#include <MutableMesh.hpp>

Inheritance diagram for MutableMesh< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for MutableMesh< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	MutableMesh ()
	MutableMesh (std::vector< Node< SPACE_DIM > * > nodes)
virtual	~MutableMesh ()
void	Clear ()
unsigned	GetNumNodes () const
unsigned	GetNumElements () const
unsigned	GetNumBoundaryElements () const
void	RescaleMeshFromBoundaryNode (ChastePoint< 1 > updatedPoint, unsigned boundaryNodeIndex)
virtual unsigned	AddNode (Node< SPACE_DIM > *pNewNode)
virtual void	SetNode (unsigned index, ChastePoint< SPACE_DIM > point, bool concreteMove=true)
void	MoveMergeNode (unsigned index, unsigned targetIndex, bool concreteMove=true)
virtual void	DeleteNode (unsigned index)
void	DeleteNodePriorToReMesh (unsigned index)
unsigned	RefineElement (Element< ELEMENT_DIM, SPACE_DIM > *pElement, ChastePoint< SPACE_DIM > point)
void	DeleteBoundaryNodeAt (unsigned index)
void	ReIndex (NodeMap &map)
virtual void	ReMesh (NodeMap &map)
void	ReMesh ()
bool	CheckIsVoronoi (double maxPenetration=0.0)
template<>
void	RescaleMeshFromBoundaryNode (ChastePoint< 1 > updatedPoint, unsigned boundaryNodeIndex)
Protected Attributes
std::vector< unsigned >	mDeletedElementIndices
std::vector< unsigned >	mDeletedBoundaryElementIndices
std::vector< unsigned >	mDeletedNodeIndices
bool	mAddedNodes
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
bool	CheckIsVoronoi (Element< ELEMENT_DIM, SPACE_DIM > *pElement, double maxPenetration)
Friends
class	boost::serialization::access

Detailed Description

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

A concrete mutable mesh class.

Definition at line 49 of file MutableMesh.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh ( )

Constructor.

Definition at line 53 of file MutableMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MutableMesh< ELEMENT_DIM, SPACE_DIM >::MutableMesh ( std::vector< Node< SPACE_DIM > * > nodes )

Constructor which takes in a vector of nodes.

Parameters:

nodes a vector of nodes

Definition at line 60 of file MutableMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

MutableMesh< ELEMENT_DIM, SPACE_DIM >::~MutableMesh ( ) [virtual]

Destructor.

Definition at line 75 of file MutableMesh.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode ( Node< SPACE_DIM > * pNewNode ) [virtual]

Add a node to the mesh.

NB. After calling this one or more times, you must then call ReMesh

Parameters:

pNewNode pointer to the new node

Reimplemented in NodesOnlyMesh< SPACE_DIM >, and NodesOnlyMesh< DIM >.

Definition at line 81 of file MutableMesh.cpp.

References Node< SPACE_DIM >::GetIndex(), and Node< SPACE_DIM >::SetIndex().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi	(	Element< ELEMENT_DIM, SPACE_DIM > *	pElement,
		double	maxPenetration
	)		`[private]`

Check whether any neighbouring node is inside the circumsphere of this element.

Parameters:

pElement	pointer to an element
maxPenetration	is the maximum distance a node is allowed to be inside the circumsphere of the element, as a proportion of the circumsphere radius.

Definition at line 760 of file MutableMesh.cpp.

References Element< ELEMENT_DIM, SPACE_DIM >::CalculateCircumsphere(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), and Node< SPACE_DIM >::rGetContainingElementIndices().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableMesh< ELEMENT_DIM, SPACE_DIM >::CheckIsVoronoi ( double maxPenetration = 0.0 )

Checks the entire mesh element by element and checks whether any neighbouring node is inside the circumsphere of this element.

Parameters:

maxPenetration is the maximum distance a node is allowed to be inside the circumsphere of an element that it is not a member of, as a proportion of the circumsphere radius.

Todo:: use ElementIterator here?

Definition at line 844 of file MutableMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::Clear ( ) [virtual]

Clear all the data in the mesh.

Reimplemented from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in NodesOnlyMesh< SPACE_DIM >, and NodesOnlyMesh< DIM >.

Definition at line 101 of file MutableMesh.cpp.

References TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::Clear().

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteBoundaryNodeAt ( unsigned index )

Remove a boundary node, and update all the appropriate data structures.

The deleted node is not removed from the list, merely marked as deleted, and can be reused when a new node is added to the mesh.

Any elements or boundary elements containing this node will be removed. The boundary nodes information will be updated with new boundary node(s). NB: New boundary elements WILL NOT be added.

Parameters:

index The index of the node to remove.

Definition at line 461 of file MutableMesh.cpp.

References EXCEPTION, AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNumNodes(), Node< SPACE_DIM >::IsDeleted(), Element< ELEMENT_DIM, SPACE_DIM >::MarkAsDeleted(), and Node< SPACE_DIM >::SetAsBoundaryNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNode ( unsigned index ) [virtual]

Delete a node from the mesh by finding an appropriate neighbour node to merge it with.

Parameters:

index is the index of the node to be deleted

Reimplemented in NodesOnlyMesh< SPACE_DIM >, and NodesOnlyMesh< DIM >.

Definition at line 208 of file MutableMesh.cpp.

References EXCEPTION, and AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::DeleteNodePriorToReMesh ( unsigned index )

Mark a node as deleted. Note that this method DOES NOT deal with the associated elements and therefore should only be called immediately prior to a ReMesh() being called. (Thus saves work compared to DeleteNode() function and does not MoveMerge the node and elements).

Parameters:

index The index of the node to delete

Definition at line 244 of file MutableMesh.cpp.

Referenced by HoneycombMeshGenerator::GetCircularMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumBoundaryElements ( ) const [virtual]

Get the number of boundary elements that are actually in use.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 112 of file MutableMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumElements ( ) const [virtual]

Get the number of elements that are actually in use.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 118 of file MutableMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::GetNumNodes ( ) const [virtual]

Get the number of nodes that are actually in use.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 124 of file MutableMesh.cpp.

Referenced by HoneycombMeshGenerator::GetCellLocationIndices(), HoneycombMeshGenerator::GetCircularMesh(), and MutableMesh< SPACE_DIM, SPACE_DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::MoveMergeNode	(	unsigned	index,
		unsigned	targetIndex,
		bool	concreteMove = `true`
	)

Move one node to another (i.e. merges the nodes), refreshing/deleting elements as appropriate.

Parameters:

index	is the index of the node to be moved
targetIndex	is the index of the node to move to
concreteMove	can be set to false if you just want to check whether this will work (defaults to true). Set it to true if you're doing the merger for real, in order to do all the bookkeeping.

Definition at line 251 of file MutableMesh.cpp.

References EXCEPTION.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

unsigned MutableMesh< ELEMENT_DIM, SPACE_DIM >::RefineElement	(	Element< ELEMENT_DIM, SPACE_DIM > *	pElement,
		ChastePoint< SPACE_DIM >	point
	)

Refine an element at a given point.

Parameters:

pElement	pointer to the element
point	a point located in the element

Definition at line 405 of file MutableMesh.cpp.

References EXCEPTION, Element< ELEMENT_DIM, SPACE_DIM >::IncludesPoint(), ChastePoint< DIM >::rGetLocation(), and Element< ELEMENT_DIM, SPACE_DIM >::UpdateNode().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReIndex ( NodeMap & map )

Re-index a mesh so that it has no deleted elements or nodes.

Parameters:

map	is a NodeMap which associates the indices of nodes in the old mesh with indices of nodes in the new mesh. This should be created with the correct size (NumAllNodes)

Definition at line 510 of file MutableMesh.cpp.

References NodeMap::Resize(), NodeMap::SetDeleted(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::SetIndex(), and NodeMap::SetNewIndex().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh ( )

Alternative version of remesh which takes no parameters does not require a NodeMap. Note: inherited classes should overload ReMesh(NodeMap&)

Definition at line 753 of file MutableMesh.cpp.

Referenced by MutableMesh< SPACE_DIM, SPACE_DIM >::serialize().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh ( NodeMap & map ) [virtual]

Re-mesh a mesh using triangle (via library calls) or tetgen

Parameters:

map	is a NodeMap which associates the indices of nodes in the old mesh with indices of nodes in the new mesh. This should be created with the correct size (NumAllNodes)

Reimplemented in Cylindrical2dMesh, NodesOnlyMesh< SPACE_DIM >, and NodesOnlyMesh< DIM >.

Definition at line 620 of file MutableMesh.cpp.

References EXCEPTION, Node< SPACE_DIM >::GetIndex(), NodeMap::Resize(), NodeMap::SetDeleted(), and NodeMap::SetNewIndex().

Referenced by CylindricalHoneycombMeshGenerator::CylindricalHoneycombMeshGenerator(), HoneycombMeshGenerator::GetCircularMesh(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update().

template<>

void MutableMesh< 1, 1 >::RescaleMeshFromBoundaryNode	(	ChastePoint< 1 >	updatedPoint,
		unsigned	boundaryNodeIndex
	)

The RescaleMeshFromBoundaryNode method is only defined for 1D meshes.

Parameters:

updatedPoint	point determining the scale factor
boundaryNodeIndex	index of the boundary node

Definition at line 136 of file MutableMesh.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::RescaleMeshFromBoundaryNode	(	ChastePoint< 1 >	updatedPoint,
		unsigned	boundaryNodeIndex
	)

Todo:: should unsigned GetNumBoundaryNodes() be overloaded too??

Rescale the mesh from a boundary node.

Parameters:

updatedPoint	point determining the scale factor
boundaryNodeIndex	index of the boundary node

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

template<class Archive >

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)		`[inline, private]`

Serialize the mesh.

Note that if you are calling this method (from subclasses) you should archive your member variables FIRST. So that this method can call a ReMesh (to convert from TrianglesMeshReader input format into your native format).

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in Cylindrical2dMesh, NodesOnlyMesh< SPACE_DIM >, and NodesOnlyMesh< DIM >.

Definition at line 65 of file MutableMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode	(	unsigned	index,
		ChastePoint< SPACE_DIM >	point,
		bool	concreteMove = `true`
	)		`[virtual]`

Move the node with a particular index to a new point in space and verifies that the signed areas of the supporting Elements are positive.

Parameters:

index	is the index of the node to be moved
point	is the new target location of the node
concreteMove	is set to false if we want to skip the signed area tests (defaults to true)

Definition at line 151 of file MutableMesh.cpp.

References EXCEPTION.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode(), MeshBasedCellPopulationWithGhostNodes< DIM >::UpdateGhostPositions(), and NodeBasedCellPopulationWithParticles< DIM >::UpdateParticlePositions().

Friends And Related Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Reimplemented in Cylindrical2dMesh, NodesOnlyMesh< SPACE_DIM >, and NodesOnlyMesh< DIM >.

Definition at line 52 of file MutableMesh.hpp.

Member Data Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

bool MutableMesh< ELEMENT_DIM, SPACE_DIM >::mAddedNodes [protected]

Whether any nodes have been added to the mesh.

Definition at line 98 of file MutableMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedBoundaryElementIndices [protected]

Indices of boundary elements that have been marked as deleted. These indices can be reused when adding new boundary elements.

Definition at line 89 of file MutableMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedElementIndices [protected]

Indices of elements that have been marked as deleted. These indices can be reused when adding new elements.

Definition at line 83 of file MutableMesh.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

std::vector<unsigned> MutableMesh< ELEMENT_DIM, SPACE_DIM >::mDeletedNodeIndices [protected]

Indices of nodes that have been marked as deleted. These indices can be reused when adding new nodes.

Definition at line 95 of file MutableMesh.hpp.

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

mesh/src/common/MutableMesh.hpp
mesh/src/common/MutableMesh.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

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

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

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