#include <AbstractTetrahedralMesh.hpp>

Inheritance diagram for AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:

Classes
class	ElementIterator

Public Types
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

Public Member Functions
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

virtual void	ConstructFromMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)=0

void	ConstructFromMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rOtherMesh)

BoundaryElementIterator	GetBoundaryElementIteratorBegin () const

BoundaryElementIterator	GetBoundaryElementIteratorEnd () 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	GetWeightedDirectionForBoundaryElement (unsigned elementIndex, c_vector< double, SPACE_DIM > &rWeightedDirection, double &rJacobianDeterminant) 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 void	ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)

virtual DistributedVectorFactory *	GetDistributedVectorFactory ()

virtual void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

virtual void	PermuteNodes ()

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)

virtual void	RefreshMesh ()

bool	IsMeshChanging () const

unsigned	CalculateMaximumContainingElementsPerProcess () const

void	SetMeshHasChangedSinceLoading ()

Protected Member Functions
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
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
virtual unsigned	SolveElementMapping (unsigned index) const =0

virtual unsigned	SolveBoundaryElementMapping (unsigned index) const =0

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

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

Friends
class	AbstractConductivityTensors< ELEMENT_DIM, SPACE_DIM >

class	CentroidWriter

class	boost::serialization::access

Detailed Description

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

Abstract base class for all tetrahedral meshes (inherits from AbstractMesh).

Definition at line 71 of file AbstractTetrahedralMesh.hpp.

Member Typedef Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef std::vector<BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *>::const_iterator AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryElementIterator

Definition of boundary element Iterator type.

Definition at line 298 of file AbstractTetrahedralMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::AbstractTetrahedralMesh ( )

Constructor.

Definition at line 66 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractTetrahedralMesh ( )

virtual

Virtual destructor, since this class has virtual methods.

Definition at line 72 of file AbstractTetrahedralMesh.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfBoundaryElement ( unsigned faceIndex )

virtual

Determine whether or not the current process owns node 0 of this boundary element (tie breaker to determine which process writes to file for when two or more share ownership of a face).

Parameters

faceIndex is the global index of the face

Returns: true if this process is designated owner

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 688 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement ( unsigned elementIndex )

virtual

Determine whether or not the current process owns node 0 of this element (tie breaker to determine which process writes to file for when two or more share ownership of an element).

Parameters

elementIndex is the global index of the element

Returns: true if this process is designated owner

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 705 of file AbstractTetrahedralMesh.cpp.

Referenced by AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumNodeConnectivityPerProcess ( ) const

Returns: Iterates through local nodes and finds two representative nodes with a maximum number of containing elements for all locally owned nodes. The two representative nodes are the most connected nodes at the boundary and the most connected node in the interior. This is because a well-element-connected boundary node is likely to be connected to more nodes since fewer of them will overlap.) At these representative node the node connectivity (number of nodes in forward star) is determined.

Useful for determining FEM matrix fill.

Definition at line 722 of file AbstractTetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

c_vector< double, 2 > AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths ( )

virtual

Computes the minimum and maximum lengths of the edges in the mesh. Overridden in Distributed case

Todo:: Should be const

Returns: The minimum and maximum edge lengths in the mesh

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 972 of file AbstractTetrahedralMesh.cpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths(), and FineCoarseMeshPair< DIM >::SetUpBoxes().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateNodeExchange	(	std::vector< std::vector< unsigned > > &	rNodesToSendPerProcess,
		std::vector< std::vector< unsigned > > &	rNodesToReceivePerProcess
	)

Get the nodes which will need to be exchanged between remote processes. If we have an element which node indices outside the local [mLo, mHi) region then we know that those nodes will need to be recieved from a remote process, while those inside the range [mLo, mHi) will need to be sent

Parameters

rNodesToSendPerProcess	(output) a vector which will be of size GetNumProcs() where each internal vector except i=GetMyRank() contains an ordered list of indices of nodes to send to process i
rNodesToReceivePerProcess	(output) a vector which will be of size GetNumProcs() for information to receive for process i

Todo:: #2426 This is where we should check that we DO HAVE a Tetrahedral (not Distributed mesh)

Definition at line 889 of file AbstractTetrahedralMesh.cpp.

References PetscTools::GetNumProcs().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals ( )

Check whether mesh has outward-facing normals.

This throws a suitable exception if an inward facing normal is found.

Returns: nothing

Definition at line 187 of file AbstractTetrahedralMesh.cpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), and Node< SPACE_DIM >::rGetLocation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid	(	unsigned	width,
		unsigned	height,
		unsigned	depth
	)

virtual

Construct a 3D cuboid grid on [0,width]x[0,height]x[0,depth].

Parameters

width	width of the mesh (in the x-direction)
height	height of the mesh (in the y-direction)
depth	depth of the mesh (in the z-direction).

In this method the width is also THE NUMBER OF ELEMENTS IN THE x-direction, and similarly with the y and z directions.

Overridden in DistributedTetrahedralMesh

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, and QuadraticMesh< DIM >.

Definition at line 388 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMesh< DIM >::ConstructCuboid(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & rOtherMesh )

Construct the mesh using another mesh. This takes a mesh of a given concrete class and produces a deep copy.

Use with caution when copying between subclasses.

Parameters

rOtherMesh the mesh to copy

Todo:: Can we make this const?

Definition at line 840 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

pure virtual

Construct the mesh using a MeshReader. This method must be overridden in concrete classes.

Parameters

rMeshReader the mesh reader

Implemented in TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, and MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh ( unsigned width )

virtual

Construct a 1D linear grid on [0,width]

ELEMENT_DIM must be equal to 1. If SPACE_DIM > 1 then the y & z default to 0.0 for every node.

Parameters

width width of the mesh (in the x-direction)

In this method the width is also THE NUMBER OF ELEMENTS IN THE x-direction.

Overridden in DistributedTetrahedralMesh

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, and QuadraticMesh< DIM >.

Definition at line 246 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMesh< DIM >::ConstructLinearMesh(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh	(	unsigned	width,
		unsigned	height,
		bool	stagger = `true`
	)

virtual

Construct a 2D rectangular grid on [0,width]x[0,height].

Diagonals can be staggered so that there is no preferred diffusion propagation direction.

Parameters

width	width of the mesh (in the x-direction)
height	height of the mesh (in the y-direction)
stagger	whether the mesh should 'jumble' up the elements (defaults to true)

In this method the width is also THE NUMBER OF ELEMENTS IN THE x-direction, and similarly with the y direction.

Overridden in DistributedTetrahedralMesh

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, and QuadraticMesh< DIM >.

Definition at line 278 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMesh< DIM >::ConstructRectangularMesh(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh	(	double	spaceStep,
		double	width,
		double	height = `0`,
		double	depth = `0`
	)

Create a 1D mesh on [0, width], 2D mesh on [0, width]x[0 height] with staggering or 3D mesh on [0, width]x[0 height]x[0 depth with a given axis-aligned space step. If SPACE_DIM > ELEMENT_DIM then the y & z default to 0.0 for every node.

Parameters

spaceStep	The axis-aligned space step
width	The width (x-dimension)
height	The height (y-dimension - ignored if ELEMENT_DIM is 1D)
depth	The depth (z-dimension -ignored in 1D and 2D)

Definition at line 573 of file AbstractTetrahedralMesh.cpp.

References EXCEPTION.

Referenced by CardiacElectroMechProbRegularGeom< DIM >::CardiacElectroMechProbRegularGeom(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), and CellBasedPdeHandler< DIM >::UseCoarsePdeMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMeshWithDimensionSplit	(	unsigned	dimension,
		double	spaceStep,
		double	width,
		double	height = `0`,
		double	depth = `0`
	)

This is a wrapper method to ConstructRegularSlabMesh() which is useful for parallel distributed meshes. By default slabs are split across processes in the top dimension (y in 2d, z in 3d) but it may be more useful to split in x or y.

Create a 1D mesh on [0, width], 2D mesh on [0, width]x[0 height] with staggering or 3D mesh on [0, width]x[0 height]x[0 depth with a given axis-aligned space step. If SPACE_DIM > ELEMENT_DIM then the y & z default to 0.0 for every node.

Parameters

dimension	The dimension/axis to be split over the processes. When dimension=0 the split is on x, dimension=1 indicates split on y etc. If dimension >= SPACE_DIM then an exception is thrown.
spaceStep	The axis-aligned space step
width	The width (x-dimension)
height	The height (y-dimension - ignored if ELEMENT_DIM is 1D)
depth	The depth (z-dimension -ignored in 1D and 2D)

Definition at line 621 of file AbstractTetrahedralMesh.cpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > * AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElement ( unsigned index ) const

Get the boundary element with a given index in the mesh.

Parameters

index the global index of the boundary element

Returns: a pointer to the boundary element.

Definition at line 148 of file AbstractTetrahedralMesh.cpp.

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::MergeFromArchive(), and Cylindrical2dMesh::ReconstructCylindricalMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryElementIterator AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin ( ) const

Returns: a pointer to the first boundary element in the mesh.

Definition at line 155 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::CheckBoundaryElements(), Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), CellBasedPdeHandlerOnCuboid< DIM >::ConstructBoundaryConditionsContainer(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), Electrodes< DIM >::Electrodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Validate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryElementIterator AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd ( ) const

Returns: a pointer to *one past* the last boundary element in the mesh (for consistency with STL iterators).

Definition at line 161 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::CheckBoundaryElements(), CellBasedPdeHandlerOnCuboid< DIM >::ConstructBoundaryConditionsContainer(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), Electrodes< DIM >::Electrodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Validate().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex	(	const ChastePoint< SPACE_DIM > &	rTestPoint,
		bool	strict = `false`,
		std::set< unsigned >	testElements = `std::set<unsigned>()`,
		bool	onlyTryWithTestElements = `false`
	)

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

Parameters

rTestPoint	reference to the point
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).

Returns: element index

Definition at line 996 of file AbstractTetrahedralMesh.cpp.

References EXCEPTION.

Referenced by CellBasedPdeHandler< DIM >::GetPdeSolutionAtPoint(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), and AveragedSourcePde< DIM >::SetupSourceTerms().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Element< ELEMENT_DIM, SPACE_DIM > * AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement ( unsigned index ) const

Get the element with a given index in the mesh.

Parameters

index the global index of the element

Returns: a pointer to the element.

Definition at line 141 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), Cylindrical2dMesh::CorrectNonPeriodicMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::EdgeIterator(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeA(), CellBasedPdeHandler< DIM >::GetPdeSolutionAtPoint(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), Cylindrical2dMesh::ReMesh(), FineCoarseMeshPair< DIM >::SetUpBoxes(), CellwiseDataGradient< DIM >::SetupGradients(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AveragedSourcePde< DIM >::SetupSourceTerms(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), and VoltageInterpolaterOntoMechanicsMesh< DIM >::VoltageInterpolaterOntoMechanicsMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ElementIterator AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin ( bool skipDeletedElements = true )

inline

Returns: an iterator to the first element in the mesh.

Parameters

skipDeletedElements whether to include deleted element

Definition at line 735 of file AbstractTetrahedralMesh.hpp.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), BidomainProblem< DIM >::AnalyseMeshForBath(), CompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), IncompressibleNonlinearElasticitySolver< DIM >::FormInitialGuess(), Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), PapillaryFibreCalculator::GetRadiusVectors(), AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::Initialise(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), Cylindrical2dMesh::ReconstructCylindricalMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), AbstractContinuumMechanicsSolver< DIM >::RemovePressureDummyValuesThroughLinearInterpolation(), PapillaryFibreCalculator::SmoothStructureTensors(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), VtkNonlinearElasticitySolutionWriter< DIM >::Write(), AbstractNonlinearElasticitySolver< DIM >::WriteCurrentStrains(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ElementIterator AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd ( )

inline

Returns: an iterator to one past the last element in the mesh.

Definition at line 742 of file AbstractTetrahedralMesh.hpp.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), PapillaryFibreCalculator::GetRadiusVectors(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), Cylindrical2dMesh::ReconstructCylindricalMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), PapillaryFibreCalculator::SmoothStructureTensors(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetHaloNodeIndices ( std::vector< unsigned > & rHaloIndices ) const

virtual

Utility method to give the functionality of iterating through the halo nodes of a process. Will return an empty std::vector (i.e. no halo nodes) unless overridden by distributed derived classes.

Parameters

rHaloIndices A vector to fill with the global indices of the nodes which are locally halos

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 833 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< 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

Compute the inverse Jacobian for a given element in the mesh.

Parameters

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

Reimplemented in TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, and NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 167 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetMaximumNodeIndex ( )

virtual

Returns: the largest index of nodes on this process. Overwritten in subclasses and used for setting up NodeMaps; the largest node index on this process.

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

Definition at line 135 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestElementIndexFromTestElements	(	const ChastePoint< SPACE_DIM > &	rTestPoint,
		std::set< unsigned >	testElements
	)

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

Parameters

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

Returns: element index

Definition at line 1045 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllBoundaryElements ( ) const

Returns: the total number of boundary elements (including those marked as deleted).

Definition at line 117 of file AbstractTetrahedralMesh.cpp.

Referenced by Cylindrical2dMesh::ReconstructCylindricalMesh(), and TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements ( ) const

Returns: the total number of elements (including those marked as deleted).

Definition at line 99 of file AbstractTetrahedralMesh.cpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::EdgeIterator(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesEnd(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), Cylindrical2dMesh::ReMesh(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements ( ) const

virtual

Returns: the number of boundary elements that are actually in use.

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

Definition at line 105 of file AbstractTetrahedralMesh.cpp.

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumCableElements ( ) const

virtual

Returns: the number of cable elements that are actually in use.

This will always return zero until overridden in the MixedDimensionMesh class

Reimplemented in MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 123 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements ( ) const

virtual

Returns: the number of elements that are actually in use.

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

Definition at line 87 of file AbstractTetrahedralMesh.cpp.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), PapillaryFibreCalculator::CalculateFibreOrientations(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), PapillaryFibreCalculator::PapillaryFibreCalculator(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetFineCoarseMeshPair(), FineCoarseMeshPair< DIM >::SetUpBoxes(), CellwiseDataGradient< DIM >::SetupGradients(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AveragedSourcePde< DIM >::SetupSourceTerms(), and XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalBoundaryElements ( ) const

virtual

Returns: the number of local boundary elements that are in use on this process (only over-ridden when the mesh is distributed).

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 111 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToBoundaryElements().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalElements ( ) const

virtual

Returns: the number of local elements that are in use on this process (only over-ridden when the mesh is distributed).

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 93 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumVertices ( ) const

virtual

Returns: the number of vertices (nodes which are also corners of elements). For a linear mesh all nodes are vertices, so this method is a synonym for GetNumNodes. However, it is over-ridden in quadratic meshes.

Reimplemented in QuadraticMesh< DIM >.

Definition at line 129 of file AbstractTetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement	(	unsigned	elementIndex,
		c_vector< double, SPACE_DIM > &	rWeightedDirection,
		double &	rJacobianDeterminant
	)		const

virtual

Compute the weighted direction for a given boundary element.

Parameters

elementIndex	index of an element
rWeightedDirection	the weighted direction vector
rJacobianDeterminant	the determinant of the Jacobian matrix

Reimplemented in TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, TetrahedralMesh< 3, 3 >, and NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 177 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

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

inlineprivate

Loads a mesh by using TrianglesMeshReader and the location in ArchiveLocationInfo.

Parameters

archive
version

Todo:: #1199 make this work for everything else...

Definition at line 190 of file AbstractTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

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

inlineprivate

Archive the AbstractTetrahedralMesh. Note that this will write out a TrianglesMeshWriter file to wherever ArchiveLocationInfo has specified.

If the mesh is MutableMesh (or a subclass) the file is written by examining the current mesh.

If the mesh is not mutable then the file is a copy of the original file the mesh was read from.

Parameters

archive	the archive
version	the current version of this class

Definition at line 118 of file AbstractTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships ( )

protectedvirtual

Sets the ownership of each element according to which nodes are owned by the process.

Information on node ownership comes from the distributed vector factory and an element is "owned" if one or more of its nodes are owned

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 45 of file AbstractTetrahedralMesh.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

privatepure virtual

Pure virtual solve boundary element mapping method. For a boundary element with a given global index, get the local index used by this process. Overridden in TetrahedralMesh and DistributedTetrahedralMesh classes.

Parameters

index the global index of the boundary element

Returns: local index

Implemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

privatepure virtual

Pure virtual solve element mapping method. For an element with a given global index, get the local index used by this process. Overridden in TetrahedralMesh and DistributedTetrahedralMesh classes.

Parameters

index the global index of the element