#include <PeriodicNodesOnlyMesh.hpp>

Inheritance diagram for PeriodicNodesOnlyMesh< SPACE_DIM >:

Collaboration diagram for PeriodicNodesOnlyMesh< SPACE_DIM >:

Public Member Functions
	PeriodicNodesOnlyMesh (c_vector< double, SPACE_DIM > width)

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

c_vector< double, SPACE_DIM >	GetVectorFromAtoB (const c_vector< double, SPACE_DIM > &rLocation1, const c_vector< double, SPACE_DIM > &rLocation2)

double	GetWidth (const unsigned &rDimension) const

c_vector< double, SPACE_DIM >	GetPeriodicWidths () const

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

unsigned	AddNode (Node< SPACE_DIM > *pNewNode)

void	RefreshMesh ()

Public Member Functions inherited from NodesOnlyMesh< SPACE_DIM >
	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 ()

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 ()

bool	GetIsPeriodicAcrossProcsFromBoxCollection () const

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	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 ()

unsigned	GetNumElements () const

unsigned	GetNumBoundaryElements () const

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

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

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 ()

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

Private Attributes
c_vector< double, SPACE_DIM >	mWidth

c_vector< bool, SPACE_DIM >	mIsDimPeriodic

Friends
class	TestPeriodicNodesOnlyMesh

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 Member Functions inherited from NodesOnlyMesh< SPACE_DIM >
void	ClearBoxCollection ()

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

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 PeriodicNodesOnlyMesh< SPACE_DIM >

A subclass of NodesOnlyMesh<SPACE_DIM> for a rectangular mesh with periodic boundaries.

The class works by overriding calls such as ReMesh() and GetVectorFromAtoB() so that simulation classes can treat this class in exactly the same way as a NodesOnlyMesh<SPACE_DIM>.

Definition at line 53 of file PeriodicNodesOnlyMesh.hpp.

Constructor & Destructor Documentation

◆ PeriodicNodesOnlyMesh()

template<unsigned SPACE_DIM>

PeriodicNodesOnlyMesh< SPACE_DIM >::PeriodicNodesOnlyMesh ( c_vector< double, SPACE_DIM > width )

Constructor.

Parameters

width the periodic widths of the mesh. (Note if width=0.0 then not periodic)

Definition at line 40 of file PeriodicNodesOnlyMesh.cpp.

References PeriodicNodesOnlyMesh< SPACE_DIM >::mIsDimPeriodic.

Member Function Documentation

◆ AddNode()

template<unsigned SPACE_DIM>

unsigned PeriodicNodesOnlyMesh< 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 NodesOnlyMesh< SPACE_DIM >.

Definition at line 167 of file PeriodicNodesOnlyMesh.cpp.

References NodesOnlyMesh< SPACE_DIM >::AddNode(), and Node< SPACE_DIM >::GetPoint().

◆ GetPeriodicWidths()

template<unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > PeriodicNodesOnlyMesh< SPACE_DIM >::GetPeriodicWidths ( ) const

Method to get the width of the periodic dimensions

Returns: The value of the mWidth vector

Definition at line 94 of file PeriodicNodesOnlyMesh.cpp.

◆ GetVectorFromAtoB()

template<unsigned SPACE_DIM>

c_vector< double, SPACE_DIM > PeriodicNodesOnlyMesh< SPACE_DIM >::GetVectorFromAtoB	(	const c_vector< double, SPACE_DIM > &	rLocation1,
		const c_vector< double, SPACE_DIM > &	rLocation2
	)

virtual

Overridden GetVectorFromAtoB() method.

Evaluates the (surface) distance between two points in ND periodic geometry.

Parameters

rLocation1	the x y and z co-ordinates of point 1
rLocation2	the x y and z co-ordinates of point 2

Returns: the vector from location1 to location2

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 181 of file PeriodicNodesOnlyMesh.cpp.

◆ GetWidth()

template<unsigned SPACE_DIM>

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

virtual

Overridden GetWidth() method.

Calculate the 'width' of any dimension of the mesh, taking periodicity into account.

Parameters

rDimension a dimension (0,1 or 2)

Returns: The maximum distance between any nodes in this dimension.

Reimplemented from NodesOnlyMesh< SPACE_DIM >.

Definition at line 100 of file PeriodicNodesOnlyMesh.cpp.

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

◆ RefreshMesh()

template<unsigned SPACE_DIM>

void PeriodicNodesOnlyMesh< SPACE_DIM >::RefreshMesh ( )

virtual

Overridden RefreshMesh() method.

If the location is outside the domain width, move it to within the boundary

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 208 of file PeriodicNodesOnlyMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::RefreshMesh().

◆ serialize()

template<unsigned SPACE_DIM>

template<class Archive >

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

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 82 of file PeriodicNodesOnlyMesh.hpp.

References PeriodicNodesOnlyMesh< SPACE_DIM >::mIsDimPeriodic, and PeriodicNodesOnlyMesh< SPACE_DIM >::mWidth.

◆ SetNode()

template<unsigned SPACE_DIM>

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

virtual

Overridden SetNode() method.

If the location should be set outside a cylindrical boundary move it back onto the cylinder.

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 NodesOnlyMesh< SPACE_DIM >.

Definition at line 118 of file PeriodicNodesOnlyMesh.cpp.

References ChastePoint< DIM >::rGetLocation(), and ChastePoint< DIM >::SetCoordinate().

◆ SetUpBoxCollection()

template<unsigned SPACE_DIM>

void PeriodicNodesOnlyMesh< SPACE_DIM >::SetUpBoxCollection	(	double	cutOffLength,
		c_vector< double, 2 *SPACE_DIM >	domainSize,
		int	numLocalRows = `PETSC_DECIDE`,
		c_vector< bool, SPACE_DIM >	isDimPeriodic = `zero_vector<bool>(SPACE_DIM)`
	)

virtual

Set up the box collection

Parameters

cutOffLength	the cut off length for node neighbours
domainSize	the size of the domain containing the nodes.
numLocalRows	the number of rows of the collection that this process should own.
isDimPeriodic	whether the box collection should be periodic in the x y and/or z direction.

Reimplemented from NodesOnlyMesh< SPACE_DIM >.

Definition at line 57 of file PeriodicNodesOnlyMesh.cpp.

References EXCEPTION, PetscTools::GetNumProcs(), and NodesOnlyMesh< SPACE_DIM >::SetUpBoxCollection().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned SPACE_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 69 of file PeriodicNodesOnlyMesh.hpp.

◆ TestPeriodicNodesOnlyMesh

template<unsigned SPACE_DIM>

friend class TestPeriodicNodesOnlyMesh

friend

Definition at line 66 of file PeriodicNodesOnlyMesh.hpp.

Member Data Documentation

◆ mIsDimPeriodic

template<unsigned SPACE_DIM>

c_vector<bool,SPACE_DIM> PeriodicNodesOnlyMesh< SPACE_DIM >::mIsDimPeriodic

private

Whether a dimension is periodic

Definition at line 64 of file PeriodicNodesOnlyMesh.hpp.

Referenced by PeriodicNodesOnlyMesh< SPACE_DIM >::PeriodicNodesOnlyMesh(), and PeriodicNodesOnlyMesh< SPACE_DIM >::serialize().

◆ mWidth

template<unsigned SPACE_DIM>

c_vector<double,SPACE_DIM> PeriodicNodesOnlyMesh< SPACE_DIM >::mWidth

private

The periodic widths of the domain

Definition at line 59 of file PeriodicNodesOnlyMesh.hpp.

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

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

mesh/src/mutable/PeriodicNodesOnlyMesh.hpp
mesh/src/mutable/PeriodicNodesOnlyMesh.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PeriodicNodesOnlyMesh()

Member Function Documentation

◆ AddNode()

◆ GetPeriodicWidths()

◆ GetVectorFromAtoB()

◆ GetWidth()

◆ RefreshMesh()

◆ serialize()

◆ SetNode()

◆ SetUpBoxCollection()

Friends And Related Symbol Documentation

◆ boost::serialization::access

◆ TestPeriodicNodesOnlyMesh

Member Data Documentation

◆ mIsDimPeriodic

◆ mWidth