#include <QuadraticMesh.hpp>

Inheritance diagram for QuadraticMesh< DIM >:

Collaboration diagram for QuadraticMesh< DIM >:

Public Member Functions
	QuadraticMesh ()

	QuadraticMesh (double spaceStep, double width, double height=0, double depth=0)

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

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

unsigned	GetNumVertices () const

Public Member Functions inherited from TetrahedralMesh< DIM, 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)

virtual void	Clear ()

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	GetNumElements () const

virtual unsigned	GetNumLocalElements () const

virtual unsigned	GetNumBoundaryElements () const

virtual unsigned	GetNumLocalBoundaryElements () const

unsigned	GetNumAllElements () const

unsigned	GetNumAllBoundaryElements () const

virtual unsigned	GetNumCableElements () 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 ()

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 ()

virtual unsigned	GetNumNodes () const

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 Member Functions
void	CountVertices ()

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

void	ConstructLinearMesh (unsigned numElemX)

void	ConstructRectangularMesh (unsigned numElemX, unsigned numElemY, bool stagger=true)

void	ConstructCuboid (unsigned numElemX, unsigned numElemY, unsigned numElemZ)

Node< DIM > *	MakeNewInternalNode (unsigned &rIndex, c_vector< double, DIM > &rLocation, c_vector< double, DIM > &rTop)

unsigned	LookupInternalNode (unsigned globalIndex1, unsigned globalIndex2, std::map< std::pair< unsigned, unsigned >, unsigned > &rEdgeMap)

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

unsigned	SolveElementMapping (unsigned index) const

unsigned	SolveBoundaryElementMapping (unsigned index) const

void	ExportToMesher (NodeMap &map, MESHER_IO &mesherInput, int *elementList=nullptr)

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
unsigned	mNumVertices

Protected Attributes inherited from TetrahedralMesh< DIM, 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

Friends
class	TestQuadraticMesh

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

Detailed Description

template<unsigned DIM>
class QuadraticMesh< DIM >

A concrete quadratic mesh class that inherits from TetrahedralMesh.

Definition at line 51 of file QuadraticMesh.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

QuadraticMesh< DIM >::QuadraticMesh ( )

inline

Constructor

Definition at line 152 of file QuadraticMesh.hpp.

References QuadraticMesh< DIM >::ConstructFromLinearMeshReader(), QuadraticMesh< DIM >::ConstructFromMeshReader(), EXPORT_TEMPLATE_CLASS_SAME_DIMS, QuadraticMesh< DIM >::GetNumVertices(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mMeshIsLinear.

template<unsigned DIM>

QuadraticMesh< DIM >::QuadraticMesh	(	double	spaceStep,
		double	width,
		double	height = `0`,
		double	depth = `0`
	)

Create a quadratic mesh on a slab (on a line in 1D, rectangle in 2d, cuboid in 3D), with the given widths and given space step. In 1D height and depth need to be passed in as 0 (the default value); in 2D depth must be zero

Parameters

spaceStep	The spatial stepsize
width	the width of the cuboid
height	the height of the cuboid
depth	the depth of the cuboid

Definition at line 65 of file QuadraticMesh.cpp.

Member Function Documentation

template<unsigned DIM>

void QuadraticMesh< DIM >::ConstructCuboid	(	unsigned	numElemX,
		unsigned	numElemY,
		unsigned	numElemZ
	)

protectedvirtual

Create a quadratic mesh on a cuobid from (0,0,0) to (numElemX,numElemY,numElemZ) with that number of elements in each direction. The method overloads the equivalent method in AbstractTetrahedralMesh. This is private, users should call ConstructRegularSlabMesh();

Parameters

numElemX	Number of elements in x-direction (also, the width of the final mesh)
numElemY	Number of elements in y-direction (also, the height of the final mesh)
numElemZ	Number of elements in y-direction (also, the depth of the final mesh)

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 243 of file QuadraticMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid().

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

template<unsigned DIM>

void QuadraticMesh< DIM >::ConstructFromLinearMeshReader ( AbstractMeshReader< DIM, DIM > & rMeshReader )

Load a quadratic mesh from a linear mesh file.

Constructs as linear mesh, then exports to triangle/tetgen

Parameters

rMeshReader the mesh reader

Definition at line 410 of file QuadraticMesh.cpp.

References QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader().

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

template<unsigned DIM>

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

Load a quadratic mesh from a file.

Parameters

rMeshReader the mesh reader

Definition at line 459 of file QuadraticMesh.cpp.

References QuadraticMeshHelper< DIM >::AddInternalNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), QuadraticMeshHelper< DIM >::CheckBoundaryElements(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), EXPORT_TEMPLATE_CLASS_SAME_DIMS, and AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetOrderOfElements().

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

template<unsigned DIM>

void QuadraticMesh< DIM >::ConstructLinearMesh ( unsigned numElemX )

protectedvirtual

Create a quadratic mesh on the interval [0,numElemX] with numElemX elements in each direction. This is private, users should call ConstructRegularSlabMesh();

Very badly named. This creates a QUADRATIC mesh, the linear just refers to the fact the mesh is a line in 1D. The name is inherited from the parent class.

Parameters

numElemX Number of elements in x-direction (also, the width of the final mesh)

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 76 of file QuadraticMesh.cpp.

References Node< SPACE_DIM >::AddElement(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh().

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

template<unsigned DIM>

void QuadraticMesh< DIM >::ConstructRectangularMesh	(	unsigned	numElemX,
		unsigned	numElemY,
		bool	stagger = `true`
	)

protectedvirtual

Create a quadratic mesh on a rectangle from (0,0) to (numElemX,numElemY) with that number of elements in each direction.

The method overloads the equivalent method in AbstractTetrahedralMesh. This is private, users should call ConstructRegularSlabMesh();

Parameters

numElemX	Number of elements in x-direction (also, the width of the final mesh)
numElemY	Number of elements in y-direction (also, the height of the final mesh)
stagger	is the same as the over-ridden method with same name in AbstractTetrahedralMesh. stagger = false gives all back-slash diagonals stagger = true check-boards the diagonals as forward and back slashes

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 103 of file QuadraticMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh().

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

template<unsigned DIM>

void QuadraticMesh< DIM >::CountVertices ( )

protected

Count nodes which are vertices (not marked as internal)

Definition at line 51 of file QuadraticMesh.cpp.

template<unsigned DIM>

unsigned QuadraticMesh< DIM >::GetNumVertices ( ) const

virtual

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

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 404 of file QuadraticMesh.cpp.

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

template<unsigned DIM>

unsigned QuadraticMesh< DIM >::LookupInternalNode	(	unsigned	globalIndex1,
		unsigned	globalIndex2,
		std::map< std::pair< unsigned, unsigned >, unsigned > &	rEdgeMap
	)

protected

A helper method used in the private structured mesh constructors (ConstructRectangularMesh etc).

Gets the internal node index between two vertex node indices assuming ordered pairs have been used as keys in the map

Parameters

globalIndex1	is the index of one of the vertex nodes
globalIndex2	is the index of the other vertex node (ordering is unimportant)
rEdgeMap	the map from ordered pairs of vertex indices to internal node index

Returns: global node index of the internal node between globalIndex1 and globalIndex2

Definition at line 225 of file QuadraticMesh.cpp.

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

template<unsigned DIM>

Node< DIM > * QuadraticMesh< DIM >::MakeNewInternalNode	(	unsigned &	rIndex,
		c_vector< double, DIM > &	rLocation,
		c_vector< double, DIM > &	rTop
	)

protected

A helper method used in the private structured mesh constructors (ConstructRectangularMesh etc).

Method uses top (and the zero vector) to calculate if the node should be designated as a boundary node. Method uses top to determine if the node is outside the cuboid – this allows for simpler loops in the caller Method creates node, pushes node onto mNodes and marks it as an internal node.

Returns: pointer to new node

Parameters

rIndex	is the index in the mesh which this node should take. Note: this method increments rIndex
rLocation	the position of the node in space (coordinates should be integers or multiples of 1/2)
rTop	the position of top-most node in the line/slab/cuboid

Definition at line 196 of file QuadraticMesh.cpp.

References Node< SPACE_DIM >::MarkAsInternal().

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

template<unsigned DIM>

template<class Archive >

void QuadraticMesh< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprotected

Serialize the mesh.

Parameters

archive	the archive
version	the current version of this class

Definition at line 73 of file QuadraticMesh.hpp.

References QuadraticMesh< DIM >::ConstructCuboid(), QuadraticMesh< DIM >::ConstructLinearMesh(), QuadraticMesh< DIM >::ConstructRectangularMesh(), QuadraticMesh< DIM >::LookupInternalNode(), and QuadraticMesh< DIM >::MakeNewInternalNode().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 65 of file QuadraticMesh.hpp.

Member Data Documentation

template<unsigned DIM>

unsigned QuadraticMesh< DIM >::mNumVertices

protected

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

Definition at line 57 of file QuadraticMesh.hpp.

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

mesh/src/common/QuadraticMesh.hpp
mesh/src/common/QuadraticMesh.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned DIM> class QuadraticMesh< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class QuadraticMesh< DIM >