TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <TetrahedralMesh.hpp>

Inherits AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Inherited by MutableMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, MutableMesh< ELEMENT_DIM, ELEMENT_DIM >, MutableMesh< SPACE_DIM, SPACE_DIM >, and NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Collaboration diagram for TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

[legend]

List of all members.

Classes
class	EdgeIterator
Public Member Functions
	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 ()
std::set< unsigned >	CalculateBoundaryOfFlaggedRegion ()
double	GetAngleBetweenNodes (unsigned indexA, unsigned indexB)
void	UnflagAllElements ()
void	FlagElementsNotContainingNodes (const std::set< unsigned > &rNodes)
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 ()
Protected Member Functions
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=NULL)
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 Attributes
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
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	TestTetrahedralMesh
class	TestCryptSimulation2d
class	boost::serialization::access

Detailed Description

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

Forward declaration for triangle helper methods (used in MutableMesh QuadraticMesh) A concrete tetrahedral mesh class.

Definition at line 64 of file TetrahedralMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::TetrahedralMesh ( ) [inline]

Constructor.

Definition at line 62 of file TetrahedralMesh.cpp.

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

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::set< unsigned > TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundaryOfFlaggedRegion ( ) [inline]

Returns:: the set of nodes which are on the boundary of the flagged region(s).

Definition at line 483 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsConforming ( ) [inline]

Check whether mesh is conforming Conforming (defn.): the intersection of two elements should be either the empty set, a vertex, an edge or a face.

It may be possible to construct non-conforming meshes which contain internal faces owned by only one element: two coplanar triangular faces of two elements form a square, but the same square on the adjacent pair of elements is formed by splitting the diagonal the other way.

Returns:: false if there are any orphaned internal faces

Definition at line 236 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear ( ) [inline, virtual]

Clear all the data in the mesh.

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

Definition at line 460 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::TetrahedralMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader ( AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > & rMeshReader ) [inline, virtual]

Construct the mesh using a MeshReader.

Parameters:

rMeshReader

the mesh reader

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 68 of file TetrahedralMesh.cpp.

Referenced by VertexBasedCellPopulation< DIM >::GetTetrahedralMeshUsingVertexMesh(), and HoneycombMeshGenerator::HoneycombMeshGenerator().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin ( ) [inline]

Returns:: iterator pointing to the first edge (i.e. connection between 2 nodes) of the mesh

Definition at line 735 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesEnd ( ) [inline]

Returns:: iterator pointing to one past the last edge (i.e. connection between 2 nodes) of the mesh

Definition at line 746 of file TetrahedralMesh.cpp.

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

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeA(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeB().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class MESHER_IO >

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher	(	NodeMap &	map,
		MESHER_IO &	mesherInput,
		int *	elementList = `NULL`
	)			`[inline, protected]`

Export the mesh (currently only the nodes) to an external mesher This is determined at compile time when the MESHER_IO template is instantiated to either

triangulateio (for triangle remesher in 2D)

tetgenio (for tetgen remesher in 3D) Since conditional compilation is not allowed, care must be taken to only use common data members in this method

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)
	mesherInput	is a triangulateio or tetgenio class (decided at compile time) Note that only nodes are exported and thus any late mesh is based on the convex hull
	elementList	is a pointer to either mesherInput.trianglelist or mesherInput.tetrahedronlist (used when we are not remeshing, but converting the form of an existing mesh) Note that this should have been re-malloced and mesherInput.numberoftriangles or mesherInput.numberoftetrahedra should be set prior to the call when elementList is non-NULL

Definition at line 901 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, NodeMap::SetDeleted(), and NodeMap::SetNewIndex().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::FlagElementsNotContainingNodes ( const std::set< unsigned > & rNodes ) [inline]

Flag all elements not containing ANY of the given nodes

Parameters:

rNodes

set of nodes to check for

Definition at line 591 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::FreeTriangulateIo ( triangulateio & mesherIo ) [inline, protected]

Convenience method to tidy up a triangleio data structure after use

Parameters:

mesherIo

is a triangulateio class

Definition at line 882 of file TetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetAngleBetweenNodes	(	unsigned	indexA,
		unsigned	indexB
	)			`[inline]`

Returns:: calculated the angle between the node at indexB and the x axis about the node at indexA. The angle returned is in the range (-pi,pi].

Parameters:

	indexA	a node index
	indexB	a node index

Definition at line 551 of file TetrahedralMesh.cpp.

References EXCEPTION, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Referenced by DiscreteSystemForceCalculator::CalculateFtAndFn(), and DiscreteSystemForceCalculator::GetSamplingAngles().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndexWithInitialGuess	(	const ChastePoint< SPACE_DIM > &	rTestPoint,
		unsigned	startingElementGuess,
		bool	strict = `false`
	)			`[inline]`

Returns:: the element index for the first element that contains a test point. Like GetContainingElementIndex but uses the user given element (M say) as the first element checked, and then checks M+1,M+2,..,Ne,0,1..

Parameters:

	rTestPoint	reference to the point
	startingElementGuess	Which element to try first.
	strict	Should the element returned contain the point in the interior and not on an edge/face/vertex (default = not strict)

Definition at line 373 of file TetrahedralMesh.cpp.

References EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by CellBasedPdeHandler< DIM >::UpdateCellPdeElementMap().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< unsigned > TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndices ( const ChastePoint< SPACE_DIM > & rTestPoint ) [inline]

Returns:: all element indices for elements that are known to contain a test point.

Parameters:

rTestPoint

reference to the point

Definition at line 445 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement	(	unsigned	elementIndex,
		c_matrix< double, SPACE_DIM, ELEMENT_DIM > &	rJacobian,
		double &	rJacobianDeterminant,
		c_matrix< double, ELEMENT_DIM, SPACE_DIM > &	rInverseJacobian
	)			const `[inline, virtual]`

Returns:: the Jacobian matrix, its inverse and its determinant for a given element.

Parameters:

	elementIndex	index of the element in the mesh
	rJacobian	the Jacobian matrix
	rJacobianDeterminant	the determinant of the Jacobian matrix
	rInverseJacobian	the inverse Jacobian matrix

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 837 of file TetrahedralMesh.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementInverseJacobians, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobianDeterminants, and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobians.

Referenced by VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), and CellwiseDataGradient< DIM >::SetupGradients().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetJacobianForElement	(	unsigned	elementIndex,
		c_matrix< double, SPACE_DIM, SPACE_DIM > &	rJacobian,
		double &	rJacobianDeterminant
	)			const `[inline, virtual]`

Returns:: the Jacobian matrix and its determinant for a given element.

Parameters:

	elementIndex	index of the element in the mesh
	rJacobian	the Jacobian matrix
	rJacobianDeterminant	the determinant of the Jacobian matrix

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 828 of file TetrahedralMesh.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobianDeterminants, and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobians.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestElementIndex ( const ChastePoint< SPACE_DIM > & rTestPoint ) [inline]

Returns:: the element index for an element is closest to the testPoint.

"Closest" means that the minimum interpolation weights for the testPoint are maximised for this element.

Parameters:

rTestPoint

reference to the point

Definition at line 419 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceArea ( ) [inline]

Returns:: the surface area of the mesh.

Definition at line 303 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementJacobianDeterminants.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume ( ) [inline]

Returns:: the volume of the mesh, calculated by adding the determinant of each element and dividing by n!, where n is the element dimension.

Definition at line 288 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobianDeterminants.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement	(	unsigned	elementIndex,
		c_vector< double, SPACE_DIM > &	rWeightedDirection,
		double &	rJacobianDeterminant
	)			const `[inline, virtual]`

Returns:: the weighted direction and the determinant of the Jacobian for a given boundary element.

Parameters:

	elementIndex	index of the element in the mesh
	rWeightedDirection	the weighted direction
	rJacobianDeterminant	the determinant of the Jacobian matrix

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 856 of file TetrahedralMesh.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementJacobianDeterminants, and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementWeightedDirections.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForElement	(	unsigned	elementIndex,
		c_vector< double, SPACE_DIM > &	rWeightedDirection,
		double &	rJacobianDeterminant
	)			const `[inline, virtual]`

Returns:: the weighted direction and the determinant of the Jacobian for a given element.

Parameters:

	elementIndex	index of the element in the mesh
	rWeightedDirection	the weighted direction
	rJacobianDeterminant	the determinant of the Jacobian matrix

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 847 of file TetrahedralMesh.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobianDeterminants, and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementWeightedDirections.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class MESHER_IO >

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher	(	MESHER_IO &	mesherOutput,
		unsigned	numberOfElements,
		int *	elementList,
		unsigned	numberOfFaces,
		int *	faceList,
		int *	edgeMarkerList
	)			`[inline, protected]`

Import the mesh from an external mesher This is determined at compile time when the MESHER_IO template is instantiated to either

triangulateio (for triangle remesher in 2D)

tetgenio (for tetgen remesher in 3D) Since conditional compilation is not allowed, care must be taken to only use common data members in this method (or add arguments

Todo:: #1545 ...)

Parameters:

	mesherOutput	is a triangulateio or tetgenio class (decided at compile time)
	numberOfElements	is a copy of either mesherOutput.numberoftriangles or mesherOutput.numberoftetrahedra
	elementList	is a pointer to either mesherOutput.trianglelist or mesherOutput.tetrahedronlist
	numberOfFaces	is a copy of either mesherOutput.edges or mesherOutput.numberoftrifaces
	faceList	is a pointer to either mesherOutput.edgelist or mesherOutput.trifacelist
	edgeMarkerList	is a pointer to either mesherOutput.edgemarkerlist or NULL

Definition at line 952 of file TetrahedralMesh.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::InitialiseTriangulateIo ( triangulateio & mesherIo ) [inline, protected]

Convenience method to tidy up a triangleio data structure before use

Parameters:

mesherIo

is a triangulateio class

Definition at line 864 of file TetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes ( const std::vector< unsigned > & perm ) [inline]

Permute the nodes so that they appear in a different order in mNodes (and their mIndex's are altered accordingly).

Parameters:

perm

is a vector containing the new indices

Definition at line 344 of file TetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodePermutation, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes ( ) [inline, virtual]

Permute the nodes randomly so that they appear in a different order in mNodes (and their mIndex's are altered accordingly).

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 332 of file TetrahedralMesh.cpp.

References RandomNumberGenerator::Instance(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and RandomNumberGenerator::Shuffle().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ReadNodesPerProcessorFile ( const std::string & rNodesPerProcessorFile ) [inline, virtual]

Read in the number of nodes per processor from file.

Parameters:

rNodesPerProcessorFile

the name of the file

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 191 of file TetrahedralMesh.cpp.

References EXCEPTION, PetscTools::GetMyRank(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), PetscTools::GetNumProcs(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mpDistributedVectorFactory.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData ( ) [inline, virtual]

Update mElementJacobians, mElementWeightedDirections and mBoundaryElementWeightedDirections.

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 779 of file TetrahedralMesh.cpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh ( ) [inline, virtual]

Overridden RefreshMesh method. This method calls RefreshJacobianCachedData.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 752 of file TetrahedralMesh.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the mesh.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NodesOnlyMesh< SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, QuadraticMesh< DIM >, Cylindrical2dMesh, Cylindrical2dNodesOnlyMesh, NodesOnlyMesh< DIM >, and NodesOnlyMesh< 2 >.

Definition at line 78 of file TetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping ( unsigned index ) const [inline, protected, virtual]

Overridden solve boundary element mapping method.

Parameters:

index

the global index of the boundary element

Returns:: local index

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 772 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

Referenced by NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping ( unsigned index ) const [inline, protected, virtual]

Overridden solve element mapping method.

Parameters:

index

the global index of the element

Returns:: local index

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 765 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping ( unsigned index ) const [inline, protected, virtual]

Overridden solve node mapping method.

Parameters:

index

the global index of the node

Returns:: local index

Implements AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

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

Definition at line 758 of file TetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::UnflagAllElements ( ) [inline]

Unflag all elements in the mesh.

Definition at line 580 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Needed for serialization.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in MutableMesh< ELEMENT_DIM, SPACE_DIM >, NodesOnlyMesh< SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, QuadraticMesh< DIM >, Cylindrical2dMesh, Cylindrical2dNodesOnlyMesh, MutableMesh< ELEMENT_DIM, ELEMENT_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, MutableMesh< SPACE_DIM, SPACE_DIM >, NodesOnlyMesh< DIM >, and NodesOnlyMesh< 2 >.

Definition at line 70 of file TetrahedralMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<double> TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementJacobianDeterminants [protected]

Vector storing the determinant of the Jacobian matrix for each boundary element in the mesh.

Definition at line 125 of file TetrahedralMesh.hpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceArea(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), and Cylindrical2dMesh::ReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< c_vector<double, SPACE_DIM> > TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementWeightedDirections [protected]

Vector storing the weighted direction for each boundary element in the mesh.

Definition at line 122 of file TetrahedralMesh.hpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), and Cylindrical2dMesh::ReMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< c_matrix<double, ELEMENT_DIM, SPACE_DIM> > TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementInverseJacobians [protected]

Vector storing the inverse Jacobian matrix for each element in the mesh.

Definition at line 116 of file TetrahedralMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<double> TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobianDeterminants [protected]

Vector storing the Jacobian determinant for each element in the mesh.

Definition at line 119 of file TetrahedralMesh.hpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< c_matrix<double, SPACE_DIM, ELEMENT_DIM> > TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobians [protected]

Vector storing the Jacobian matrix for each element in the mesh.

Definition at line 113 of file TetrahedralMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector< c_vector<double, SPACE_DIM> > TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementWeightedDirections [protected]

Vector storing the weighted direction for each element in the mesh.

Definition at line 110 of file TetrahedralMesh.hpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

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

mesh/src/common/TetrahedralMesh.hpp
mesh/src/common/TetrahedralMesh.cpp

TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

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