#include <PottsMesh.hpp>

Inheritance diagram for PottsMesh< DIM >:

Collaboration diagram for PottsMesh< DIM >:

Classes
class	PottsElementIterator

Public Member Functions
PottsElementIterator	GetElementIteratorBegin (bool skipDeletedElements=true)

PottsElementIterator	GetElementIteratorEnd ()

	PottsMesh (std::vector< Node< DIM > * > nodes, std::vector< PottsElement< DIM > * > pottsElements, std::vector< std::set< unsigned > > vonNeumannNeighbouringNodeIndices, std::vector< std::set< unsigned > > mooreNeighbouringNodeIndices)

	PottsMesh ()

virtual	~PottsMesh ()

virtual unsigned	GetNumNodes () const

virtual unsigned	GetNumElements () const

unsigned	GetNumAllElements () const

PottsElement< DIM > *	GetElement (unsigned index) const

virtual c_vector< double, DIM >	GetCentroidOfElement (unsigned index)

void	ConstructFromMeshReader (AbstractMeshReader< DIM, DIM > &rMeshReader)

virtual void	Clear ()

virtual double	GetVolumeOfElement (unsigned index)

virtual double	GetSurfaceAreaOfElement (unsigned index)

std::set< unsigned >	GetMooreNeighbouringNodeIndices (unsigned nodeIndex)

std::set< unsigned >	GetVonNeumannNeighbouringNodeIndices (unsigned nodeIndex)

void	DeleteNode (unsigned index)

void	DeleteElement (unsigned index)

void	RemoveDeletedElements ()

unsigned	DivideElement (PottsElement< DIM > *pElement, bool placeOriginalElementBelow=false)

unsigned	AddElement (PottsElement< DIM > *pNewElement)

std::set< unsigned >	GetNeighbouringElementIndices (unsigned elementIndex)

Public Member Functions inherited from AbstractMesh< DIM, DIM >
virtual ChasteCuboid< SPACE_DIM >	CalculateBoundingBox () const

NodeIterator	GetNodeIteratorBegin (bool skipDeletedNodes=true)

NodeIterator	GetNodeIteratorEnd ()

	AbstractMesh ()

virtual	~AbstractMesh ()

unsigned	GetNumBoundaryNodes () const

virtual unsigned	GetNumAllNodes () const

unsigned	GetNumNodeAttributes () const

Node< SPACE_DIM > *	GetNode (unsigned index) const

virtual Node< SPACE_DIM > *	GetNodeOrHaloNode (unsigned index) const

Node< SPACE_DIM > *	GetNodeFromPrePermutationIndex (unsigned index) const

virtual void	ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)

virtual DistributedVectorFactory *	GetDistributedVectorFactory ()

virtual void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

virtual void	PermuteNodes ()

BoundaryNodeIterator	GetBoundaryNodeIteratorBegin () const

BoundaryNodeIterator	GetBoundaryNodeIteratorEnd () const

std::string	GetMeshFileBaseName () const

bool	IsMeshOnDisk () const

const std::vector< unsigned > &	rGetNodePermutation () const

virtual c_vector< double, SPACE_DIM >	GetVectorFromAtoB (const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB)

double	GetDistanceBetweenNodes (unsigned indexA, unsigned indexB)

virtual double	GetWidth (const unsigned &rDimension) const

virtual unsigned	GetNearestNodeIndex (const ChastePoint< SPACE_DIM > &rTestPoint)

virtual void	Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)

virtual void	Translate (const c_vector< double, SPACE_DIM > &rDisplacement)

void	Translate (const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0)

virtual void	Rotate (c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix)

void	Rotate (c_vector< double, 3 > axis, double angle)

void	Rotate (double theta)

void	RotateX (const double theta)

void	RotateY (const double theta)

void	RotateZ (const double theta)

virtual void	RefreshMesh ()

bool	IsMeshChanging () const

unsigned	CalculateMaximumContainingElementsPerProcess () const

void	SetMeshHasChangedSinceLoading ()

Protected Member Functions
unsigned	SolveNodeMapping (unsigned index) const

unsigned	SolveElementMapping (unsigned index) const

unsigned	SolveBoundaryElementMapping (unsigned index) const

template<class Archive >
void	save (Archive &archive, const unsigned int version) const

template<class Archive >
void	load (Archive &archive, const unsigned int version)

Protected Member Functions inherited from AbstractMesh< DIM, DIM >
virtual void	SetElementOwnerships ()

ChasteCuboid< SPACE_DIM >	CalculateBoundingBox (const std::vector< Node< SPACE_DIM > * > &rNodes) const

Protected Attributes
std::vector< PottsElement< DIM > * >	mElements

std::vector< unsigned >	mDeletedElementIndices

std::vector< std::set< unsigned > >	mVonNeumannNeighbouringNodeIndices

std::vector< std::set< unsigned > >	mMooreNeighbouringNodeIndices

Protected Attributes inherited from AbstractMesh< DIM, DIM >
std::vector< Node< SPACE_DIM > * >	mNodes

std::vector< Node< SPACE_DIM > * >	mBoundaryNodes

DistributedVectorFactory *	mpDistributedVectorFactory

std::vector< unsigned >	mNodePermutation

std::string	mMeshFileBaseName

bool	mMeshChangesDuringSimulation

Friends
class	TestPottsMesh

class	boost::serialization::access

Additional Inherited Members
Public Types inherited from AbstractMesh< DIM, DIM >
typedef std::vector< Node < SPACE_DIM > * >::const_iterator	BoundaryNodeIterator

Detailed Description

template<unsigned DIM>
class PottsMesh< DIM >

A Potts-based mesh class, for use in Cellular Potts model simulations.

Definition at line 63 of file PottsMesh.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

PottsMesh< DIM >::PottsMesh	(	std::vector< Node< DIM > * >	nodes,
		std::vector< PottsElement< DIM > * >	pottsElements,
		std::vector< std::set< unsigned > >	vonNeumannNeighbouringNodeIndices,
		std::vector< std::set< unsigned > >	mooreNeighbouringNodeIndices
	)

Default constructor.

Parameters

nodes	vector of pointers to nodes
pottsElements	vector of pointers to PottsElements
vonNeumannNeighbouringNodeIndices	vector of set of Moore neighbours for each node
mooreNeighbouringNodeIndices	vector of set of Von Neumann neighbours for each node

Definition at line 41 of file PottsMesh.cpp.

References EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

PottsMesh< DIM >::PottsMesh ( )

Default constructor for use by serializer.

Definition at line 87 of file PottsMesh.cpp.

template<unsigned DIM>

PottsMesh< DIM >::~PottsMesh ( )

virtual

Destructor.

Definition at line 94 of file PottsMesh.cpp.

Member Function Documentation

template<unsigned DIM>

unsigned PottsMesh< DIM >::AddElement ( PottsElement< DIM > * pNewElement )

Add an element to the mesh.

Parameters

pNewElement the new element

Returns: the index of the new element in the mesh

Definition at line 513 of file PottsMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), and MutableElement< DIM, DIM >::RegisterWithNodes().

template<unsigned DIM>

void PottsMesh< DIM >::Clear ( )

virtual

Delete mNodes and mElements.

Definition at line 120 of file PottsMesh.cpp.

template<unsigned DIM>

void PottsMesh< DIM >::ConstructFromMeshReader ( AbstractMeshReader< DIM, DIM > & rMeshReader )

Construct the mesh using a MeshReader.

Parameters

rMeshReader the mesh reader

Definition at line 574 of file PottsMesh.cpp.

Referenced by PottsMesh< SPACE_DIM >::load().

template<unsigned DIM>

void PottsMesh< DIM >::DeleteElement ( unsigned index )

Mark an element as deleted. Note that in a Potts mesh this does not delete the nodes so no remeshing is required.

Parameters

index the global index of a specified Potts element

Definition at line 245 of file PottsMesh.cpp.

template<unsigned DIM>

void PottsMesh< DIM >::DeleteNode ( unsigned index )

Mark a node as deleted. Note that in a Potts mesh this requires the elements and connectivity to be updated accordingley.

Parameters

index the global index of a specified node

Definition at line 272 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::DivideElement	(	PottsElement< DIM > *	pElement,
		bool	placeOriginalElementBelow = `false`
	)

Divide an element by assigning half the nodes to each new element in numerical order. If an odd number of nodes then the existing element has one more node than the new element.

Parameters

pElement	the element to divide
placeOriginalElementBelow	whether to place the original element below (in the y direction) the new element (defaults to false)

Returns: the index of the new element

Not implemented in 1d

Remove the correct nodes from each element. If placeOriginalElementBelow is true, place the original element below (in the y direction or z in 3d) the new element; otherwise, place it above.

Todo:: this could be more efficient

Definition at line 386 of file PottsMesh.cpp.

References MutableElement< DIM, DIM >::DeleteNode(), EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

c_vector< double, DIM > PottsMesh< DIM >::GetCentroidOfElement ( unsigned index )

virtual

Compute the centroid of an element.

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters

index the global index of a specified vertex element

Returns: (centroid_x,centroid_y).

Todo:: This should probably be returning the nearest node

Definition at line 169 of file PottsMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeLocation(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

PottsElement< DIM > * PottsMesh< DIM >::GetElement ( unsigned index ) const

Parameters

index the global index of a specified PottsElement.

Returns: a pointer to the PottsElement

Definition at line 162 of file PottsMesh.cpp.

template<unsigned DIM>

PottsMesh< DIM >::PottsElementIterator PottsMesh< DIM >::GetElementIteratorBegin ( bool skipDeletedElements = true )

inline

Returns: an iterator to the first element in the mesh.

Parameters

skipDeletedElements whether to include deleted element

Definition at line 422 of file PottsMesh.hpp.

template<unsigned DIM>

PottsMesh< DIM >::PottsElementIterator PottsMesh< DIM >::GetElementIteratorEnd ( )

inline

Returns: an iterator to one past the last element in the mesh.

Definition at line 429 of file PottsMesh.hpp.

template<unsigned DIM>

std::set< unsigned > PottsMesh< DIM >::GetMooreNeighbouringNodeIndices ( unsigned nodeIndex )

Given a node, return a set containing the indices of its Moore neighbouring nodes.

Parameters

nodeIndex global index of the node

Returns: neighbouring node indices in Moore neighbourhood

Definition at line 233 of file PottsMesh.cpp.

Referenced by ExclusionCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), ShovingCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), CaBasedCellPopulation< DIM >::GetNeighbouringLocationIndices(), ExclusionCaBasedDivisionRule< SPACE_DIM >::IsRoomToDivide(), and CaBasedCellPopulation< DIM >::UpdateCellLocations().

template<unsigned DIM>

std::set< unsigned > PottsMesh< DIM >::GetNeighbouringElementIndices ( unsigned elementIndex )

Given an element, find a set containing the indices of its neighbouring elements.

Parameters

elementIndex global index of the element

Returns: its neighbouring element indices

Definition at line 530 of file PottsMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

unsigned PottsMesh< DIM >::GetNumAllElements ( ) const

Returns: the number of PottsElements in the mesh, including those marked as deleted.

Definition at line 156 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::GetNumElements ( ) const

virtual

Returns: the number of PottsElements in the mesh.

Definition at line 150 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::GetNumNodes ( ) const

virtual

Returns: the number of Nodes in the mesh.

Reimplemented from AbstractMesh< DIM, DIM >.

Definition at line 144 of file PottsMesh.cpp.

Referenced by PottsMeshWriter< DIM >::WriteFilesUsingMesh().

template<unsigned DIM>

double PottsMesh< DIM >::GetSurfaceAreaOfElement ( unsigned index )

virtual

Compute the surface area (or perimeter in 2D) of a PottsElement.

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters

index the global index of a specified PottsElement

Returns: the surface area of the element

Todo:: not implemented in 3d yet

Definition at line 198 of file PottsMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

double PottsMesh< DIM >::GetVolumeOfElement ( unsigned index )

virtual

Get the volume (or area in 2D, or length in 1D) of a PottsElement.

This needs to be overridden in daughter classes for non-Euclidean metrics.

Parameters

index the global index of a specified PottsElement element

Returns: the volume of the element

Definition at line 189 of file PottsMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes().

template<unsigned DIM>

std::set< unsigned > PottsMesh< DIM >::GetVonNeumannNeighbouringNodeIndices ( unsigned nodeIndex )

Given a node, return a set containing the indices of its Von Neumann neighbouring nodes.

Parameters

nodeIndex global index of the node

Returns: neighbouring node indices in Von Neumann neighbourhood

Definition at line 239 of file PottsMesh.cpp.

Referenced by CryptShovingCaBasedDivisionRule::CalculateDaughterNodeIndex(), and CryptShovingCaBasedDivisionRule::IsNodeOnBase().

template<unsigned DIM>

template<class Archive >

void PottsMesh< DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)

inlineprotected

Loads a mesh by using PottsMeshReader and the location in ArchiveLocationInfo.

Parameters

archive	the archive
version	the current version of this class

Definition at line 143 of file PottsMesh.hpp.

template<unsigned DIM>

void PottsMesh< DIM >::RemoveDeletedElements ( )

Remove deleted elements and reorder them appropriately

Definition at line 253 of file PottsMesh.cpp.

template<unsigned DIM>

template<class Archive >

void PottsMesh< DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const

inlineprotected

Archive the PottsMesh and its member variables. Note that this will write out a PottsMeshWriter file to wherever ArchiveLocationInfo has specified.

Parameters

archive	the archive
version	the current version of this class

Definition at line 121 of file PottsMesh.hpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::SolveBoundaryElementMapping ( unsigned index ) const

protected

Solve boundary element mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters

index the global index of the boundary element

Returns: local index

Definition at line 114 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::SolveElementMapping ( unsigned index ) const

protected

Solve element mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters

index the global index of the element

Returns: local index

Definition at line 107 of file PottsMesh.cpp.

template<unsigned DIM>

unsigned PottsMesh< DIM >::SolveNodeMapping ( unsigned index ) const

protectedvirtual

Solve node mapping method. This overridden method is required as it is pure virtual in the base class.

Parameters

index the global index of the node

Returns: local index

Implements AbstractMesh< DIM, DIM >.

Definition at line 100 of file PottsMesh.cpp.

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 111 of file PottsMesh.hpp.

Member Data Documentation

template<unsigned DIM>

std::vector<unsigned> PottsMesh< DIM >::mDeletedElementIndices

protected

Indices of elements that have been marked as deleted. These indices can be reused when adding new elements.

Definition at line 75 of file PottsMesh.hpp.

Referenced by PottsMesh< SPACE_DIM >::load(), and PottsMesh< SPACE_DIM >::save().

template<unsigned DIM>

std::vector<PottsElement<DIM>*> PottsMesh< DIM >::mElements

protected

Vector of pointers to PottsElements.

Definition at line 69 of file PottsMesh.hpp.

template<unsigned DIM>

std::vector< std::set<unsigned> > PottsMesh< DIM >::mMooreNeighbouringNodeIndices

protected

Vector of set of Moore neighbours for each node.

Definition at line 81 of file PottsMesh.hpp.

Referenced by PottsMesh< SPACE_DIM >::load(), and PottsMesh< SPACE_DIM >::save().

template<unsigned DIM>

std::vector< std::set<unsigned> > PottsMesh< DIM >::mVonNeumannNeighbouringNodeIndices

protected

Vector of set of Von Neumann neighbours for each node.

Definition at line 78 of file PottsMesh.hpp.

Referenced by PottsMesh< SPACE_DIM >::load(), and PottsMesh< SPACE_DIM >::save().

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

cell_based/src/mesh/PottsMesh.hpp
cell_based/src/mesh/PottsMesh.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned DIM> class PottsMesh< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class PottsMesh< DIM >