Container to store the particles for simulation using the linked cells algorithm. More...

#include <LinkedCellsContainer.h>

Inheritance diagram for LinkedCellsContainer:

Collaboration diagram for LinkedCellsContainer:

Public Member Functions
	LinkedCellsContainer (std::array< double, 3 > domainSize, double rCutOff, BoundarySet boundarySet)
	Constructor of the LinkedCellsContainer class. More...

int	calcCellIndex (const std::array< double, 3 > &position)
	Calculate the index of the cell to which a particle decided by its position belongs. More...

void	add (Particle &p) override
	Add a particle to this container. More...

int	threeDToOneD (int x, int y, int z) const
	Convert 3 dimensional coordinates to one dimensional coordinates. More...

int	threeDToOneDDomain (int x, int y, int z) const

std::array< int, 3 >	oneDToThreeD (int index) const
	Convert a one dimensional coordinate to three dimensional coordinates. More...

void	updateCells ()
	Assign each particle to its correct cell after there positions have been changed. More...

void	clearHaloCells (Side side)
	Delete all particles in all halo cells being part of a specific size. More...

void	applyToEachParticle (const std::function< void(Particle &)> &function) override
	Iterate over all particles in this container and apply a lambda function to them. More...

void	applyToEachParticleInDomain (const std::function< void(Particle &)> &function) override
	Iterate over all particles that are part of the domain and apply a lambda function to them. More...

void	applyToAllUniquePairsInDomain (const std::function< void(Particle &, Particle &)> &function) override
	Iterate over all unique pairs of particles being part of the simulation domain and apply a lambda function to them. More...

void	applyToAllUniquePairsInDomainOptimized (const std::function< void(Particle &, Particle &, std::array< double, 3 >, double)> &function)
	Implements the optimization we presented as our second idea. At the moment this is dead code, because we did not have time yet to make it compatible with our current program structure and only integrated it once when doing the time measurements. More...

void	applyToAllBoundaryParticles (const std::function< void(Particle &, std::array< double, 3 > &)> &function, Side boundary)
	Iterate over all particles in the boundary cells of a specific side which have a distance to that side that is smaller or equal than the threshold. More...

size_t	size () const override
	Get the number of particles stored in this container. More...

std::array< double, 3 >	fromLowToHigh (const std::array< double, 3 > &position, int dimension)
	Move a particle along a certain dimension that underflows the domain int that dimension to the opposite side of the domain in that dimension. More...

std::array< double, 3 >	fromHighToLow (const std::array< double, 3 > &position, int dimension)
	Move a particle along a certain dimension that overflows the domain int that dimension to the opposite side of the domain in that dimension. More...

void	teleportParticlesToOppositeSide (Side sideStart)
	Moves particles along a certain dimension from the halo cells back into the simulation domain. More...

void	applyForcesFromOppositeSide (Side side)
	Used for periodic boundaries to calculate the force that all particles from the opposite edge exert on the particles on the specified cell on the specified side. More...

std::vector< std::vector< Particle > > &	getCells ()

std::array< std::vector< int >, 6 > &	getHaloCells ()

std::array< std::vector< int >, 6 > &	getBoundaries ()

std::vector< std::vector< int > > &	getDomainCellIterationScheme ()

int	getNX () const

int	getNY () const

int	getNZ () const

double	getCellSizeX () const

double	getCellSizeY () const

double	getCellSizeZ () const

double	getRCutOff () const

bool	isTwoD () const

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

Public Member Functions inherited from ParticleContainer
virtual	~ParticleContainer ()=default
	Virtual default constructor to guarantee appropriate memory clean up. More...

Private Member Functions
void	calculateHaloCellIndices ()
	Pre-calculation of all halo cell indices. More...

void	calculateBoundaryCellIndices ()
	Pre-calculation of all boundary cell indices. More...

void	calculateDomainCellsIterationScheme ()
	Pre-calculation of the indices defining the processing order of cells. More...

void	calculateScheduleParallelSophisticatedHelper (int xStart, int yStart, int zStart)

void	calculateScheduleNaive ()

void	calculateScheduleParallelSophisticated ()

double	calcDistanceFromBoundary (Particle &p, Side side)
	Calculate the distance that a particle has to a specific side of the domain. In 2D the distance to sides top and bottom is always 0. More...

std::array< double, 3 >	calcGhostParticle (Particle &p, Side side)
	Calculate the position of the ghost particle with respect to a specific side used for reflective boundaries. More...

void	teleportParticlesToOppositeSideHelper (Side sideStart, int dimension, int modus)
	Moves particles along a certain dimension from the halo cells back into the simulation domain. More...

void	applyForceToOppositeCellsHelper (Side side, std::array< int, 3 > cellToProcess)
	Used for periodic boundaries to calculate the force that all particles from the opposite edge exert on the particles on the specified cell on the specified side. More...

void	applyForceToOppositeEdgeHelper (std::array< int, 3 > cellToProcess, std::array< int, 3 > offsetCell, std::array< double, 3 > offsetPosition, int dim)
	Used for periodic boundaries to calculate the force that all particles from the opposite edge exert on the particles of the specified cell. More...

bool	isCellInDomain (std::array< int, 3 > cell) const
	Checks, if the specified cell is part of the domain. More...

bool	isParticleInDomain (const std::array< double, 3 > &position) const
	Checks, if the specified particle is inside the domain. More...

void	applyForcesBetweenTwoCells (int cellTarget, int cellSource, std::array< double, 3 > offsetSource)
	Calculates the forces that particles in the cell source apply to the particles in cell target. More...

Private Attributes
std::vector< std::vector< Particle > >	cells

size_t	currentSize

std::array< std::vector< int >, 6 >	haloCells

std::array< std::vector< int >, 6 >	boundaries

std::vector< std::vector< int > >	domainCellIterationScheme

std::vector< int >	scheduleParallelNaive

std::vector< int >	scheduleParallelSophisticated

int	nX

int	nY

int	nZ

int	baseY

int	baseZ

int	baseYDomain

int	baseZDomain

double	cellSizeX

double	cellSizeY

double	cellSizeZ

double	rCutOff

bool	twoD

std::array< double, 3 >	domainSize

outputWriter::VTKWriter	vtk_writer

LennardJonesForce	lJF

BoundarySet	boundariesSet

Detailed Description

Container to store the particles for simulation using the linked cells algorithm.

Constructor & Destructor Documentation

◆ LinkedCellsContainer()

LinkedCellsContainer::LinkedCellsContainer	(	std::array< double, 3 >	domainSize,
		double	rCutOff,
		BoundarySet	boundarySet
	)

Constructor of the LinkedCellsContainer class.

Constructor and methods

Parameters

domainSize	Size of the simulation domain. Syntax {x, y, z}. Front lower left corner is by definition (0,0,0).
rCutOff	The cut-off radius

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Member Function Documentation

◆ add()

void LinkedCellsContainer::add ( Particle & p )

overridevirtual

Add a particle to this container.

Parameters

p	Particle to be added.

If the simulation environment is 2D, only particles living in 2D space are accepted. Try adding particles living in 3D space to 2D simulation environment will lead to the termination of the program.

Implements ParticleContainer.

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◆ applyForcesBetweenTwoCells()

void LinkedCellsContainer::applyForcesBetweenTwoCells	(	int	cellTarget,
		int	cellSource,
		std::array< double, 3 >	offsetSource
	)

private

Calculates the forces that particles in the cell source apply to the particles in cell target.

Parameters

cellTarget	Index of the cell containing the particles to which the force is applied.
cellSource	Index of the cell containing the particles which exert the force.
offsetSource	Offset to move the particles of the cell source in the right position for force calculations.

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◆ applyForcesFromOppositeSide()

void LinkedCellsContainer::applyForcesFromOppositeSide ( Side side )

Used for periodic boundaries to calculate the force that all particles from the opposite edge exert on the particles on the specified cell on the specified side.

Parameters

side	Side on which the force is exerted.

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◆ applyForceToOppositeCellsHelper()

void LinkedCellsContainer::applyForceToOppositeCellsHelper	(	Side	side,
		std::array< int, 3 >	cellToProcess
	)

private

Used for periodic boundaries to calculate the force that all particles from the opposite edge exert on the particles on the specified cell on the specified side.

Parameters

side	Side on which the force is exerted.
cellToProcess	Specific cell of that side.

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◆ applyForceToOppositeEdgeHelper()

void LinkedCellsContainer::applyForceToOppositeEdgeHelper	(	std::array< int, 3 >	cellToProcess,
		std::array< int, 3 >	offsetCell,
		std::array< double, 3 >	offsetPosition,
		int	dim
	)

private

Used for periodic boundaries to calculate the force that all particles from the opposite edge exert on the particles of the specified cell.

Parameters

cellToProcess	Cell on which particles the force is exerted.
offsetCell	Offset to reach the cell of the opposite edge.
offsetPosition	Offset to move the particles of the opposite edge to the current edge for proper force calculation.
dim	Dimension in which the edge is living.

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◆ applyToAllBoundaryParticles()

void LinkedCellsContainer::applyToAllBoundaryParticles	(	const std::function< void(Particle &, std::array< double, 3 > &)> &	function,
		Side	boundary
	)

Iterate over all particles in the boundary cells of a specific side which have a distance to that side that is smaller or equal than the threshold.

Parameters

function	Lambda function that is applied to each particle fulfilling the requirements.
boundary	Side to which the boundary cells belong.

Additionally, the position of the corresponding ghost particle of each particle is calculated and passed in the lambda function as second input. This information makes the implementation of reflective boundaries a lot easier.

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◆ applyToAllUniquePairsInDomain()

void LinkedCellsContainer::applyToAllUniquePairsInDomain ( const std::function< void(Particle &, Particle &)> & function )

overridevirtual

Iterate over all unique pairs of particles being part of the simulation domain and apply a lambda function to them.

Parameters

function Lambda function that is applied to each unique pair of particles.

The purpose of this function is provide an easy way of calculating the force between all particles by using Newton's third law of motion.

Implements ParticleContainer.

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◆ applyToAllUniquePairsInDomainOptimized()

void LinkedCellsContainer::applyToAllUniquePairsInDomainOptimized ( const std::function< void(Particle &, Particle &, std::array< double, 3 >, double)> & function )

Implements the optimization we presented as our second idea. At the moment this is dead code, because we did not have time yet to make it compatible with our current program structure and only integrated it once when doing the time measurements.

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◆ applyToEachParticle()

void LinkedCellsContainer::applyToEachParticle ( const std::function< void(Particle &)> & function )

overridevirtual

Iterate over all particles in this container and apply a lambda function to them.

Parameters

function Lambda function that is applied to each particle.

Implements ParticleContainer.

◆ applyToEachParticleInDomain()

void LinkedCellsContainer::applyToEachParticleInDomain ( const std::function< void(Particle &)> & function )

overridevirtual

Iterate over all particles that are part of the domain and apply a lambda function to them.

Parameters

function Lambda function that is applied to each particle.

Implements ParticleContainer.

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◆ calcCellIndex()

int LinkedCellsContainer::calcCellIndex ( const std::array< double, 3 > & position )

Calculate the index of the cell to which a particle decided by its position belongs.

Parameters

position Position of the particle to calculate the cell index of.

Returns: Corresponding cell index.

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◆ calcDistanceFromBoundary()

double LinkedCellsContainer::calcDistanceFromBoundary	(	Particle &	p,
		Side	side
	)

private

Calculate the distance that a particle has to a specific side of the domain. In 2D the distance to sides top and bottom is always 0.

Parameters

p	Particle used for distance calculation
side	Side of the domain to which the distance is calculated

Returns: Distance of particle p to the specified side.

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◆ calcGhostParticle()

std::array< double, 3 > LinkedCellsContainer::calcGhostParticle	(	Particle &	p,
		Side	side
	)

private

Calculate the position of the ghost particle with respect to a specific side used for reflective boundaries.

Parameters

p	Particle to calculate the corresponding ghost particle of.
side	Side of the domain at which the particle is mirrored.

Returns: Position of the ghost particle.

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◆ calculateBoundaryCellIndices()

void LinkedCellsContainer::calculateBoundaryCellIndices ( )

private

Pre-calculation of all boundary cell indices.

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◆ calculateDomainCellsIterationScheme()

void LinkedCellsContainer::calculateDomainCellsIterationScheme ( )

private

Pre-calculation of the indices defining the processing order of cells.

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◆ calculateHaloCellIndices()

void LinkedCellsContainer::calculateHaloCellIndices ( )

private

Pre-calculation of all halo cell indices.

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◆ calculateScheduleNaive()

void LinkedCellsContainer::calculateScheduleNaive ( )

private

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◆ calculateScheduleParallelSophisticated()

void LinkedCellsContainer::calculateScheduleParallelSophisticated ( )

private

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◆ calculateScheduleParallelSophisticatedHelper()

void LinkedCellsContainer::calculateScheduleParallelSophisticatedHelper	(	int	xStart,
		int	yStart,
		int	zStart
	)

private

◆ clearHaloCells()

void LinkedCellsContainer::clearHaloCells ( Side side )

Delete all particles in all halo cells being part of a specific size.

Parameters

side	Side at which all halo cells are cleared.

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◆ fromHighToLow()

std::array< double, 3 > LinkedCellsContainer::fromHighToLow	(	const std::array< double, 3 > &	position,
		int	dimension
	)

Move a particle along a certain dimension that overflows the domain int that dimension to the opposite side of the domain in that dimension.

Parameters

position	Current position of the particle.
dimension	Dimension along the particle is moved.

Returns: New position.

◆ fromLowToHigh()

std::array< double, 3 > LinkedCellsContainer::fromLowToHigh	(	const std::array< double, 3 > &	position,
		int	dimension
	)

Move a particle along a certain dimension that underflows the domain int that dimension to the opposite side of the domain in that dimension.

Parameters

position	Current position of the particle.
dimension	Dimension along the particle is moved.

Returns: New position.

◆ getBoundaries()

std::array<std::vector<int>, 6>& LinkedCellsContainer::getBoundaries ( )

inline

◆ getCells()

std::vector<std::vector<Particle> >& LinkedCellsContainer::getCells ( )

inline

◆ getCellSizeX()

double LinkedCellsContainer::getCellSizeX ( ) const

inline

◆ getCellSizeY()

double LinkedCellsContainer::getCellSizeY ( ) const

inline

◆ getCellSizeZ()

double LinkedCellsContainer::getCellSizeZ ( ) const

inline

◆ getDomainCellIterationScheme()

std::vector<std::vector<int> >& LinkedCellsContainer::getDomainCellIterationScheme ( )

inline

◆ getDomainSize()

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

inline

◆ getHaloCells()

std::array<std::vector<int>, 6>& LinkedCellsContainer::getHaloCells ( )

inline

◆ getNX()

int LinkedCellsContainer::getNX ( ) const

inline

◆ getNY()

int LinkedCellsContainer::getNY ( ) const

inline

◆ getNZ()

int LinkedCellsContainer::getNZ ( ) const

inline

◆ getRCutOff()

double LinkedCellsContainer::getRCutOff ( ) const

inline

◆ isCellInDomain()

bool LinkedCellsContainer::isCellInDomain ( std::array< int, 3 > cell ) const

private

Checks, if the specified cell is part of the domain.

Parameters

cell	Cell to check.

Returns: True if cell is part of the domain, false otherwise.

◆ isParticleInDomain()

bool LinkedCellsContainer::isParticleInDomain ( const std::array< double, 3 > & position ) const

private

Checks, if the specified particle is inside the domain.

Parameters

position Position of the particle.

Returns: True if the particle is inside the domain, false otherwise.

◆ isTwoD()

bool LinkedCellsContainer::isTwoD ( ) const

inline

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◆ oneDToThreeD()

std::array< int, 3 > LinkedCellsContainer::oneDToThreeD ( int index ) const

Convert a one dimensional coordinate to three dimensional coordinates.

Parameters

index One dimensional coordinate

Returns: Corresponding coordinates in three dimensional space.

◆ size()

size_t LinkedCellsContainer::size ( ) const

overridevirtual

Get the number of particles stored in this container.

Returns: Number of particles stored in this container.

Implements ParticleContainer.

◆ teleportParticlesToOppositeSide()

void LinkedCellsContainer::teleportParticlesToOppositeSide ( Side sideStart )

Moves particles along a certain dimension from the halo cells back into the simulation domain.

Parameters

sideStart Side from which the particles will be teleported to the opposite side.

Only updates the cell of the particle, if the particle is back into the domain in all three dimensions.

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◆ teleportParticlesToOppositeSideHelper()

void LinkedCellsContainer::teleportParticlesToOppositeSideHelper	(	Side	sideStart,
		int	dimension,
		int	modus
	)

private

Moves particles along a certain dimension from the halo cells back into the simulation domain.

Parameters

sideStart	Side from which the particles will be teleported to the opposite side.
dimension	Dimension along which the particles are moved (x := 0, y := 1, z := 2)
modus	Specify if the particles are moved up or down along the dimension (down := 0, up := 1)

Only updates the cell of the particle, if the particle is back into the domain in all three dimensions.

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◆ threeDToOneD()

int LinkedCellsContainer::threeDToOneD	(	int	x,
		int	y,
		int	z
	)		const

Convert 3 dimensional coordinates to one dimensional coordinates.

Parameters

x	x coordinate
y	y coordinate
z	z coordinate

Returns: Corresponding coordinate in one dimensional space.

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◆ threeDToOneDDomain()

int LinkedCellsContainer::threeDToOneDDomain	(	int	x,
		int	y,
		int	z
	)		const

◆ updateCells()

void LinkedCellsContainer::updateCells ( )

Assign each particle to its correct cell after there positions have been changed.

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Member Data Documentation

◆ baseY

int LinkedCellsContainer::baseY

private

Number of cells in one row (nX many).

◆ baseYDomain

int LinkedCellsContainer::baseYDomain

private

Number of cells in one layer halo cells excluded (nX - 2 many).

◆ baseZ

int LinkedCellsContainer::baseZ

private

Number of cells in one layer (nX * nY many).

◆ baseZDomain

int LinkedCellsContainer::baseZDomain

private

Number of cells in one layer halo cells excluded ((nX - 2) * (nY - 2) many).

◆ boundaries

std::array<std::vector<int>, 6> LinkedCellsContainer::boundaries

private

The indices of all boundary cells belonging to one or more of the 6 sides

◆ boundariesSet

BoundarySet LinkedCellsContainer::boundariesSet

private

◆ cells

std::vector<std::vector<Particle> > LinkedCellsContainer::cells

private

We use an 1D vector to store the flattened 3D cell structure being an essential property of the linked cells algorithm. Each cell is represented itself by an 1D vector of particles.

◆ cellSizeX

double LinkedCellsContainer::cellSizeX

private

Size of each cell in dimension x.

◆ cellSizeY

double LinkedCellsContainer::cellSizeY

private

Size of each cell in dimension y.

◆ cellSizeZ

double LinkedCellsContainer::cellSizeZ

private

Size of each cell in dimension z.

◆ currentSize

size_t LinkedCellsContainer::currentSize

private

The current number of particles that is contained in this container is tracked by the attribute currentSize and kept up-to-date through every operation.

◆ domainCellIterationScheme

std::vector<std::vector<int> > LinkedCellsContainer::domainCellIterationScheme

private

The indices of the order in which all cells within the domain are processed to process each pair of particles only ones

◆ domainSize

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

private

Size of the domain {x, y , z}. The front lower left corner of the domain is set to (0,0,0) by definition.

◆ haloCells

std::array<std::vector<int>, 6> LinkedCellsContainer::haloCells

private

The indices of all halo cells belonging to one or more of the 6 sides,

◆ lJF

LennardJonesForce LinkedCellsContainer::lJF

private

◆ nX

int LinkedCellsContainer::nX

private

Number of cells in dimension x (halo cells inclusive).

◆ nY

int LinkedCellsContainer::nY

private

Number of cells in dimension y (halo cells inclusive).

◆ nZ

int LinkedCellsContainer::nZ

private

Number of cells in dimension z (halo cells inclusive).

◆ rCutOff

double LinkedCellsContainer::rCutOff

private

Cut-off radius.

◆ scheduleParallelNaive

std::vector<int> LinkedCellsContainer::scheduleParallelNaive

private

◆ scheduleParallelSophisticated

std::vector<int> LinkedCellsContainer::scheduleParallelSophisticated

private

◆ twoD

bool LinkedCellsContainer::twoD

private

Specifies, if the simulation only uses 2 of 3 dimensions. If this is the case, resources can be saved.

◆ vtk_writer

outputWriter::VTKWriter LinkedCellsContainer::vtk_writer

private

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

/home/runner/work/MolSim/MolSim/src/particleRepresentation/container/linkedCellsContainer/LinkedCellsContainer.h
/home/runner/work/MolSim/MolSim/src/particleRepresentation/container/linkedCellsContainer/LinkedCellsContainer.cpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ LinkedCellsContainer()

Member Function Documentation

◆ add()

◆ applyForcesBetweenTwoCells()

◆ applyForcesFromOppositeSide()

◆ applyForceToOppositeCellsHelper()

◆ applyForceToOppositeEdgeHelper()

◆ applyToAllBoundaryParticles()

◆ applyToAllUniquePairsInDomain()

◆ applyToAllUniquePairsInDomainOptimized()

◆ applyToEachParticle()

◆ applyToEachParticleInDomain()

◆ calcCellIndex()

◆ calcDistanceFromBoundary()

◆ calcGhostParticle()

◆ calculateBoundaryCellIndices()

◆ calculateDomainCellsIterationScheme()

◆ calculateHaloCellIndices()

◆ calculateScheduleNaive()

◆ calculateScheduleParallelSophisticated()

◆ calculateScheduleParallelSophisticatedHelper()

◆ clearHaloCells()

◆ fromHighToLow()

◆ fromLowToHigh()

◆ getBoundaries()

◆ getCells()

◆ getCellSizeX()

◆ getCellSizeY()

◆ getCellSizeZ()

◆ getDomainCellIterationScheme()

◆ getDomainSize()

◆ getHaloCells()

◆ getNX()

◆ getNY()

◆ getNZ()

◆ getRCutOff()

◆ isCellInDomain()

◆ isParticleInDomain()

◆ isTwoD()

◆ oneDToThreeD()

◆ size()

◆ teleportParticlesToOppositeSide()

◆ teleportParticlesToOppositeSideHelper()

◆ threeDToOneD()

◆ threeDToOneDDomain()

◆ updateCells()

Member Data Documentation

◆ baseY

◆ baseYDomain

◆ baseZ

◆ baseZDomain

◆ boundaries

◆ boundariesSet

◆ cells

◆ cellSizeX

◆ cellSizeY

◆ cellSizeZ

◆ currentSize

◆ domainCellIterationScheme

◆ domainSize

◆ haloCells

◆ lJF

◆ nX

◆ nY

◆ nZ

◆ rCutOff

◆ scheduleParallelNaive

◆ scheduleParallelSophisticated

◆ twoD

◆ vtk_writer