#include <Toroidal2dMesh.hpp>

Inheritance diagram for Toroidal2dMesh:

Collaboration diagram for Toroidal2dMesh:

Public Member Functions
	Toroidal2dMesh (double width, double depth)

	Toroidal2dMesh (double width, double depth, std::vector< Node< 2 > * > nodes)

	~Toroidal2dMesh ()

void	ReMesh (NodeMap &rMap)

c_vector< double, 2 >	GetVectorFromAtoB (const c_vector< double, 2 > &rLocation1, const c_vector< double, 2 > &rLocation2)

void	SetNode (unsigned index, ChastePoint< 2 > point, bool concreteMove)

double	GetWidth (const unsigned &rDimension) const

unsigned	AddNode (Node< 2 > *pNewNode)

bool	GetInstanceOfMismatchedBoundaryNodes ()

void	RefreshMesh ()

Public Member Functions inherited from MutableMesh< 2, 2 >
bool	CheckIsVoronoi (double maxPenetration=0.0)

	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)

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)

void	ReMesh ()

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

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

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	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 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 ()

Private Member Functions
void	CreateMirrorNodes ()

void	ReconstructCylindricalMesh ()

void	ReconstructToroidalMesh ()

void	CorrectCylindricalNonPeriodicMesh ()

void	CorrectToroidalNonPeriodicMesh ()

void	GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries ()

void	GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries ()

unsigned	GetCorrespondingCylindricalNodeIndex (unsigned nodeIndex)

unsigned	GetCorrespondingToroidalNodeIndex (unsigned nodeIndex)

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

Private Attributes
double	mWidth

double	mHeight

std::vector< unsigned >	mLeftOriginals

std::vector< unsigned >	mLeftImages

std::map< unsigned, unsigned >	mImageToLeftOriginalNodeMap

std::vector< unsigned >	mRightOriginals

std::vector< unsigned >	mRightImages

std::map< unsigned, unsigned >	mImageToRightOriginalNodeMap

std::set< unsigned >	mLeftPeriodicBoundaryElementIndices

std::set< unsigned >	mRightPeriodicBoundaryElementIndices

std::vector< unsigned >	mBottomOriginals

std::vector< unsigned >	mBottomImages

std::map< unsigned, unsigned >	mImageToBottomOriginalNodeMap

std::vector< unsigned >	mTopOriginals

std::vector< unsigned >	mTopImages

std::map< unsigned, unsigned >	mImageToTopOriginalNodeMap

std::set< unsigned >	mBottomPeriodicBoundaryElementIndices

std::set< unsigned >	mTopPeriodicBoundaryElementIndices

bool	mMismatchedBoundaryElements

Friends
class	TestToroidal2dMesh

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

Protected Attributes inherited from MutableMesh< 2, 2 >
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

Detailed Description

A subclass of MutableMesh<2,2> for a rectangular mesh with periodic left and right boundaries, representing a Toroidal geometry.

The class works by overriding calls such as ReMesh() and GetVectorFromAtoB() so that simulation classes can treat this class in exactly the same way as a MutableMesh<2,2>.

Definition at line 55 of file Toroidal2dMesh.hpp.

Constructor & Destructor Documentation

◆ Toroidal2dMesh() [1/2]

Toroidal2dMesh::Toroidal2dMesh	(	double	width,
		double	depth
	)

Con+structor.

Parameters

width	the periodic width of the mesh
depth	the periodic depth of the mesh

Definition at line 47 of file Toroidal2dMesh.cpp.

◆ Toroidal2dMesh() [2/2]

Toroidal2dMesh::Toroidal2dMesh	(	double	width,
		double	depth,
		std::vector< Node< 2 > * >	nodes
	)

A constructor which reads in a width and collection of nodes, then calls a ReMesh() command to create the elements of the mesh.

Parameters

width	the periodic width of the mesh
depth	the periodic depth of the mesh
nodes	a collection of nodes to construct the mesh with

Definition at line 60 of file Toroidal2dMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, MutableMesh< 2, 2 >::ReMesh(), Node< SPACE_DIM >::rGetLocation(), and UNUSED_OPT.

◆ ~Toroidal2dMesh()

Toroidal2dMesh::~Toroidal2dMesh ( )

Destructor.

Definition at line 56 of file Toroidal2dMesh.cpp.

Member Function Documentation

◆ AddNode()

unsigned Toroidal2dMesh::AddNode ( Node< 2 > * pNewNode )

Overridden AddNode() method.

Parameters

pNewNode the node to be added to the mesh

Returns: the global index of the new node

Definition at line 800 of file Toroidal2dMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), Node< SPACE_DIM >::GetPoint(), and SetNode().

◆ CorrectCylindricalNonPeriodicMesh()

void Toroidal2dMesh::CorrectCylindricalNonPeriodicMesh ( )

private

This method should only ever be called by the public ReMesh() method.

Uses mLeftPeriodicBoundaryElementIndices and mRightPeriodicBoundaryElementIndices and compares the nodes in each to ensure that both boundaries have been meshed identically. If they have not it calls UseTheseElementsToDecideMeshing() to sort out the troublesome elements which have been meshed differently on each side and uses the meshing of the elements on the right hand boundary to decide on how to mesh the left hand side.

Definition at line 811 of file Toroidal2dMesh.cpp.

References GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries(), GetCorrespondingCylindricalNodeIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), mLeftPeriodicBoundaryElementIndices, mRightPeriodicBoundaryElementIndices, and NEVER_REACHED.

Referenced by ReMesh().

◆ CorrectToroidalNonPeriodicMesh()

void Toroidal2dMesh::CorrectToroidalNonPeriodicMesh ( )

private

This method should only ever be called by the public ReMesh() method.

Uses mLeftPeriodicBoundaryElementIndices and mRightPeriodicBoundaryElementIndices and compares the nodes in each to ensure that both boundaries have been meshed identically. If they have not it calls UseTheseElementsToDecideMeshing() to sort out the troublesome elements which have been meshed differently on each side and uses the meshing of the elements on the right hand boundary to decide on how to mesh the left hand side.

Definition at line 917 of file Toroidal2dMesh.cpp.

References GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries(), GetCorrespondingToroidalNodeIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), mBottomPeriodicBoundaryElementIndices, mTopPeriodicBoundaryElementIndices, and NEVER_REACHED.

Referenced by ReMesh().

◆ CreateMirrorNodes()

void Toroidal2dMesh::CreateMirrorNodes ( )

private

Creates a set of mirrored nodes for a Toroidal re-mesh. Updates mRightImages, mLeftImages, mTopImages and mBottomImages . All mesh points should be 0 < x < mWidth and 0 < y < mHeight

This method should only ever be called by the public ReMesh() method.

Definition at line 84 of file Toroidal2dMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), mBottomImages, mBottomOriginals, mBottomPeriodicBoundaryElementIndices, mHeight, mImageToBottomOriginalNodeMap, mImageToLeftOriginalNodeMap, mImageToRightOriginalNodeMap, mImageToTopOriginalNodeMap, mLeftImages, mLeftOriginals, mLeftPeriodicBoundaryElementIndices, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, mRightImages, mRightOriginals, mRightPeriodicBoundaryElementIndices, mTopImages, mTopOriginals, mTopPeriodicBoundaryElementIndices, and mWidth.

Referenced by ReMesh().

◆ GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries()

void Toroidal2dMesh::GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries ( )

private

This method should only ever be called by the public ReMesh method.

The elements which straddle the periodic boundaries need to be identified in order to compare the list on the right with the list on the left and reconstruct a Toroidal mesh.

Empties and repopulates the member variables mLeftPeriodicBoundaryElementIndices and mRightPeriodicBoundaryElementIndices

Definition at line 1024 of file Toroidal2dMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), mImageToLeftOriginalNodeMap, mImageToRightOriginalNodeMap, mLeftPeriodicBoundaryElementIndices, and mRightPeriodicBoundaryElementIndices.

Referenced by CorrectCylindricalNonPeriodicMesh().

◆ GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries()

void Toroidal2dMesh::GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries ( )

private

This method should only ever be called by the public ReMesh method.

The elements which straddle the periodic boundaries need to be identified in order to compare the list on the right with the list on the left and reconstruct a Toroidal mesh.

Empties and repopulates the member variables mLeftPeriodicBoundaryElementIndices and mRightPeriodicBoundaryElementIndices

Definition at line 1117 of file Toroidal2dMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), mBottomPeriodicBoundaryElementIndices, mImageToBottomOriginalNodeMap, mImageToTopOriginalNodeMap, and mTopPeriodicBoundaryElementIndices.

Referenced by CorrectToroidalNonPeriodicMesh().

◆ GetCorrespondingCylindricalNodeIndex()

unsigned Toroidal2dMesh::GetCorrespondingCylindricalNodeIndex ( unsigned nodeIndex )

private

This method should only ever be called by the public ReMesh() method.

Parameters

nodeIndex The index of an original/mirrored node

Returns: the index of the corresponding mirror image of that node (can be either an original or mirror node)

Definition at line 1180 of file Toroidal2dMesh.cpp.

References mRightImages, mRightOriginals, and NEVER_REACHED.

Referenced by CorrectCylindricalNonPeriodicMesh().

◆ GetCorrespondingToroidalNodeIndex()

unsigned Toroidal2dMesh::GetCorrespondingToroidalNodeIndex ( unsigned nodeIndex )

private

This method should only ever be called by the public ReMesh() method.

Parameters

nodeIndex The index of an original/mirrored node

Returns: the index of the corresponding mirror image of that node (can be either an original or mirror node)

Definition at line 1229 of file Toroidal2dMesh.cpp.

References mTopImages, mTopOriginals, and NEVER_REACHED.

Referenced by CorrectToroidalNonPeriodicMesh().

◆ GetInstanceOfMismatchedBoundaryNodes()

bool Toroidal2dMesh::GetInstanceOfMismatchedBoundaryNodes ( )

Returns: whether you have mismatched numbers of left and right boundary nodes

◆ GetVectorFromAtoB()

c_vector< double, 2 > Toroidal2dMesh::GetVectorFromAtoB	(	const c_vector< double, 2 > &	rLocation1,
		const c_vector< double, 2 > &	rLocation2
	)

Overridden GetVectorFromAtoB() method.

Evaluates the (surface) distance between two points in a 2D Toroidal geometry.

Parameters

rLocation1	the x and y co-ordinates of point 1
rLocation2	the x and y co-ordinates of point 2

Returns: the vector from location1 to location2

Definition at line 722 of file Toroidal2dMesh.cpp.

References mHeight, and mWidth.

◆ GetWidth()

double Toroidal2dMesh::GetWidth ( const unsigned & rDimension ) const

virtual

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the mesh, taking periodicity into account.

Parameters

rDimension a dimension (0 or 1)

Returns: The maximum distance between any nodes in this dimension.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 785 of file Toroidal2dMesh.cpp.

References mHeight, and mWidth.

◆ ReconstructCylindricalMesh()

void Toroidal2dMesh::ReconstructCylindricalMesh ( )

private

After any corrections have been made to the boundary elements (see UseTheseElementsToDecideMeshing()) this method deletes the mirror image nodes, elements and boundary elements created for a Toroidal remesh by cycling through the elements and changing elements with partly real and partly imaginary elements to be real with periodic real nodes instead of mirror image nodes. We end up with very strangely shaped elements which cross the whole mesh but specify the correct connections between nodes.

This method should only ever be called by the public ReMesh() method.

Definition at line 451 of file Toroidal2dMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), MutableMesh< 2, 2 >::mDeletedElementIndices, MutableMesh< 2, 2 >::mDeletedNodeIndices, mImageToLeftOriginalNodeMap, mImageToRightOriginalNodeMap, mLeftImages, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and mRightImages.

Referenced by ReMesh().

◆ ReconstructToroidalMesh()

void Toroidal2dMesh::ReconstructToroidalMesh ( )

private

After any corrections have been made to the boundary elements (see UseTheseElementsToDecideMeshing()) this method deletes the mirror image nodes, elements and boundary elements created for a Toroidal remesh by cycling through the elements and changing elements with partly real and partly imaginary elements to be real with periodic real nodes instead of mirror image nodes. We end up with very strangely shaped elements which cross the whole mesh but specify the correct connections between nodes.

This method should only ever be called by the public ReMesh() method.

Definition at line 588 of file Toroidal2dMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), mBottomImages, MutableMesh< 2, 2 >::mDeletedElementIndices, MutableMesh< 2, 2 >::mDeletedNodeIndices, mImageToBottomOriginalNodeMap, mImageToTopOriginalNodeMap, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and mTopImages.

Referenced by ReMesh().

◆ RefreshMesh()

void Toroidal2dMesh::RefreshMesh ( )

virtual

Overridden RefreshMesh method. This method moves node backinto domain and calls RefreshJacobianCachedData.

Reimplemented from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1278 of file Toroidal2dMesh.cpp.

References mHeight, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and mWidth.

◆ ReMesh()

void Toroidal2dMesh::ReMesh ( NodeMap & rMap )

virtual

Overridden ReMesh() method.

Conduct a Toroidal remesh by calling CreateMirrorNodes() to create mirror image nodes, then calling ReMesh() on the parent class, then mapping the new node indices and calling ReconstructToroidalMesh() to remove surplus nodes, leaving a fully periodic mesh.

Parameters

rMap	a reference to a nodemap which should be created with the required number of nodes.

Reimplemented from MutableMesh< 2, 2 >.

Definition at line 199 of file Toroidal2dMesh.cpp.

◆ serialize()

template<class Archive >

void Toroidal2dMesh::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archives the member variables of the Toroidal2dMesh class which have to be preserved during the lifetime of the mesh.

The remaining member variables are re-initialised before being used by each ReMesh() call so they do not need to be archived.

Parameters

archive	the archive
version	the current version of this class the current version of this class

Definition at line 236 of file Toroidal2dMesh.hpp.

References mHeight, and mWidth.

◆ SetNode()

void Toroidal2dMesh::SetNode	(	unsigned	index,
		ChastePoint< 2 >	point,
		bool	concreteMove
	)

Overridden SetNode() method.

If the location should be set outside a Toroidal boundary, it is moved back onto the cylinder.

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

Definition at line 754 of file Toroidal2dMesh.cpp.

References mHeight, mWidth, ChastePoint< DIM >::rGetLocation(), ChastePoint< DIM >::SetCoordinate(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

Referenced by AddNode().

Friends And Related Symbol Documentation

◆ boost::serialization::access

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 223 of file Toroidal2dMesh.hpp.

◆ TestToroidal2dMesh

friend class TestToroidal2dMesh

friend

Definition at line 57 of file Toroidal2dMesh.hpp.

Member Data Documentation

◆ mBottomImages

std::vector<unsigned> Toroidal2dMesh::mBottomImages

private

The image nodes corresponding to these Bottom nodes (on Top of mesh).

Definition at line 94 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), ReconstructToroidalMesh(), and ReMesh().

◆ mBottomOriginals

std::vector<unsigned> Toroidal2dMesh::mBottomOriginals

private

The Bottom nodes which have been mirrored during the remesh.

Definition at line 91 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), and ReMesh().

◆ mBottomPeriodicBoundaryElementIndices

std::set<unsigned> Toroidal2dMesh::mBottomPeriodicBoundaryElementIndices

private

The indices of elements which straddle the Bottom periodic boundary.

Definition at line 109 of file Toroidal2dMesh.hpp.

Referenced by CorrectToroidalNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries(), and ReMesh().

◆ mHeight

double Toroidal2dMesh::mHeight

private

The periodic height of the domain.

Definition at line 64 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetVectorFromAtoB(), GetWidth(), RefreshMesh(), ReMesh(), serialize(), and SetNode().

◆ mImageToBottomOriginalNodeMap

std::map<unsigned, unsigned> Toroidal2dMesh::mImageToBottomOriginalNodeMap

private

A map from image node index (on Top of mesh) to original node index (on Bottom of mesh).

Definition at line 97 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries(), ReconstructToroidalMesh(), and ReMesh().

◆ mImageToLeftOriginalNodeMap

std::map<unsigned, unsigned> Toroidal2dMesh::mImageToLeftOriginalNodeMap

private

A map from image node index (on right of mesh) to original node index (on left of mesh).

Definition at line 73 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries(), ReconstructCylindricalMesh(), and ReMesh().

◆ mImageToRightOriginalNodeMap

std::map<unsigned, unsigned> Toroidal2dMesh::mImageToRightOriginalNodeMap

private

A map from image node index (on left of mesh) to original node index (on right of mesh).

Definition at line 82 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries(), ReconstructCylindricalMesh(), and ReMesh().

◆ mImageToTopOriginalNodeMap

std::map<unsigned, unsigned> Toroidal2dMesh::mImageToTopOriginalNodeMap

private

A map from image node index (on Bottom of mesh) to original node index (on Top of mesh).

Definition at line 106 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries(), ReconstructToroidalMesh(), and ReMesh().

◆ mLeftImages

std::vector<unsigned> Toroidal2dMesh::mLeftImages

private

The image nodes corresponding to these left nodes (on right of mesh).

Definition at line 70 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), ReconstructCylindricalMesh(), and ReMesh().

◆ mLeftOriginals

std::vector<unsigned> Toroidal2dMesh::mLeftOriginals

private

The left nodes which have been mirrored during the remesh.

Definition at line 67 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), and ReMesh().

◆ mLeftPeriodicBoundaryElementIndices

std::set<unsigned> Toroidal2dMesh::mLeftPeriodicBoundaryElementIndices

private

The indices of elements which straddle the left periodic boundary.

Definition at line 85 of file Toroidal2dMesh.hpp.

Referenced by CorrectCylindricalNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries(), and ReMesh().

◆ mMismatchedBoundaryElements

bool Toroidal2dMesh::mMismatchedBoundaryElements

private

Whether the number of left hand boundary nodes does not equal the number of right hand boundary nodes (and top=bottom)

Definition at line 116 of file Toroidal2dMesh.hpp.

◆ mRightImages

std::vector<unsigned> Toroidal2dMesh::mRightImages

private

The image nodes corresponding to these right nodes (on left of mesh).

Definition at line 79 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetCorrespondingCylindricalNodeIndex(), ReconstructCylindricalMesh(), and ReMesh().

◆ mRightOriginals

std::vector<unsigned> Toroidal2dMesh::mRightOriginals

private

The right nodes which have been mirrored during the remesh.

Definition at line 76 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetCorrespondingCylindricalNodeIndex(), and ReMesh().

◆ mRightPeriodicBoundaryElementIndices

std::set<unsigned> Toroidal2dMesh::mRightPeriodicBoundaryElementIndices

private

The indices of elements which straddle the right periodic boundary.

Definition at line 88 of file Toroidal2dMesh.hpp.

Referenced by CorrectCylindricalNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries(), and ReMesh().

◆ mTopImages

std::vector<unsigned> Toroidal2dMesh::mTopImages

private

The image nodes corresponding to these Top nodes (on Bottom of mesh).

Definition at line 103 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetCorrespondingToroidalNodeIndex(), ReconstructToroidalMesh(), and ReMesh().

◆ mTopOriginals

std::vector<unsigned> Toroidal2dMesh::mTopOriginals

private

The Top nodes which have been mirrored during the remesh.

Definition at line 100 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetCorrespondingToroidalNodeIndex(), and ReMesh().

◆ mTopPeriodicBoundaryElementIndices

std::set<unsigned> Toroidal2dMesh::mTopPeriodicBoundaryElementIndices

private

The indices of elements which straddle the Top periodic boundary.

Definition at line 112 of file Toroidal2dMesh.hpp.

Referenced by CorrectToroidalNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries(), and ReMesh().

◆ mWidth

double Toroidal2dMesh::mWidth

private

The periodic width of the domina.

Definition at line 61 of file Toroidal2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetVectorFromAtoB(), GetWidth(), RefreshMesh(), ReMesh(), serialize(), and SetNode().

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

mesh/src/mutable/Toroidal2dMesh.hpp
mesh/src/mutable/Toroidal2dMesh.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ Toroidal2dMesh() [1/2]

◆ Toroidal2dMesh() [2/2]

◆ ~Toroidal2dMesh()

Member Function Documentation

◆ AddNode()

◆ CorrectCylindricalNonPeriodicMesh()

◆ CorrectToroidalNonPeriodicMesh()

◆ CreateMirrorNodes()

◆ GenerateVectorsOfElementsStraddlingCylindricalPeriodicBoundaries()

◆ GenerateVectorsOfElementsStraddlingToroidalPeriodicBoundaries()

◆ GetCorrespondingCylindricalNodeIndex()

◆ GetCorrespondingToroidalNodeIndex()

◆ GetInstanceOfMismatchedBoundaryNodes()

◆ GetVectorFromAtoB()

◆ GetWidth()

◆ ReconstructCylindricalMesh()

◆ ReconstructToroidalMesh()

◆ RefreshMesh()

◆ ReMesh()

◆ serialize()

◆ SetNode()

Friends And Related Symbol Documentation

◆ boost::serialization::access

◆ TestToroidal2dMesh

Member Data Documentation

◆ mBottomImages

◆ mBottomOriginals

◆ mBottomPeriodicBoundaryElementIndices

◆ mHeight

◆ mImageToBottomOriginalNodeMap

◆ mImageToLeftOriginalNodeMap

◆ mImageToRightOriginalNodeMap

◆ mImageToTopOriginalNodeMap

◆ mLeftImages

◆ mLeftOriginals

◆ mLeftPeriodicBoundaryElementIndices

◆ mMismatchedBoundaryElements

◆ mRightImages

◆ mRightOriginals

◆ mRightPeriodicBoundaryElementIndices

◆ mTopImages

◆ mTopOriginals

◆ mTopPeriodicBoundaryElementIndices

◆ mWidth