Cylindrical2dMesh Class Reference

#include <Cylindrical2dMesh.hpp>

Inheritance diagram for Cylindrical2dMesh:

Collaboration diagram for Cylindrical2dMesh:

List of all members.

Public Member Functions

Cylindrical2dMesh (double width)

Cylindrical2dMesh (double width, std::vector< Node< 2 > * > nodes)

~Cylindrical2dMesh ()

void ReMesh (NodeMap &map)

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)

Private Member Functions

void UpdateTopAndBottom ()

void CreateHaloNodes ()

void CreateMirrorNodes ()

void ReconstructCylindricalMesh ()

void DeleteHaloNodes ()

void CorrectNonPeriodicMesh ()

void GenerateVectorsOfElementsStraddlingPeriodicBoundaries ()

unsigned GetCorrespondingNodeIndex (unsigned nodeIndex)

void UseTheseElementsToDecideMeshing (std::set< unsigned > mainSideElements)

bool IsThisIndexInList (const unsigned &rNodeIndex, const std::vector< unsigned > &rListOfNodes)

template<class Archive>

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

Private Attributes

double mWidth

double mTop

double mBottom

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 > mTopHaloNodes

std::vector< unsigned > mBottomHaloNodes

Friends

class TestCylindrical2dMesh

class boost::serialization::access

Detailed Description

A subclass of MutableMesh<2,2> for a rectangular mesh with periodic left and right boundaries, representing a cylindrical 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 50 of file Cylindrical2dMesh.hpp.

Constructor & Destructor Documentation

Cylindrical2dMesh::Cylindrical2dMesh ( double width )

Constructor.

Parameters:

width

the width of the crypt (circumference)

Definition at line 34 of file Cylindrical2dMesh.cpp.

Cylindrical2dMesh::Cylindrical2dMesh	(	double	width,
		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 length scale.
	nodes	a collection of nodes to construct the mesh with.

Definition at line 42 of file Cylindrical2dMesh.cpp.

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

Cylindrical2dMesh::~Cylindrical2dMesh ( ) [inline]

Destructor.

Definition at line 237 of file Cylindrical2dMesh.hpp.

Member Function Documentation

void Cylindrical2dMesh::UpdateTopAndBottom ( ) [private]

Calls TetrahedralMesh<2,2>::GetWidthExtremes() to calculate mTop and mBottom for the cylindrical mesh.

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

Definition at line 61 of file Cylindrical2dMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidthExtremes(), mBottom, and mTop.

Referenced by CreateHaloNodes().

void Cylindrical2dMesh::CreateHaloNodes ( ) [private]

This method creates a compressed row of nodes, just above and below the main mesh at a constant height (a 'halo'). These will mesh to a known configuration (each one on the boundary), this avoids boundary elements of lengths over half a crypt width which prevent the process of cylindrical meshing.

The nodes which are created are later removed by DeleteHaloNodes().

Definition at line 132 of file Cylindrical2dMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), mBottom, mBottomHaloNodes, mTop, mTopHaloNodes, mWidth, and UpdateTopAndBottom().

Referenced by ReMesh().

void Cylindrical2dMesh::CreateMirrorNodes ( ) [private]

Creates a set of mirrored nodes for a cylindrical re-mesh. Updates mRightImages and mLeftImages. All mesh points should be 0<x<mWidth.

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

Definition at line 69 of file Cylindrical2dMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), mImageToLeftOriginalNodeMap, mImageToRightOriginalNodeMap, mLeftImages, mLeftOriginals, mLeftPeriodicBoundaryElementIndices, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, mRightImages, mRightOriginals, mRightPeriodicBoundaryElementIndices, and mWidth.

Referenced by ReMesh().

void Cylindrical2dMesh::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 cylindrical 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 288 of file Cylindrical2dMesh.cpp.

Referenced by ReMesh().

void Cylindrical2dMesh::DeleteHaloNodes ( ) [private]

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

This method removes the nodes which were added by CreateHaloNodes() before the remeshing algorithm was called.

Definition at line 422 of file Cylindrical2dMesh.cpp.

References MutableMesh< 2, 2 >::DeleteBoundaryNodeAt(), mBottomHaloNodes, and mTopHaloNodes.

Referenced by ReMesh().

void Cylindrical2dMesh::CorrectNonPeriodicMesh ( ) [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 520 of file Cylindrical2dMesh.cpp.

References GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), GetCorrespondingNodeIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), mLeftPeriodicBoundaryElementIndices, mRightPeriodicBoundaryElementIndices, and UseTheseElementsToDecideMeshing().

Referenced by ReMesh().

void Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries ( ) [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 cylindrical mesh.

Empties and repopulates the member variables mLeftPeriodicBoundaryElementIndices and mRightPeriodicBoundaryElementIndices

Definition at line 690 of file Cylindrical2dMesh.cpp.

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

Referenced by CorrectNonPeriodicMesh().

unsigned Cylindrical2dMesh::GetCorrespondingNodeIndex ( 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 731 of file Cylindrical2dMesh.cpp.

References IsThisIndexInList(), mLeftImages, mLeftOriginals, mRightImages, and mRightOriginals.

Referenced by CorrectNonPeriodicMesh(), and UseTheseElementsToDecideMeshing().

void Cylindrical2dMesh::UseTheseElementsToDecideMeshing ( std::set< unsigned > mainSideElements ) [private]

This method takes in two elements which are not meshed in the same way on the opposite boundary. It deletes the corresponding two elements (connecting the same four nodes) and makes two new elements which are connected in the same way. We should then be able to reconstruct the cylindrical mesh properly.

Parameters:

mainSideElements

two elements (usually in a square) which have been meshed differently on the opposite boundary

Definition at line 611 of file Cylindrical2dMesh.cpp.

References GetCorrespondingNodeIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), MutableMesh< 2, 2 >::mDeletedElementIndices, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementInverseJacobians, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobianDeterminants, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobians, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and MutableMesh< 2, 2 >::ReIndex().

Referenced by CorrectNonPeriodicMesh().

bool Cylindrical2dMesh::IsThisIndexInList	(	const unsigned &	rNodeIndex,
		const std::vector< unsigned > &	rListOfNodes
	)			`[private]`

Returns true if an unsigned is contained in a vector of unsigneds

Parameters:

	rNodeIndex	an unsigned value
	rListOfNodes	a list of unsigned values

Returns:: whether the unsigned is in this std::vector

Definition at line 479 of file Cylindrical2dMesh.cpp.

Referenced by GetCorrespondingNodeIndex().

template<class Archive>

void Cylindrical2dMesh::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Archives the member variables of the Cylindrical2dMesh 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

Reimplemented from MutableMesh< 2, 2 >.

Definition at line 207 of file Cylindrical2dMesh.hpp.

References mBottom, mTop, and mWidth.

void Cylindrical2dMesh::ReMesh ( NodeMap & map ) [virtual]

Conducts a cylindrical remesh (OVERRIDDEN constructor of main ReMesh function)

Firstly calls CreateMirrorNodes to create mirror image nodes Then calls remesher Maps new node indices calls ReconstructCylindricalMesh to remove surplus nodes to create a fully periodic mesh.

Parameters:

&map

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

Reimplemented from MutableMesh< 2, 2 >.

Definition at line 162 of file Cylindrical2dMesh.cpp.

c_vector< double, 2 > Cylindrical2dMesh::GetVectorFromAtoB	(	const c_vector< double, 2 > &	rLocation1,
		const c_vector< double, 2 > &	rLocation2
	)

This OVERRIDDEN method evaluates the (surface) distance between two points in a 2D Cylindrical 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 433 of file Cylindrical2dMesh.cpp.

References mWidth.

void Cylindrical2dMesh::SetNode	(	unsigned	index,
		ChastePoint< 2 >	point,
		bool	concreteMove
	)

OVERRIDDEN function to set the location of a node.

If the location should be set outside a cylindrical boundary move it back onto the cylinder.

SetNode moves 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

Definition at line 460 of file Cylindrical2dMesh.cpp.

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

Referenced by AddNode().

double Cylindrical2dMesh::GetWidth ( const unsigned & rDimension ) const [virtual]

OVERRIDDEN FUNCTION

Parameters:

rDimension

must be 0 (x) or 1 (y)

Returns:: width the CryptWidth or current height

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 492 of file Cylindrical2dMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and mWidth.

unsigned Cylindrical2dMesh::AddNode ( Node< 2 > * pNewNode )

Add a node to the mesh.

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

Parameters:

pNewNode

the node to be added to the mesh

Returns:: the global index of the new node

Definition at line 508 of file Cylindrical2dMesh.cpp.

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

Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from MutableMesh< 2, 2 >.

Definition at line 195 of file Cylindrical2dMesh.hpp.

Member Data Documentation

double Cylindrical2dMesh::mWidth [private]

The circumference of the cylinder

Definition at line 56 of file Cylindrical2dMesh.hpp.

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

double Cylindrical2dMesh::mTop [private]

The top of the cylinder (y coordinate)

Definition at line 59 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), serialize(), and UpdateTopAndBottom().

double Cylindrical2dMesh::mBottom [private]

The bottom of the cylinder (y coordinate)

Definition at line 62 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), serialize(), and UpdateTopAndBottom().

std::vector<unsigned> Cylindrical2dMesh::mLeftOriginals [private]

The left nodes which have been mirrored during the remesh

Definition at line 65 of file Cylindrical2dMesh.hpp.

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

std::vector<unsigned> Cylindrical2dMesh::mLeftImages [private]

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

Definition at line 68 of file Cylindrical2dMesh.hpp.

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

std::map<unsigned, unsigned> Cylindrical2dMesh::mImageToLeftOriginalNodeMap [private]

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

Definition at line 71 of file Cylindrical2dMesh.hpp.

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

std::vector<unsigned> Cylindrical2dMesh::mRightOriginals [private]

The right nodes which have been mirrored during the remesh

Definition at line 74 of file Cylindrical2dMesh.hpp.

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

std::vector<unsigned> Cylindrical2dMesh::mRightImages [private]

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

Definition at line 77 of file Cylindrical2dMesh.hpp.

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

std::map<unsigned, unsigned> Cylindrical2dMesh::mImageToRightOriginalNodeMap [private]

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

Definition at line 80 of file Cylindrical2dMesh.hpp.

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

std::set<unsigned> Cylindrical2dMesh::mLeftPeriodicBoundaryElementIndices [private]

The indices of elements which straddle the left periodic boundary

Definition at line 83 of file Cylindrical2dMesh.hpp.

Referenced by CorrectNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), and ReMesh().

std::set<unsigned> Cylindrical2dMesh::mRightPeriodicBoundaryElementIndices [private]

The indices of elements which straddle the right periodic boundary

Definition at line 86 of file Cylindrical2dMesh.hpp.

Referenced by CorrectNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), and ReMesh().

std::vector<unsigned > Cylindrical2dMesh::mTopHaloNodes [private]

The indices of nodes on the top boundary

Definition at line 89 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), DeleteHaloNodes(), and ReMesh().

std::vector<unsigned > Cylindrical2dMesh::mBottomHaloNodes [private]

The indices of nodes on the bottom boundary

Definition at line 92 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), DeleteHaloNodes(), and ReMesh().

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

/tmp/release_1.1/cancer/src/mesh/Cylindrical2dMesh.hpp
/tmp/release_1.1/cancer/src/mesh/Cylindrical2dMesh.cpp


Public Member Functions
	Cylindrical2dMesh (double width)
	Cylindrical2dMesh (double width, std::vector< Node< 2 > * > nodes)
	~Cylindrical2dMesh ()
void	ReMesh (NodeMap &map)
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)
Private Member Functions
void	UpdateTopAndBottom ()
void	CreateHaloNodes ()
void	CreateMirrorNodes ()
void	ReconstructCylindricalMesh ()
void	DeleteHaloNodes ()
void	CorrectNonPeriodicMesh ()
void	GenerateVectorsOfElementsStraddlingPeriodicBoundaries ()
unsigned	GetCorrespondingNodeIndex (unsigned nodeIndex)
void	UseTheseElementsToDecideMeshing (std::set< unsigned > mainSideElements)
bool	IsThisIndexInList (const unsigned &rNodeIndex, const std::vector< unsigned > &rListOfNodes)
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
double	mWidth
double	mTop
double	mBottom
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 >	mTopHaloNodes
std::vector< unsigned >	mBottomHaloNodes
Friends
class	TestCylindrical2dMesh
class	boost::serialization::access