#include <TetrahedralMesh.hpp>

Inheritance diagram for TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

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 ()

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	GetNumVertices () 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 ()

virtual void	ConstructLinearMesh (unsigned width)

virtual void	ConstructRectangularMesh (unsigned width, unsigned height, bool stagger=true)

virtual void	ConstructCuboid (unsigned width, unsigned height, unsigned depth)

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
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=nullptr)

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 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
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

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

Friends
class	TestTetrahedralMesh

class	TestCryptSimulation2d

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 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

◆ TetrahedralMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::TetrahedralMesh ( )

Constructor.

Definition at line 62 of file TetrahedralMesh.cpp.

Member Function Documentation

◆ CheckIsConforming()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsConforming ( )

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.

◆ Clear()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear ( )

virtual

Clear all the data in the mesh.

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

Definition at line 459 of file TetrahedralMesh.cpp.

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

◆ ConstructFromMeshReader()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader ( AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > & rMeshReader )

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.

References AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetMeshFileBaseName(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::HasNodePermutation(), and AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset().

Referenced by QuadraticMesh< DIM >::ConstructFromLinearMeshReader(), QuadraticMesh< DIM >::ConstructFromMeshReader(), NodesOnlyMesh< SPACE_DIM >::ConstructFromMeshReader(), ImmersedBoundaryCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), and VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier().

◆ EdgesBegin()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin ( )

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

Definition at line 625 of file TetrahedralMesh.cpp.

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

◆ EdgesEnd()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesEnd ( )

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

Definition at line 636 of file TetrahedralMesh.cpp.

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

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SpringIterator::SpringIterator(), MeshBasedCellPopulationWithGhostNodes< DIM >::ApplyGhostForces(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeA().

◆ ExportToMesher()

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 = `nullptr`
	)

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 791 of file TetrahedralMesh.cpp.

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

◆ FreeTriangulateIo()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::FreeTriangulateIo ( triangulateio & mesherIo )

protected

Convenience method to tidy up a triangleio data structure after use

Parameters

mesherIo is a triangulateio class

Definition at line 772 of file TetrahedralMesh.cpp.

◆ GetAngleBetweenNodes()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetAngleBetweenNodes	(	unsigned	indexA,
		unsigned	indexB
	)

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 482 of file TetrahedralMesh.cpp.

References EXCEPTION.

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

◆ GetContainingElementIndexWithInitialGuess()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 372 of file TetrahedralMesh.cpp.

◆ GetContainingElementIndices()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

Parameters

rTestPoint reference to the point

Definition at line 444 of file TetrahedralMesh.cpp.

◆ GetInverseJacobianForElement()

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

virtual

Returns the Jacobian matrix, its inverse and its determinant for a given element (via arguments).

Parameters

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

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 727 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 CellwiseDataGradient< DIM >::SetupGradients().

◆ GetJacobianForElement()

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

virtual

Returns the Jacobian matrix and its determinant for a given element (via arguments).

Parameters

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

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 718 of file TetrahedralMesh.cpp.

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

◆ GetNearestElementIndex()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 417 of file TetrahedralMesh.cpp.

References EXCEPT_IF_NOT.

◆ GetSurfaceArea()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceArea ( )

Returns: the surface area of the mesh.

Definition at line 302 of file TetrahedralMesh.cpp.

◆ GetVolume()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

double TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume ( )

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 287 of file TetrahedralMesh.cpp.

Referenced by CellPopulationAreaWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

◆ GetWeightedDirectionForBoundaryElement()

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

virtual

Returns the weighted direction and the determinant of the Jacobian for a given boundary element (via arguments).

Parameters

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

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 746 of file TetrahedralMesh.cpp.

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

◆ GetWeightedDirectionForElement()

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

virtual

Returns the weighted direction and the determinant of the Jacobian for a given element (via arguments).

Parameters

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

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 737 of file TetrahedralMesh.cpp.

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

◆ ImportFromMesher()

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
	)

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

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

Todo:: #1545: (or add arguments ...)

Definition at line 842 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().

◆ InitialiseTriangulateIo()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::InitialiseTriangulateIo ( triangulateio & mesherIo )

protected

Convenience method to tidy up a triangleio data structure before use

Parameters

mesherIo is a triangulateio class

Definition at line 754 of file TetrahedralMesh.cpp.

◆ PermuteNodes() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes ( )

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 331 of file TetrahedralMesh.cpp.

References RandomNumberGenerator::Instance(), and RandomNumberGenerator::Shuffle().

◆ PermuteNodes() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 343 of file TetrahedralMesh.cpp.

◆ ReadNodesPerProcessorFile()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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 190 of file TetrahedralMesh.cpp.

◆ RefreshJacobianCachedData()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData ( )

virtual

Update mElementJacobians, mElementWeightedDirections and mBoundaryElementWeightedDirections.

Reimplemented in NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 669 of file TetrahedralMesh.cpp.

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

◆ RefreshMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh ( )

virtual

Overridden RefreshMesh method. This method calls RefreshJacobianCachedData.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in Toroidal2dMesh.

Definition at line 642 of file TetrahedralMesh.cpp.

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

◆ serialize()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the mesh.

Parameters

archive	the archive
version	the current version of this class

Definition at line 78 of file TetrahedralMesh.hpp.

◆ SolveBoundaryElementMapping()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping ( unsigned index ) const

protectedvirtual

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 662 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

◆ SolveElementMapping()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping ( unsigned index ) const

protectedvirtual

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 655 of file TetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

◆ SolveNodeMapping()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping ( unsigned index ) const

protectedvirtual

Overridden solve node mapping method.

Parameters

index the global index of the node

Returns: local index

Implements AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 648 of file TetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 70 of file TetrahedralMesh.hpp.

◆ TestCryptSimulation2d

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class TestCryptSimulation2d

friend

Definition at line 67 of file TetrahedralMesh.hpp.

◆ TestTetrahedralMesh

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class TestTetrahedralMesh

friend

Definition at line 66 of file TetrahedralMesh.hpp.

Member Data Documentation

◆ mBoundaryElementJacobianDeterminants

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 >::GetWeightedDirectionForBoundaryElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), Cylindrical2dMesh::ReMesh(), and Toroidal2dMesh::ReMesh().

◆ mBoundaryElementWeightedDirections

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(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), Cylindrical2dMesh::ReMesh(), and Toroidal2dMesh::ReMesh().

◆ mElementInverseJacobians

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 TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

◆ mElementJacobianDeterminants

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 >::GetWeightedDirectionForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

◆ mElementJacobians

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 TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

◆ mElementWeightedDirections

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

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

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

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TetrahedralMesh()

Member Function Documentation

◆ CheckIsConforming()

◆ Clear()

◆ ConstructFromMeshReader()

◆ EdgesBegin()

◆ EdgesEnd()

◆ ExportToMesher()

◆ FreeTriangulateIo()

◆ GetAngleBetweenNodes()

◆ GetContainingElementIndexWithInitialGuess()

◆ GetContainingElementIndices()

◆ GetInverseJacobianForElement()

◆ GetJacobianForElement()

◆ GetNearestElementIndex()

◆ GetSurfaceArea()

◆ GetVolume()

◆ GetWeightedDirectionForBoundaryElement()

◆ GetWeightedDirectionForElement()

◆ ImportFromMesher()

◆ InitialiseTriangulateIo()

◆ PermuteNodes() [1/2]

◆ PermuteNodes() [2/2]

◆ ReadNodesPerProcessorFile()

◆ RefreshJacobianCachedData()

◆ RefreshMesh()

◆ serialize()

◆ SolveBoundaryElementMapping()

◆ SolveElementMapping()

◆ SolveNodeMapping()

Friends And Related Symbol Documentation

◆ boost::serialization::access

◆ TestCryptSimulation2d

◆ TestTetrahedralMesh

Member Data Documentation

◆ mBoundaryElementJacobianDeterminants

◆ mBoundaryElementWeightedDirections

◆ mElementInverseJacobians

◆ mElementJacobianDeterminants

◆ mElementJacobians

◆ mElementWeightedDirections