#include <NodesOnlyMesh.hpp>

Inheritance diagram for NodesOnlyMesh< SPACE_DIM >:

Collaboration diagram for NodesOnlyMesh< SPACE_DIM >:

Public Member Functions
	NodesOnlyMesh ()

virtual	~NodesOnlyMesh ()

void	ConstructNodesWithoutMesh (const std::vector< Node< SPACE_DIM > * > &rNodes, double maxInteractionDistance)

void	ConstructNodesWithoutMesh (const std::vector< boost::shared_ptr< Node< SPACE_DIM > > > &rNodes, double maxInteractionDistance)

void	ConstructNodesWithoutMesh (const AbstractMesh< SPACE_DIM, SPACE_DIM > &rGeneratingMesh, double maxInteractionDistance)

std::vector< bool > &	rGetInitiallyOwnedNodes ()

void	Clear ()

unsigned	SolveNodeMapping (unsigned index) const

Node< SPACE_DIM > *	GetNodeOrHaloNode (unsigned index) const

bool	IsOwned (c_vector< double, SPACE_DIM > &location)

unsigned	GetNumNodes () const

virtual unsigned	GetMaximumNodeIndex ()

void	SetMaximumInteractionDistance (double maxDistance)

double	GetMaximumInteractionDistance ()

double	GetWidth (const unsigned &rDimension) const

void	SetCalculateNodeNeighbours (bool calculateNodeNeighbours)

void	CalculateInteriorNodePairs (std::vector< std::pair< Node< SPACE_DIM > , Node< SPACE_DIM > > > &rNodePairs)

void	CalculateBoundaryNodePairs (std::vector< std::pair< Node< SPACE_DIM > , Node< SPACE_DIM > > > &rNodePairs)

void	ReMesh (NodeMap &rMap)

void	SetInitialBoxCollection (const c_vector< double, 2 *SPACE_DIM > domainSize, double maxInteractionDistance)

void	UpdateBoxCollection ()

void	ResizeBoxCollection ()

void	AddNodesToBoxes ()

void	AddHaloNodesToBoxes ()

void	CalculateNodesOutsideLocalDomain ()

std::vector< unsigned > &	rGetNodesToSendLeft ()

std::vector< unsigned > &	rGetNodesToSendRight ()

std::vector< unsigned > &	rGetHaloNodesToSendRight ()

std::vector< unsigned > &	rGetHaloNodesToSendLeft ()

void	AddHaloNode (boost::shared_ptr< Node< SPACE_DIM > > pNewNode)

void	ClearHaloNodes ()

void	SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > point, bool concreteMove=false)

unsigned	AddNode (Node< SPACE_DIM > *pNewNode)

void	AddMovedNode (boost::shared_ptr< Node< SPACE_DIM > > pMovedNode)

void	DeleteNode (unsigned index)

void	DeleteMovedNode (unsigned index)

void	SetMinimumNodeDomainBoundarySeparation (double separation)

void	LoadBalanceMesh ()

void	ConstructFromMeshReader (AbstractMeshReader< SPACE_DIM, SPACE_DIM > &rMeshReader)

std::vector< unsigned >	GetAllNodeIndices () const

Public Member Functions inherited from MutableMesh< SPACE_DIM, SPACE_DIM >
bool	CheckIsVoronoi (double maxPenetration=0.0)

	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)

unsigned	AddElement (Element< ELEMENT_DIM, SPACE_DIM > *pNewElement)

void	MoveMergeNode (unsigned index, unsigned targetIndex, bool concreteMove=true)

virtual void	DeleteElement (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)

void	ReMesh ()

std::vector< c_vector < unsigned, 5 > >	SplitLongEdges (double cutoffLength)

c_vector< unsigned, 3 >	SplitEdge (Node< SPACE_DIM > pNodeA, Node< SPACE_DIM > pNodeB)

Public Member Functions inherited from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
	TetrahedralMesh ()

void	ConstructFromMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)

void	ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)

bool	CheckIsConforming ()

double	GetVolume ()

double	GetSurfaceArea ()

void	RefreshMesh ()

void	PermuteNodes ()

void	PermuteNodes (const std::vector< unsigned > &perm)

unsigned	GetContainingElementIndexWithInitialGuess (const ChastePoint< SPACE_DIM > &rTestPoint, unsigned startingElementGuess, bool strict=false)

unsigned	GetNearestElementIndex (const ChastePoint< SPACE_DIM > &rTestPoint)

std::vector< unsigned >	GetContainingElementIndices (const ChastePoint< SPACE_DIM > &rTestPoint)

double	GetAngleBetweenNodes (unsigned indexA, unsigned indexB)

virtual void	RefreshJacobianCachedData ()

virtual void	GetJacobianForElement (unsigned elementIndex, c_matrix< double, SPACE_DIM, SPACE_DIM > &rJacobian, double &rJacobianDeterminant) const

virtual void	GetInverseJacobianForElement (unsigned elementIndex, c_matrix< double, SPACE_DIM, ELEMENT_DIM > &rJacobian, double &rJacobianDeterminant, c_matrix< double, ELEMENT_DIM, SPACE_DIM > &rInverseJacobian) const

virtual void	GetWeightedDirectionForElement (unsigned elementIndex, c_vector< double, SPACE_DIM > &rWeightedDirection, double &rJacobianDeterminant) const

virtual void	GetWeightedDirectionForBoundaryElement (unsigned elementIndex, c_vector< double, SPACE_DIM > &rWeightedDirection, double &rJacobianDeterminant) const

EdgeIterator	EdgesBegin ()

EdgeIterator	EdgesEnd ()

Public Member Functions inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
ElementIterator	GetElementIteratorBegin (bool skipDeletedElements=true)

ElementIterator	GetElementIteratorEnd ()

	AbstractTetrahedralMesh ()

virtual	~AbstractTetrahedralMesh ()

virtual unsigned	GetNumLocalElements () const

virtual unsigned	GetNumLocalBoundaryElements () const

unsigned	GetNumAllElements () const

unsigned	GetNumAllBoundaryElements () const

virtual unsigned	GetNumCableElements () const

virtual unsigned	GetNumVertices () const

Element< ELEMENT_DIM, SPACE_DIM > *	GetElement (unsigned index) const

BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > *	GetBoundaryElement (unsigned index) const

void	ConstructFromMesh (AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rOtherMesh)

BoundaryElementIterator	GetBoundaryElementIteratorBegin () const

BoundaryElementIterator	GetBoundaryElementIteratorEnd () const

void	CheckOutwardNormals ()

virtual void	ConstructLinearMesh (unsigned width)

virtual void	ConstructRectangularMesh (unsigned width, unsigned height, bool stagger=true)

virtual void	ConstructCuboid (unsigned width, unsigned height, unsigned depth)

void	ConstructRegularSlabMesh (double spaceStep, double width, double height=0, double depth=0)

void	ConstructRegularSlabMeshWithDimensionSplit (unsigned dimension, double spaceStep, double width, double height=0, double depth=0)

virtual bool	CalculateDesignatedOwnershipOfBoundaryElement (unsigned faceIndex)

virtual bool	CalculateDesignatedOwnershipOfElement (unsigned elementIndex)

unsigned	CalculateMaximumNodeConnectivityPerProcess () const

virtual void	GetHaloNodeIndices (std::vector< unsigned > &rHaloIndices) const

void	CalculateNodeExchange (std::vector< std::vector< unsigned > > &rNodesToSendPerProcess, std::vector< std::vector< unsigned > > &rNodesToReceivePerProcess)

virtual c_vector< double, 2 >	CalculateMinMaxEdgeLengths ()

unsigned	GetContainingElementIndex (const ChastePoint< SPACE_DIM > &rTestPoint, bool strict=false, std::set< unsigned > testElements=std::set< unsigned >(), bool onlyTryWithTestElements=false)

unsigned	GetNearestElementIndexFromTestElements (const ChastePoint< SPACE_DIM > &rTestPoint, std::set< unsigned > testElements)

Public Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
NodeIterator	GetNodeIteratorBegin (bool skipDeletedNodes=true)

NodeIterator	GetNodeIteratorEnd ()

	AbstractMesh ()

virtual	~AbstractMesh ()

unsigned	GetNumBoundaryNodes () const

virtual unsigned	GetNumAllNodes () const

unsigned	GetNumNodeAttributes () const

Node< SPACE_DIM > *	GetNode (unsigned index) const

Node< SPACE_DIM > *	GetNodeFromPrePermutationIndex (unsigned index) const

virtual DistributedVectorFactory *	GetDistributedVectorFactory ()

virtual void	SetDistributedVectorFactory (DistributedVectorFactory *pFactory)

BoundaryNodeIterator	GetBoundaryNodeIteratorBegin () const

BoundaryNodeIterator	GetBoundaryNodeIteratorEnd () const

std::string	GetMeshFileBaseName () const

bool	IsMeshOnDisk () const

const std::vector< unsigned > &	rGetNodePermutation () const

virtual c_vector< double, SPACE_DIM >	GetVectorFromAtoB (const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB)

double	GetDistanceBetweenNodes (unsigned indexA, unsigned indexB)

virtual ChasteCuboid< SPACE_DIM >	CalculateBoundingBox () const

virtual unsigned	GetNearestNodeIndex (const ChastePoint< SPACE_DIM > &rTestPoint)

virtual void	Scale (const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0)

virtual void	Translate (const c_vector< double, SPACE_DIM > &rDisplacement)

void	Translate (const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0)

virtual void	Rotate (c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix)

void	Rotate (c_vector< double, 3 > axis, double angle)

void	RotateX (const double theta)

void	RotateY (const double theta)

void	RotateZ (const double theta)

void	Rotate (double theta)

bool	IsMeshChanging () const

unsigned	CalculateMaximumContainingElementsPerProcess () const

void	SetMeshHasChangedSinceLoading ()

Protected Member Functions
void	ClearBoxCollection ()

virtual void	SetUpBoxCollection (double cutOffLength, c_vector< double, 2 *SPACE_DIM > domainSize, int numLocalRows=PETSC_DECIDE, bool isPeriodic=false)

DistributedBoxCollection < SPACE_DIM > *	GetBoxCollection ()

Protected Member Functions inherited from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
unsigned	SolveNodeMapping (unsigned index) const

unsigned	SolveElementMapping (unsigned index) const

unsigned	SolveBoundaryElementMapping (unsigned index) const

template<class MESHER_IO >
void	ExportToMesher (NodeMap &map, MESHER_IO &mesherInput, int *elementList=nullptr)

template<class MESHER_IO >
void	ImportFromMesher (MESHER_IO &mesherOutput, unsigned numberOfElements, int elementList, unsigned numberOfFaces, int faceList, int *edgeMarkerList)

void	InitialiseTriangulateIo (triangulateio &mesherIo)

void	FreeTriangulateIo (triangulateio &mesherIo)

Protected Member Functions inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
void	SetElementOwnerships ()

Protected Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
ChasteCuboid< SPACE_DIM >	CalculateBoundingBox (const std::vector< Node< SPACE_DIM > * > &rNodes) const

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

template<class Archive >
void	load (Archive &archive, const unsigned int version)

unsigned	GetNextAvailableIndex ()

void	EnlargeBoxCollection ()

bool	IsANodeCloseToDomainBoundary ()

void	SetUpBoxCollection (const std::vector< Node< SPACE_DIM > * > &rNodes)

void	RemoveDeletedNodes (NodeMap &map)

void	UpdateNodeIndices ()

void	AddNodeWithFixedIndex (Node< SPACE_DIM > *pNewNode)

Private Attributes
std::vector< boost::shared_ptr < Node< SPACE_DIM > > >	mHaloNodes

double	mMaximumInteractionDistance

std::map< unsigned, unsigned >	mNodesMapping

std::map< unsigned, unsigned >	mHaloNodesMapping

unsigned	mIndexCounter

double	mMinimumNodeDomainBoundarySeparation

std::vector< unsigned >	mDeletedGlobalNodeIndices

std::vector< unsigned >	mNodesToSendRight

std::vector< unsigned >	mNodesToSendLeft

std::vector< bool >	mLocalInitialNodes

unsigned	mMaxAddedNodeIndex

DistributedBoxCollection < SPACE_DIM > *	mpBoxCollection

bool	mCalculateNodeNeighbours

Friends
class	TestNodesOnlyMesh

class	boost::serialization::access

Additional Inherited Members
Public Types inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector < BoundaryElement< ELEMENT_DIM-1, SPACE_DIM > * >::const_iterator	BoundaryElementIterator

Public Types inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector< Node < SPACE_DIM > * >::const_iterator	BoundaryNodeIterator

Protected Attributes inherited from MutableMesh< SPACE_DIM, SPACE_DIM >
std::vector< unsigned >	mDeletedElementIndices

std::vector< unsigned >	mDeletedBoundaryElementIndices

std::vector< unsigned >	mDeletedNodeIndices

bool	mAddedNodes

Protected Attributes inherited from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
std::vector< c_vector< double, SPACE_DIM > >	mElementWeightedDirections

std::vector< c_matrix< double, SPACE_DIM, ELEMENT_DIM > >	mElementJacobians

std::vector< c_matrix< double, ELEMENT_DIM, SPACE_DIM > >	mElementInverseJacobians

std::vector< double >	mElementJacobianDeterminants

std::vector< c_vector< double, SPACE_DIM > >	mBoundaryElementWeightedDirections

std::vector< double >	mBoundaryElementJacobianDeterminants

Protected Attributes inherited from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >
bool	mMeshIsLinear

std::vector< Element < ELEMENT_DIM, SPACE_DIM > * >	mElements

std::vector< BoundaryElement < ELEMENT_DIM-1, SPACE_DIM > * >	mBoundaryElements

Protected Attributes inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
std::vector< Node< SPACE_DIM > * >	mNodes

std::vector< Node< SPACE_DIM > * >	mBoundaryNodes

DistributedVectorFactory *	mpDistributedVectorFactory

std::vector< unsigned >	mNodePermutation

std::string	mMeshFileBaseName

bool	mMeshChangesDuringSimulation

Detailed Description

template<unsigned SPACE_DIM>
class NodesOnlyMesh< SPACE_DIM >

Mesh class for storing lists of nodes (no elements). This inherits from MutableMesh because we want to be able to add and delete nodes.

Definition at line 52 of file NodesOnlyMesh.hpp.

Constructor & Destructor Documentation

template<unsigned SPACE_DIM>

NodesOnlyMesh< SPACE_DIM >::NodesOnlyMesh ( )

Default constructor to initialise BoxCollection to NULL.

Definition at line 41 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

NodesOnlyMesh< SPACE_DIM >::~NodesOnlyMesh ( )

virtual

Over-written destructor to delete pointer to BoxCollection.

Definition at line 53 of file NodesOnlyMesh.cpp.

Member Function Documentation

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::AddHaloNode ( boost::shared_ptr< Node< SPACE_DIM > > pNewNode )

Add a temporary halo node on this process.

Parameters

pNewNode a shared pointer to the new node to add.

Definition at line 370 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::AddHaloNodesToBoxes ( )

Iterate through each halo node and add it to its appropriate box.

Definition at line 606 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::AddMovedNode ( boost::shared_ptr< Node< SPACE_DIM > > pMovedNode )

Add a node to this process that has moved from another process.

Parameters

pMovedNode the node to add to this mesh.

Definition at line 406 of file NodesOnlyMesh.cpp.

References Node< SPACE_DIM >::AddNodeAttribute(), Node< SPACE_DIM >::GetRadius(), Node< SPACE_DIM >::SetIsParticle(), Node< SPACE_DIM >::SetRadius(), and Node< SPACE_DIM >::SetRegion().

template<unsigned SPACE_DIM>

unsigned NodesOnlyMesh< SPACE_DIM >::AddNode ( Node< SPACE_DIM > * pNewNode )

virtual

Overridden AddNode() method.

Parameters

pNewNode pointer to the new node.

Returns: index of new node.

Reimplemented from MutableMesh< SPACE_DIM, SPACE_DIM >.

Definition at line 385 of file NodesOnlyMesh.cpp.

References Node< SPACE_DIM >::SetIndex().

Referenced by Cylindrical2dNodesOnlyMesh::AddNode(), and ParallelCellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateParallelCells().

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::AddNodesToBoxes ( )

Iterate through each node and add it to its appropriate box.

Definition at line 593 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::AddNodeWithFixedIndex ( Node< SPACE_DIM > * pNewNode )

private

Add pNewNode to the mesh, maintaining its current global index. Called by AddNode and AddMovedNode.

Parameters

pNewNode the new node to add to this mesh.

Definition at line 341 of file NodesOnlyMesh.cpp.

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

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::CalculateBoundaryNodePairs ( std::vector< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > & rNodePairs )

Calculate pairs of nodes from boxes on the process boundary using the BoxCollection

Parameters

rNodePairs reference to the set of node pairs to populate.

Definition at line 234 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::CalculateInteriorNodePairs ( std::vector< std::pair< Node< SPACE_DIM > *, Node< SPACE_DIM > * > > & rNodePairs )

Calculate pairs of nodes from interior boxes using the BoxCollection.

Parameters

rNodePairs reference to the set of node pairs to populate.

Definition at line 226 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::CalculateNodesOutsideLocalDomain ( )

Work out which nodes lie outside the local domain and add their indices to the vectors mNodesToSendLeft and mNodesToSendRight.

Definition at line 291 of file NodesOnlyMesh.cpp.

References PetscTools::GetMyRank().

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::Clear ( )

virtual

Overridden Clear() method for NodesOnlyMesh.

Reimplemented from TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 140 of file NodesOnlyMesh.cpp.

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

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::ClearBoxCollection ( )

protected

Clear the BoxCollection

Definition at line 550 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::ClearHaloNodes ( )

Delete all the halo nodes on this process.

Definition at line 377 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::ConstructFromMeshReader ( AbstractMeshReader< SPACE_DIM, SPACE_DIM > & rMeshReader )

Overridden ConstructFromMeshReader to correctly assign global node indices on load.

Parameters

rMeshReader the mesh reader for input.

Definition at line 665 of file NodesOnlyMesh.cpp.

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

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh	(	const std::vector< Node< SPACE_DIM > * > &	rNodes,
		double	maxInteractionDistance
	)

Construct the mesh using only nodes. No mesh is created, but the nodes are stored. The original vector of nodes is deep-copied: new node objects are made with are independent of the pointers in the input so that they can be safely deleted.

If this is the only way of constructing a mesh of this type, then we can be certain that elements and boundary elements are always unused.

Parameters

rNodes	a vector of pointers to nodes.
maxInteractionDistance	the distance that defines node neighbours in CalculateNodePairs.

Definition at line 60 of file NodesOnlyMesh.cpp.

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

Referenced by CaBasedCellPopulation< DIM >::WriteVtkResultsToFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh	(	const std::vector< boost::shared_ptr< Node< SPACE_DIM > > > &	rNodes,
		double	maxInteractionDistance
	)

Construct the mesh using only nodes. No mesh is created, but the nodes are stored. The original vector of nodes is deep-copied: new node objects are made with are independent of the pointers in the input so that they can be safely deleted.

If this is the only way of constructing a mesh of this type, then we can be certain that elements and boundary elements are always unused.

Parameters

rNodes	a vector of shared pointers to nodes.
maxInteractionDistance	the distance that defines node neighbours in CalculateNodePairs.

Definition at line 102 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::ConstructNodesWithoutMesh	(	const AbstractMesh< SPACE_DIM, SPACE_DIM > &	rGeneratingMesh,
		double	maxInteractionDistance
	)

A Helper method to enable you to construct a nodes-only mesh by stripping the nodes TetrahedralMesh, this calls the ConstructNodesWithoutMesh method with the nodes

Parameters

rGeneratingMesh	any mesh with nodes, used to generate the NodesOnlyMesh.
maxInteractionDistance	the distance that defines node neighbours in CalculateNodePairs.

Definition at line 115 of file NodesOnlyMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::DeleteMovedNode ( unsigned index )

Make a clean delete of a node that has moved off this process.

Parameters

index the global index of the node moving off this process.

Definition at line 451 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::DeleteNode ( unsigned index )

virtual

Overridden DeleteNode() method.

Parameters

index of the node to be deleted

Reimplemented from MutableMesh< SPACE_DIM, SPACE_DIM >.

Definition at line 436 of file NodesOnlyMesh.cpp.

References EXCEPTION.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::EnlargeBoxCollection ( )

private

Increase box collection size by adding an extra row/face to each edge.

Definition at line 488 of file NodesOnlyMesh.cpp.

References PetscTools::AmMaster(), and PetscTools::AmTopMost().

template<unsigned SPACE_DIM>

std::vector< unsigned > NodesOnlyMesh< SPACE_DIM >::GetAllNodeIndices ( ) const

Get all node indices in order of appearance.

Returns: Node vector of node indices for this process ignoring all delete nodes

Definition at line 677 of file NodesOnlyMesh.cpp.

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

template<unsigned SPACE_DIM>

DistributedBoxCollection< SPACE_DIM > * NodesOnlyMesh< SPACE_DIM >::GetBoxCollection ( )

protected

Returns: mpBoxCollection

Definition at line 152 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

double NodesOnlyMesh< SPACE_DIM >::GetMaximumInteractionDistance ( )

Returns: mMaxInteractionDistance.

Definition at line 203 of file NodesOnlyMesh.cpp.

Referenced by ParallelCellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateParallelCells().

template<unsigned SPACE_DIM>

unsigned NodesOnlyMesh< SPACE_DIM >::GetMaximumNodeIndex ( )

virtual

Get the largest node global index on this process.

Returns: the maximum node index.

Reimplemented from AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 191 of file NodesOnlyMesh.cpp.

References PetscTools::GetMyRank(), and PetscTools::GetNumProcs().

Referenced by ParallelCellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateParallelCells().

template<unsigned SPACE_DIM>

unsigned NodesOnlyMesh< SPACE_DIM >::GetNextAvailableIndex ( )

private

Calculate the next unique global index available on this process. Uses a hashing function to ensure that a unique index is given to every node.

For example for 3 process they will have access to the following integers:

Proc 0: 0 3 6 9 12 ...

Proc 1: 1 4 7 10 13 ...

Proc 2: 2 5 8 11 14 ...

Deleted node indices can be locally re-used.

Deleted node indices of nodes that have *moved* process cannot be re-used.

Returns: the next available index.

Definition at line 468 of file NodesOnlyMesh.cpp.

References PetscTools::GetMyRank(), and PetscTools::GetNumProcs().

template<unsigned SPACE_DIM>

Node< SPACE_DIM > * NodesOnlyMesh< SPACE_DIM >::GetNodeOrHaloNode ( unsigned index ) const

virtual

Overridden method to get node or halo node from the mesh.

Parameters

index the global index of the node.

Returns: a pointer to the node.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 158 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

unsigned NodesOnlyMesh< SPACE_DIM >::GetNumNodes ( ) const

virtual

Returns: the local number of nodes that are actually in use. Does not include halo nodes.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 185 of file NodesOnlyMesh.cpp.

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

template<unsigned SPACE_DIM>

double NodesOnlyMesh< SPACE_DIM >::GetWidth ( const unsigned & rDimension ) const

virtual

Overridden GetWidth method to work in parallel.

Parameters

rDimension the dimension along which to get the width.

Returns: the width.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 209 of file NodesOnlyMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and PetscTools::GetWorld().

Referenced by CaBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<unsigned SPACE_DIM>

bool NodesOnlyMesh< SPACE_DIM >::IsANodeCloseToDomainBoundary ( )

private

Returns: Whether any node (deleted or otherwise) is close to the domain boundary.

Definition at line 510 of file NodesOnlyMesh.cpp.

References PetscTools::GetWorld().

template<unsigned SPACE_DIM>

bool NodesOnlyMesh< SPACE_DIM >::IsOwned ( c_vector< double, SPACE_DIM > & location )

A method to identify whether a location is owned in the parallel space decomposition.

Parameters

location the location to test

Returns: whether the point is owned.

Definition at line 179 of file NodesOnlyMesh.cpp.

Referenced by ParallelCellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateParallelCells().

template<unsigned SPACE_DIM>

template<class Archive >

void NodesOnlyMesh< SPACE_DIM >::load	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Load member variables of the object which have to be preserved during its lifetime.

Note that we must archive any member variables FIRST so that this method can call a ReMesh (to convert from TrianglesMeshReader input format into our native format).

Parameters

archive	the archive
version	the current version of this class

Definition at line 94 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::LoadBalanceMesh ( )

Re-allocate the underlaying BoxCollection rows based on the load-balance algorithm implemented in the box collection.

Definition at line 646 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::ReMesh ( NodeMap & rMap )

virtual

Overridden ReMesh() method. Since only Nodes are stored, this method cleans up mNodes by removing nodes marked as deleted and reallocating mNodes to 'fill the gaps'.

Parameters

rMap	a reference to a NodeMap which associates the indices of the old mesh with the new mesh. It should be large enough to contain all node indices.

Reimplemented from MutableMesh< SPACE_DIM, SPACE_DIM >.

Definition at line 242 of file NodesOnlyMesh.cpp.

References NodeMap::ResetToIdentity().

Referenced by ParallelCellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateParallelCells().

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::RemoveDeletedNodes ( NodeMap & map )

private

Remove all nodes that return mIsDeleted as true.

Parameters

map	the NodeMap to record which nodes have been removed.

Definition at line 257 of file NodesOnlyMesh.cpp.

References NodeMap::SetDeleted().

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::ResizeBoxCollection ( )

Check whether any nodes are close to the edge of the box collection and increase the size of it if necessary.

Definition at line 632 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

std::vector< unsigned > & NodesOnlyMesh< SPACE_DIM >::rGetHaloNodesToSendLeft ( )

Returns: the indices of halo nodes, owned by this process, on the left hand boundary.

Definition at line 335 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

std::vector< unsigned > & NodesOnlyMesh< SPACE_DIM >::rGetHaloNodesToSendRight ( )

Returns: the indices of halo nodes, owned by this process, on the right hand boundary.

Definition at line 329 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

std::vector< bool > & NodesOnlyMesh< SPACE_DIM >::rGetInitiallyOwnedNodes ( )

Returns: whether each initial node given to ConstructNodesWithoutMesh is owned by this process.

Definition at line 121 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

std::vector< unsigned > & NodesOnlyMesh< SPACE_DIM >::rGetNodesToSendLeft ( )

Returns: mNodesToSendLeft.

Definition at line 317 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

std::vector< unsigned > & NodesOnlyMesh< SPACE_DIM >::rGetNodesToSendRight ( )

Returns: mNodesToSendRight.

Definition at line 323 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

template<class Archive >

void NodesOnlyMesh< SPACE_DIM >::save	(	Archive &	archive,
		const unsigned int	version
	)		const

inlineprivate

Archives the member variables of the object which have to be preserved during its lifetime.

Note that we must archive any member variables FIRST so that this method can call a ReMesh (to convert from TrianglesMeshReader input format into our native format).

Parameters

archive	the archive
version	the current version of this class

Definition at line 73 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::SetCalculateNodeNeighbours ( bool calculateNodeNeighbours )

Set whether to calculate node neighbours for the rNodeNeigbours set in CalculateNodePairs. Switch off for efficiency

Parameters

calculateNodeNeighbours whether to store the neighbours.

Definition at line 220 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::SetInitialBoxCollection	(	const c_vector< double, 2 *SPACE_DIM >	domainSize,
		double	maxInteractionDistance
	)

Set the initial box collection without passing nodes to the mesh. Used for memory efficient construction in parallel.

Parameters

domainSize	the initial domain size of the mesh.
maxInteractionDistance	the max interaction distance between nodes.

Definition at line 560 of file NodesOnlyMesh.cpp.

Referenced by ParallelCellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateParallelCells().

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::SetMaximumInteractionDistance ( double maxDistance )

Set the maximum node interaction distance.

Parameters

maxDistance the new maximum distance.

Definition at line 197 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::SetMinimumNodeDomainBoundarySeparation ( double separation )

Set the value of mMinimumNodeDomainBoundarySeparation.

Parameters

separation the new value for the separation.

Definition at line 460 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::SetNode	(	unsigned	nodeIndex,
		ChastePoint< SPACE_DIM >	point,
		bool	concreteMove = `false`
	)

virtual

Overridden SetNode() method.

Parameters

nodeIndex	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 in the parent Class Note this should always be false here

Reimplemented from MutableMesh< SPACE_DIM, SPACE_DIM >.

Definition at line 396 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::SetUpBoxCollection ( const std::vector< Node< SPACE_DIM > * > & rNodes )

private

Set up a DistributedBoxCollection by calculating the correct domain size from the node locations.

Parameters

rNodes the nodes that will be contained in the box collection.

Definition at line 566 of file NodesOnlyMesh.cpp.

References ChasteCuboid< SPACE_DIM >::rGetLowerCorner(), and ChasteCuboid< SPACE_DIM >::rGetUpperCorner().

Referenced by Cylindrical2dNodesOnlyMesh::SetUpBoxCollection().

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::SetUpBoxCollection	(	double	cutOffLength,
		c_vector< double, 2 *SPACE_DIM >	domainSize,
		int	numLocalRows = `PETSC_DECIDE`,
		bool	isPeriodic = `false`
	)

protectedvirtual

Set up the box collection. Overridden in subclasses to implement periodicity.

Parameters

cutOffLength	the cut off length for node neighbours.
domainSize	the size of the domain containing the nodes.
numLocalRows	the number of rows that should be owned by this process.
isPeriodic	whether the DistributedBoxCollection should be periodic.

Definition at line 583 of file NodesOnlyMesh.cpp.

References DistributedBoxCollection< DIM >::SetupLocalBoxesHalfOnly().

template<unsigned SPACE_DIM>

unsigned NodesOnlyMesh< SPACE_DIM >::SolveNodeMapping ( unsigned index ) const

virtual

Overridden solve node mapping method

Parameters

index the global index of the node.

Returns: the local index of the node in mNodes.

Implements AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 127 of file NodesOnlyMesh.cpp.

References EXCEPTION, and PetscTools::GetMyRank().

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::UpdateBoxCollection ( )

Clear the old box collection and set up a new one if necessary.

Definition at line 619 of file NodesOnlyMesh.cpp.

template<unsigned SPACE_DIM>

void NodesOnlyMesh< SPACE_DIM >::UpdateNodeIndices ( )

private

Make sure that node indices match their location, and update mNodesMapping.

Definition at line 280 of file NodesOnlyMesh.cpp.

Friends And Related Function Documentation

template<unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 59 of file NodesOnlyMesh.hpp.

Member Data Documentation

template<unsigned SPACE_DIM>

bool NodesOnlyMesh< SPACE_DIM >::mCalculateNodeNeighbours

private

Whether to calculate node neighbours in the box collection. Switch off for efficiency

Definition at line 153 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

std::vector<unsigned> NodesOnlyMesh< SPACE_DIM >::mDeletedGlobalNodeIndices

private

A list of the global indices of nodes that have been deleted from this process and can be reused.

Definition at line 133 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

std::vector<boost::shared_ptr<Node<SPACE_DIM> > > NodesOnlyMesh< SPACE_DIM >::mHaloNodes

private

Vector of shared-pointers to halo nodes used by this process.

Definition at line 115 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

std::map<unsigned, unsigned> NodesOnlyMesh< SPACE_DIM >::mHaloNodesMapping

private

A map from halo node global index to local index in mHaloNodes.

Definition at line 124 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

unsigned NodesOnlyMesh< SPACE_DIM >::mIndexCounter

private

A counter of the number of fresh node indices used on this process. Ensures unique indices in parallel.

Definition at line 127 of file NodesOnlyMesh.hpp.

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

template<unsigned SPACE_DIM>

std::vector<bool> NodesOnlyMesh< SPACE_DIM >::mLocalInitialNodes

private

A list of flags showing which initial nodes passed to ConstructNodesWithoutMesh were created on this process.

Definition at line 143 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

unsigned NodesOnlyMesh< SPACE_DIM >::mMaxAddedNodeIndex

private

A variable to keep track of added node indices so we know the largest on this process. Used to create a large enough NodeMap when remeshing.

Definition at line 147 of file NodesOnlyMesh.hpp.

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

template<unsigned SPACE_DIM>

double NodesOnlyMesh< SPACE_DIM >::mMaximumInteractionDistance

private

Nodes separated by a distance less than mMaximumInteractionDistance are neighbours.

Definition at line 118 of file NodesOnlyMesh.hpp.

Referenced by NodesOnlyMesh< 2 >::load(), and NodesOnlyMesh< 2 >::save().

template<unsigned SPACE_DIM>

double NodesOnlyMesh< SPACE_DIM >::mMinimumNodeDomainBoundarySeparation

private

A minimum separation to maintain between nodes and the boundary of mpBoxCollection, which grows with the mesh.

Definition at line 130 of file NodesOnlyMesh.hpp.

Referenced by NodesOnlyMesh< 2 >::load(), and NodesOnlyMesh< 2 >::save().

template<unsigned SPACE_DIM>

std::map<unsigned, unsigned> NodesOnlyMesh< SPACE_DIM >::mNodesMapping

private

A map from node global index to local index in mNodes.

Definition at line 121 of file NodesOnlyMesh.hpp.

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

template<unsigned SPACE_DIM>

std::vector<unsigned> NodesOnlyMesh< SPACE_DIM >::mNodesToSendLeft

private

A list of global indices of nodes that need to be moved to the left hand process.

Definition at line 139 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

std::vector<unsigned> NodesOnlyMesh< SPACE_DIM >::mNodesToSendRight

private

A list of global indices of nodes that need to be moved to the right hand process.

Definition at line 136 of file NodesOnlyMesh.hpp.

template<unsigned SPACE_DIM>

DistributedBoxCollection<SPACE_DIM>* NodesOnlyMesh< SPACE_DIM >::mpBoxCollection

private

A pointer to the DistributedBoxCollection.

Definition at line 150 of file NodesOnlyMesh.hpp.

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

mesh/src/common/NodesOnlyMesh.hpp
mesh/src/common/NodesOnlyMesh.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<unsigned SPACE_DIM> class NodesOnlyMesh< SPACE_DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned SPACE_DIM>
class NodesOnlyMesh< SPACE_DIM >