AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractTetrahedralMesh.hpp>

Inherits AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Inherited by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< 3, 3 >, and TetrahedralMesh< DIM, DIM >.

Collaboration diagram for AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:
Collaboration graph
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List of all members.

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 GetNumBoundaryElements () const
unsigned GetNumAllElements () const
unsigned GetNumAllBoundaryElements () const
Element< ELEMENT_DIM, SPACE_DIM > * GetElement (unsigned index) const
BoundaryElement< ELEMENT_DIM-1,
SPACE_DIM > * 		GetBoundaryElement (unsigned index) const
virtual void SetElementOwnerships (unsigned lo, unsigned hi)
virtual void ConstructFromMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)=0
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
virtual void ConstructLinearMesh (unsigned width)
virtual void ConstructRectangularMesh (unsigned width, unsigned height, bool stagger=true)
virtual void ConstructCuboid (unsigned width, unsigned height, unsigned depth)
virtual bool CalculateDesignatedOwnershipOfBoundaryElement (unsigned faceIndex)
virtual bool CalculateDesignatedOwnershipOfElement (unsigned elementIndex)

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 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 54 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 204 of file AbstractTetrahedralMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::AbstractTetrahedralMesh (  )  [inline]

Constructor.

Definition at line 57 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractTetrahedralMesh (  )  [inline, virtual]

Virtual destructor, since this class has virtual methods.

Definition at line 63 of file AbstractTetrahedralMesh.cpp.

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

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfBoundaryElement ( unsigned  faceIndex  )  [inline, 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 >.

Definition at line 472 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElement(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory().

Referenced by Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement ( unsigned  elementIndex  )  [inline, 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 >.

Definition at line 489 of file AbstractTetrahedralMesh.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid ( unsigned  width,
unsigned  height,
unsigned  depth 
) [inline, 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) Overridden in DistributedTetrahedralMesh

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 286 of file AbstractTetrahedralMesh.cpp.

References 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 AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

Referenced by CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::ConstructHyperCube().

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 >, TetrahedralMesh< ELEMENT_DIM, SPACE_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  )  [inline, virtual]

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

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) Overridden in DistributedTetrahedralMesh

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 148 of file AbstractTetrahedralMesh.cpp.

References 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 AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

Referenced by CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::ConstructHyperCube().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh ( unsigned  width,
unsigned  height,
bool  stagger = true 
) [inline, 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) Overridden in DistributedTetrahedralMesh

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 179 of file AbstractTetrahedralMesh.cpp.

References 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 AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

Referenced by CardiacElectroMechProbRegularGeom< DIM >::CardiacElectroMechProbRegularGeom(), and CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::ConstructHyperCube().

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

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 110 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping().

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfBoundaryElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::MergeFromArchive(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), Cylindrical2dMesh::ReconstructCylindricalMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryElementIterator AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin (  )  const [inline]

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

Definition at line 117 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

Referenced by QuadraticMesh< DIM >::AddNodesToBoundaryElements(), Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), QuadraticMesh< DIM >::ConstructFromMeshReader(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), Electrodes< DIM >::Electrodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceArea(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Validate(), and QuadraticMesh< DIM >::WriteBoundaryElementFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryElementIterator AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd (  )  const [inline]

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

Definition at line 123 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

Referenced by QuadraticMesh< DIM >::AddNodesToBoundaryElements(), Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), QuadraticMesh< DIM >::ConstructFromMeshReader(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), Electrodes< DIM >::Electrodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceArea(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Validate(), and QuadraticMesh< DIM >::WriteBoundaryElementFile().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
Element< ELEMENT_DIM, SPACE_DIM > * AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement ( unsigned  index  )  const [inline]

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 103 of file AbstractTetrahedralMesh.cpp.

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

Referenced by QuadraticMesh< DIM >::AddNodesToBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseQuadPoints(), QuadraticMesh< DIM >::ConstructFromMeshReader(), Cylindrical2dMesh::CorrectNonPeriodicMesh(), BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::EdgeIterator(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgesBegin(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), VoronoiTessellation< DIM >::GenerateVerticesFromElementCircumcentres(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeA(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeB(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), VoronoiTessellation< DIM >::Initialise(), Node< SPACE_DIM >::IsFlagged(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::operator++(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), Cylindrical2dMesh::ReMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode(), FineCoarseMeshPair< DIM >::SetUpBoxesOnFineMesh(), CardiacElectroMechanicsProblem< DIM >::Solve(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), and VertexMesh< 2, 2 >::VertexMesh().

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 457 of file AbstractTetrahedralMesh.hpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundaryOfFlaggedRegion(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsConforming(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::FlagElementsNotContainingNodes(), Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), PapillaryFibreCalculator::GetRadiusVectors(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), Cylindrical2dMesh::ReconstructCylindricalMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), PapillaryFibreCalculator::SmoothStructureTensors(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::UnflagAllElements(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), and MeshBasedTissue< DIM >::WriteResultsToFiles().

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 464 of file AbstractTetrahedralMesh.hpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundaryOfFlaggedRegion(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsConforming(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::FlagElementsNotContainingNodes(), Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), PapillaryFibreCalculator::GetRadiusVectors(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), Cylindrical2dMesh::ReconstructCylindricalMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), PapillaryFibreCalculator::SmoothStructureTensors(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::UnflagAllElements(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), and MeshBasedTissue< DIM >::WriteResultsToFiles().

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 [inline, 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 129 of file AbstractTetrahedralMesh.cpp.

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

Referenced by StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllBoundaryElements (  )  const [inline]

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

Definition at line 90 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements (  )  const [inline]

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

Definition at line 84 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

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 >::PermuteNodesWithMetisBinaries(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), Cylindrical2dMesh::ReMesh(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh(), and VertexMesh< 2, 2 >::VertexMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements (  )  const [inline, virtual]

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

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

Definition at line 96 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsConforming(), QuadraticMesh< DIM >::ConstructFromMeshReader(), and BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements (  )  const [inline, virtual]

Get the number of elements that are actually in use.

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

Definition at line 78 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by AbstractCardiacMechanicsAssembler< DIM >::AbstractCardiacMechanicsAssembler(), QuadraticMesh< DIM >::AddNodesToBoundaryElements(), PapillaryFibreCalculator::CalculateFibreOrientations(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), QuadraticMesh< DIM >::ConstructFromMeshReader(), BidomainPde< SPACE_DIM >::CreateExtracellularConductivityTensors(), StreeterFibreGenerator< SPACE_DIM >::GenerateOrthotropicFibreOrientation(), VoronoiTessellation< DIM >::GenerateVerticesFromElementCircumcentres(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndexWithInitialGuess(), VoronoiTessellation< DIM >::Initialise(), NonlinearElasticityAssembler< DIM >::NonlinearElasticityAssembler(), PapillaryFibreCalculator::PapillaryFibreCalculator(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodesWithMetisBinaries(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), FineCoarseMeshPair< DIM >::SetUpBoxesOnFineMesh(), and VertexMesh< 2, 2 >::VertexMesh().

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 [inline, 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 139 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping().

Referenced by Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality().

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 124 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

Always write the in-memory mesh to disk, to make sure we have a properly permuted version of it.

Todo:
#1200 This is bad for very large meshes. Consider making a symlink and just writing the permutation. Perhaps even copy the permutation file from an earlier checkpoint?

Definition at line 96 of file AbstractTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships ( unsigned  lo,
unsigned  hi 
) [inline, virtual]

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

Parameters:
lo is the lowest node number owned by the process
hi is one higher than the highest node number owned by the process ie. this process owns nodes [lo..hi) and element is "owned" if one or more of its nodes are owned

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 37 of file AbstractTetrahedralMesh.cpp.

References AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, 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 >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElement(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement().

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 >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

Referenced by AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< ELEMENT_DIM, SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, QuadraticMesh< DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, Cylindrical2dMesh, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 82 of file AbstractTetrahedralMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<BoundaryElement<ELEMENT_DIM-1, SPACE_DIM> *> AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements [protected]

Vector of pointers to boundary elements in the mesh.

Definition at line 195 of file AbstractTetrahedralMesh.hpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllBoundaryElements(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalBoundaryElements(), NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetWeightedDirectionForBoundaryElement(), QuadraticMesh< DIM >::QuadraticMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterBoundaryElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), Cylindrical2dMesh::ReMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveBoundaryElementMapping(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractTetrahedralMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<Element<ELEMENT_DIM, SPACE_DIM> *> AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements [protected]

Vector of pointers to elements in the mesh.

Definition at line 192 of file AbstractTetrahedralMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ElementIterator::ElementIterator(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndexWithInitialGuess(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndices(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetInverseJacobianForElement(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestElementIndex(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNearestElementIndexFromTestElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ElementIterator::IsAtEnd(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodesWithMetisBinaries(), QuadraticMesh< DIM >::QuadraticMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveElementMapping(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::~AbstractTetrahedralMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mMeshIsLinear [protected]

Most tet meshes are linear (set to true). Set to false in quadratics.

Definition at line 60 of file AbstractTetrahedralMesh.hpp.

Referenced by AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::load(), QuadraticMesh< DIM >::QuadraticMesh(), and AbstractTetrahedralMesh< SPACE_DIM, SPACE_DIM >::save().

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