#include <ObsoleteBoxCollection.hpp>

Collaboration diagram for ObsoleteBoxCollection< DIM >:

Public Member Functions
	ObsoleteBoxCollection (double boxWidth, c_vector< double, 2 *DIM > domainSize, bool isPeriodicInX=false, bool isPeriodicInY=false, bool isPeriodicInZ=false)

void	EmptyBoxes ()

unsigned	CalculateContainingBox (Node< DIM > *pNode)

unsigned	CalculateContainingBox (c_vector< double, DIM > &rLocation)

Box< DIM > &	rGetBox (unsigned boxIndex)

unsigned	GetNumBoxes ()

void	SetupLocalBoxesHalfOnly ()

void	SetupAllLocalBoxes ()

std::set< unsigned > &	rGetLocalBoxes (unsigned boxIndex)

const c_vector< double, 2 *DIM > &	rGetDomainSize () const

void	CalculateNodePairs (std::vector< Node< DIM > * > &rNodes, std::vector< std::pair< Node< DIM > , Node< DIM > > > &rNodePairs)

bool	IsOwned (Node< DIM > *pNode)

bool	IsBoxOwned (unsigned globalIndex)

Private Member Functions
unsigned	GetLinearIndex (c_vector< int, DIM > gridIndices)

c_vector< unsigned, DIM >	GetGridIndices (unsigned linearIndex)

bool	IsBoxInDomain (c_vector< unsigned, DIM > gridIndices)

c_vector< bool, DIM >	IsIndexPenultimate (c_vector< unsigned, DIM > gridIndices)

void	SetupLocalBoxes (const std::vector< c_vector< int, DIM > > &rNeighbours)

Private Attributes
std::vector< Box< DIM > >	mBoxes

c_vector< double, 2 *DIM >	mDomainSize

double	mBoxWidth

c_vector< unsigned, DIM >	mNumBoxesEachDirection

std::vector< std::set< unsigned > >	mLocalBoxes

c_vector< bool, DIM >	mIsDomainPeriodic

Static Private Attributes
static const double	msFudge = 5e-14

Friends
class	TestObsoleteBoxCollection

Detailed Description

template<unsigned DIM>
class ObsoleteBoxCollection< DIM >

A collection of 'boxes' partitioning the domain with information on which nodes are located in which box Not archived - in cell_based constructed in NodeBasedCellPopulation constructor.

This is to be merged with DistributedBoxCollection.

Definition at line 52 of file ObsoleteBoxCollection.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

ObsoleteBoxCollection< DIM >::ObsoleteBoxCollection	(	double	boxWidth,
		c_vector< double, 2 *DIM >	domainSize,
		bool	isPeriodicInX = `false`,
		bool	isPeriodicInY = `false`,
		bool	isPeriodicInZ = `false`
	)

Constructor.

Parameters

boxWidth	the width of each box (cut-off length in NodeBasedCellPopulation simulations)
domainSize	the size of the domain, in the form (xmin, xmax, ymin, ymax) (etc)
isPeriodicInX	whether the domain is periodic in the x direction
isPeriodicInY	whether the domain is periodic in the y direction
isPeriodicInZ	whether the domain is periodic in the z direction

Todo:: #2725 example: domain width of 1.0 and box width of 0.25, the following line will create 5 boxes not 4

Definition at line 48 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mBoxes, ObsoleteBoxCollection< DIM >::mIsDomainPeriodic, ObsoleteBoxCollection< DIM >::mNumBoxesEachDirection, ObsoleteBoxCollection< DIM >::msFudge, and NEVER_REACHED.

Member Function Documentation

template<unsigned DIM>

unsigned ObsoleteBoxCollection< DIM >::CalculateContainingBox ( Node< DIM > * pNode )

Returns: the index of the box this node is contained in.

Parameters

pNode address of the node

Definition at line 104 of file ObsoleteBoxCollection.cpp.

References Node< SPACE_DIM >::rGetLocation().

Referenced by ObsoleteBoxCollection< DIM >::CalculateNodePairs().

template<unsigned DIM>

unsigned ObsoleteBoxCollection< DIM >::CalculateContainingBox ( c_vector< double, DIM > & rLocation )

Returns: the index of the box a point is contained in

Parameters

rLocation The point

Definition at line 112 of file ObsoleteBoxCollection.cpp.

References EXCEPTION, ObsoleteBoxCollection< DIM >::GetLinearIndex(), ObsoleteBoxCollection< DIM >::mBoxWidth, ObsoleteBoxCollection< DIM >::mDomainSize, and ObsoleteBoxCollection< DIM >::msFudge.

template<unsigned DIM>

void ObsoleteBoxCollection< DIM >::CalculateNodePairs	(	std::vector< Node< DIM > * > &	rNodes,
		std::vector< std::pair< Node< DIM > , Node< DIM > > > &	rNodePairs
	)

Compute all the pairs of (potentially) connected nodes for cell_based simulations, ie nodes which are in a local box to the box containing the first node. **Note: the user still has to check that the node pairs are less than the cut-off distance apart.** The pairs are checked so that index1 < index2, so each connected pair of nodes is only in the set once.

Parameters

rNodes	all the nodes to be considered
rNodePairs	the return value, a set of pairs of nodes

Definition at line 634 of file ObsoleteBoxCollection.cpp.

References Node< SPACE_DIM >::AddNeighbour(), ObsoleteBoxCollection< DIM >::CalculateContainingBox(), ObsoleteBoxCollection< DIM >::EmptyBoxes(), Node< SPACE_DIM >::GetIndex(), ObsoleteBoxCollection< DIM >::mBoxes, and ObsoleteBoxCollection< DIM >::rGetLocalBoxes().

template<unsigned DIM>

void ObsoleteBoxCollection< DIM >::EmptyBoxes ( )

Remove the list of nodes stored in each box.

Definition at line 95 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mBoxes.

Referenced by ObsoleteBoxCollection< DIM >::CalculateNodePairs().

template<unsigned DIM>

c_vector< unsigned, DIM > ObsoleteBoxCollection< DIM >::GetGridIndices ( unsigned linearIndex )

private

Parameters

linearIndex the linear index in row-major form

Returns: the grid indices (i), (i,j), or (i,j,k) depending on DIM

Definition at line 211 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mNumBoxesEachDirection, and NEVER_REACHED.

Referenced by ObsoleteBoxCollection< DIM >::SetupLocalBoxes().

template<unsigned DIM>

unsigned ObsoleteBoxCollection< DIM >::GetLinearIndex ( c_vector< int, DIM > gridIndices )

private

Parameters

gridIndices the grid indices (i), (i,j), or (i,j,k) depending on DIM

Returns: the linear index in row-major form

Definition at line 151 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mIsDomainPeriodic, ObsoleteBoxCollection< DIM >::mNumBoxesEachDirection, and NEVER_REACHED.

Referenced by ObsoleteBoxCollection< DIM >::CalculateContainingBox(), and ObsoleteBoxCollection< DIM >::SetupLocalBoxes().

template<unsigned DIM>

unsigned ObsoleteBoxCollection< DIM >::GetNumBoxes ( )

Returns: the total (global) number of boxes.

Definition at line 145 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mBoxes.

template<unsigned DIM>

bool ObsoleteBoxCollection< DIM >::IsBoxInDomain ( c_vector< unsigned, DIM > gridIndices )

private

Parameters

gridIndices the coordinates (i), (i,j), or (i,j,k) depending on DIM

Returns: whether the box is in the domain

Definition at line 248 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mIsDomainPeriodic, and ObsoleteBoxCollection< DIM >::mNumBoxesEachDirection.

Referenced by ObsoleteBoxCollection< DIM >::SetupLocalBoxes().

template<unsigned DIM>

bool ObsoleteBoxCollection< DIM >::IsBoxOwned ( unsigned globalIndex )

inline

Helper function for transition to distributed version of box collection.

This method allows us to insert of dummy test for whether a box/point/node/location is located on the local process.

Parameters

globalIndex the global index of the box.

Returns: true (whether the point at pNode->rGetLocation() is owned on this process)

Definition at line 224 of file ObsoleteBoxCollection.hpp.

template<unsigned DIM>

c_vector< bool, DIM > ObsoleteBoxCollection< DIM >::IsIndexPenultimate ( c_vector< unsigned, DIM > gridIndices )

private

This method is used for periodicity. It is necessary to consider additional boxes as being local to a candidate box if and only if the candidate box is in the penultimate location of any dimension.

Parameters

gridIndices the coordinates (i), (i,j), or (i,j,k) depending on DIM

Returns: whether the box is in the penultimate location in each dimension

Definition at line 276 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mNumBoxesEachDirection.

Referenced by ObsoleteBoxCollection< DIM >::SetupLocalBoxes().

template<unsigned DIM>

bool ObsoleteBoxCollection< DIM >::IsOwned ( Node< DIM > * pNode )

inline

Helper function for transition to distributed version of box collection.

This method allows us to insert of dummy test for whether a box/point/node/location is located on the local process.

Parameters

pNode the node to test.

Returns: true (whether the point at pNode->rGetLocation() is owned on this process)

Definition at line 211 of file ObsoleteBoxCollection.hpp.

template<unsigned DIM>

Box< DIM > & ObsoleteBoxCollection< DIM >::rGetBox ( unsigned boxIndex )

Parameters

boxIndex the index of the box to return

Returns: a reference to the box with global index boxIndex.

Definition at line 138 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mBoxes.

template<unsigned DIM>

const c_vector< double, 2 *DIM > & ObsoleteBoxCollection< DIM >::rGetDomainSize ( ) const

Return the size of the domain partitioned by this collection

Returns: the vector of the domain edges (xmin, xmax etc).

Definition at line 628 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mDomainSize.

template<unsigned DIM>

std::set< unsigned > & ObsoleteBoxCollection< DIM >::rGetLocalBoxes ( unsigned boxIndex )

Get the set of all the local boxes, i.e. itself and its nearest-neighbours.

Parameters

boxIndex the index of the box

Returns: the set containing the indices of boxes local to box boxIndex. i.e. the box boxIndex itself and its nearest-neighbours.

Definition at line 621 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::mLocalBoxes.

Referenced by ObsoleteBoxCollection< DIM >::CalculateNodePairs().

template<unsigned DIM>

void ObsoleteBoxCollection< DIM >::SetupAllLocalBoxes ( )

Generates a list of vectors representing all the possible neighbour locations in DIM-dimensions, and calls SetupLocalBoxes().

Definition at line 384 of file ObsoleteBoxCollection.cpp.

References NEVER_REACHED, and ObsoleteBoxCollection< DIM >::SetupLocalBoxes().

template<unsigned DIM>

void ObsoleteBoxCollection< DIM >::SetupLocalBoxes ( const std::vector< c_vector< int, DIM > > & rNeighbours )

private

Helper function for SetupLocalBoxesHalfOnly() and SetupAllLocalBoxes().

Accepts a vector of neighbours that should be considered for each box and populates mLocalBoxes based on these neighbours. The set of neighbours is either half or all of the neighbours, depending on the function calling this method.

Parameters

rNeighbours a vector of neighbours

Definition at line 459 of file ObsoleteBoxCollection.cpp.

References ObsoleteBoxCollection< DIM >::GetGridIndices(), ObsoleteBoxCollection< DIM >::GetLinearIndex(), ObsoleteBoxCollection< DIM >::IsBoxInDomain(), ObsoleteBoxCollection< DIM >::IsIndexPenultimate(), ObsoleteBoxCollection< DIM >::mBoxes, ObsoleteBoxCollection< DIM >::mIsDomainPeriodic, ObsoleteBoxCollection< DIM >::mLocalBoxes, and NEVER_REACHED.

Referenced by ObsoleteBoxCollection< DIM >::SetupAllLocalBoxes(), and ObsoleteBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned DIM>

void ObsoleteBoxCollection< DIM >::SetupLocalBoxesHalfOnly ( )

Generates a list of vectors representing half the possible neighbour locations in DIM-dimensions ({0} and {1} in 1D, rather than {-1}, {0}, {1}), and similar in higher dimensions, and calls SetupLocalBoxes().

Definition at line 289 of file ObsoleteBoxCollection.cpp.

References NEVER_REACHED, and ObsoleteBoxCollection< DIM >::SetupLocalBoxes().