AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractTetrahedralMesh.hpp>

Inherits AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

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

Collaboration diagram for AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >:
Collaboration graph
[legend]

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 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)
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)

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 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 (  )  [inline]

Constructor.

Definition at line 67 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 73 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
Returns:
true if this process is designated owner

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

Definition at line 622 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
Returns:
true if this process is designated owner

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

Definition at line 639 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().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumNodeConnectivityPerProcess (  )  const [inline]
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 656 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector< double, 2 > AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths (  )  [inline, 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 870 of file AbstractTetrahedralMesh.cpp.

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

Referenced by 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 
) [inline]

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 787 of file AbstractTetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), PetscTools::GetNumProcs(), and DistributedVectorFactory::rGetGlobalLows().

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

Check whether mesh has outward-facing normals.

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

Returns:
nothing

Definition at line 188 of file AbstractTetrahedralMesh.cpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), EXCEPTION, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorEnd(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), and Node< SPACE_DIM >::rGetLocation().

Referenced by AbstractNonlinearElasticitySolver< DIM >::Solve().

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).

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 389 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 DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &  rOtherMesh  )  [inline]

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 738 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), Node< SPACE_DIM >::IsBoundaryNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::IsDeleted(), Node< SPACE_DIM >::IsDeleted(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryNodes, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh(), BoundaryElement< ELEMENT_DIM, SPACE_DIM >::RegisterWithNodes(), Element< ELEMENT_DIM, SPACE_DIM >::RegisterWithNodes(), and Node< SPACE_DIM >::rGetLocation().

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  )  [inline, 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 247 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 DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh().

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)

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 279 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 DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRegularSlabMesh ( double  spaceStep,
double  width,
double  height = 0,
double  depth = 0 
) [inline]

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 574 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), EXCEPTION, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale().

Referenced by CardiacElectroMechProbRegularGeom< DIM >::CardiacElectroMechProbRegularGeom(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), QuadraticMesh< DIM >::QuadraticMesh(), 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 [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 149 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(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::MergeFromArchive(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), Cylindrical2dMesh::ReconstructCylindricalMesh(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::BoundaryElementIterator AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElementIteratorBegin (  )  const [inline]
Returns:
a pointer to the first boundary element in the mesh.

Definition at line 156 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::CheckBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals(), Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), CellBasedPdeHandlerOnCuboid< DIM >::ConstructBoundaryConditionsContainer(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), QuadraticMesh< DIM >::ConstructCuboid(), QuadraticMesh< DIM >::ConstructRectangularMesh(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), Electrodes< DIM >::Electrodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceArea(), 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 [inline]
Returns:
a pointer to *one past* the last boundary element in the mesh (for consistency with STL iterators).

Definition at line 162 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

Referenced by QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), QuadraticMeshHelper< DIM >::CheckBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals(), Electrodes< DIM >::ComputeElectrodesAreasAndCheckEquality(), CellBasedPdeHandlerOnCuboid< DIM >::ConstructBoundaryConditionsContainer(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), QuadraticMesh< DIM >::ConstructCuboid(), QuadraticMesh< DIM >::ConstructRectangularMesh(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::DefineZeroNeumannOnMeshBoundary(), Electrodes< DIM >::Electrodes(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetSurfaceArea(), 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 
) [inline]

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 894 of file AbstractTetrahedralMesh.cpp.

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

Referenced by FineCoarseMeshPair< DIM >::ComputeCoarseElementForGivenPoint(), FineCoarseMeshPair< DIM >::ComputeFineElementAndWeightForGivenPoint(), CellBasedPdeHandler< DIM >::FindCoarseElementContainingCell(), CellBasedPdeHandler< DIM >::GetPdeSolutionAtPoint(), CellBasedPdeHandler< DIM >::InitialiseCellPdeElementMap(), 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 [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 142 of file AbstractTetrahedralMesh.cpp.

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

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), AbstractNonlinearElasticitySolver< DIM >::AssembleOnBoundaryElementForPressureOnDeformedBc(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumNodeConnectivityPerProcess(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals(), FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineElementCentroids(), ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux(), FineCoarseMeshPair< DIM >::ComputeFineElementAndWeightForGivenPoint(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), Cylindrical2dMesh::CorrectNonPeriodicMesh(), 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(), CellBasedPdeHandler< DIM >::FindCoarseElementContainingCell(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeA(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::GetNodeB(), CellBasedPdeHandler< DIM >::GetPdeSolutionAtPoint(), PapillaryFibreCalculator::GetRadiusVectorForOneElement(), Node< SPACE_DIM >::IsFlagged(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::EdgeIterator::operator++(), Cylindrical2dMesh::ReMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode(), FineCoarseMeshPair< DIM >::SetUpBoxes(), CellwiseDataGradient< DIM >::SetupGradients(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AveragedSourcePde< DIM >::SetupSourceTerms(), CardiacElectroMechanicsProblem< DIM, ELEC_PROB_DIM >::Solve(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge(), 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 718 of file AbstractTetrahedralMesh.hpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), CompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundaryOfFlaggedRegion(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateNodeExchange(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsConforming(), QuadraticMesh< DIM >::ConstructCuboid(), QuadraticMesh< DIM >::ConstructRectangularMesh(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::FlagElementsNotContainingNodes(), IncompressibleNonlinearElasticitySolver< DIM >::FormInitialGuess(), Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), PapillaryFibreCalculator::GetRadiusVectors(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), Cylindrical2dMesh::ReconstructCylindricalMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), AbstractContinuumMechanicsSolver< DIM >::RemovePressureDummyValuesThroughLinearInterpolation(), PapillaryFibreCalculator::SmoothStructureTensors(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitLongEdges(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::UnflagAllElements(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), 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 725 of file AbstractTetrahedralMesh.hpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), CompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), AbstractFunctionalCalculator< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::Calculate(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundaryOfFlaggedRegion(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMinMaxEdgeLengths(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateNodeExchange(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsConforming(), QuadraticMesh< DIM >::ConstructCuboid(), QuadraticMesh< DIM >::ConstructRectangularMesh(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), AbstractContinuumMechanicsSolver< DIM >::CreateVtkOutput(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ExportToMesher(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::FlagElementsNotContainingNodes(), IncompressibleNonlinearElasticitySolver< DIM >::FormInitialGuess(), Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), PapillaryFibreCalculator::GetRadiusVectors(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetVolume(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), Cylindrical2dMesh::ReconstructCylindricalMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RefreshJacobianCachedData(), AbstractContinuumMechanicsSolver< DIM >::RemovePressureDummyValuesThroughLinearInterpolation(), PapillaryFibreCalculator::SmoothStructureTensors(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitLongEdges(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::UnflagAllElements(), Cylindrical2dMesh::UseTheseElementsToDecideMeshing(), AbstractNonlinearElasticitySolver< DIM >::WriteCurrentStrains(), 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 [inline, 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 731 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 [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 168 of file AbstractTetrahedralMesh.cpp.

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

Referenced by AbstractNonlinearElasticitySolver< DIM >::AssembleOnBoundaryElementForPressureOnDeformedBc(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleOnElement(), CompressibleNonlinearElasticitySolver< DIM >::AssembleOnElement(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::AssembleOnElement(), ElectrodesStimulusFactory< DIM >::ComputeElectrodeTotalFlux(), and AbstractNonlinearElasticitySolver< DIM >::GetElementCentroidStrain().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetMaximumNodeIndex (  )  [inline, 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 136 of file AbstractTetrahedralMesh.cpp.

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

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

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 942 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by FineCoarseMeshPair< DIM >::ComputeCoarseElementForGivenPoint(), and FineCoarseMeshPair< DIM >::ComputeFineElementAndWeightForGivenPoint().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllBoundaryElements (  )  const [inline]
Returns:
the total number of boundary elements (including those marked as deleted).

Definition at line 118 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

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

Definition at line 100 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 >::RefreshJacobianCachedData(), Cylindrical2dMesh::ReMesh(), and Cylindrical2dMesh::UseTheseElementsToDecideMeshing().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements (  )  const [inline, virtual]
Returns:
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 106 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumCableElements (  )  const [inline, 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 124 of file AbstractTetrahedralMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements (  )  const [inline, virtual]
Returns:
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 88 of file AbstractTetrahedralMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements.

Referenced by AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AbstractCorrectionTermAssembler(), AbstractNonlinearElasticitySolver< DIM >::AddStressToAverageStressPerElement(), IncompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), CompressibleNonlinearElasticitySolver< DIM >::AssembleSystem(), PapillaryFibreCalculator::CalculateFibreOrientations(), FineCoarseMeshPair< DIM >::ComputeCoarseElementsForFineElementCentroids(), CuboidMeshConstructor< ELEMENT_DIM, SPACE_DIM >::Construct(), CellBasedPdeHandler< DIM >::ConstructBoundaryConditionsContainer(), QuadraticMesh< DIM >::ConstructFromLinearMeshReader(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), ExtendedBidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors(), ExtendedBidomainTissue< SPACE_DIM >::CreateIntracellularConductivityTensorSecondCell(), AbstractContinuumMechanicsAssembler< DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX >::DoAssemble(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), AbstractNonlinearElasticitySolver< DIM >::GetAverageStressPerElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndex(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetContainingElementIndexWithInitialGuess(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalElements(), PapillaryFibreCalculator::PapillaryFibreCalculator(), QuadraturePointsGroup< DIM >::QuadraturePointsGroup(), AbstractNonlinearElasticitySolver< DIM >::SetComputeAverageStressPerElementDuringSolve(), AbstractCardiacMechanicsSolver< ELASTICITY_SOLVER, DIM >::SetFineCoarseMeshPair(), SolidMechanicsProblemDefinition< DIM >::SetMaterialLaw(), FineCoarseMeshPair< DIM >::SetUpBoxes(), CellwiseDataGradient< DIM >::SetupGradients(), VolumeDependentAveragedSourcePde< DIM >::SetupSourceTerms(), AveragedSourcePde< DIM >::SetupSourceTerms(), AbstractNonlinearElasticitySolver< DIM >::WriteCurrentAverageElementStresses(), and XdmfMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalBoundaryElements (  )  const [inline, 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 112 of file AbstractTetrahedralMesh.cpp.

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

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalElements (  )  const [inline, 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 94 of file AbstractTetrahedralMesh.cpp.

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

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), and BidomainTissue< SPACE_DIM >::CreateExtracellularConductivityTensors().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumVertices (  )  const [inline, 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 130 of file AbstractTetrahedralMesh.cpp.

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

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 [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 178 of file AbstractTetrahedralMesh.cpp.

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

Referenced by ContinuumMechanicsNeumannBcsAssembler< DIM >::AssembleOnBoundaryElement(), AbstractNonlinearElasticitySolver< DIM >::AssembleOnBoundaryElement(), AbstractNonlinearElasticitySolver< DIM >::AssembleOnBoundaryElementForPressureOnDeformedBc(), and 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...

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

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 [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

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

Definition at line 118 of file AbstractTetrahedralMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SetElementOwnerships (  )  [inline, 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 46 of file AbstractTetrahedralMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory(), DistributedVectorFactory::GetHigh(), DistributedVectorFactory::GetLow(), 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
Returns:
local index

Implemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, 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
Returns:
local index

Implemented in DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, DistributedTetrahedralMesh< DIM, 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 DistributedQuadraticMesh< DIM >, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >, MutableMesh< ELEMENT_DIM, SPACE_DIM >, NodesOnlyMesh< SPACE_DIM >, NonCachedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, QuadraticMesh< DIM >, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >, Cylindrical2dMesh, Cylindrical2dNodesOnlyMesh, DistributedTetrahedralMesh< DIM, DIM >, MutableMesh< ELEMENT_DIM, ELEMENT_DIM >, MutableMesh< 2, 2 >, MutableMesh< DIM, DIM >, MutableMesh< SPACE_DIM, SPACE_DIM >, NodesOnlyMesh< DIM >, NodesOnlyMesh< 2 >, TetrahedralMesh< DIM, DIM >, and TetrahedralMesh< 3, 3 >.

Definition at line 104 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 280 of file AbstractTetrahedralMesh.hpp.

Referenced by TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), 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(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElement(), 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(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher(), 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 277 of file AbstractTetrahedralMesh.hpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CalculateMaximumNodeConnectivityPerProcess(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructCuboid(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), QuadraticMesh< DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructLinearMesh(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructRectangularMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ElementIterator::ElementIterator(), AbstractTetrahedralMesh< 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(), AbstractTetrahedralMesh< 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(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ImportFromMesher(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ElementIterator::IsAtEnd(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::RegisterElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), 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 79 of file AbstractTetrahedralMesh.hpp.

Referenced by QuadraticMesh< DIM >::ConstructCuboid(), DistributedQuadraticMesh< DIM >::ConstructFromMeshReader(), QuadraticMesh< DIM >::ConstructRectangularMesh(), 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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