Node< SPACE_DIM > Class Template Reference

#include <Node.hpp>

Collaboration diagram for Node< SPACE_DIM >:

List of all members.

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)

void SetPoint (ChastePoint< SPACE_DIM > point)

void SetIndex (unsigned index)

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::set< unsigned > & rGetContainingBoundaryElementIndices ()

unsigned GetNumContainingElements () const

unsigned GetNumBoundaryElements () const

void MarkAsDeleted ()

bool IsDeleted () const

template<unsigned ELEMENT_DIM>

bool IsFlagged (TetrahedralMesh< 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

void CommonConstructor (unsigned index, bool isBoundaryNode)

Private Attributes

unsigned mIndex

unsigned mRegion

c_vector< double, SPACE_DIM > mLocation

bool mIsBoundaryNode

bool mIsDeleted

std::set< unsigned > mElementIndices

std::set< unsigned > mBoundaryElementIndices

Classes

class ContainingBoundaryElementIterator

class ContainingElementIterator

Detailed Description

template<unsigned SPACE_DIM>
class Node< SPACE_DIM >

A node in a finite element mesh.

Definition at line 46 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 which takes 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 48 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 which takes 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 55 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 which takes 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 65 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 which takes the coordinates if 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 72 of file Node.cpp.

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

Member Function Documentation

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 39 of file Node.cpp.

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

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

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. Jacobian and JacobianDeterminant of element need to be updated.

Parameters:

point

the new location of the node

Definition at line 91 of file Node.cpp.

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

template<unsigned SPACE_DIM>

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

Set the index of this node in the mesh.

Parameters:

index

the index of the node

Definition at line 97 of file Node.cpp.

References Node< SPACE_DIM >::mIndex.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), and NodeBasedTissue< DIM >::AddNode().

template<unsigned SPACE_DIM>

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

Set whether this node is a boundary node.

Parameters:

value

whether the node is a boundary node

Definition at line 103 of file Node.cpp.

References Node< SPACE_DIM >::mIsBoundaryNode.

Referenced by QuadraticMesh< DIM >::AddNodeToBoundaryElement(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt().

template<unsigned SPACE_DIM>

ChastePoint< SPACE_DIM > Node< SPACE_DIM >::GetPoint ( ) const [inline]

Get the node's location as a ChastePoint.

Definition at line 110 of file Node.cpp.

References Node< SPACE_DIM >::mLocation.

Referenced by Cylindrical2dMesh::AddNode(), AbstractLinearEllipticPde< ELEM_DIM, SPACE_DIM >::ComputeConstantInUSourceTermAtNode(), AbstractLinearEllipticPde< ELEM_DIM, SPACE_DIM >::ComputeLinearInUCoeffInSourceTermAtNode(), AbstractLinearParabolicPde< ELEM_DIM, SPACE_DIM >::ComputeLinearSourceTermAtNode(), AbstractLinearParabolicPde< ELEM_DIM, SPACE_DIM >::ComputeNonlinearSourceTermAtNode(), AbstractBoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::GetDirichletBCValue(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned SPACE_DIM>

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

Get 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 116 of file Node.cpp.

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

Referenced by CryptSimulation2d::ApplyTissueBoundaryConditions(), AbstractStaticAssembler< ELEMENT_DIM, SPACE_DIM, PROBLEM_DIM, NON_HEART, CONCRETE >::AssembleOnElement(), NodeBoxCollection< DIM >::CalculateContainingBox(), DistanceMapCalculator< SPACE_DIM >::ComputeDistanceMap(), AbstractConvergenceTester< CELL, CARDIAC_PROBLEM, DIM, PROBLEM_DIM >::Converge(), Cylindrical2dMesh::Cylindrical2dMesh(), and VoronoiTessellation< DIM >::Initialise().

template<unsigned SPACE_DIM>

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

Get 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 123 of file Node.cpp.

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

Referenced by CryptSimulation2d::ApplyTissueBoundaryConditions().

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetIndex ( ) const [inline]

Get the index of this node in the mesh.

Definition at line 130 of file Node.cpp.

References Node< SPACE_DIM >::mIndex.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), NodeBasedTissue< DIM >::AddNode(), DistanceMapCalculator< SPACE_DIM >::ComputeDistanceMap(), MonodomainPde< ELEM_DIM, SPACE_DIM >::ComputeNonlinearSourceTermAtNode(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThickness(), MonodomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), BidomainDg0Assembler< ELEMENT_DIM, SPACE_DIM >::IncrementInterpolatedQuantities(), VoronoiTessellation< DIM >::Initialise(), LessThanNode< SPACE_DIM >::operator()(), and CellwiseData< DIM >::SetValue().

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::IsBoundaryNode ( ) const [inline]

Get whether this node is a boundary node.

Definition at line 136 of file Node.cpp.

References Node< SPACE_DIM >::mIsBoundaryNode.

Referenced by BoundaryConditionsContainer< ELEM_DIM, SPACE_DIM, PROBLEM_DIM >::AddDirichletBoundaryCondition(), QuadraticMesh< DIM >::AddNodeToBoundaryElement(), and VoronoiTessellation< DIM >::Initialise().

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 148 of file Node.cpp.

References Node< SPACE_DIM >::mElementIndices.

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 154 of file Node.cpp.

References Node< SPACE_DIM >::mElementIndices.

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 164 of file Node.cpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

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 174 of file Node.cpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>

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

Return a set of indices of elements containing this node as a vertex.

Definition at line 180 of file Node.cpp.

References Node< SPACE_DIM >::mElementIndices.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckVoronoi(), VoronoiTessellation< DIM >::Initialise(), and MeshBasedTissue< DIM >::Update().

template<unsigned SPACE_DIM>

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

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

Definition at line 186 of file Node.cpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetNumContainingElements ( ) const [inline]

Get the number of elements in the mesh that contain this node.

Definition at line 192 of file Node.cpp.

References Node< SPACE_DIM >::mElementIndices.

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetNumBoundaryElements ( ) const [inline]

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

Definition at line 198 of file Node.cpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>

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

Mark the node as having been removed from the mesh.

Definition at line 208 of file Node.cpp.

References Node< SPACE_DIM >::mIsDeleted.

template<unsigned SPACE_DIM>

bool Node< SPACE_DIM >::IsDeleted ( ) const [inline]

Get whether the node is marked as deleted.

Definition at line 214 of file Node.cpp.

References Node< SPACE_DIM >::mIsDeleted.

Referenced by MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt(), and AbstractTetrahedralMeshWriter< ELEMENT_DIM, SPACE_DIM >::WriteFilesUsingMesh().

template<unsigned SPACE_DIM>

template<unsigned ELEMENT_DIM>

bool Node< SPACE_DIM >::IsFlagged ( TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > & rMesh ) [inline]

Determine if a node lives within a flagged element.

Parameters:

rMesh

the mesh containing the nodes and elements

Definition at line 248 of file Node.hpp.

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

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 220 of file Node.cpp.

References Node< SPACE_DIM >::mRegion.

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::GetRegion ( ) const [inline]

Get the node's region ID.

Definition at line 226 of file Node.cpp.

References Node< SPACE_DIM >::mRegion.

template<unsigned SPACE_DIM>

ContainingElementIterator Node< SPACE_DIM >::ContainingElementsBegin ( ) const [inline]

Get a ContainingElementIterator pointing to the first containing element

Definition at line 330 of file Node.hpp.

References Node< SPACE_DIM >::mElementIndices.

Referenced by DistanceMapCalculator< SPACE_DIM >::ComputeDistanceMap(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThickness(), Node< SPACE_DIM >::IsFlagged(), and MeshBasedTissue< DIM >::Update().

template<unsigned SPACE_DIM>

ContainingElementIterator Node< SPACE_DIM >::ContainingElementsEnd ( ) const [inline]

Get a ContainingElementIterator pointing to one past the last containing element

Definition at line 338 of file Node.hpp.

References Node< SPACE_DIM >::mElementIndices.

Referenced by DistanceMapCalculator< SPACE_DIM >::ComputeDistanceMap(), StreeterFibreGenerator< SPACE_DIM >::GetAveragedThickness(), Node< SPACE_DIM >::IsFlagged(), and MeshBasedTissue< DIM >::Update().

template<unsigned SPACE_DIM>

ContainingBoundaryElementIterator Node< SPACE_DIM >::ContainingBoundaryElementsBegin ( ) const [inline]

Get a ContainingBoundaryElementIterator pointing to the first containing boundary element

Definition at line 397 of file Node.hpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

template<unsigned SPACE_DIM>

ContainingBoundaryElementIterator Node< SPACE_DIM >::ContainingBoundaryElementsEnd ( ) const [inline]

Get a ContainingBoundaryElementIterator pointing to one past the last containing boundary element

Definition at line 405 of file Node.hpp.

References Node< SPACE_DIM >::mBoundaryElementIndices.

Member Data Documentation

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::mIndex [private]

The index of this node within the mesh.

Definition at line 51 of file Node.hpp.

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

template<unsigned SPACE_DIM>

unsigned Node< SPACE_DIM >::mRegion [private]

A region ID.

Definition at line 54 of file Node.hpp.

Referenced by Node< SPACE_DIM >::CommonConstructor(), Node< SPACE_DIM >::GetRegion(), and Node< SPACE_DIM >::SetRegion().

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 57 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>

bool Node< SPACE_DIM >::mIsBoundaryNode [private]

Whether this node is a boundary node.

Definition at line 60 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.

Definition at line 66 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>

std::set<unsigned> Node< SPACE_DIM >::mElementIndices [private]

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

Definition at line 69 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>

std::set<unsigned> Node< SPACE_DIM >::mBoundaryElementIndices [private]

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

Definition at line 72 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().

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

/tmp/release_1.1/mesh/src/common/Node.hpp
/tmp/release_1.1/mesh/src/common/Node.cpp


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)
void	SetPoint (ChastePoint< SPACE_DIM > point)
void	SetIndex (unsigned index)
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::set< unsigned > &	rGetContainingBoundaryElementIndices ()
unsigned	GetNumContainingElements () const
unsigned	GetNumBoundaryElements () const
void	MarkAsDeleted ()
bool	IsDeleted () const
template<unsigned ELEMENT_DIM>
bool	IsFlagged (TetrahedralMesh< 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
void	CommonConstructor (unsigned index, bool isBoundaryNode)
Private Attributes
unsigned	mIndex
unsigned	mRegion
c_vector< double, SPACE_DIM >	mLocation
bool	mIsBoundaryNode
bool	mIsDeleted
std::set< unsigned >	mElementIndices
std::set< unsigned >	mBoundaryElementIndices
Classes
class	ContainingBoundaryElementIterator
class	ContainingElementIterator

Node< SPACE_DIM > Class Template Reference

Public Member Functions

Private Member Functions

Private Attributes

Classes

Detailed Description

template<unsigned SPACE_DIM> class Node< SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<unsigned SPACE_DIM>
class Node< SPACE_DIM >