#include <Node.hpp>

Inheritance diagram for Node< SPACE_DIM >:

Collaboration diagram for Node< SPACE_DIM >:

Classes
class	ContainingBoundaryElementIterator

class	ContainingElementIterator

Public Member Functions
	Node (unsigned index, ChastePoint< SPACE_DIM > point, bool isBoundaryNode=false)

	Node (unsigned index, std::vector< double > coords, bool isBoundaryNode=false)

	Node (unsigned index, c_vector< double, SPACE_DIM > location, bool isBoundaryNode=false)

	Node (unsigned index, bool isBoundaryNode=false, double v1=0, double v2=0, double v3=0)

	Node (unsigned index, double *location, bool isBoundaryNode=false)

	~Node ()

void	SetPoint (ChastePoint< SPACE_DIM > point)

void	SetIndex (unsigned index)

void	AddNodeAttribute (double attribute)

void	SetAsBoundaryNode (bool value=true)

ChastePoint< SPACE_DIM >	GetPoint () const

const c_vector< double, SPACE_DIM > &	rGetLocation () const

c_vector< double, SPACE_DIM > &	rGetModifiableLocation ()

unsigned	GetIndex () const

bool	IsBoundaryNode () const

void	AddElement (unsigned index)

void	RemoveElement (unsigned index)

void	RemoveBoundaryElement (unsigned index)

void	AddBoundaryElement (unsigned index)

void	AddNeighbour (unsigned index)

void	ClearNeighbours ()

void	RemoveDuplicateNeighbours ()

bool	NeighboursIsEmpty ()

void	SetNeighboursSetUp (bool flag)

bool	GetNeighboursSetUp ()

std::vector< unsigned > &	rGetNeighbours ()

std::set< unsigned > &	rGetContainingElementIndices ()

std::vector< double > &	rGetNodeAttributes ()

unsigned	GetNumNodeAttributes ()

bool	HasNodeAttributes ()

std::set< unsigned > &	rGetContainingBoundaryElementIndices ()

unsigned	GetNumContainingElements () const

unsigned	GetNumBoundaryElements () const

c_vector< double, SPACE_DIM > &	rGetAppliedForce ()

void	ClearAppliedForce ()

void	AddAppliedForceContribution (const c_vector< double, SPACE_DIM > &rForceContribution)

bool	IsParticle ()

void	SetIsParticle (bool isParticle)

double	GetRadius ()

void	SetRadius (double radius)

void	MarkAsDeleted ()

bool	IsDeleted () const

void	MarkAsInternal ()

bool	IsInternal () const

void	SetRegion (unsigned region)

unsigned	GetRegion () const

ContainingElementIterator	ContainingElementsBegin () const

ContainingElementIterator	ContainingElementsEnd () const

ContainingBoundaryElementIterator	ContainingBoundaryElementsBegin () const

ContainingBoundaryElementIterator	ContainingBoundaryElementsEnd () const

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

void	CommonConstructor (unsigned index, bool isBoundaryNode)

void	ConstructNodeAttributes ()

void	CheckForNodeAttributes () const

Private Attributes
unsigned	mIndex

c_vector< double, SPACE_DIM >	mLocation

NodeAttributes< SPACE_DIM > *	mpNodeAttributes

bool	mIsBoundaryNode

bool	mIsInternal

bool	mIsDeleted

std::set< unsigned >	mElementIndices

std::set< unsigned >	mBoundaryElementIndices

Friends
class	boost::serialization::access

class	TestNode

Detailed Description

template<unsigned SPACE_DIM>
class Node< SPACE_DIM >

A node in a finite element mesh.

Definition at line 58 of file Node.hpp.

Constructor & Destructor Documentation

◆ Node() [1/5]

template<unsigned SPACE_DIM>

Node< SPACE_DIM >::Node	(	unsigned	index,
		ChastePoint< SPACE_DIM >	point,
		bool	isBoundaryNode = `false`
	)

There are many ways of creating a node, depending on how you wish to specify its spatial location.

Constructor that takes in the node's location as a ChastePoint.

Parameters

index	the index of the node in the mesh
point	the location of the node in the mesh
isBoundaryNode	whether the node is a boundary node (defaults to false)

Definition at line 56 of file Node.cpp.

References ChastePoint< DIM >::rGetLocation().

◆ Node() [2/5]

template<unsigned SPACE_DIM>

Node< SPACE_DIM >::Node	(	unsigned	index,
		std::vector< double >	coords,
		bool	isBoundaryNode = `false`
	)

Constructor that takes in the node's location as a std::vector.

Parameters

index	the index of the node in the mesh
coords	the location of the node in the mesh
isBoundaryNode	whether the node is a boundary node (defaults to false)

Definition at line 63 of file Node.cpp.

◆ Node() [3/5]

template<unsigned SPACE_DIM>

Node< SPACE_DIM >::Node	(	unsigned	index,
		c_vector< double, SPACE_DIM >	location,
		bool	isBoundaryNode = `false`
	)

Constructor that takes in the node's location as a c_vector.

Parameters

index	the index of the node in the mesh
location	the location of the node in the mesh
isBoundaryNode	whether the node is a boundary node (defaults to false)

Definition at line 73 of file Node.cpp.

◆ Node() [4/5]

template<unsigned SPACE_DIM>

Node< SPACE_DIM >::Node	(	unsigned	index,
		bool	isBoundaryNode = `false`,
		double	v1 = `0`,
		double	v2 = `0`,
		double	v3 = `0`
	)

Constructor that takes the coordinates of the node's location as separate input arguments.

Parameters

index	the index of the node in the mesh
isBoundaryNode	whether the node is a boundary node (defaults to false)
v1	the x-coordinate of the node in the mesh (defaults to 0)
v2	the y-coordinate of the node in the mesh (defaults to 0)
v3	the z-coordinate of the node in the mesh (defaults to 0)

Definition at line 80 of file Node.cpp.

◆ Node() [5/5]

template<unsigned SPACE_DIM>

Node< SPACE_DIM >::Node	(	unsigned	index,
		double *	location,
		bool	isBoundaryNode = `false`
	)

Constructor that takes in the coordinates of the node's location as an array pointer.

Parameters

index	the index of the node in the mesh
isBoundaryNode	whether the node is a boundary node (defaults to false)
location	address of the x-coordinate of the node in the mesh (other coordinates are assumed to be in contiguous memory)

Definition at line 95 of file Node.cpp.

◆ ~Node()

template<unsigned SPACE_DIM>

Node< SPACE_DIM >::~Node ( )

Explicit destructor to free memory from mpNodeAttributes.

Definition at line 105 of file Node.cpp.

Member Function Documentation

◆ AddAppliedForceContribution()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::AddAppliedForceContribution ( const c_vector< double, SPACE_DIM > & rForceContribution )

Add a contribution to the force applied to this node.

Parameters

rForceContribution the force vector to add to mAppliedForce

Definition at line 224 of file Node.cpp.

◆ AddBoundaryElement()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::AddBoundaryElement ( unsigned index )

Add an boundary element that contains this node.

Parameters

index of the element to add.

Definition at line 294 of file Node.cpp.

◆ AddElement()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::AddElement ( unsigned index )

Add an element that contains this node.

Parameters

index of the element to add.

Definition at line 268 of file Node.cpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::MutableVertexMesh(), QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), PottsElement< DIM >::AddNode(), QuadraticMesh< DIM >::ConstructLinearMesh(), and MutableElement< 1, SPACE_DIM >::UpdateNode().

◆ AddNeighbour()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::AddNeighbour ( unsigned index )

Add a neighbour to this node's vector of neighbouring node indices.

Parameters

index of the node to add.

Definition at line 328 of file Node.cpp.

Referenced by ObsoleteBoxCollection< DIM >::CalculateNodePairs().

◆ AddNodeAttribute()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::AddNodeAttribute ( double attribute )

Add an attribute to the list of node attributes.

Parameters

attribute the value of the attribute to be added

Definition at line 170 of file Node.cpp.

Referenced by DistributedTetrahedralMesh< DIM, DIM >::CalculateBoundingBox(), NodesOnlyMesh< 2 >::SetNode(), and TetrahedralMesh< DIM, DIM >::SolveNodeMapping().

◆ CheckForNodeAttributes()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::CheckForNodeAttributes ( ) const

private

Check that node attributes have been set up, and throw an exception if not.

Definition at line 388 of file Node.cpp.

References EXCEPTION.

◆ ClearAppliedForce()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::ClearAppliedForce ( )

Clear the vector associated with the force.

Definition at line 216 of file Node.cpp.

◆ ClearNeighbours()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::ClearNeighbours ( )

Clear this node's vector of neighbour indices.

Definition at line 336 of file Node.cpp.

◆ CommonConstructor()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::CommonConstructor	(	unsigned	index,
		bool	isBoundaryNode
	)

private

Extraction of commonality between the constructors.

Parameters

index	the index of the node in the mesh
isBoundaryNode	whether the node is a boundary node

Definition at line 46 of file Node.cpp.

◆ ConstructNodeAttributes()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::ConstructNodeAttributes ( )

private

Construct an empty NodeAttributes container.

Definition at line 397 of file Node.cpp.

◆ ContainingBoundaryElementsBegin()

template<unsigned SPACE_DIM>

ContainingBoundaryElementIterator Node< SPACE_DIM >::ContainingBoundaryElementsBegin ( ) const

inline

Returns: a ContainingBoundaryElementIterator pointing to the first containing boundary element

Definition at line 554 of file Node.hpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

◆ ContainingBoundaryElementsEnd()

template<unsigned SPACE_DIM>

ContainingBoundaryElementIterator Node< SPACE_DIM >::ContainingBoundaryElementsEnd ( ) const

inline

Returns: a ContainingBoundaryElementIterator pointing to one past the last containing boundary element

Definition at line 562 of file Node.hpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

◆ ContainingElementsBegin()

template<unsigned SPACE_DIM>

ContainingElementIterator Node< SPACE_DIM >::ContainingElementsBegin ( ) const

inline

Returns: a ContainingElementIterator pointing to the first containing element

Definition at line 485 of file Node.hpp.

References Node< SPACE_DIM >::mElementIndices.

Referenced by ImmersedBoundaryKinematicFeedbackForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearDifferentialAdhesionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryLinearInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryMorseInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell(), ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::NodesInDifferentElementOrLamina(), AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), and DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::WorkOnLocalQueue().

◆ ContainingElementsEnd()

template<unsigned SPACE_DIM>

ContainingElementIterator Node< SPACE_DIM >::ContainingElementsEnd ( ) const

inline

Returns: a ContainingElementIterator pointing to one past the last containing element

Definition at line 493 of file Node.hpp.

References Node< SPACE_DIM >::mElementIndices.

Referenced by QuadraticMeshHelper< DIM >::AddNodesToBoundaryElements(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell(), AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), and DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::WorkOnLocalQueue().

◆ GetIndex()

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetIndex ( ) const

Returns: the index of this node in the mesh.

Definition at line 158 of file Node.cpp.

◆ GetNeighboursSetUp()

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::GetNeighboursSetUp ( )

Returns: a flag to indicate that the neighbours of this node have/have not been updated.

Definition at line 368 of file Node.cpp.

Referenced by NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), and NodeBasedCellPopulation< DIM >::GetNodesWithinNeighbourhoodRadius().

◆ GetNumBoundaryElements()

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetNumBoundaryElements ( ) const

Returns: the number of boundary elements in the mesh that contain this node.

Definition at line 318 of file Node.cpp.

◆ GetNumContainingElements()

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetNumContainingElements ( ) const

Returns: the number of elements in the mesh that contain this node.

Definition at line 312 of file Node.cpp.

Referenced by AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), and PottsBasedCellPopulation< DIM >::UpdateCellLocations().

◆ GetNumNodeAttributes()

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetNumNodeAttributes ( )

Returns: the number of node attributes associated with this node.

Definition at line 186 of file Node.cpp.

◆ GetPoint()

template<unsigned SPACE_DIM>

ChastePoint< SPACE_DIM > Node< SPACE_DIM >::GetPoint ( ) const

Returns: the node's location as a ChastePoint.

Definition at line 133 of file Node.cpp.

Referenced by Cylindrical2dMesh::AddNode(), Cylindrical2dNodesOnlyMesh::AddNode(), Toroidal2dMesh::AddNode(), PeriodicNodesOnlyMesh< SPACE_DIM >::AddNode(), AbstractLinearEllipticPde< ELEMENT_DIM, SPACE_DIM >::ComputeConstantInUSourceTermAtNode(), AbstractLinearEllipticPde< ELEMENT_DIM, SPACE_DIM >::ComputeLinearInUCoeffInSourceTermAtNode(), AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeSourceTermAtNode(), AbstractLinearParabolicPde< ELEMENT_DIM, SPACE_DIM >::ComputeSourceTermAtNode(), RampedQuarterStimulusCellFactory< CELL, DIM >::CreateCardiacCellForTissueNode(), BathCellFactory< DIM, CELLTYPE >::CreateCardiacCellForTissueNode(), HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCardiacCellForTissueNode(), PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode(), ExtendedBidomainTissue< DIM >::CreateExtracellularConductivityTensors(), ElectrodesStimulusFactory< DIM >::CreateStimulusForNode(), ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), and AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetDirichletBCValue().

◆ GetRadius()

template<unsigned SPACE_DIM>

double Node< SPACE_DIM >::GetRadius ( )

Returns: the radius of this node. An exception is thrown if the node has no attributes.

Definition at line 248 of file Node.cpp.

Referenced by NodeBasedCellPopulation< DIM >::AddCell(), BuskeCompressionForce< DIM >::AddForceContribution(), RepulsionForce< DIM >::AddForceContribution(), BuskeAdhesiveForce< DIM >::CalculateForceBetweenNodes(), BuskeElasticForce< DIM >::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), NodeBasedCellPopulation< DIM >::GetVolumeOfCell(), VolumeDependentAveragedSourceEllipticPde< DIM >::SetupSourceTerms(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), and HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit().

◆ GetRegion()

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetRegion ( ) const

Returns: the node's region ID. Defaults to 0 if no NodeAttributes have been setup.

Definition at line 437 of file Node.cpp.

Referenced by ImmersedBoundaryLinearInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), ImmersedBoundaryMorseInteractionForce< DIM >::AddImmersedBoundaryForceContribution(), AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode(), BathCellFactory< DIM, CELLTYPE >::CreateCardiacCellForTissueNode(), and ImmersedBoundaryMesh< ELEMENT_DIM, SPACE_DIM >::NodesInDifferentElementOrLamina().

◆ HasNodeAttributes()

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::HasNodeAttributes ( )

Returns: Whether mpNodeAttributes has been set. Used in archiving of attributes in a mesh.

Definition at line 202 of file Node.cpp.

◆ IsBoundaryNode()

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::IsBoundaryNode ( ) const

Returns: whether this node is a boundary node.

Definition at line 164 of file Node.cpp.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, 3 >::BoundaryConditionsContainer(), QuadraticMeshHelper< DIM >::AddNodeToBoundaryElement(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddPeriodicBoundaryCondition(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshForPdeModifier(), and SlidingBoundaryCondition< DIM >::ImposeBoundaryCondition().

◆ IsDeleted()

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::IsDeleted ( ) const

Returns: whether the node is marked as deleted.

Definition at line 412 of file Node.cpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForRosettes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval().

◆ IsInternal()

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::IsInternal ( ) const

Returns: whether the node is internal (not vertex) in a quadratic element.

Definition at line 424 of file Node.cpp.

◆ IsParticle()

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::IsParticle ( )

Returns: whether this node is a particle or not

Definition at line 232 of file Node.cpp.

◆ MarkAsDeleted()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::MarkAsDeleted ( )

Mark the node as having been removed from the mesh.

Definition at line 406 of file Node.cpp.

◆ MarkAsInternal()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::MarkAsInternal ( )

Mark the node as being internal (not vertex) in a quadratic element.

Definition at line 418 of file Node.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddInternalNodesToElements(), and QuadraticMesh< DIM >::MakeNewInternalNode().

◆ NeighboursIsEmpty()

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::NeighboursIsEmpty ( )

Check whether the node neighbours collection is empty.

Returns: whether this node has any neighbours.

Definition at line 352 of file Node.cpp.

◆ RemoveBoundaryElement()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::RemoveBoundaryElement ( unsigned index )

Remove an boundary element that contains this node.

Parameters

index of the boundary element to be removed.

Definition at line 284 of file Node.cpp.

◆ RemoveDuplicateNeighbours()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::RemoveDuplicateNeighbours ( )

Remove duplicates from the vector of node neighbour indices.

Definition at line 344 of file Node.cpp.

◆ RemoveElement()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::RemoveElement ( unsigned index )

Remove an element that contains this node.

Parameters

index of the element to be removed.

Definition at line 274 of file Node.cpp.

◆ rGetAppliedForce()

template<unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > & Node< SPACE_DIM >::rGetAppliedForce ( )

Returns: the force applied to this node.

Definition at line 208 of file Node.cpp.

Referenced by AbstractImmersedBoundaryForce< DIM >::AddNormalNoiseToNodes(), and ImmersedBoundarySimulationModifier< DIM >::PropagateForcesToFluidGrid().

◆ rGetContainingBoundaryElementIndices()

template<unsigned SPACE_DIM>

std::set< unsigned > & Node< SPACE_DIM >::rGetContainingBoundaryElementIndices ( )

Returns: a set of indices of boundary elements containing this node as a vertex.

Definition at line 306 of file Node.cpp.

◆ rGetContainingElementIndices()

template<unsigned SPACE_DIM>

std::set< unsigned > & Node< SPACE_DIM >::rGetContainingElementIndices ( )

Returns: a set of indices of elements containing this node as a vertex.

Definition at line 300 of file Node.cpp.

◆ rGetLocation()

template<unsigned SPACE_DIM>

const c_vector< double, SPACE_DIM > & Node< SPACE_DIM >::rGetLocation ( ) const

Returns: the node's location as a c_vector.

The returned location may not be modified; if you want that functionality use rGetModifiableLocation instead.

Definition at line 139 of file Node.cpp.

◆ rGetModifiableLocation()

template<unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > & Node< SPACE_DIM >::rGetModifiableLocation ( )

Returns: the node's location as a c_vector.

If you modify the returned location, Jacobian and JacobianDeterminant of elements need to be updated.

Don't forget to assign the result of this call to a reference!

Definition at line 151 of file Node.cpp.

Referenced by Cylindrical2dVertexMesh::CheckNodeLocation(), Toroidal2dVertexMesh::CheckNodeLocation(), FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseNodes(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), SlidingBoundaryCondition< DIM >::ImposeBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::ImposeBoundaryCondition(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), PlaneBoundaryCondition< ELEMENT_DIM, SPACE_DIM >::ImposeBoundaryCondition(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval(), and ExtrinsicPullModifier< DIM >::UpdateAtEndOfTimeStep().

◆ rGetNeighbours()

template<unsigned SPACE_DIM>

std::vector< unsigned > & Node< SPACE_DIM >::rGetNeighbours ( )

Returns: this node's vector of neighbour indices.

Definition at line 376 of file Node.cpp.

Referenced by NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), and NodeBasedCellPopulation< DIM >::GetNodesWithinNeighbourhoodRadius().

◆ rGetNodeAttributes()

template<unsigned SPACE_DIM>

std::vector< double > & Node< SPACE_DIM >::rGetNodeAttributes ( )

Returns: a vector containing the node attributes. An exception is thrown if the node has no attributes.

Definition at line 178 of file Node.cpp.

Referenced by NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh().

◆ serialize()

template<unsigned SPACE_DIM>

template<class Archive >

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

inlineprivate

Archive the member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 99 of file Node.hpp.

References Node< SPACE_DIM >::mpNodeAttributes.

◆ SetAsBoundaryNode()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::SetAsBoundaryNode ( bool value = true )

Set whether the node is a boundary node.

Parameters

value whether the node is a boundary node

Definition at line 127 of file Node.cpp.

Referenced by QuadraticMeshHelper< DIM >::AddNodeToBoundaryElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval().

◆ SetIndex()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::SetIndex ( unsigned index )

Set the index of the node in the mesh.

Parameters

index the index of the node

Definition at line 121 of file Node.cpp.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), NodesOnlyMesh< SPACE_DIM >::AddNode(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), and ImmersedBoundaryMesh< DIM, DIM >::ReMesh().

◆ SetIsParticle()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::SetIsParticle ( bool isParticle )

Set whether this node is a particle, for cell_based simulations.

Parameters

isParticle whether this node is a particle or not.

Definition at line 240 of file Node.cpp.

Referenced by NodesOnlyMesh< 2 >::ClearHaloNodes().

◆ SetNeighboursSetUp()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::SetNeighboursSetUp ( bool flag )

Sets a flag to indicate that the neighbours of this node have/have not been updated.

Parameters

flag	whether the neighbours are set up or not.

Definition at line 360 of file Node.cpp.

◆ SetPoint()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::SetPoint ( ChastePoint< SPACE_DIM > point )

Set the node's location.

Note: setting the point in space is dangerous, because the Jacobian and JacobianDeterminant of any corresponding elements need to be updated.

Parameters

point the new location of the node

Definition at line 115 of file Node.cpp.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge().

◆ SetRadius()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::SetRadius ( double radius )

Set the radius of the node.

Parameters

radius the value to assign to the radius property. Should be >= 0.0

Definition at line 256 of file Node.cpp.

Referenced by NodeBasedCellPopulation< DIM >::AddCell(), NodesOnlyMesh< 2 >::ClearHaloNodes(), and NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh().

◆ SetRegion()

template<unsigned SPACE_DIM>

void Node< SPACE_DIM >::SetRegion ( unsigned region )

Set the node's region ID.

Parameters

region the new region ID

Definition at line 430 of file Node.cpp.

Referenced by ImmersedBoundaryPalisadeMeshGenerator::ImmersedBoundaryPalisadeMeshGenerator(), and NodesOnlyMesh< 2 >::ClearHaloNodes().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 90 of file Node.hpp.

◆ TestNode

template<unsigned SPACE_DIM>

friend class TestNode

friend

Definition at line 91 of file Node.hpp.

Member Data Documentation

◆ mBoundaryElementIndices

template<unsigned SPACE_DIM>

std::set<unsigned> Node< SPACE_DIM >::mBoundaryElementIndices

private

Set of indices of boundary elements containing this node as a vertex.

Definition at line 87 of file Node.hpp.

Referenced by Node< SPACE_DIM >::ContainingBoundaryElementsBegin(), and Node< SPACE_DIM >::ContainingBoundaryElementsEnd().

◆ mElementIndices

template<unsigned SPACE_DIM>

std::set<unsigned> Node< SPACE_DIM >::mElementIndices

private

Set of indices of elements containing this node as a vertex.

Definition at line 84 of file Node.hpp.

Referenced by Node< SPACE_DIM >::ContainingElementsBegin(), and Node< SPACE_DIM >::ContainingElementsEnd().

◆ mIndex

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::mIndex

private

The index of this node within the mesh.

Definition at line 63 of file Node.hpp.

◆ mIsBoundaryNode

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::mIsBoundaryNode

private

Whether this node is a boundary node.

Definition at line 72 of file Node.hpp.

◆ mIsDeleted

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::mIsDeleted

private

Whether this node has been deleted, and hence whether its location in the mesh can be re-used (for use in the MutableMesh class).

Definition at line 81 of file Node.hpp.

◆ mIsInternal

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::mIsInternal

private

Whether this node is an internal node (for use in the QuadraticMesh class).

Definition at line 75 of file Node.hpp.

◆ mLocation

template<unsigned SPACE_DIM>

c_vector<double, SPACE_DIM> Node< SPACE_DIM >::mLocation

private

The location of this node within the mesh.

Definition at line 66 of file Node.hpp.

◆ mpNodeAttributes

template<unsigned SPACE_DIM>

NodeAttributes<SPACE_DIM>* Node< SPACE_DIM >::mpNodeAttributes

private

A pointer to a NodeAttributes object associated with this node.

Definition at line 69 of file Node.hpp.

Referenced by Node< SPACE_DIM >::serialize().

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

mesh/src/common/Node.hpp
mesh/src/common/Node.cpp

Classes

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ Node() [1/5]

◆ Node() [2/5]

◆ Node() [3/5]

◆ Node() [4/5]

◆ Node() [5/5]

◆ ~Node()

Member Function Documentation

◆ AddAppliedForceContribution()

◆ AddBoundaryElement()

◆ AddElement()

◆ AddNeighbour()

◆ AddNodeAttribute()

◆ CheckForNodeAttributes()

◆ ClearAppliedForce()

◆ ClearNeighbours()

◆ CommonConstructor()

◆ ConstructNodeAttributes()

◆ ContainingBoundaryElementsBegin()

◆ ContainingBoundaryElementsEnd()

◆ ContainingElementsBegin()

◆ ContainingElementsEnd()

◆ GetIndex()

◆ GetNeighboursSetUp()

◆ GetNumBoundaryElements()

◆ GetNumContainingElements()

◆ GetNumNodeAttributes()

◆ GetPoint()

◆ GetRadius()

◆ GetRegion()

◆ HasNodeAttributes()

◆ IsBoundaryNode()

◆ IsDeleted()

◆ IsInternal()

◆ IsParticle()

◆ MarkAsDeleted()

◆ MarkAsInternal()

◆ NeighboursIsEmpty()

◆ RemoveBoundaryElement()

◆ RemoveDuplicateNeighbours()

◆ RemoveElement()

◆ rGetAppliedForce()

◆ rGetContainingBoundaryElementIndices()

◆ rGetContainingElementIndices()

◆ rGetLocation()

◆ rGetModifiableLocation()

◆ rGetNeighbours()

◆ rGetNodeAttributes()

◆ serialize()

◆ SetAsBoundaryNode()

◆ SetIndex()

◆ SetIsParticle()

◆ SetNeighboursSetUp()

◆ SetPoint()

◆ SetRadius()

◆ SetRegion()

Friends And Related Symbol Documentation

◆ boost::serialization::access

◆ TestNode

Member Data Documentation

◆ mBoundaryElementIndices

◆ mElementIndices

◆ mIndex

◆ mIsBoundaryNode

◆ mIsDeleted

◆ mIsInternal

◆ mLocation

◆ mpNodeAttributes