QuadraticMesh< DIM > Class Template Reference

#include <QuadraticMesh.hpp>

Inheritance diagram for QuadraticMesh< DIM >:

Collaboration diagram for QuadraticMesh< DIM >:

List of all members.

Public Member Functions

QuadraticMesh (const std::string &rFileName, bool boundaryElemFileIsQuadratic)

QuadraticMesh (double xEnd, double yEnd, unsigned numElemX, unsigned numElemY)

QuadraticMesh (double xEnd, double yEnd, double zEnd, unsigned numElemX, unsigned numElemY, unsigned numElemZ)

void WriteBoundaryElementFile (std::string directory, std::string fileName)

unsigned GetNumVertices ()

Private Member Functions

void LoadFromFile (const std::string &rFileName, bool boundaryElemFileIsQuadratic)

void AddNodesToBoundaryElements ()

void AddNodeToBoundaryElement (BoundaryElement< DIM-1, DIM > *pBoundaryElement, Element< DIM, DIM > *pElement, unsigned internalNode)

void AddExtraBoundaryNodes (BoundaryElement< DIM-1, DIM > *pBoundaryElement, Element< DIM, DIM > *pElement, unsigned nodeIndexOppositeToFace)

void HelperMethod1 (unsigned boundaryElemNode0, unsigned boundaryElemNode1, Element< DIM, DIM > *pElement, unsigned node0, unsigned node1, unsigned node2, unsigned &rOffset, bool &rReverse)

void HelperMethod2 (BoundaryElement< DIM-1, DIM > *pBoundaryElement, Element< DIM, DIM > *pElement, unsigned internalNode0, unsigned internalNode1, unsigned internalNode2, unsigned offset, bool reverse)

void RunMesherAndReadMesh (std::string binary, std::string outputDir, std::string fileStem)

Private Attributes

std::vector< bool > mIsInternalNode

unsigned mNumVertices

Detailed Description

template<unsigned DIM>
class QuadraticMesh< DIM >

A concrete quadratic mesh class that inherits from TetrahedralMesh.

Definition at line 40 of file QuadraticMesh.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

QuadraticMesh< DIM >::QuadraticMesh	(	const std::string &	rFileName,
		bool	boundaryElemFileIsQuadratic
	)			`[inline]`

Constructs a new Quadratic Mesh

Parameters:

	rFileName	The name of the quadratic mesh file to load
	boundaryElemFileIsQuadratic	Whether the boundary element file has a quadratic number of nodes (eg 3 in 2d) or linear number. Note tetgen with '-o2' creates files with quadratic elements but linear boundary elements. The AddExtraBoundaryNodes method will compute the extra info in boundaryElemFileIsQuadratic==false (slow).

Definition at line 41 of file QuadraticMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), and QuadraticMesh< DIM >::LoadFromFile().

template<unsigned DIM>

QuadraticMesh< DIM >::QuadraticMesh	(	double	xEnd,
		double	yEnd,
		unsigned	numElemX,
		unsigned	numElemY
	)			`[inline]`

Todo:: 1d constructor

Create a quadratic mesh on a rectangle (so 2D only) from (0,0) to (xEnd,yEnd) with the given number of elements in each direction. This writes a temporary node file and uses triangle to mesh this nodefile.

Parameters:

	xEnd	the width of the rectangle
	yEnd	the breadth of the rectangle
	numElemX	the number of elements in the x direction
	numElemY	the number of elements in the y direction

Definition at line 60 of file QuadraticMesh.cpp.

References QuadraticMesh< DIM >::AddNodesToBoundaryElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, QuadraticMesh< DIM >::mIsInternalNode, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, QuadraticMesh< DIM >::mNumVertices, and TetrahedralMesh< DIM, DIM >::RefreshJacobianCachedData().

template<unsigned DIM>

QuadraticMesh< DIM >::QuadraticMesh	(	double	xEnd,
		double	yEnd,
		double	zEnd,
		unsigned	numElemX,
		unsigned	numElemY,
		unsigned	numElemZ
	)			`[inline]`

Create a quadratic mesh on a cuboid (so 3D only!) from (0,0,0) to (xEnd,yEnd,zEnd) with the given number of elements in each direction. This writes a temporary node file and uses triangle to mesh this nodefile.

Parameters:

	xEnd	the width of the cuboid
	yEnd	the breadth of the cuboid
	zEnd	the height of the cuboid
	numElemX	the number of elements in the x direction
	numElemY	the number of elements in the y direction
	numElemZ	the number of elements in the z direction

Definition at line 201 of file QuadraticMesh.cpp.

References OutputFileHandler::GetOutputDirectoryFullPath(), OutputFileHandler::OpenOutputFile(), and QuadraticMesh< DIM >::RunMesherAndReadMesh().

Member Function Documentation

template<unsigned DIM>

void QuadraticMesh< DIM >::LoadFromFile	(	const std::string &	rFileName,
		bool	boundaryElemFileIsQuadratic
	)			`[inline, private]`

Load a quadratic mesh from a file.

Parameters:

	rFileName	the name of the file to load the mesh from.
	boundaryElemFileIsQuadratic	Whether the boundary element file has a quadratic number of nodes (eg 3 in 2d) or linear number. Note tetgen with '-o2' creates files with quadratic elements but linear boundary elements. QuadraticMesh will compute the extra info in boundaryElemFileIsQuadratic==false (slow).

Definition at line 301 of file QuadraticMesh.cpp.

Referenced by QuadraticMesh< DIM >::QuadraticMesh(), and QuadraticMesh< DIM >::RunMesherAndReadMesh().

template<unsigned DIM>

void QuadraticMesh< DIM >::AddNodesToBoundaryElements ( ) [inline, private]

Top level method for making 2D edges have 3 nodes not 2 and making 3D faces have 6 nodes not 3.

Definition at line 389 of file QuadraticMesh.cpp.

References QuadraticMesh< DIM >::AddExtraBoundaryNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements().

Referenced by QuadraticMesh< DIM >::LoadFromFile(), and QuadraticMesh< DIM >::QuadraticMesh().

template<unsigned DIM>

void QuadraticMesh< DIM >::AddNodeToBoundaryElement	(	BoundaryElement< DIM-1, DIM > *	pBoundaryElement,
		Element< DIM, DIM > *	pElement,
		unsigned	internalNode
	)			`[inline, private]`

This method adds the given node (defined by an element and a node index) to the given boundary element, and also sets the node as a boundary element and adds it to the std::vector of boundary elements.

Parameters:

	pBoundaryElement	pointer to a boundary element in the mesh
	pElement	pointer to an element in the mesh
	internalNode	index of a node in the mesh

Definition at line 471 of file QuadraticMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::AddNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), Node< SPACE_DIM >::IsBoundaryNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, and Node< SPACE_DIM >::SetAsBoundaryNode().

Referenced by QuadraticMesh< DIM >::AddExtraBoundaryNodes(), and QuadraticMesh< DIM >::HelperMethod2().

template<unsigned DIM>

void QuadraticMesh< DIM >::AddExtraBoundaryNodes	(	BoundaryElement< DIM-1, DIM > *	pBoundaryElement,
		Element< DIM, DIM > *	pElement,
		unsigned	nodeIndexOppositeToFace
	)			`[inline, private]`

Given a face in an element (defined by giving an element and the opposite node number to the face) that corresponds to a given boundary element, this method adds in the face's internal nodes to the boundary element (in the correct order).

Parameters:

	pBoundaryElement	pointer to a boundary element in the mesh
	pElement	pointer to an element in the mesh
	nodeIndexOppositeToFace	index of a node in the mesh

Definition at line 492 of file QuadraticMesh.cpp.

References QuadraticMesh< DIM >::AddNodeToBoundaryElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), QuadraticMesh< DIM >::HelperMethod1(), and QuadraticMesh< DIM >::HelperMethod2().

Referenced by QuadraticMesh< DIM >::AddNodesToBoundaryElements().

template<unsigned DIM>

void QuadraticMesh< DIM >::HelperMethod1	(	unsigned	boundaryElemNode0,
		unsigned	boundaryElemNode1,
		Element< DIM, DIM > *	pElement,
		unsigned	node0,
		unsigned	node1,
		unsigned	node2,
		unsigned &	rOffset,
		bool &	rReverse
	)			`[inline, private]`

Nasty helper method for AddNodeToBoundaryElement() in 3D.

This method takes in the three vertices of a face which match the given boundary element, and figure out if the order of the nodes in the face is reversed in the boundary element (returned in the bool 'rReverse'). Also, the offset between the first node in the face (as given to this method) and the first node in the boundary element is computed (returned in the variable 'rOffset'). Offset should then be applied before reverse to match the face nodes to the boundary element nodes.

Todo:: document these parameters

Parameters:

	boundaryElemNode0
	boundaryElemNode1
	pElement
	node0
	node1
	node2
	rOffset
	rReverse

Definition at line 594 of file QuadraticMesh.cpp.

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

Referenced by QuadraticMesh< DIM >::AddExtraBoundaryNodes().

template<unsigned DIM>

void QuadraticMesh< DIM >::HelperMethod2	(	BoundaryElement< DIM-1, DIM > *	pBoundaryElement,
		Element< DIM, DIM > *	pElement,
		unsigned	internalNode0,
		unsigned	internalNode1,
		unsigned	internalNode2,
		unsigned	offset,
		bool	reverse
	)			`[inline, private]`

Nasty helper method for AddNodeToBoundaryElement() in 3D.

This method takes the three internal nodes for some face in some element, applies the given offset and reverse (see HelperMethod1) to them, to get the ordered internal nodes which should given to the boundary element. It then calls AddNodeToBoundaryElement with each of the three internal nodes.

Todo:: document these parameters

Parameters:

	pBoundaryElement
	pElement
	internalNode0
	internalNode1
	internalNode2
	offset
	reverse

Definition at line 646 of file QuadraticMesh.cpp.

References QuadraticMesh< DIM >::AddNodeToBoundaryElement().

Referenced by QuadraticMesh< DIM >::AddExtraBoundaryNodes().

template<unsigned DIM>

void QuadraticMesh< DIM >::RunMesherAndReadMesh	(	std::string	binary,
		std::string	outputDir,
		std::string	fileStem
	)			`[inline, private]`

Helper method which runs triangle or tetgen and reads in the created mesh files.

Todo:: document these parameters (also shouldn't they be references?)

Parameters:

	binary
	outputDir
	fileStem

Definition at line 257 of file QuadraticMesh.cpp.

References QuadraticMesh< DIM >::LoadFromFile().

Referenced by QuadraticMesh< DIM >::QuadraticMesh().

template<unsigned DIM>

void QuadraticMesh< DIM >::WriteBoundaryElementFile	(	std::string	directory,
		std::string	fileName
	)			`[inline]`

Write the boundary elements to file (in case the boundary elements were linear when read and the quadratic versions have been computed.

Parameters:

	directory	Directory relative to CHASTE_TEST_OUTPUT. Not cleaned
	fileName	Boundary element file name.

Definition at line 542 of file QuadraticMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), and OutputFileHandler::OpenOutputFile().

template<unsigned DIM>

unsigned QuadraticMesh< DIM >::GetNumVertices ( ) [inline]

Get the number of vertices, ie non-internal (non-quadratic), nodes.

Definition at line 250 of file QuadraticMesh.cpp.

References QuadraticMesh< DIM >::mNumVertices.

Member Data Documentation

template<unsigned DIM>

std::vector<bool> QuadraticMesh< DIM >::mIsInternalNode [private]

Vector of bools, one for one node, saying whether the node is internal (if not, it is a vertex).

Definition at line 48 of file QuadraticMesh.hpp.

Referenced by QuadraticMesh< DIM >::LoadFromFile(), and QuadraticMesh< DIM >::QuadraticMesh().

template<unsigned DIM>

unsigned QuadraticMesh< DIM >::mNumVertices [private]

Number of vertices, ie non-internal (non-quadratic), nodes.

Definition at line 51 of file QuadraticMesh.hpp.

Referenced by QuadraticMesh< DIM >::GetNumVertices(), QuadraticMesh< DIM >::LoadFromFile(), and QuadraticMesh< DIM >::QuadraticMesh().

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

/tmp/release_1.1/mesh/src/common/QuadraticMesh.hpp
/tmp/release_1.1/mesh/src/common/QuadraticMesh.cpp


Public Member Functions
	QuadraticMesh (const std::string &rFileName, bool boundaryElemFileIsQuadratic)
	QuadraticMesh (double xEnd, double yEnd, unsigned numElemX, unsigned numElemY)
	QuadraticMesh (double xEnd, double yEnd, double zEnd, unsigned numElemX, unsigned numElemY, unsigned numElemZ)
void	WriteBoundaryElementFile (std::string directory, std::string fileName)
unsigned	GetNumVertices ()
Private Member Functions
void	LoadFromFile (const std::string &rFileName, bool boundaryElemFileIsQuadratic)
void	AddNodesToBoundaryElements ()
void	AddNodeToBoundaryElement (BoundaryElement< DIM-1, DIM > pBoundaryElement, Element< DIM, DIM > pElement, unsigned internalNode)
void	AddExtraBoundaryNodes (BoundaryElement< DIM-1, DIM > pBoundaryElement, Element< DIM, DIM > pElement, unsigned nodeIndexOppositeToFace)
void	HelperMethod1 (unsigned boundaryElemNode0, unsigned boundaryElemNode1, Element< DIM, DIM > *pElement, unsigned node0, unsigned node1, unsigned node2, unsigned &rOffset, bool &rReverse)
void	HelperMethod2 (BoundaryElement< DIM-1, DIM > pBoundaryElement, Element< DIM, DIM > pElement, unsigned internalNode0, unsigned internalNode1, unsigned internalNode2, unsigned offset, bool reverse)
void	RunMesherAndReadMesh (std::string binary, std::string outputDir, std::string fileStem)
Private Attributes
std::vector< bool >	mIsInternalNode
unsigned	mNumVertices

QuadraticMesh< DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

template<unsigned DIM> class QuadraticMesh< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned DIM>
class QuadraticMesh< DIM >