	SpecialParticleIterator
	A special iterator for iterating over the boundary and halo cell containers. More...

Public Member Functions
	CellContainer (const std::array< double, 3 > &domainSize, const std::array< BoundaryCondition, 6 > &conditions, double cutoff, ParticleContainer &particles, size_t dim=3)
	Constructs a new CellContainer and initializes all Cell objects and locks.

	~CellContainer ()
	Destroys the CellContainer object and frees the reserved locks.

ContainerType::iterator	begin ()
	Standard library iterator function for marking the beginning of the iteration process.

ContainerType::iterator	end ()
	Standard library iterator function for marking the end of the iteration process.

ParticleContainer::PairIterator	beginPairs ()
	Direct access to the beginning of the ParticleContainer's PairIterator.

ParticleContainer::PairIterator	endPairs ()
	Direct access to the end of the ParticleContainer's PairIterator.

ContainerType::const_iterator	begin () const
	Standard library iterator function for marking the beginning of the iteration process of a const CellContainer.

ContainerType::const_iterator	end () const
	Standard library iterator function for marking the end of the iteration process of a const CellContainer.

SpecialParticleIterator	boundaryBegin ()
	Gets a SpecialParticleIterator pointing to the beginning of the boundary Cell pointer container.

SpecialParticleIterator	boundaryEnd ()
	Gets a SpecialParticleIterator pointing to the end of the boundary Cell pointer container.

SpecialParticleIterator	haloBegin ()
	Gets a SpecialParticleIterator pointing to the beginning of the halo Cell pointer container.

SpecialParticleIterator	haloEnd ()
	Gets a SpecialParticleIterator pointing to the end of the halo Cell pointer container.

Cell &	operator[] (size_t index)
	Dereference of the [] operator.

const Cell &	operator[] (size_t index) const
	Dereference of the [] operator (const).

std::vector< Cell > &	getCells ()
	Gets a reference to the Cell container.

const std::vector< Cell > &	getCells () const
	Gets a const reference to the Cell container.

std::vector< std::reference_wrapper< Cell > > &	getBorderCells ()
	Gets a reference to the border Cell container.

const std::vector< std::reference_wrapper< Cell > > &	getBorderCells () const
	Gets a const reference to the border Cell container.

std::vector< std::reference_wrapper< Cell > > &	getHaloCells ()
	Gets a reference to the halo Cell container.

const std::vector< std::reference_wrapper< Cell > > &	getHaloCells () const
	Gets a const reference to the halo Cell container.

std::vector< std::reference_wrapper< Cell > > &	getIterableCells ()
	Gets a reference to the iterable Cell container.

const std::vector< std::reference_wrapper< Cell > > &	getIterableCells () const
	Gets a const reference to the iterable Cell container.

void	removeHaloCellParticles ()
	Removes the active halo Cell Particle objects.

int	getCellIndex (const std::array< double, 3 > &position)
	Gets the 1D index in the Cell container based on the given position.

void	deleteParticle (Particle &p)
	Removes a Particle from a Cell and marks it inactive.

bool	addParticle (Particle &p)
	Adds a Particle to the Cell container.

bool	moveParticle (Particle &p)
	Moves a particle from one Cell to another.

std::array< int, 3 >	getVirtualCellCoordinates (int index) const
	Gets the coordinates of a Cell from its index.

std::array< double, 3 >	getMirrorPosition (const std::array< double, 3 > &position, const Cell &from, const Cell &to, int direction) const
	Mirrors a position from a source Cell to a destination Cell.

int	getOppositeNeighbor (int cellIndex, HaloLocation direction) const
	Gets the index of the opposing Cell in the specified direction.

void	calculateNeighbors (int cellIndex)
	Computes the vector of neighbouring Cell indices, including the Cell itself.

const std::vector< int > &	getNeighbors (int cellIndex) const
	Gets a vector of neighbouring Cell indices, including the Cell itself.

std::vector< std::reference_wrapper< Cell > >	getNeighborCells (int cellIndex)

int	getOppositeOfHalo (const Cell &from, HaloLocation location)
	For a halo cell returns the index of the border cell on the opposite side of the domain.

int	getOppositeOfBorder (const Cell &from, BorderLocation location)
	For a border cell returns the index of the halo cell on the opposite side of the domain.

std::vector< int >	getOppositeOfBorderCorner (const Cell &from, std::vector< BorderLocation > &locations)
	For a border cell returns the indices of the corner cells on the opposite sides of the domain.

std::vector< std::vector< BorderLocation > >	getBorderCombinations (std::vector< BorderLocation > &locations)
	For a collection of border locations, returns all unique pairs.

const std::array< double, 3 > &	getDomainSize () const
	Gets a const reference to the CellContainer's domain size.

const std::array< double, 3 > &	getCellSize () const
	Gets a const reference to the CellContainer's cell size.

const std::array< size_t, 3 > &	getNumCells () const
	Gets a const reference to the CellContainer's cell count in each dimension.

const std::array< BoundaryCondition, 6 > &	getConditions () const
	Gets the boundary conditions at each boundary.

double	getCutoff () const
	Gets the cutoff radius used for calculating the cell size.

size_t	getDim () const
	Gets the number of dimensions of the linked cells.

bool	getAnyPeriodic () const
	Checks if any boundary condition is periodic.

ParticleContainer &	getParticles ()
	Gets a reference to the primary ParticleContainer.

const ParticleContainer &	getParticles () const
	Gets a const reference to the primary ParticleContainer.

size_t	size () const
	Gets the size of the ParticleContainer, including all inactive Cells.

size_t	activeSize () const
	Gets the amount of active Particle objects in the ParticleContainer.

void	printCellIndices () const
	Debug function to print the indices of all cells for a 2D container.

void	printCellContents () const
	Debug function to print the contents of each cell.

Private Types
using	ContainerType = std::vector< Cell >
	Typedef for the underlying Cell container type.

Private Attributes
ContainerType	cells
	The container of Cell objects itself.

std::vector< omp_lock_t >	cellLocks
	Container of mutual exclusion locks for each cell.

std::vector< std::reference_wrapper< Cell > >	borderCells
	Container of references to border cells.

std::vector< std::reference_wrapper< Cell > >	haloCells
	Container of references to halo cells.

std::vector< std::reference_wrapper< Cell > >	iterableCells
	Container of references to cells to iterate over when calculating the forces between particles.

std::array< double, 3 >	domainSize
	The size of the domain in each dimension.

std::array< double, 3 >	cellSize {0, 0, 0}
	The size of each cell in each dimension (default: 0, 0, 0).

std::array< size_t, 3 >	numCells {1, 1, 1}
	The number of cells in each dimension (default: 1, 1, 1).

std::array< BoundaryCondition, 6 >	conditions
	An array of boundary conditions to be applied at each boundary (North, South, West, East, Above, Below).

double	cutoff
	The cutoff radius.

size_t	dim
	The number of dimensions (2/3)

bool	anyPeriodic {false}
	Determines if there are any periodic halo cells.

ParticleContainer &	particles
	A reference to the overarching ParticleContainer.

Detailed Description

Cell encapsulation class for implementing the linked cell method.

Member Typedef Documentation

◆ ContainerType

using CellContainer::ContainerType = std::vector<Cell>

private

Typedef for the underlying Cell container type.

Constructor & Destructor Documentation

◆ CellContainer()

CellContainer::CellContainer	(	const std::array< double, 3 > &	domainSize,
		const std::array< BoundaryCondition, 6 > &	conditions,
		double	cutoff,
		ParticleContainer &	particles,
		size_t	dim = `3`
	)

Constructs a new CellContainer and initializes all Cell objects and locks.

Parameters

domainSize	The size of the domain.
conditions	The boundary conditions to be applied at each boundary.
cutoff	The cutoff radius.
particles	The main ParticleContainer.
dim	The dimension of the container. May either be two- (2) or three-dimensional (3).

◆ ~CellContainer()

CellContainer::~CellContainer ( )

Destroys the CellContainer object and frees the reserved locks.

Member Function Documentation

◆ activeSize()

size_t CellContainer::activeSize ( ) const

Gets the amount of active Particle objects in the ParticleContainer.

Returns: The total number of active Particle objects.

◆ addParticle()

bool CellContainer::addParticle ( Particle & p )

Adds a Particle to the Cell container.

The 1D container index is computed from the Particle's current position. If the index is valid, the Particle is added there, otherwise nothing happens.

Parameters

p

Returns: true if the Particle was successfully added.; false if the Particle could not be added.

◆ begin() [1/2]

ContainerType::iterator CellContainer::begin ( )

Standard library iterator function for marking the beginning of the iteration process.

Returns: An iterator pointing to the first element of cells.

◆ begin() [2/2]

ContainerType::const_iterator CellContainer::begin ( ) const

Standard library iterator function for marking the beginning of the iteration process of a const CellContainer.

Returns: An iterator pointing to the first element of cells.

◆ beginPairs()

ParticleContainer::PairIterator CellContainer::beginPairs ( )

Direct access to the beginning of the ParticleContainer's PairIterator.

Use this to iterate over all distinct pairs of Particle objects in the domain.

Returns: The beginning of the ParticleContainer's PairIterator.

◆ boundaryBegin()

SpecialParticleIterator CellContainer::boundaryBegin ( )

Gets a SpecialParticleIterator pointing to the beginning of the boundary Cell pointer container.

Returns: A SpecialParticleIterator pointing to the beginning of the boundary Cell pointer container.

◆ boundaryEnd()

SpecialParticleIterator CellContainer::boundaryEnd ( )

Gets a SpecialParticleIterator pointing to the end of the boundary Cell pointer container.

Returns: A SpecialParticleIterator pointing to the end of the boundary Cell pointer container.

◆ calculateNeighbors()

void CellContainer::calculateNeighbors ( int cellIndex )

Computes the vector of neighbouring Cell indices, including the Cell itself.

Parameters

cellIndex The index of the Cell for which the neighbours should be determined.

◆ deleteParticle()

void CellContainer::deleteParticle ( Particle & p )

Removes a Particle from a Cell and marks it inactive.

First, the function finds the 1D index of the Particle's Cell. From there, it is removed, then marked as inactive. Note that, in order for this function to work, the Particle must have its correct index stored, and the index must be valid (i.e. not -1).

Parameters

p	The Particle to remove.

◆ end() [1/2]

ContainerType::iterator CellContainer::end ( )

Standard library iterator function for marking the end of the iteration process.

Returns: An iterator pointing to the last element of cells.

◆ end() [2/2]

ContainerType::const_iterator CellContainer::end ( ) const

Standard library iterator function for marking the end of the iteration process of a const CellContainer.

Returns: An iterator pointing to the last element of cells.

◆ endPairs()

ParticleContainer::PairIterator CellContainer::endPairs ( )

Direct access to the end of the ParticleContainer's PairIterator.

Use this to iterate over all distinct pairs of Particle objects in the domain.

Returns: The end of the ParticleContainer's PairIterator.

◆ getAnyPeriodic()

bool CellContainer::getAnyPeriodic ( ) const

Checks if any boundary condition is periodic.

Returns: true if at least one boundary condition is periodic.; false if there are no periodic boundary conditions.

◆ getBorderCells() [1/2]

std::vector< std::reference_wrapper< Cell > > & CellContainer::getBorderCells ( )

Gets a reference to the border Cell container.

Returns: A reference to the border Cell container.

◆ getBorderCells() [2/2]

const std::vector< std::reference_wrapper< Cell > > & CellContainer::getBorderCells ( ) const

Gets a const reference to the border Cell container.

Returns: A const reference to the border Cell container.

◆ getBorderCombinations()

std::vector< std::vector< BorderLocation > > CellContainer::getBorderCombinations ( std::vector< BorderLocation > & locations )

For a collection of border locations, returns all unique pairs.

Parameters

locations The border locations/directions which form the pairs

Returns: A vector of vectors representing the unique pairs

◆ getCellIndex()

int CellContainer::getCellIndex ( const std::array< double, 3 > & position )

Gets the 1D index in the Cell container based on the given position.

Parameters

position The position from which to compute the corresponding 1D index.

Returns: The 1D index in the Cell container.

◆ getCells() [1/2]

std::vector< Cell > & CellContainer::getCells ( )

Gets a reference to the Cell container.

Returns: A reference to the Cell container.

◆ getCells() [2/2]

const std::vector< Cell > & CellContainer::getCells ( ) const

Gets a const reference to the Cell container.

Returns: A const reference to the Cell container.

◆ getCellSize()

const std::array< double, 3 > & CellContainer::getCellSize ( ) const

Gets a const reference to the CellContainer's cell size.

Returns: A const reference to the CellContainer's cell size.

◆ getConditions()

const std::array< BoundaryCondition, 6 > & CellContainer::getConditions ( ) const

Gets the boundary conditions at each boundary.

Returns: A reference to the array containing the boundary conditions at each boundary.

◆ getCutoff()

double CellContainer::getCutoff ( ) const

Gets the cutoff radius used for calculating the cell size.

Returns: The cutoff radius.

◆ getDim()

size_t CellContainer::getDim ( ) const

Gets the number of dimensions of the linked cells.

Returns: The number of dimensions

◆ getDomainSize()

const std::array< double, 3 > & CellContainer::getDomainSize ( ) const

Gets a const reference to the CellContainer's domain size.

Returns: A const reference to the CellContainer's domain size.

◆ getHaloCells() [1/2]

std::vector< std::reference_wrapper< Cell > > & CellContainer::getHaloCells ( )

Gets a reference to the halo Cell container.

Returns: A reference to the halo Cell container.

◆ getHaloCells() [2/2]

const std::vector< std::reference_wrapper< Cell > > & CellContainer::getHaloCells ( ) const

Gets a const reference to the halo Cell container.

Returns: A const reference to the halo Cell container.

◆ getIterableCells() [1/2]

std::vector< std::reference_wrapper< Cell > > & CellContainer::getIterableCells ( )

Gets a reference to the iterable Cell container.

Returns: A reference to the iterable Cell container.

◆ getIterableCells() [2/2]

const std::vector< std::reference_wrapper< Cell > > & CellContainer::getIterableCells ( ) const

Gets a const reference to the iterable Cell container.

Returns: A const reference to the iterable Cell container.

◆ getMirrorPosition()

std::array< double, 3 > CellContainer::getMirrorPosition	(	const std::array< double, 3 > &	position,
		const Cell &	from,
		const Cell &	to,
		int	direction
	)		const

Mirrors a position from a source Cell to a destination Cell.

To be used primarily when incorporating reflective boundaries.

Parameters

position	The position in the source Cell.
from	The source Cell.
to	The destination Cell.
direction	The direction(s) in which to mirror the coordinates.

Returns: The mirrored position inside the destination Cell.

◆ getNeighborCells()

std::vector< std::reference_wrapper< Cell > > CellContainer::getNeighborCells ( int cellIndex )

◆ getNeighbors()

const std::vector< int > & CellContainer::getNeighbors ( int cellIndex ) const

Gets a vector of neighbouring Cell indices, including the Cell itself.

Parameters

cellIndex The index of the Cell for which the neighbours should be determined.

Returns: A vector of neighbouring Cell indices, including the Cell itself.

◆ getNumCells()

const std::array< size_t, 3 > & CellContainer::getNumCells ( ) const

Gets a const reference to the CellContainer's cell count in each dimension.

Returns: A const reference to the CellContainer's cell count in each dimension.

◆ getOppositeNeighbor()

int CellContainer::getOppositeNeighbor	(	int	cellIndex,
		HaloLocation	direction
	)		const

Gets the index of the opposing Cell in the specified direction.

For example, if the direction is NORTH, this function will return the southern neighbor.

Parameters

cellIndex	The Cell from which to get the opposing Cell index.
direction	The opposite direction of the desired neighbor Cell.

Returns: The index of the opposing Cell in the specified direction.

◆ getOppositeOfBorder()

int CellContainer::getOppositeOfBorder	(	const Cell &	from,
		BorderLocation	location
	)

For a border cell returns the index of the halo cell on the opposite side of the domain.

Parameters

from	The Cell for which the opposite halo cell should be determined
location	The orientation of the Border Cell

Returns: The index of the opposite halo cell

◆ getOppositeOfBorderCorner()

std::vector< int > CellContainer::getOppositeOfBorderCorner	(	const Cell &	from,
		std::vector< BorderLocation > &	locations
	)

For a border cell returns the indices of the corner cells on the opposite sides of the domain.

Parameters

from	The Cell for which the opposite halo cell should be determined
locations	The orientations of the Border Cell

Returns: The indices of the opposite halo cells

◆ getOppositeOfHalo()

int CellContainer::getOppositeOfHalo	(	const Cell &	from,
		HaloLocation	location
	)

For a halo cell returns the index of the border cell on the opposite side of the domain.

Parameters

from	The Cell for which the opposite border cell should be determined
location	The orientation of the Halo Cell

Returns: The index of the opposite border cell

◆ getParticles() [1/2]

ParticleContainer & CellContainer::getParticles ( )

Gets a reference to the primary ParticleContainer.

Returns: A reference to the overarching ParticleContainer.

◆ getParticles() [2/2]

const ParticleContainer & CellContainer::getParticles ( ) const

Gets a const reference to the primary ParticleContainer.

Returns: A const reference to the overarching ParticleContainer.

◆ getVirtualCellCoordinates()

std::array< int, 3 > CellContainer::getVirtualCellCoordinates ( int index ) const

Gets the coordinates of a Cell from its index.

Parameters

index The index of the Cell in the container.

Returns: The lower-left origin coordinates of the corresponding Cell.

◆ haloBegin()

SpecialParticleIterator CellContainer::haloBegin ( )

Gets a SpecialParticleIterator pointing to the beginning of the halo Cell pointer container.

Returns: A SpecialParticleIterator pointing to the beginning of the halo Cell pointer container.

◆ haloEnd()

SpecialParticleIterator CellContainer::haloEnd ( )

Gets a SpecialParticleIterator pointing to the end of the halo Cell pointer container.

Returns: A SpecialParticleIterator pointing to the end of the halo Cell pointer container.

◆ moveParticle()

bool CellContainer::moveParticle ( Particle & p )

Moves a particle from one Cell to another.

The Particle is first deleted, then added again. The source and destionation cells may be the same. Even if the Particle might not have moved, it will definitely be removed, even if something goes wrong.

Parameters

p

Returns: true if the Particle was successfully moved.; false if the Particle could not be moved. Here, the Particle is removed from the Cell container.

◆ operator[]() [1/2]

Cell & CellContainer::operator[] ( size_t index )

Dereference of the [] operator.

Gets a Cell by index. Does NOT perform bounds checking.

Parameters

index The index of the Cell to get.

Returns: A reference to the Cell at the specified index.

◆ operator[]() [2/2]

const Cell & CellContainer::operator[] ( size_t index ) const

Dereference of the [] operator (const).

Gets a Cell by index. Does NOT perform bounds checking.

Parameters

index The index of the Cell to get.

Returns: A const reference to the Cell at the specified index.

◆ printCellContents()

void CellContainer::printCellContents ( ) const

Debug function to print the contents of each cell.

◆ printCellIndices()

void CellContainer::printCellIndices ( ) const

Debug function to print the indices of all cells for a 2D container.

Halo cells are marked red, border cells are marked yellow, inner cells are marked green.

◆ removeHaloCellParticles()

void CellContainer::removeHaloCellParticles ( )

Removes the active halo Cell Particle objects.

For each halo Cell particle, if the Particle is active, it is removed from the Cell's linked list and is marked inactive.

◆ size()

size_t CellContainer::size ( ) const

Gets the size of the ParticleContainer, including all inactive Cells.

Returns: The total size of the ParticleContainer.

Member Data Documentation

◆ anyPeriodic

bool CellContainer::anyPeriodic {false}

private

Determines if there are any periodic halo cells.

◆ borderCells

std::vector<std::reference_wrapper<Cell> > CellContainer::borderCells

private

Container of references to border cells.

◆ cellLocks

std::vector<omp_lock_t> CellContainer::cellLocks

private

Container of mutual exclusion locks for each cell.

◆ cells

ContainerType CellContainer::cells

private

The container of Cell objects itself.

◆ cellSize

std::array<double, 3> CellContainer::cellSize {0, 0, 0}

private

The size of each cell in each dimension (default: 0, 0, 0).

◆ conditions

std::array<BoundaryCondition, 6> CellContainer::conditions

private

An array of boundary conditions to be applied at each boundary (North, South, West, East, Above, Below).

◆ cutoff

double CellContainer::cutoff

private

The cutoff radius.

◆ dim

size_t CellContainer::dim

private

The number of dimensions (2/3)

◆ domainSize

std::array<double, 3> CellContainer::domainSize

private

The size of the domain in each dimension.

◆ haloCells

std::vector<std::reference_wrapper<Cell> > CellContainer::haloCells

private

Container of references to halo cells.

◆ iterableCells

std::vector<std::reference_wrapper<Cell> > CellContainer::iterableCells

private

Container of references to cells to iterate over when calculating the forces between particles.

◆ numCells

std::array<size_t, 3> CellContainer::numCells {1, 1, 1}

private

The number of cells in each dimension (default: 1, 1, 1).

◆ particles

ParticleContainer& CellContainer::particles

private

A reference to the overarching ParticleContainer.

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

src/objects/CellContainer.h

Classes

Public Member Functions

Private Types

Private Attributes

Detailed Description

Member Typedef Documentation

◆ ContainerType

Constructor & Destructor Documentation

◆ CellContainer()

◆ ~CellContainer()

Member Function Documentation

◆ activeSize()

◆ addParticle()

◆ begin() [1/2]

◆ begin() [2/2]

◆ beginPairs()

◆ boundaryBegin()

◆ boundaryEnd()

◆ calculateNeighbors()

◆ deleteParticle()

◆ end() [1/2]

◆ end() [2/2]

◆ endPairs()

◆ getAnyPeriodic()

◆ getBorderCells() [1/2]

◆ getBorderCells() [2/2]

◆ getBorderCombinations()

◆ getCellIndex()

◆ getCells() [1/2]

◆ getCells() [2/2]

◆ getCellSize()

◆ getConditions()

◆ getCutoff()

◆ getDim()

◆ getDomainSize()

◆ getHaloCells() [1/2]

◆ getHaloCells() [2/2]

◆ getIterableCells() [1/2]

◆ getIterableCells() [2/2]

◆ getMirrorPosition()

◆ getNeighborCells()

◆ getNeighbors()

◆ getNumCells()

◆ getOppositeNeighbor()

◆ getOppositeOfBorder()

◆ getOppositeOfBorderCorner()

◆ getOppositeOfHalo()

◆ getParticles() [1/2]

◆ getParticles() [2/2]

◆ getVirtualCellCoordinates()

◆ haloBegin()

◆ haloEnd()

◆ moveParticle()

◆ operator[]() [1/2]

◆ operator[]() [2/2]

◆ printCellContents()

◆ printCellIndices()

◆ removeHaloCellParticles()

◆ size()

Member Data Documentation

◆ anyPeriodic

◆ borderCells

◆ cellLocks

◆ cells

◆ cellSize

◆ conditions

◆ cutoff

◆ dim

◆ domainSize

◆ haloCells

◆ iterableCells

◆ numCells

◆ particles