#include <MixedDimensionMesh.hpp>

Inheritance diagram for MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >:

Public Types
typedef std::multimap< constNode< SPACE_DIM > , Element< 1u, SPACE_DIM > >::iterator	NodeCableIterator

typedef std::pair< NodeCableIterator, NodeCableIterator >	CableRangeAtNode

typedef std::vector< Element< 1, SPACE_DIM > * >::const_iterator	CableElementIterator

Public Types inherited from DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector< Node< SPACE_DIM > * >::const_iterator	HaloNodeIterator

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

Public Types inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector< Node< SPACE_DIM > * >::const_iterator	BoundaryNodeIterator

Public Member Functions
	MixedDimensionMesh (DistributedTetrahedralMeshPartitionType::type partitioningMethod=DistributedTetrahedralMeshPartitionType::METIS_LIBRARY)

	~MixedDimensionMesh ()

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

void	RegisterCableElement (unsigned index)

unsigned	GetNumCableElements () const

unsigned	GetNumLocalCableElements () const

Element< 1u, SPACE_DIM > *	GetCableElement (unsigned globalElementIndex) const

bool	CalculateDesignatedOwnershipOfCableElement (unsigned globalElementIndex)

CableRangeAtNode	GetCablesAtNode (const Node< SPACE_DIM > *pNode)

CableElementIterator	GetCableElementIteratorBegin () const

CableElementIterator	GetCableElementIteratorEnd () const

Public Member Functions inherited from DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
	DistributedTetrahedralMesh (DistributedTetrahedralMeshPartitionType::type partitioningMethod=DistributedTetrahedralMeshPartitionType::PARMETIS_LIBRARY)

virtual	~DistributedTetrahedralMesh ()

void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

unsigned	GetNumLocalNodes () const

unsigned	GetNumHaloNodes () const

unsigned	GetNumLocalElements () const

unsigned	GetNumLocalBoundaryElements () const

unsigned	GetNumNodes () const

unsigned	GetNumAllNodes () const

unsigned	GetNumElements () const

DistributedTetrahedralMeshPartitionType::type	GetPartitionType () const

unsigned	GetNumBoundaryElements () const

void	GetHaloNodeIndices (std::vector< unsigned > &rHaloIndices) const

void	SetProcessRegion (ChasteCuboid< SPACE_DIM > *pRegion)

ChasteCuboid< SPACE_DIM > *	GetProcessRegion ()

bool	CalculateDesignatedOwnershipOfElement (unsigned elementIndex)

bool	CalculateDesignatedOwnershipOfBoundaryElement (unsigned faceIndex)

void	ConstructLinearMesh (unsigned width)

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

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

virtual void	Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)

Node< SPACE_DIM > *	GetNodeOrHaloNode (unsigned index) const

virtual ChasteCuboid< SPACE_DIM >	CalculateBoundingBox () const

virtual unsigned	GetNearestNodeIndex (const ChastePoint< SPACE_DIM > &rTestPoint)

virtual c_vector< double, 2 >	CalculateMinMaxEdgeLengths ()

void	Rotate (c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix)

void	Translate (const c_vector< double, SPACE_DIM > &rDisplacement)

HaloNodeIterator	GetHaloNodeIteratorBegin () const

HaloNodeIterator	GetHaloNodeIteratorEnd () const

Public Member Functions inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
ElementIterator	GetElementIteratorBegin (bool skipDeletedElements=true)

ElementIterator	GetElementIteratorEnd ()

	AbstractTetrahedralMesh ()

virtual	~AbstractTetrahedralMesh ()

unsigned	GetNumAllElements () const

unsigned	GetNumAllBoundaryElements () const

virtual unsigned	GetNumVertices () const

virtual unsigned	GetMaximumNodeIndex ()

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

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

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

BoundaryElementIterator	GetBoundaryElementIteratorBegin () const

BoundaryElementIterator	GetBoundaryElementIteratorEnd () const

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 ()

void	ConstructRegularSlabMesh (double spaceStep, double width, double height=0, double depth=0)

void	ConstructRegularSlabMeshWithDimensionSplit (unsigned dimension, double spaceStep, double width, double height=0, double depth=0)

unsigned	CalculateMaximumNodeConnectivityPerProcess () const

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

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

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

Public Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
NodeIterator	GetNodeIteratorBegin (bool skipDeletedNodes=true)

NodeIterator	GetNodeIteratorEnd ()

	AbstractMesh ()

virtual	~AbstractMesh ()

unsigned	GetNumBoundaryNodes () const

unsigned	GetNumNodeAttributes () const

Node< SPACE_DIM > *	GetNode (unsigned index) const

Node< SPACE_DIM > *	GetNodeFromPrePermutationIndex (unsigned index) const

virtual void	ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)

virtual DistributedVectorFactory *	GetDistributedVectorFactory ()

virtual void	PermuteNodes ()

BoundaryNodeIterator	GetBoundaryNodeIteratorBegin () const

BoundaryNodeIterator	GetBoundaryNodeIteratorEnd () const

std::string	GetMeshFileBaseName () const

bool	IsMeshOnDisk () const

const std::vector< unsigned > &	rGetNodePermutation () const

virtual c_vector< double, SPACE_DIM >	GetVectorFromAtoB (const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB)

double	GetDistanceBetweenNodes (unsigned indexA, unsigned indexB)

virtual double	GetWidth (const unsigned &rDimension) const

void	Translate (const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0)

void	Rotate (c_vector< double, 3 > axis, double angle)

void	RotateX (const double theta)

void	RotateY (const double theta)

void	RotateZ (const double theta)

void	Rotate (double theta)

virtual void	RefreshMesh ()

bool	IsMeshChanging () const

unsigned	CalculateMaximumContainingElementsPerProcess () const

void	SetMeshHasChangedSinceLoading ()

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

Private Attributes
std::vector< Element< 1u, SPACE_DIM > * >	mCableElements

unsigned	mNumCableElements

std::map< unsigned, unsigned >	mCableElementsMapping

std::multimap< const Node< SPACE_DIM > , Element< 1u, SPACE_DIM > >	mNodeToCablesMapping

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
unsigned	SolveNodeMapping (unsigned index) const

unsigned	SolveElementMapping (unsigned index) const

unsigned	SolveBoundaryElementMapping (unsigned index) const

Protected Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
ChasteCuboid< SPACE_DIM >	CalculateBoundingBox (const std::vector< Node< SPACE_DIM > * > &rNodes) const

Protected Attributes inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
bool	mMeshIsLinear

std::vector< Element< ELEMENT_DIM, SPACE_DIM > * >	mElements

std::vector< BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > * >	mBoundaryElements

Protected Attributes inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
std::vector< Node< SPACE_DIM > * >	mNodes

std::vector< Node< SPACE_DIM > * >	mBoundaryNodes

DistributedVectorFactory *	mpDistributedVectorFactory

std::vector< unsigned >	mNodePermutation

std::string	mMeshFileBaseName

bool	mMeshChangesDuringSimulation

Detailed Description

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

A tetrahedral mesh that also supports embedded 1D cable elements.

Could be used for Purkinje or blood vessels, etc.

Definition at line 51 of file MixedDimensionMesh.hpp.

Member Typedef Documentation

◆ CableElementIterator

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef std::vector<Element<1,SPACE_DIM>*>::const_iterator MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::CableElementIterator

Definition of cable element Iterator type.

Definition at line 156 of file MixedDimensionMesh.hpp.

◆ CableRangeAtNode

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef std::pair<NodeCableIterator, NodeCableIterator> MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::CableRangeAtNode

The type returned by GetCablesAtNode.

Definition at line 112 of file MixedDimensionMesh.hpp.

◆ NodeCableIterator

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef std::multimap<constNode<SPACE_DIM>*,Element<1u,SPACE_DIM>*>::iterator MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::NodeCableIterator

Iterator type over mNodeToCablesMapping.

Definition at line 109 of file MixedDimensionMesh.hpp.

Constructor & Destructor Documentation

◆ MixedDimensionMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::MixedDimensionMesh ( DistributedTetrahedralMeshPartitionType::type partitioningMethod = DistributedTetrahedralMeshPartitionType::METIS_LIBRARY )

Constructor.

Parameters

partitioningMethod defaults to METIS_LIBRARY, but in 1-D is always overridden in this constructor to be the DUMB partition

Definition at line 40 of file MixedDimensionMesh.cpp.

◆ ~MixedDimensionMesh()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

Destructor - cleans up the cables

Definition at line 46 of file MixedDimensionMesh.cpp.

Member Function Documentation

◆ CalculateDesignatedOwnershipOfCableElement()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfCableElement ( unsigned globalElementIndex )

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

Returns: true if designated owner

Parameters

globalElementIndex is the global index of the cable element

Definition at line 170 of file MixedDimensionMesh.cpp.

◆ ConstructFromMeshReader()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Construct the mesh using a MeshReader.

Parameters

rMeshReader the mesh reader

Reimplemented from DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 55 of file MixedDimensionMesh.cpp.

References DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader().

◆ GetCableElement()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

Element< 1u, SPACE_DIM > * MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElement ( unsigned globalElementIndex ) const

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

Parameters

globalElementIndex the global index of the cable element

Returns: a pointer to the cable element.

Definition at line 155 of file MixedDimensionMesh.cpp.

◆ GetCableElementIteratorBegin()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::CableElementIterator MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElementIteratorBegin ( ) const

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

Definition at line 203 of file MixedDimensionMesh.cpp.

Referenced by MonodomainPurkinjeCableAssembler< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeCableAssembler().

◆ GetCableElementIteratorEnd()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::CableElementIterator MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElementIteratorEnd ( ) const

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

Definition at line 209 of file MixedDimensionMesh.cpp.

Referenced by MonodomainPurkinjeCableAssembler< ELEMENT_DIM, SPACE_DIM >::MonodomainPurkinjeCableAssembler().

◆ GetCablesAtNode()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::CableRangeAtNode MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCablesAtNode ( const Node< SPACE_DIM > * pNode )

Returns: the cables that are attached to the given node.

Parameters

pNode a node to find the adjoining cables of

Returns: the adjoining cables.

Definition at line 196 of file MixedDimensionMesh.cpp.

◆ GetNumCableElements()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

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

virtual

Returns: the number of cable elements.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 143 of file MixedDimensionMesh.cpp.

◆ GetNumLocalCableElements()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalCableElements ( ) const

Returns: the number of cable elements on this process.

Definition at line 149 of file MixedDimensionMesh.cpp.

◆ RegisterCableElement()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::RegisterCableElement ( unsigned index )

Add the most recently constructed cable element to the global->local cable element mapping

Parameters

index is the global index of cable element to be registered

Definition at line 137 of file MixedDimensionMesh.cpp.

◆ serialize()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

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

inlineprivate

Serialize the mesh.

Parameters

archive	the archive
version	the current version of this class

Definition at line 144 of file MixedDimensionMesh.hpp.

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 136 of file MixedDimensionMesh.hpp.

Member Data Documentation

◆ mCableElements

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<Element<1u, SPACE_DIM>*> MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElements

private

The elements making up the 1D cables

Definition at line 124 of file MixedDimensionMesh.hpp.

◆ mCableElementsMapping

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::map<unsigned, unsigned> MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElementsMapping

private

A map from global cable index to local index used by this process.

Definition at line 130 of file MixedDimensionMesh.hpp.

◆ mNodeToCablesMapping

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::multimap<const Node<SPACE_DIM>*, Element<1u, SPACE_DIM>*> MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mNodeToCablesMapping

private

Records which cables are attached to each node.

Definition at line 133 of file MixedDimensionMesh.hpp.

◆ mNumCableElements

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mNumCableElements

private

The global number of cables over all processes

Definition at line 127 of file MixedDimensionMesh.hpp.

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

mesh/src/common/MixedDimensionMesh.hpp
mesh/src/common/MixedDimensionMesh.cpp

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ CableElementIterator

◆ CableRangeAtNode

◆ NodeCableIterator

Constructor & Destructor Documentation

◆ MixedDimensionMesh()

◆ ~MixedDimensionMesh()

Member Function Documentation

◆ CalculateDesignatedOwnershipOfCableElement()

◆ ConstructFromMeshReader()

◆ GetCableElement()

◆ GetCableElementIteratorBegin()

◆ GetCableElementIteratorEnd()

◆ GetCablesAtNode()

◆ GetNumCableElements()

◆ GetNumLocalCableElements()

◆ RegisterCableElement()

◆ serialize()

Friends And Related Symbol Documentation

◆ boost::serialization::access

Member Data Documentation

◆ mCableElements

◆ mCableElementsMapping

◆ mNodeToCablesMapping

◆ mNumCableElements