#include <MutableMesh.hpp>

Inheritance diagram for MutableMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MutableMesh< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	MutableMesh ()

	MutableMesh (std::vector< Node< SPACE_DIM > * > nodes)

virtual	~MutableMesh ()

void	Clear ()

unsigned	GetNumNodes () const

unsigned	GetNumElements () const

unsigned	GetNumBoundaryElements () const

void	RescaleMeshFromBoundaryNode (ChastePoint< 1 > updatedPoint, unsigned boundaryNodeIndex)

virtual unsigned	AddNode (Node< SPACE_DIM > *pNewNode)

unsigned	AddElement (Element< ELEMENT_DIM, SPACE_DIM > *pNewElement)

virtual void	SetNode (unsigned index, ChastePoint< SPACE_DIM > point, bool concreteMove=true)

void	MoveMergeNode (unsigned index, unsigned targetIndex, bool concreteMove=true)

virtual void	DeleteNode (unsigned index)

virtual void	DeleteElement (unsigned index)

void	DeleteNodePriorToReMesh (unsigned index)

unsigned	RefineElement (Element< ELEMENT_DIM, SPACE_DIM > *pElement, ChastePoint< SPACE_DIM > point)

void	DeleteBoundaryNodeAt (unsigned index)

void	ReIndex (NodeMap &map)

virtual void	ReMesh (NodeMap &map)

void	ReMesh ()

std::vector< c_vector< unsigned, 5 > >	SplitLongEdges (double cutoffLength)

c_vector< unsigned, 3 >	SplitEdge (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB)

bool	CheckIsVoronoi (double maxPenetration=0.0)

template<>
void	RescaleMeshFromBoundaryNode (ChastePoint< 1 > updatedPoint, unsigned boundaryNodeIndex)

Public Member Functions inherited from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
	TetrahedralMesh ()

void	ConstructFromMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)

void	ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)

bool	CheckIsConforming ()

double	GetVolume ()

double	GetSurfaceArea ()

void	RefreshMesh ()

void	PermuteNodes ()

void	PermuteNodes (const std::vector< unsigned > &perm)

unsigned	GetContainingElementIndexWithInitialGuess (const ChastePoint< SPACE_DIM > &rTestPoint, unsigned startingElementGuess, bool strict=false)

unsigned	GetNearestElementIndex (const ChastePoint< SPACE_DIM > &rTestPoint)

std::vector< unsigned >	GetContainingElementIndices (const ChastePoint< SPACE_DIM > &rTestPoint)

double	GetAngleBetweenNodes (unsigned indexA, unsigned indexB)

virtual void	RefreshJacobianCachedData ()

virtual void	GetJacobianForElement (unsigned elementIndex, c_matrix< double, SPACE_DIM, SPACE_DIM > &rJacobian, double &rJacobianDeterminant) const

virtual void	GetInverseJacobianForElement (unsigned elementIndex, c_matrix< double, SPACE_DIM, ELEMENT_DIM > &rJacobian, double &rJacobianDeterminant, c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian) const

virtual void	GetWeightedDirectionForElement (unsigned elementIndex, c_vector< double, SPACE_DIM > &rWeightedDirection, double &rJacobianDeterminant) const

virtual void	GetWeightedDirectionForBoundaryElement (unsigned elementIndex, c_vector< double, SPACE_DIM > &rWeightedDirection, double &rJacobianDeterminant) const

EdgeIterator	EdgesBegin ()

EdgeIterator	EdgesEnd ()

Public Member Functions inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
ElementIterator	GetElementIteratorBegin (bool skipDeletedElements=true)

ElementIterator	GetElementIteratorEnd ()

	AbstractTetrahedralMesh ()

virtual	~AbstractTetrahedralMesh ()

virtual unsigned	GetNumLocalElements () const

virtual unsigned	GetNumLocalBoundaryElements () const

unsigned	GetNumAllElements () const

unsigned	GetNumAllBoundaryElements () const

virtual unsigned	GetNumCableElements () const

virtual unsigned	GetNumVertices () const

virtual unsigned	GetMaximumNodeIndex ()

Element< ELEMENT_DIM, SPACE_DIM > *	GetElement (unsigned index) const

BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *	GetBoundaryElement (unsigned index) const

void	ConstructFromMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rOtherMesh)

BoundaryElementIterator	GetBoundaryElementIteratorBegin () const

BoundaryElementIterator	GetBoundaryElementIteratorEnd () const

void	CheckOutwardNormals ()

virtual void	ConstructLinearMesh (unsigned width)

virtual void	ConstructRectangularMesh (unsigned width, unsigned height, bool stagger=true)

virtual void	ConstructCuboid (unsigned width, unsigned height, unsigned depth)

void	ConstructRegularSlabMesh (double spaceStep, double width, double height=0, double depth=0)

void	ConstructRegularSlabMeshWithDimensionSplit (unsigned dimension, double spaceStep, double width, double height=0, double depth=0)

virtual bool	CalculateDesignatedOwnershipOfBoundaryElement (unsigned faceIndex)

virtual bool	CalculateDesignatedOwnershipOfElement (unsigned elementIndex)

unsigned	CalculateMaximumNodeConnectivityPerProcess () const

virtual void	GetHaloNodeIndices (std::vector< unsigned > &rHaloIndices) const

void	CalculateNodeExchange (std::vector< std::vector< unsigned > > &rNodesToSendPerProcess, std::vector< std::vector< unsigned > > &rNodesToReceivePerProcess)

virtual c_vector< double, 2 >	CalculateMinMaxEdgeLengths ()

unsigned	GetContainingElementIndex (const ChastePoint< SPACE_DIM > &rTestPoint, bool strict=false, std::set< unsigned > testElements=std::set< unsigned >(), bool onlyTryWithTestElements=false)

unsigned	GetNearestElementIndexFromTestElements (const ChastePoint< SPACE_DIM > &rTestPoint, std::set< unsigned > testElements)

Public Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
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 DistributedVectorFactory *	GetDistributedVectorFactory ()

virtual void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

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 ChasteCuboid< SPACE_DIM >	CalculateBoundingBox () 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	RotateX (const double theta)

void	RotateY (const double theta)

void	RotateZ (const double theta)

void	Rotate (double theta)

bool	IsMeshChanging () const

unsigned	CalculateMaximumContainingElementsPerProcess () const

void	SetMeshHasChangedSinceLoading ()

Protected Attributes
std::vector< unsigned >	mDeletedElementIndices

std::vector< unsigned >	mDeletedBoundaryElementIndices

std::vector< unsigned >	mDeletedNodeIndices

bool	mAddedNodes

Protected Attributes inherited from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
std::vector< c_vector< double, SPACE_DIM > >	mElementWeightedDirections

std::vector< c_matrix< double, SPACE_DIM, ELEMENT_DIM > >	mElementJacobians

std::vector< c_matrix< double, ELEMENT_DIM, SPACE_DIM > >	mElementInverseJacobians

std::vector< double >	mElementJacobianDeterminants

std::vector< c_vector< double, SPACE_DIM > >	mBoundaryElementWeightedDirections

std::vector< double >	mBoundaryElementJacobianDeterminants

Protected Attributes inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
bool	mMeshIsLinear

std::vector< Element< ELEMENT_DIM, SPACE_DIM > * >	mElements

std::vector< BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > * >	mBoundaryElements

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

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

DistributedVectorFactory *	mpDistributedVectorFactory

std::vector< unsigned >	mNodePermutation

std::string	mMeshFileBaseName

bool	mMeshChangesDuringSimulation

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

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

bool	CheckIsVoronoi (Element< ELEMENT_DIM, SPACE_DIM > *pElement, double maxPenetration)

Friends
class	boost::serialization::access

Additional Inherited Members
Public Types inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector< BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > * >::const_iterator	BoundaryElementIterator

Public Types inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector< Node< SPACE_DIM > * >::const_iterator	BoundaryNodeIterator

Protected Member Functions inherited from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
unsigned	SolveNodeMapping (unsigned index) const

unsigned	SolveElementMapping (unsigned index) const

unsigned	SolveBoundaryElementMapping (unsigned index) const

template<class MESHER_IO >
void	ExportToMesher (NodeMap &map, MESHER_IO &mesherInput, int *elementList=nullptr)

template<class MESHER_IO >
void	ImportFromMesher (MESHER_IO &mesherOutput, unsigned numberOfElements, int elementList, unsigned numberOfFaces, int faceList, int *edgeMarkerList)

void	InitialiseTriangulateIo (triangulateio &mesherIo)

void	FreeTriangulateIo (triangulateio &mesherIo)

Protected Member Functions inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
void	SetElementOwnerships ()

Protected Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
ChasteCuboid< SPACE_DIM >	CalculateBoundingBox (const std::vector< Node< SPACE_DIM > * > &rNodes) const

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MutableMesh< ELEMENT_DIM, SPACE_DIM >

A concrete mutable mesh class.

Definition at line 50 of file MutableMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh ( )

Constructor.

Definition at line 52 of file MutableMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh ( std::vector< Node< SPACE_DIM > * > nodes )

Constructor which takes in a vector of nodes.

Parameters

nodes a vector of nodes

Definition at line 59 of file MutableMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::mAddedNodes, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MutableMesh< ELEMENT_DIM, SPACE_DIM >::~MutableMesh ( )

virtual

Destructor.

Definition at line 74 of file MutableMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::Clear().

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddElement ( Element< ELEMENT_DIM, SPACE_DIM > * pNewElement )

Helper method to add an element to the mesh.

Parameters

pNewElement pointer to the new element object. The object will be updated with the index assigned to the element.

Returns: new element index

Definition at line 100 of file MutableMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and Element< ELEMENT_DIM, SPACE_DIM >::ResetIndex().

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode ( Node< SPACE_DIM > * pNewNode )

virtual

Add a node to the mesh.

NB. After calling this one or more times, you must then call ReMesh

Parameters

pNewNode pointer to the new node

Returns: the index of the new node in the mesh

Reimplemented in NodesOnlyMesh< SPACE_DIM >, NodesOnlyMesh< DIM >, and NodesOnlyMesh< 2 >.

Definition at line 80 of file MutableMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::mAddedNodes, MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and Node< SPACE_DIM >::SetIndex().

Referenced by Cylindrical2dMesh::AddNode(), Cylindrical2dMesh::CreateHaloNodes(), Cylindrical2dMesh::CreateMirrorNodes(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi	(	Element< ELEMENT_DIM, SPACE_DIM > *	pElement,
		double	maxPenetration
	)

private

Returns: true if the mesh is Voronoi local to the given element. Check whether any neighbouring node is inside the circumsphere of this element.

Parameters

pElement	pointer to an element
maxPenetration	is the maximum distance a node is allowed to be inside the circumsphere of the element, as a proportion of the circumsphere radius.

Definition at line 993 of file MutableMesh.cpp.

References Element< ELEMENT_DIM, SPACE_DIM >::CalculateCircumsphere(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementInverseJacobians, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobians, and Node< SPACE_DIM >::rGetContainingElementIndices().

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi ( double maxPenetration = 0.0 )

Returns: true if Voronoi. Checks the entire mesh element by element and checks whether any neighbouring node is inside the circumsphere of this element.

Parameters

maxPenetration is the maximum distance a node is allowed to be inside the circumsphere of an element that it is not a member of, as a proportion of the circumsphere radius.

Todo:: use ElementIterator here?

Definition at line 1078 of file MutableMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), EXPORT_TEMPLATE_CLASS_ALL_DIMS, and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::Clear ( )

virtual

Clear all the data in the mesh.

Reimplemented from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NodesOnlyMesh< DIM >, and NodesOnlyMesh< 2 >.

Definition at line 124 of file MutableMesh.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::mAddedNodes, MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedBoundaryElementIndices, MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, and MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices.

Referenced by NodesOnlyMesh< SPACE_DIM >::Clear(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::~MutableMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt ( unsigned index )

Remove a boundary node, and update all the appropriate data structures.

The deleted node is not removed from the list, merely marked as deleted, and can be reused when a new node is added to the mesh.

Any elements or boundary elements containing this node will be removed. The boundary nodes information will be updated with new boundary node(s). NB: New boundary elements WILL NOT be added.

Parameters

index The index of the node to remove.

Definition at line 515 of file MutableMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElement ( unsigned index )

virtual

Delete an element from the mesh. Any remaining nodes not connected to an element are also removed.

Parameters

index The index of the element to be deleted

Definition at line 267 of file MutableMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedBoundaryElementIndices, MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNode ( unsigned index )

virtual

Delete a node from the mesh by finding an appropriate neighbour node to merge it with.

Parameters

index is the index of the node to be deleted

Reimplemented in NodesOnlyMesh< SPACE_DIM >, NodesOnlyMesh< DIM >, and NodesOnlyMesh< 2 >.

Definition at line 231 of file MutableMesh.cpp.

References EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh ( unsigned index )

Mark a node as deleted. Note that this method DOES NOT deal with the associated elements and therefore should only be called immediately prior to a ReMesh() being called. (Thus saves work compared to DeleteNode() function and does not MoveMerge the node and elements).

Parameters

index The index of the node to delete

Definition at line 298 of file MutableMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by HoneycombMeshGenerator::GetCircularMesh(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells(), and NodeBasedCellPopulation< DIM >::RemoveDeadCells().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements ( ) const

virtual

Returns: the number of boundary elements that are actually in use.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 135 of file MutableMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, and MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedBoundaryElementIndices.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElement().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements ( ) const

virtual

Returns: the number of elements that are actually in use.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 141 of file MutableMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( ) const

virtual

Returns: the number of nodes that are actually in use.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NodesOnlyMesh< DIM >, and NodesOnlyMesh< 2 >.

Definition at line 147 of file MutableMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by HoneycombMeshGenerator::GetCellLocationIndices(), HoneycombMeshGenerator::GetCircularMesh(), MutableMesh< SPACE_DIM, SPACE_DIM >::load(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Load the mesh, along with attributes if saved nodes have attributes. Loading of attributes is covered in TestNodesOnlyMesh.

Parameters

archive	the archive to save to.
version	the version number.

Definition at line 93 of file MutableMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode	(	unsigned	index,
		unsigned	targetIndex,
		bool	concreteMove = `true`
	)

Move one node to another (i.e. merges the nodes), refreshing/deleting elements as appropriate.

Parameters

index	is the index of the node to be moved
targetIndex	is the index of the node to move to
concreteMove	can be set to false if you just want to check whether this will work (defaults to true). Set it to true if you're doing the merger for real, in order to do all the bookkeeping.

Definition at line 305 of file MutableMesh.cpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement	(	Element< ELEMENT_DIM, SPACE_DIM > *	pElement,
		ChastePoint< SPACE_DIM >	point
	)

Refine an element at a given point.

Parameters

pElement	pointer to the element
point	a point located in the element

Returns: index of the new node which has been created at the given location

Definition at line 459 of file MutableMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), EXCEPTION, Element< ELEMENT_DIM, SPACE_DIM >::IncludesPoint(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, ChastePoint< DIM >::rGetLocation(), and Element< ELEMENT_DIM, SPACE_DIM >::UpdateNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex ( NodeMap & map )

Re-index a mesh so that it has no deleted elements or nodes.

Parameters

map	is a NodeMap which associates the indices of nodes in the old mesh with indices of nodes in the new mesh. This should be created with the correct size (NumAllNodes)

Definition at line 564 of file MutableMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh ( NodeMap & map )

virtual

Re-mesh a mesh using triangle (via library calls) or tetgen

Parameters

map	is a NodeMap which associates the indices of nodes in the old mesh with indices of nodes in the new mesh. This should be created with the correct size (NumAllNodes)

Reimplemented in NodesOnlyMesh< SPACE_DIM >, NodesOnlyMesh< DIM >, NodesOnlyMesh< 2 >, and Cylindrical2dMesh.

Definition at line 676 of file MutableMesh.cpp.

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator::GetCircularMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh ( )

Alternative version of remesh which takes no parameters, i.e. does not require a NodeMap. It will create one and call the other ReMesh method. Note: inherited classes should overload ReMesh(NodeMap&)

Definition at line 809 of file MutableMesh.cpp.

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

Referenced by MutableMesh< SPACE_DIM, SPACE_DIM >::load(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), and Cylindrical2dMesh::ReMesh().

template<>

void MutableMesh< 1, 1 >::RescaleMeshFromBoundaryNode	(	ChastePoint< 1 >	updatedPoint,
		unsigned	boundaryNodeIndex
	)

The RescaleMeshFromBoundaryNode method is only defined for 1D meshes.

Parameters

updatedPoint	point determining the scale factor
boundaryNodeIndex	index of the boundary node

Definition at line 159 of file MutableMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::RescaleMeshFromBoundaryNode	(	ChastePoint< 1 >	updatedPoint,
		unsigned	boundaryNodeIndex
	)

Todo:: should unsigned GetNumBoundaryNodes() be overloaded too??

Rescale the mesh from a boundary node.

Parameters

updatedPoint	point determining the scale factor
boundaryNodeIndex	index of the boundary node

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const

inlineprivate

Save the mesh, along with attributes if nodes have attributes. Saving of attributes is covered in TestNodesOnlyMesh.

Parameters

archive	the archive to save to.
version	the version number.

Definition at line 62 of file MutableMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode	(	unsigned	index,
		ChastePoint< SPACE_DIM >	point,
		bool	concreteMove = `true`
	)

virtual

Move the node with a particular index to a new point in space and verifies that the signed areas of the supporting Elements are positive.

Parameters

index	is the index of the node to be moved
point	is the new target location of the node
concreteMove	is set to false if we want to skip the signed area tests (defaults to true)

Reimplemented in NodesOnlyMesh< SPACE_DIM >, NodesOnlyMesh< DIM >, and NodesOnlyMesh< 2 >.

Definition at line 174 of file MutableMesh.cpp.

References EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementWeightedDirections, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode(), and Cylindrical2dMesh::SetNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< unsigned, 3 > MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge	(	Node< SPACE_DIM > *	pNodeA,
		Node< SPACE_DIM > *	pNodeB
	)

Splits an edge in two and create all the relevant new elements and nodes

Parameters

pNodeA	first point defining the edge
pNodeB	second point defining the edge

Returns: the index of the new node

Definition at line 912 of file MutableMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), Node< SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetVectorFromAtoB(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, NEVER_REACHED, AbstractElement< ELEMENT_DIM, SPACE_DIM >::ReplaceNode(), Node< SPACE_DIM >::rGetContainingElementIndices(), Node< SPACE_DIM >::rGetLocation(), and UNSIGNED_UNSET.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitLongEdges().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< c_vector< unsigned, 5 > > MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitLongEdges ( double cutoffLength )

Find edges in the mesh longer than the given cutoff length and split them creating new elements as required.

Parameters

cutoffLength cutoff length for edge splitting

Returns: returns a vector of triples with pointers to the new node followed by pointers to the nodes defining the bisected edge.

Todo:: use iterators to tidy this up

Definition at line 816 of file MutableMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistanceBetweenNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), Node< SPACE_DIM >::GetIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 53 of file MutableMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableMesh< ELEMENT_DIM, SPACE_DIM >::mAddedNodes

protected

Whether any nodes have been added to the mesh.

Definition at line 151 of file MutableMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedBoundaryElementIndices

protected

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

Definition at line 142 of file MutableMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices

protected

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

Definition at line 136 of file MutableMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices

protected

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

Definition at line 148 of file MutableMesh.hpp.

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

mesh/src/common/MutableMesh.hpp
mesh/src/common/MutableMesh.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM> class MutableMesh< ELEMENT_DIM, SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class MutableMesh< ELEMENT_DIM, SPACE_DIM >