#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 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
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)
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 ()
Protected Member Functions
void	SetElementOwnerships ()
Protected Attributes
bool	mMeshIsLinear
std::vector< Element < ELEMENT_DIM, SPACE_DIM > * >	mElements
std::vector< BoundaryElement < ELEMENT_DIM-1, SPACE_DIM > * >	mBoundaryElements
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	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 295 of file AbstractTetrahedralMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::AbstractTetrahedralMesh ( )

Constructor.

Definition at line 65 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 71 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

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

Definition at line 614 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

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

Definition at line 631 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 the node with the/a maximum number of containing elements for all locally owned nodes. At that representative node the node connectivity (number of nodes in forward star) is determined.

Useful for determining FEM matrix fill.

Definition at line 648 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]

Calculate the bounding box (width extremes for all dimensions of 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 837 of file AbstractTetrahedralMesh.cpp.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths().

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

Definition at line 754 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 180 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 >, QuadraticMesh< DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 381 of file AbstractTetrahedralMesh.cpp.

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.

Todo:: Can we make this const?

Parameters:

rOtherMesh the mesh to copy

Definition at line 705 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 DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, DIM >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

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 >, QuadraticMesh< DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 239 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMesh< 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 >, QuadraticMesh< DIM >, and DistributedTetrahedralMesh< DIM, DIM >.

Definition at line 271 of file AbstractTetrahedralMesh.cpp.

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 566 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>

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 141 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

Return a pointer to the first boundary element in the mesh.

Definition at line 148 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::CheckBoundaryElements(), Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), Electrodes< DIM >::Electrodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), 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

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

Definition at line 154 of file AbstractTetrahedralMesh.cpp.

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

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 134 of file AbstractTetrahedralMesh.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), AdaptiveTetrahedralMesh::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(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), Node< SPACE_DIM >::IsFlagged(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), Cylindrical2dMesh::ReMesh(), FineCoarseMeshPair< DIM >::SetUpBoxes(), CellwiseDataGradient< DIM >::SetupGradients(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AveragedSourcePde< DIM >::SetupSourceTerms(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), 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]

Get an iterator to the first element in the mesh.

Parameters:

skipDeletedElements whether to include deleted element

Definition at line 671 of file AbstractTetrahedralMesh.hpp.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), BidomainProblem< DIM >::AnalyseMeshForBath(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), CompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), AdaptiveTetrahedralMesh::ConstructFromDistributedMesh(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), PapillaryFibreCalculator::GetRadiusVectors(), AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::Initialise(), Cylindrical2dMesh::ReconstructCylindricalMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), AbstractContinuumMechanicsSolver< DIM >::RemovePressureDummyValuesThroughLinearInterpolation(), PapillaryFibreCalculator::SmoothStructureTensors(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), AbstractNonlinearElasticitySolver< DIM >::WriteCurrentDeformationGradients(), 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]

Get an iterator to one past the last element in the mesh.

Definition at line 678 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(), AdaptiveTetrahedralMesh::ConstructFromDistributedMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), PapillaryFibreCalculator::GetRadiusVectors(), Cylindrical2dMesh::ReconstructCylindricalMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), PapillaryFibreCalculator::SmoothStructureTensors(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), VtkMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles().

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 698 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 NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 160 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

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

Definition at line 116 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

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

Definition at line 98 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 >::EdgeIterator::operator++(), 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]

Get the number of boundary elements that are actually in use.

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

Definition at line 104 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]

Get 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]

Get the number of elements that are actually in use.

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

Definition at line 86 of file AbstractTetrahedralMesh.cpp.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), PapillaryFibreCalculator::CalculateFibreOrientations(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), AdaptiveTetrahedralMesh::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 CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Get 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 110 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]

Get 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 92 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]

Get 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 128 of file AbstractTetrahedralMesh.cpp.

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

Definition at line 170 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
	)		`[inline, private]`

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 187 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 `[inline, private]`

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 115 of file AbstractTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships ( ) [protected, virtual]

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 44 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 [private, pure 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

Implemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, 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 [private, pure 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

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