Node< SPACE_DIM > Class Template Reference

#include <Node.hpp>

Collaboration diagram for Node< SPACE_DIM >:
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List of all members.

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)
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 (c_vector< double, SPACE_DIM > &forceContribution)
bool IsParticle ()
void SetIsParticle (bool isParticle)
double GetRadius ()
void SetRadius (double radius)
void MarkAsDeleted ()
bool IsDeleted () const
void MarkAsInternal ()
bool IsInternal () const
template<unsigned ELEMENT_DIM>
bool IsFlagged (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
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

template<unsigned SPACE_DIM>
Node< SPACE_DIM >::Node ( unsigned  index,
ChastePoint< SPACE_DIM >  point,
bool  isBoundaryNode = false 
) [inline]

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 Node< SPACE_DIM >::CommonConstructor(), Node< SPACE_DIM >::mLocation, and ChastePoint< DIM >::rGetLocation().

template<unsigned SPACE_DIM>
Node< SPACE_DIM >::Node ( unsigned  index,
std::vector< double >  coords,
bool  isBoundaryNode = false 
) [inline]

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.

References Node< SPACE_DIM >::CommonConstructor(), and Node< SPACE_DIM >::mLocation.

template<unsigned SPACE_DIM>
Node< SPACE_DIM >::Node ( unsigned  index,
c_vector< double, SPACE_DIM >  location,
bool  isBoundaryNode = false 
) [inline]

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.

References Node< SPACE_DIM >::CommonConstructor(), and Node< SPACE_DIM >::mLocation.

template<unsigned SPACE_DIM>
Node< SPACE_DIM >::Node ( unsigned  index,
bool  isBoundaryNode = false,
double  v1 = 0,
double  v2 = 0,
double  v3 = 0 
) [inline]

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.

References Node< SPACE_DIM >::CommonConstructor(), and Node< SPACE_DIM >::mLocation.

template<unsigned SPACE_DIM>
Node< SPACE_DIM >::Node ( unsigned  index,
double *  location,
bool  isBoundaryNode = false 
) [inline]

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.

References Node< SPACE_DIM >::CommonConstructor(), and Node< SPACE_DIM >::mLocation.

template<unsigned SPACE_DIM>
Node< SPACE_DIM >::~Node (  )  [inline]

Explicit destructor to free memory from mpNodeAttributes.

Definition at line 105 of file Node.cpp.

References Node< SPACE_DIM >::mpNodeAttributes.

Member Function Documentation

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::AddAppliedForceContribution ( c_vector< double, SPACE_DIM > &  forceContribution  )  [inline]

Add a contribution to the force applied to this node.

Parameters:
forceContribution the force vector to add to mAppliedForce

Definition at line 225 of file Node.cpp.

References Node< SPACE_DIM >::ConstructNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

Referenced by RepulsionForce< DIM >::AddForceContribution(), DiffusionForce< DIM >::AddForceContribution(), and BuskeCompressionForce< DIM >::AddForceContribution().

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::AddBoundaryElement ( unsigned  index  )  [inline]

Add an boundary element that contains this node.

Parameters:
index of the element to add.

Definition at line 295 of file Node.cpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::AddElement ( unsigned  index  )  [inline]

Add an element that contains this node.

Parameters:
index of the element to add.

Definition at line 269 of file Node.cpp.

References Node< SPACE_DIM >::mElementIndices.

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

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::AddNodeAttribute ( double  attribute  )  [inline]

Add an attribute to the list of node attributes.

Parameters:
attribute,: the value of the attribute to be added

Definition at line 171 of file Node.cpp.

References Node< SPACE_DIM >::ConstructNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

Referenced by NodesOnlyMesh< SPACE_DIM >::AddMovedNode(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader(), and DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMeshReader().

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::CheckForNodeAttributes (  )  const [inline, private]

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

Definition at line 329 of file Node.cpp.

References EXCEPTION, and Node< SPACE_DIM >::mpNodeAttributes.

Referenced by Node< SPACE_DIM >::GetRadius(), Node< SPACE_DIM >::IsParticle(), Node< SPACE_DIM >::rGetAppliedForce(), and Node< SPACE_DIM >::rGetNodeAttributes().

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::ClearAppliedForce (  )  [inline]

Clear the vector associated with the force.

Definition at line 217 of file Node.cpp.

References Node< SPACE_DIM >::ConstructNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::CommonConstructor ( unsigned  index,
bool  isBoundaryNode 
) [inline, 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.

References Node< SPACE_DIM >::mIndex, Node< SPACE_DIM >::mIsBoundaryNode, Node< SPACE_DIM >::mIsDeleted, Node< SPACE_DIM >::mIsInternal, and Node< SPACE_DIM >::mpNodeAttributes.

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

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::ConstructNodeAttributes (  )  [inline, private]

Construct an empty NodeAttributes container.

Definition at line 338 of file Node.cpp.

References Node< SPACE_DIM >::mpNodeAttributes.

Referenced by Node< SPACE_DIM >::AddAppliedForceContribution(), Node< SPACE_DIM >::AddNodeAttribute(), Node< SPACE_DIM >::ClearAppliedForce(), Node< SPACE_DIM >::SetIsParticle(), Node< SPACE_DIM >::SetRadius(), and Node< SPACE_DIM >::SetRegion().

template<unsigned SPACE_DIM>
ContainingBoundaryElementIterator Node< SPACE_DIM >::ContainingBoundaryElementsBegin (  )  const [inline]
Returns:
a ContainingBoundaryElementIterator pointing to the first containing boundary element

Definition at line 535 of file Node.hpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

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 543 of file Node.hpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>
ContainingElementIterator Node< SPACE_DIM >::ContainingElementsBegin (  )  const [inline]
Returns:
a ContainingElementIterator pointing to the first containing element

Definition at line 466 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(), Node< SPACE_DIM >::IsFlagged(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), and DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::WorkOnLocalQueue().

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 474 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(), Node< SPACE_DIM >::IsFlagged(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), and DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::WorkOnLocalQueue().

template<unsigned SPACE_DIM>
unsigned Node< SPACE_DIM >::GetIndex (  )  const [inline]
Returns:
the index of this node in the mesh.

Definition at line 159 of file Node.cpp.

References Node< SPACE_DIM >::mIndex.

Referenced by RepulsionForce< DIM >::AddForceContribution(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), NodesOnlyMesh< SPACE_DIM >::AddNodeWithFixedIndex(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges(), CellwiseSourcePde< DIM >::ComputeLinearInUCoeffInSourceTermAtNode(), NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh(), HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCardiacCellForTissueNode(), LuoRudySpiralWaveCellFactory::CreateCardiacCellForTissueNode(), AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateJunctionFromFile(), AbstractPurkinjeCellFactory< ELEMENT_DIM, SPACE_DIM >::CreatePurkinjeCellForNode(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThicknessLocalNode(), Toroidal2dVertexMesh::GetMeshForVtk(), Cylindrical2dVertexMesh::GetMeshForVtk(), PottsMesh< DIM >::GetNeighbouringElementIndices(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshUsingVertexMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), LinearParabolicPdeSystemWithCoupledOdeSystemSolver< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::IncrementInterpolatedQuantities(), AbstractCorrectionTermAssembler< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::IncrementInterpolatedQuantities(), LessThanNode< SPACE_DIM >::operator()(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitLongEdges(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh(), and DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::WorkOnLocalQueue().

template<unsigned SPACE_DIM>
unsigned Node< SPACE_DIM >::GetNumBoundaryElements (  )  const [inline]
Returns:
the number of boundary elements in the mesh that contain this node.

Definition at line 319 of file Node.cpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>
unsigned Node< SPACE_DIM >::GetNumContainingElements (  )  const [inline]
Returns:
the number of elements in the mesh that contain this node.

Definition at line 313 of file Node.cpp.

References Node< SPACE_DIM >::mElementIndices.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), and PottsBasedCellPopulation< DIM >::UpdateCellLocations().

template<unsigned SPACE_DIM>
unsigned Node< SPACE_DIM >::GetNumNodeAttributes (  )  [inline]
Returns:
the number of node attributes associated with this node.

Definition at line 187 of file Node.cpp.

References Node< SPACE_DIM >::mpNodeAttributes.

template<unsigned SPACE_DIM>
ChastePoint< SPACE_DIM > Node< SPACE_DIM >::GetPoint (  )  const [inline]
Returns:
the node's location as a ChastePoint.

Definition at line 134 of file Node.cpp.

References Node< SPACE_DIM >::mLocation.

Referenced by Toroidal2dVertexMesh::AddNode(), Cylindrical2dVertexMesh::AddNode(), Cylindrical2dNodesOnlyMesh::AddNode(), Cylindrical2dMesh::AddNode(), AbstractLinearEllipticPde< ELEMENT_DIM, SPACE_DIM >::ComputeLinearInUCoeffInSourceTermAtNode(), AbstractLinearParabolicPdeSystemForCoupledOdeSystem< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::ComputeSourceTermAtNode(), AbstractLinearParabolicPde< ELEMENT_DIM, SPACE_DIM >::ComputeSourceTermAtNode(), PlaneStimulusCellFactory< CELL, ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForTissueNode(), HeartConfigRelatedCellFactory< SPACE_DIM >::CreateCardiacCellForTissueNode(), BathCellFactory< DIM, CELLTYPE >::CreateCardiacCellForTissueNode(), RampedQuarterStimulusCellFactory< CELL, DIM >::CreateCardiacCellForTissueNode(), ExtendedBidomainTissue< SPACE_DIM >::CreateGGapConductivities(), ZeroNetChargeElectrodes< DIM >::CreateStimulusForNode(), ElectrodesStimulusFactory< DIM >::CreateStimulusForNode(), and AbstractBoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::GetDirichletBCValue().

template<unsigned SPACE_DIM>
double Node< SPACE_DIM >::GetRadius (  )  [inline]
Returns:
the radius of this node.

Definition at line 249 of file Node.cpp.

References Node< SPACE_DIM >::CheckForNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

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

template<unsigned SPACE_DIM>
unsigned Node< SPACE_DIM >::GetRegion (  )  const [inline]
Returns:
the node's region ID. Defaults to 0 if no NodeAttributes have been setup.

Definition at line 378 of file Node.cpp.

References Node< SPACE_DIM >::mpNodeAttributes.

Referenced by AbstractCardiacCellFactory< ELEMENT_DIM, SPACE_DIM >::CreateCardiacCellForNode(), and BathCellFactory< DIM, CELLTYPE >::CreateCardiacCellForTissueNode().

template<unsigned SPACE_DIM>
bool Node< SPACE_DIM >::HasNodeAttributes (  )  [inline]
Returns:
Whether mpNodeAttributes has been set. Used in archiving of attributes in a mesh.

Definition at line 203 of file Node.cpp.

References Node< SPACE_DIM >::mpNodeAttributes.

template<unsigned SPACE_DIM>
bool Node< SPACE_DIM >::IsBoundaryNode (  )  const [inline]
Returns:
whether this node is a boundary node.

Definition at line 165 of file Node.cpp.

References Node< SPACE_DIM >::mIsBoundaryNode.

Referenced by BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition(), QuadraticMeshHelper< DIM >::AddNodeToBoundaryElement(), BoundaryConditionsContainer< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM >::AddPeriodicBoundaryCondition(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshUsingVertexMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

template<unsigned SPACE_DIM>
bool Node< SPACE_DIM >::IsDeleted (  )  const [inline]
Returns:
whether the node is marked as deleted.

Definition at line 353 of file Node.cpp.

References Node< SPACE_DIM >::mIsDeleted.

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

template<unsigned SPACE_DIM>
template<unsigned ELEMENT_DIM>
bool Node< SPACE_DIM >::IsFlagged ( AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &  rMesh  )  [inline]
Returns:
true if a node lives within a flagged element.
Parameters:
rMesh the mesh containing the nodes and elements

Definition at line 381 of file Node.hpp.

References Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), and AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement().

template<unsigned SPACE_DIM>
bool Node< SPACE_DIM >::IsInternal (  )  const [inline]
Returns:
whether the node is internal (not vertex) in a quadratic element.

Definition at line 365 of file Node.cpp.

References Node< SPACE_DIM >::mIsInternal.

template<unsigned SPACE_DIM>
bool Node< SPACE_DIM >::IsParticle (  )  [inline]
Returns:
whether this node is a particle or not

Definition at line 233 of file Node.cpp.

References Node< SPACE_DIM >::CheckForNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::MarkAsDeleted (  )  [inline]

Mark the node as having been removed from the mesh.

Definition at line 347 of file Node.cpp.

References Node< SPACE_DIM >::mIsDeleted.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap().

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::MarkAsInternal (  )  [inline]

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

Definition at line 359 of file Node.cpp.

References Node< SPACE_DIM >::mIsInternal.

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

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::RemoveBoundaryElement ( unsigned  index  )  [inline]

Remove an boundary element that contains this node.

Parameters:
index of the boundary element to be removed.

Definition at line 285 of file Node.cpp.

References EXCEPTION, and Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::RemoveElement ( unsigned  index  )  [inline]

Remove an element that contains this node.

Parameters:
index of the element to be removed.

Definition at line 275 of file Node.cpp.

References EXCEPTION, and Node< SPACE_DIM >::mElementIndices.

template<unsigned SPACE_DIM>
c_vector< double, SPACE_DIM > & Node< SPACE_DIM >::rGetAppliedForce (  )  [inline]
Returns:
the force applied to this node.

Definition at line 209 of file Node.cpp.

References Node< SPACE_DIM >::CheckForNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

template<unsigned SPACE_DIM>
std::set< unsigned > & Node< SPACE_DIM >::rGetContainingBoundaryElementIndices (  )  [inline]
Returns:
a set of indices of boundary elements containing this node as a vertex.

Definition at line 307 of file Node.cpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>
std::set< unsigned > & Node< SPACE_DIM >::rGetContainingElementIndices (  )  [inline]
Returns:
a set of indices of elements containing this node as a vertex.

Definition at line 301 of file Node.cpp.

References Node< SPACE_DIM >::mElementIndices.

Referenced by MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::CheckForSwapsFromShortEdges(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), NagaiHondaForce< DIM >::GetAdhesionParameter(), NagaiHondaDifferentialAdhesionForce< DIM >::GetAdhesionParameter(), FarhadifarForce< DIM >::GetLineTensionParameter(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringElementIndices(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::IdentifySwapType(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT2Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), and VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh().

template<unsigned SPACE_DIM>
const c_vector< double, SPACE_DIM > & Node< SPACE_DIM >::rGetLocation (  )  const [inline]
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 140 of file Node.cpp.

References Node< SPACE_DIM >::mIsDeleted, and Node< SPACE_DIM >::mLocation.

Referenced by RepulsionForce< DIM >::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), AbstractFeCableIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AssembleOnCableElement(), AbstractFeVolumeIntegralAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, CAN_ASSEMBLE_VECTOR, CAN_ASSEMBLE_MATRIX, INTERPOLATION_LEVEL >::AssembleOnElement(), DistributedBoxCollection< DIM >::CalculateContainingBox(), BoxCollection< DIM >::CalculateContainingBox(), GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), BuskeElasticForce< DIM >::CalculateForceBetweenNodes(), BuskeAdhesiveForce< DIM >::CalculateForceBetweenNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::CheckOutwardNormals(), FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ConstructFromMesh(), LuoRudySpiralWaveCellFactory::CreateCardiacCellForTissueNode(), Cylindrical2dMesh::Cylindrical2dMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideEdge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DivideElementAlongGivenAxis(), NodeBasedCellPopulation< DIM >::GetNeighbouringNodeIndices(), VertexBasedCellPopulation< DIM >::GetTetrahedralMeshUsingVertexMesh(), NodeBasedCellPopulation< DIM >::GetVolumeOfCell(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), PlaneBoundaryCondition< DIM >::ImposeBoundaryCondition(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformIntersectionSwap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::SplitEdge(), NodeBasedCellPopulationWithBuskeUpdate< DIM >::UpdateNodeLocations(), CryptSimulationBoundaryCondition< DIM >::VerifyBoundaryCondition(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::VertexMesh(), and DistanceMapCalculator< ELEMENT_DIM, SPACE_DIM >::WorkOnLocalQueue().

template<unsigned SPACE_DIM>
c_vector< double, SPACE_DIM > & Node< SPACE_DIM >::rGetModifiableLocation (  )  [inline]
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 152 of file Node.cpp.

References Node< SPACE_DIM >::mIsDeleted, and Node< SPACE_DIM >::mLocation.

Referenced by FineCoarseMeshPair< DIM >::ComputeFineElementsAndWeightsForCoarseNodes(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), SphereGeometryBoundaryCondition< DIM >::ImposeBoundaryCondition(), PlaneBoundaryCondition< DIM >::ImposeBoundaryCondition(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformNodeMerge(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval().

template<unsigned SPACE_DIM>
std::vector< double > & Node< SPACE_DIM >::rGetNodeAttributes (  )  [inline]
Returns:
a vector containing the node attributes.

Definition at line 179 of file Node.cpp.

References Node< SPACE_DIM >::CheckForNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

template<unsigned SPACE_DIM>
template<class Archive >
void Node< SPACE_DIM >::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

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.

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::SetAsBoundaryNode ( bool  value = true  )  [inline]

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.

References Node< SPACE_DIM >::mIsBoundaryNode.

Referenced by QuadraticMeshHelper< DIM >::AddNodeToBoundaryElement(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::DeleteElementPriorToReMesh(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT1Swap(), MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformT3Swap(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::PerformVoidRemoval().

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::SetIndex ( unsigned  index  )  [inline]

Set the index of the node in the mesh.

Parameters:
index the index of the node

Definition at line 121 of file Node.cpp.

References Node< SPACE_DIM >::mIndex.

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

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::SetIsParticle ( bool  isParticle  )  [inline]

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

Parameters:
isParticle whether this node is a particle or not.

Definition at line 241 of file Node.cpp.

References Node< SPACE_DIM >::ConstructNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

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

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::SetPoint ( ChastePoint< SPACE_DIM >  point  )  [inline]

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.

References Node< SPACE_DIM >::mLocation, and ChastePoint< DIM >::rGetLocation().

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

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::SetRadius ( double  radius  )  [inline]

Set the radius of the node.

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

Definition at line 257 of file Node.cpp.

References Node< SPACE_DIM >::ConstructNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

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

template<unsigned SPACE_DIM>
void Node< SPACE_DIM >::SetRegion ( unsigned  region  )  [inline]

Set the node's region ID.

Parameters:
region the new region ID

Definition at line 371 of file Node.cpp.

References Node< SPACE_DIM >::ConstructNodeAttributes(), and Node< SPACE_DIM >::mpNodeAttributes.

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

Friends And Related Function Documentation

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

Needed for serialization.

Definition at line 90 of file Node.hpp.

Member Data Documentation

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 >::AddBoundaryElement(), Node< SPACE_DIM >::ContainingBoundaryElementsBegin(), Node< SPACE_DIM >::ContainingBoundaryElementsEnd(), Node< SPACE_DIM >::GetNumBoundaryElements(), Node< SPACE_DIM >::RemoveBoundaryElement(), and Node< SPACE_DIM >::rGetContainingBoundaryElementIndices().

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 >::AddElement(), Node< SPACE_DIM >::ContainingElementsBegin(), Node< SPACE_DIM >::ContainingElementsEnd(), Node< SPACE_DIM >::GetNumContainingElements(), Node< SPACE_DIM >::RemoveElement(), and Node< SPACE_DIM >::rGetContainingElementIndices().

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.

Referenced by Node< SPACE_DIM >::CommonConstructor(), Node< SPACE_DIM >::GetIndex(), and Node< SPACE_DIM >::SetIndex().

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.

Referenced by Node< SPACE_DIM >::CommonConstructor(), Node< SPACE_DIM >::IsBoundaryNode(), and Node< SPACE_DIM >::SetAsBoundaryNode().

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.

Referenced by Node< SPACE_DIM >::CommonConstructor(), Node< SPACE_DIM >::IsDeleted(), Node< SPACE_DIM >::MarkAsDeleted(), Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().

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.

Referenced by Node< SPACE_DIM >::CommonConstructor(), Node< SPACE_DIM >::IsInternal(), and Node< SPACE_DIM >::MarkAsInternal().

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.

Referenced by Node< SPACE_DIM >::GetPoint(), Node< SPACE_DIM >::Node(), Node< SPACE_DIM >::rGetLocation(), Node< SPACE_DIM >::rGetModifiableLocation(), and Node< SPACE_DIM >::SetPoint().

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 >::AddAppliedForceContribution(), Node< SPACE_DIM >::AddNodeAttribute(), Node< SPACE_DIM >::CheckForNodeAttributes(), Node< SPACE_DIM >::ClearAppliedForce(), Node< SPACE_DIM >::CommonConstructor(), Node< SPACE_DIM >::ConstructNodeAttributes(), Node< SPACE_DIM >::GetNumNodeAttributes(), Node< SPACE_DIM >::GetRadius(), Node< SPACE_DIM >::GetRegion(), Node< SPACE_DIM >::HasNodeAttributes(), Node< SPACE_DIM >::IsParticle(), Node< SPACE_DIM >::rGetAppliedForce(), Node< SPACE_DIM >::rGetNodeAttributes(), Node< SPACE_DIM >::serialize(), Node< SPACE_DIM >::SetIsParticle(), Node< SPACE_DIM >::SetRadius(), Node< SPACE_DIM >::SetRegion(), and Node< SPACE_DIM >::~Node().

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