MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <MixedDimensionMesh.hpp>

Inheritance diagram for MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >:

Public Types
typedef std::multimap< const Node< 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

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.

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.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

typedef std::multimap<const Node<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

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.

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.

References MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElements.

Member Function Documentation

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.

References MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElement(), and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetDistributedVectorFactory().

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 ElementData::AttributeValue, DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNextCableElementData(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeOrHaloNode(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumCableElementAttributes(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::GetNumCableElements(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodePermutation, MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mNodeToCablesMapping, MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mNumCableElements, NEVER_REACHED, ElementData::NodeIndices, MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::RegisterCableElement(), AbstractMeshReader< ELEMENT_DIM, SPACE_DIM >::Reset(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::SetAttribute(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::SolveNodeMapping().

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.

References EXCEPTION, PetscTools::GetMyRank(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElements, and MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElementsMapping.

Referenced by MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::CalculateDesignatedOwnershipOfCableElement().

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.

References MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElements.

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

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.

References EXPORT_TEMPLATE_CLASS_ALL_DIMS, and MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElements.

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

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.

References MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mNodeToCablesMapping.

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.

References MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mNumCableElements.

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.

References MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElements.

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.

References MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElements, and MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::mCableElementsMapping.

Referenced by MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader().

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 Function Documentation

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

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.

Referenced by MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElement(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElementIteratorBegin(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElementIteratorEnd(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetNumLocalCableElements(), MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::RegisterCableElement(), and MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::~MixedDimensionMesh().

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.

Referenced by MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCableElement(), and MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::RegisterCableElement().

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.

Referenced by MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), and MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetCablesAtNode().

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.

Referenced by MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), and MixedDimensionMesh< ELEMENT_DIM, SPACE_DIM >::GetNumCableElements().

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

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