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 >, 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	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)
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)
void	RefreshMesh ()
void	PermuteNodes ()
void	PermuteNodesWithMetisBinaries (unsigned numProcs)
void	PermuteNodes (std::vector< unsigned > &perm)
unsigned	GetContainingElementIndex (ChastePoint< SPACE_DIM > testPoint, bool strict=false, std::set< unsigned > testElements=std::set< unsigned >(), bool onlyTryWithTestElements=false)
unsigned	GetContainingElementIndexWithInitialGuess (ChastePoint< SPACE_DIM > testPoint, unsigned startingElementGuess, bool strict=false)
unsigned	GetNearestElementIndex (ChastePoint< SPACE_DIM > testPoint)
unsigned	GetNearestElementIndexFromTestElements (ChastePoint< SPACE_DIM > testPoint, std::set< unsigned > testElements)
	todo #1299 refactor common code with GetNearestElementIndex
std::vector< unsigned >	GetContainingElementIndices (ChastePoint< SPACE_DIM > testPoint)
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
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 >

A concrete tetrahedral mesh class.

Definition at line 54 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 50 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]

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

Definition at line 818 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 214 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 >, MutableMesh< 2, 2 >, and MutableMesh< DIM, DIM >.

Definition at line 795 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 >::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 56 of file TetrahedralMesh.cpp.

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

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 (ie connection between 2 nodes) of the mesh

Definition at line 1051 of file TetrahedralMesh.cpp.

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

Referenced by VoronoiTessellation< DIM >::Initialise(), FineCoarseMeshPair< DIM >::SetUpBoxesOnFineMesh(), MeshBasedTissue< DIM >::SpringsBegin(), MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

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 (ie connection between 2 nodes) of the mesh

Definition at line 1062 of file TetrahedralMesh.cpp.

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

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeA(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeB(), VoronoiTessellation< DIM >::Initialise(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::operator++(), FineCoarseMeshPair< DIM >::SetUpBoxesOnFineMesh(), MeshBasedTissue< DIM >::SpringsEnd(), MeshBasedTissueWithGhostNodes< DIM >::UpdateGhostPositions(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

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 924 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>

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

Calcuate 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 884 of file TetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex	(	ChastePoint< SPACE_DIM >	testPoint,
		bool	strict = `false`,
		std::set< unsigned >	testElements = `std::set<unsigned>()`,
		bool	onlyTryWithTestElements = `false`
	)			`[inline]`

Return the element index for the first element that contains a test point

Parameters:

	testPoint
	strict	Should the element returned contain the point in the interior and not on an edge/face/vertex (default = not strict)
	testElements	a set of guesses for the element (a set of element indices), to be checked first for potential efficiency improvements. (default = empty set)
	onlyTryWithTestElements	Do not continue with other elements after trying the with testElements (for cases where you know the testPoint must be in the set of test elements or maybe outside the mesh).

Todo:: #1299 What if the element is deleted?

Todo:: #1299 Polling every element is unnecessary. We ought to start from a likely place and hill climb

Todo:: #1299 What if the element is deleted?

Definition at line 621 of file TetrahedralMesh.cpp.

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

Referenced by FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseQuadPoints().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Return 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:

	testPoint
	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)

Todo:: #1299 What if the element is deleted?

Definition at line 669 of file TetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

Parameters:

testPoint

the point

Todo:: #1299 What if the element is deleted?

Definition at line 779 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]`

Get 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 1150 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 VoronoiTessellation< DIM >::GenerateVerticesFromElementCircumcentres(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres().

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]`

Get 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 1141 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 ( ChastePoint< SPACE_DIM > testPoint ) [inline]

Return 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:

testPoint

the point

Todo:: #1299 This ought to return a set of all elements that contain the point (if the point is a node in the mesh then it's contained in multiple elements)

Todo:: #1299 Polling every element is unnecessary. We ought to start from a likely place and hill climb

Todo:: #1299 What if the element is deleted?

Definition at line 714 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestElementIndexFromTestElements	(	ChastePoint< SPACE_DIM >	testPoint,
		std::set< unsigned >	testElements
	)			`[inline]`

todo #1299 refactor common code with GetNearestElementIndex

As with GetNearestElementIndex() except only searches in the given set of elements.

Parameters:

	testPoint	the point
	testElements	a set of elements (element indices) to look in

Definition at line 747 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseQuadPoints().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Return the surface area of the mesh.

Definition at line 278 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]

Return 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 263 of file TetrahedralMesh.cpp.

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

Referenced by MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile().

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]`

Get 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 1169 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]`

Get 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 1160 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>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes ( 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 462 of file TetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), 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 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 440 of file TetrahedralMesh.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodesWithMetisBinaries ( unsigned numProcs ) [inline]

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

Parameters:

numProcs

Number of processors (e.g. number of partitions)

Definition at line 487 of file TetrahedralMesh.cpp.

References PetscTools::AmMaster(), PetscTools::Barrier(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), OutputFileHandler::GetOutputDirectoryFullPath(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, OutputFileHandler::OpenOutputFile(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes().

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 167 of file TetrahedralMesh.cpp.

References 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 1095 of file TetrahedralMesh.cpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), 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 1068 of file TetrahedralMesh.cpp.

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

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::RescaleMeshFromBoundaryNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate ( double theta ) [inline]

Rotating a 2D mesh equates that rotation around the z-axis.

Parameters:

theta

is the angle of rotation in radians

Definition at line 434 of file TetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate	(	c_vector< double, 3 >	axis,
		double	angle
	)			`[inline]`

Do an angle axis rotation.

Parameters:

	axis	is the axis of rotation (does not need to be normalised)
	angle	is the angle of rotation in radians

Definition at line 357 of file TetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate ( c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix ) [inline]

Do a general mesh rotation with a positive determinant orthonormal rotation matrix. This is the rotation method that actually does the work.

Parameters:

rotationMatrix

is a Ublas rotation matrix of the correct form

Definition at line 342 of file TetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Rotate(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RotateX(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RotateY(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RotateZ().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RotateX ( const double theta ) [inline]

Rotate the mesh about the x-axis.

Parameters:

theta

is the angle of rotation in radians

Definition at line 382 of file TetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RotateY ( const double theta ) [inline]

Rotate the mesh about the y-axis.

Parameters:

theta

is the angle of rotation in radians

Definition at line 398 of file TetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RotateZ ( const double theta ) [inline]

Rotate the mesh about the z-axis.

Parameters:

theta

is the angle of rotation in radians

Definition at line 416 of file TetrahedralMesh.cpp.

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

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

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 MutableMesh< ELEMENT_DIM, SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, QuadraticMesh< DIM >, Cylindrical2dMesh, MutableMesh< 2, 2 >, and MutableMesh< DIM, DIM >.

Definition at line 69 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

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1088 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

Implements AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1081 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

Implements AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 1074 of file TetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate	(	const double	xMovement = `0.0`,
		const double	yMovement = `0.0`,
		const double	zMovement = `0.0`
	)			`[inline]`

Translate the mesh given the coordinate displacements separately.

Parameters:

	xMovement	is the x-displacement (defaults to 0.0)
	yMovement	is the y-displacement (defaults to 0.0)
	zMovement	is the z-displacement (defaults to 0.0)

Definition at line 307 of file TetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate ( const c_vector< double, SPACE_DIM > & rDisplacement ) [inline]

Translate the mesh given the displacement vector. This is the translation method that actually does the work.

Parameters:

rDisplacement

is a translation vector of the correct size

Definition at line 328 of file TetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

Referenced by HoneycombMeshGenerator::GetCircularMesh(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Translate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Unflag all elements in the mesh.

Definition at line 913 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 >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, QuadraticMesh< DIM >, Cylindrical2dMesh, MutableMesh< 2, 2 >, and MutableMesh< DIM, DIM >.

Definition at line 61 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 113 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 110 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 104 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 107 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 101 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 98 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:

/tmp/release_2.0/mesh/src/common/TetrahedralMesh.hpp
/tmp/release_2.0/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 >