Chaste  Release::2017.1
Toroidal2dVertexMesh Class Reference

#include <Toroidal2dVertexMesh.hpp>

+ Inheritance diagram for Toroidal2dVertexMesh:
+ Collaboration diagram for Toroidal2dVertexMesh:

Public Member Functions

 Toroidal2dVertexMesh (double width, double height, std::vector< Node< 2 > * > nodes, std::vector< VertexElement< 2, 2 > * > vertexElements, double cellRearrangementThreshold=0.01, double t2Threshold=0.001)
 
 Toroidal2dVertexMesh ()
 
 ~Toroidal2dVertexMesh ()
 
c_vector< double, 2 > GetVectorFromAtoB (const c_vector< double, 2 > &rLocation1, const c_vector< double, 2 > &rLocation2)
 
void SetNode (unsigned nodeIndex, ChastePoint< 2 > point)
 
double GetWidth (const unsigned &rDimension) const
 
unsigned AddNode (Node< 2 > *pNewNode)
 
MutableVertexMesh< 2, 2 > * GetMeshForVtk ()
 
void ConstructFromMeshReader (AbstractMeshReader< 2, 2 > &rMeshReader, double width, double height)
 
- Public Member Functions inherited from MutableVertexMesh< 2, 2 >
 MutableVertexMesh (std::vector< Node< SPACE_DIM > * > nodes, std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > vertexElements, double cellRearrangementThreshold=0.01, double t2Threshold=0.001, double cellRearrangementRatio=1.5, double protorosetteFormationProbability=0.0, double protorosetteResolutionProbabilityPerTimestep=0.0, double rosetteResolutionProbabilityPerTimestep=0.0)
 
 MutableVertexMesh ()
 
virtual ~MutableVertexMesh ()
 
void SetCellRearrangementThreshold (double cellRearrangementThreshold)
 
void SetT2Threshold (double t2Threshold)
 
void SetCellRearrangementRatio (double cellRearrangementRatio)
 
void SetProtorosetteFormationProbability (double protorosetteFormationProbability)
 
void SetProtorosetteResolutionProbabilityPerTimestep (double protorosetteResolutionProbabilityPerTimestep)
 
void SetRosetteResolutionProbabilityPerTimestep (double rosetteResolutionProbabilityPerTimestep)
 
virtual void SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > point)
 
void SetCheckForInternalIntersections (bool checkForInternalIntersections)
 
double GetCellRearrangementThreshold () const
 
double GetT2Threshold () const
 
double GetCellRearrangementRatio () const
 
double GetProtorosetteFormationProbability () const
 
double GetProtorosetteResolutionProbabilityPerTimestep () const
 
double GetRosetteResolutionProbabilityPerTimestep () const
 
void SetDistanceForT3SwapChecking (double distanceForT3SwapChecking)
 
double GetDistanceForT3SwapChecking () const
 
unsigned GetNumNodes () const
 
unsigned GetNumElements () const
 
bool GetCheckForInternalIntersections () const
 
std::vector< c_vector< double, SPACE_DIM > > GetLocationsOfT1Swaps ()
 
c_vector< double, SPACE_DIM > GetLastT2SwapLocation ()
 
std::vector< c_vector< double, SPACE_DIM > > GetLocationsOfT3Swaps ()
 
void ClearLocationsOfT1Swaps ()
 
void ClearLocationsOfT3Swaps ()
 
unsigned AddNode (Node< SPACE_DIM > *pNewNode)
 
void DeleteElementPriorToReMesh (unsigned index)
 
void DeleteNodePriorToReMesh (unsigned index)
 
unsigned DivideElementAlongShortAxis (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, bool placeOriginalElementBelow=false)
 
unsigned DivideElementAlongGivenAxis (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, c_vector< double, SPACE_DIM > axisOfDivision, bool placeOriginalElementBelow=false)
 
unsigned AddElement (VertexElement< ELEMENT_DIM, SPACE_DIM > *pNewElement)
 
bool CheckForT2Swaps (VertexElementMap &rElementMap)
 
void Clear ()
 
void DivideEdge (Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB)
 
void RemoveDeletedNodesAndElements (VertexElementMap &rElementMap)
 
void RemoveDeletedNodes ()
 
virtual void ReMesh (VertexElementMap &rElementMap)
 
void ReMesh ()
 
- Public Member Functions inherited from VertexMesh< ELEMENT_DIM, SPACE_DIM >
VertexElementIterator GetElementIteratorBegin (bool skipDeletedElements=true)
 
VertexElementIterator GetElementIteratorEnd ()
 
 VertexMesh (std::vector< Node< SPACE_DIM > * > nodes, std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > vertexElements)
 
 VertexMesh (std::vector< Node< SPACE_DIM > * > nodes, std::vector< VertexElement< ELEMENT_DIM-1, SPACE_DIM > * > faces, std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > vertexElements)
 
 VertexMesh (TetrahedralMesh< 2, 2 > &rMesh, bool isPeriodic=false)
 
 VertexMesh (TetrahedralMesh< 3, 3 > &rMesh)
 
 VertexMesh ()
 
virtual ~VertexMesh ()
 
unsigned GetNumAllElements () const
 
virtual unsigned GetNumFaces () const
 
VertexElement< ELEMENT_DIM, SPACE_DIM > * GetElement (unsigned index) const
 
VertexElement< ELEMENT_DIM-1, SPACE_DIM > * GetFace (unsigned index) const
 
virtual c_vector< double, SPACE_DIM > GetCentroidOfElement (unsigned index)
 
void ConstructFromMeshReader (AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader)
 
unsigned GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex (unsigned elementIndex)
 
unsigned GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex (unsigned nodeIndex)
 
unsigned GetRosetteRankOfElement (unsigned index)
 
virtual c_vector< double, SPACE_DIM > GetVectorFromAtoB (const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB)
 
virtual double GetVolumeOfElement (unsigned index)
 
virtual double GetSurfaceAreaOfElement (unsigned index)
 
c_vector< double, SPACE_DIM > GetAreaGradientOfElementAtNode (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)
 
c_vector< double, SPACE_DIM > GetPreviousEdgeGradientOfElementAtNode (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)
 
c_vector< double, SPACE_DIM > GetNextEdgeGradientOfElementAtNode (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)
 
c_vector< double, SPACE_DIM > GetPerimeterGradientOfElementAtNode (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex)
 
virtual c_vector< double, 3 > CalculateMomentsOfElement (unsigned index)
 
double GetEdgeLength (unsigned elementIndex1, unsigned elementIndex2)
 
double GetElongationShapeFactorOfElement (unsigned elementIndex)
 
double CalculateUnitNormalToFaceWithArea (VertexElement< ELEMENT_DIM-1, SPACE_DIM > *pFace, c_vector< double, SPACE_DIM > &rNormal)
 
virtual double CalculateAreaOfFace (VertexElement< ELEMENT_DIM-1, SPACE_DIM > *pFace)
 
c_vector< double, SPACE_DIM > GetShortAxisOfElement (unsigned index)
 
std::set< unsignedGetNeighbouringNodeIndices (unsigned nodeIndex)
 
std::set< unsignedGetNeighbouringNodeNotAlsoInElement (unsigned nodeIndex, unsigned elemIndex)
 
std::set< unsignedGetNeighbouringElementIndices (unsigned elementIndex)
 
template<>
 VertexMesh (TetrahedralMesh< 2, 2 > &rMesh, bool isPeriodic)
 
template<>
 VertexMesh (TetrahedralMesh< 3, 3 > &rMesh)
 
- 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
 
virtual Node< SPACE_DIM > * GetNodeOrHaloNode (unsigned index) const
 
Node< SPACE_DIM > * GetNodeFromPrePermutationIndex (unsigned index) const
 
virtual void ReadNodesPerProcessorFile (const std::string &rNodesPerProcessorFile)
 
virtual DistributedVectorFactoryGetDistributedVectorFactory ()
 
virtual void SetDistributedVectorFactory (DistributedVectorFactory *pFactory)
 
virtual void PermuteNodes ()
 
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)
 
virtual void RefreshMesh ()
 
bool IsMeshChanging () const
 
unsigned CalculateMaximumContainingElementsPerProcess () const
 
void SetMeshHasChangedSinceLoading ()
 

Private Member Functions

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

Private Attributes

double mWidth
 
double mHeight
 

Friends

class TestToroidal2dVertexMesh
 
class boost::serialization::access
 

Additional Inherited Members

- Public Types inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
typedef std::vector< Node< SPACE_DIM > * >::const_iterator BoundaryNodeIterator
 
- Protected Member Functions inherited from MutableVertexMesh< 2, 2 >
unsigned DivideElement (VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned nodeAIndex, unsigned nodeBIndex, bool placeOriginalElementBelow=false)
 
virtual bool CheckForSwapsFromShortEdges ()
 
bool CheckForIntersections ()
 
virtual void IdentifySwapType (Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB)
 
void PerformNodeMerge (Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB)
 
void PerformT1Swap (Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB, std::set< unsigned > &rElementsContainingNodes)
 
void PerformIntersectionSwap (Node< SPACE_DIM > *pNode, unsigned elementIndex)
 
void PerformT2Swap (VertexElement< ELEMENT_DIM, SPACE_DIM > &rElement)
 
void PerformT3Swap (Node< SPACE_DIM > *pNode, unsigned elementIndex)
 
void PerformVoidRemoval (Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB, Node< SPACE_DIM > *pNodeC)
 
virtual void HandleHighOrderJunctions (Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB)
 
void PerformRosetteRankIncrease (Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB)
 
void PerformProtorosetteResolution (Node< SPACE_DIM > *pProtorosetteNode)
 
void PerformRosetteRankDecrease (Node< SPACE_DIM > *pRosetteNode)
 
void CheckForRosettes ()
 
c_vector< double, 2 > WidenEdgeOrCorrectIntersectionLocationIfNecessary (unsigned indexA, unsigned indexB, c_vector< double, 2 > intersection)
 
void serialize (Archive &archive, const unsigned int version)
 
- Protected Member Functions inherited from VertexMesh< ELEMENT_DIM, SPACE_DIM >
unsigned SolveNodeMapping (unsigned index) const
 
unsigned SolveElementMapping (unsigned index) const
 
unsigned SolveBoundaryElementMapping (unsigned index) const
 
void GenerateVerticesFromElementCircumcentres (TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
 
bool ElementIncludesPoint (const c_vector< double, SPACE_DIM > &rTestPoint, unsigned elementIndex)
 
unsigned GetLocalIndexForElementEdgeClosestToPoint (const c_vector< double, SPACE_DIM > &rTestPoint, unsigned elementIndex)
 
template<class Archive >
void save (Archive &archive, const unsigned int version) const
 
template<class Archive >
void load (Archive &archive, const unsigned int version)
 
- Protected Member Functions inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
virtual void SetElementOwnerships ()
 
ChasteCuboid< SPACE_DIM > CalculateBoundingBox (const std::vector< Node< SPACE_DIM > * > &rNodes) const
 
- Protected Attributes inherited from MutableVertexMesh< 2, 2 >
double mCellRearrangementThreshold
 
double mCellRearrangementRatio
 
double mT2Threshold
 
double mProtorosetteFormationProbability
 
double mProtorosetteResolutionProbabilityPerTimestep
 
double mRosetteResolutionProbabilityPerTimestep
 
bool mCheckForInternalIntersections
 
std::vector< unsignedmDeletedNodeIndices
 
std::vector< unsignedmDeletedElementIndices
 
double mDistanceForT3SwapChecking
 
std::vector< c_vector< double, SPACE_DIM > > mLocationsOfT1Swaps
 
c_vector< double, SPACE_DIM > mLastT2SwapLocation
 
std::vector< c_vector< double, SPACE_DIM > > mLocationsOfT3Swaps
 
- Protected Attributes inherited from VertexMesh< ELEMENT_DIM, SPACE_DIM >
std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > mElements
 
std::vector< VertexElement< ELEMENT_DIM-1, SPACE_DIM > * > mFaces
 
std::map< unsigned, unsignedmVoronoiElementIndexMap
 
TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * mpDelaunayMesh
 
- Protected Attributes inherited from AbstractMesh< ELEMENT_DIM, SPACE_DIM >
std::vector< Node< SPACE_DIM > * > mNodes
 
std::vector< Node< SPACE_DIM > * > mBoundaryNodes
 
DistributedVectorFactorympDistributedVectorFactory
 
std::vector< unsignedmNodePermutation
 
std::string mMeshFileBaseName
 
bool mMeshChangesDuringSimulation
 

Detailed Description

A subclass of MutableVertexMesh<2,2> for a rectangular mesh with periodic left and right boundaries and top and bottom boundaries, representing a toroidal geometry.

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 MutableMesh<2,2>.

Definition at line 53 of file Toroidal2dVertexMesh.hpp.

Constructor & Destructor Documentation

Toroidal2dVertexMesh::Toroidal2dVertexMesh ( double  width,
double  height,
std::vector< Node< 2 > * >  nodes,
std::vector< VertexElement< 2, 2 > * >  vertexElements,
double  cellRearrangementThreshold = 0.01,
double  t2Threshold = 0.001 
)

Default constructor.

Parameters
widththe width of the mesh
heightthe height of the mesh
nodesvector of pointers to nodes
vertexElementsvector of pointers to VertexElements
cellRearrangementThresholdthe minimum threshold distance for element rearrangement (defaults to 0.01)
t2Thresholdthe maximum threshold distance for Type 2 swaps (defaults to 0.001)

Definition at line 38 of file Toroidal2dVertexMesh.cpp.

References MutableVertexMesh< 2, 2 >::ReMesh().

Toroidal2dVertexMesh::Toroidal2dVertexMesh ( )

Constructor.

Definition at line 52 of file Toroidal2dVertexMesh.cpp.

Referenced by serialize().

Toroidal2dVertexMesh::~Toroidal2dVertexMesh ( )

Destructor.

Definition at line 56 of file Toroidal2dVertexMesh.cpp.

Referenced by serialize().

Member Function Documentation

unsigned Toroidal2dVertexMesh::AddNode ( Node< 2 > *  pNewNode)

Overridden AddNode() method.

Parameters
pNewNodethe node to be added to the mesh
Returns
the global index of the new node

Definition at line 135 of file Toroidal2dVertexMesh.cpp.

References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), Node< SPACE_DIM >::GetPoint(), and SetNode().

Referenced by serialize().

c_vector< double, 2 > Toroidal2dVertexMesh::GetVectorFromAtoB ( const c_vector< double, 2 > &  rLocation1,
const c_vector< double, 2 > &  rLocation2 
)

Overridden GetVectorFromAtoB() method.

This method evaluates the (surface) distance between two points in a 2D toroidal geometry.

Parameters
rLocation1the x and y co-ordinates of point 1
rLocation2the x and y co-ordinates of point 2
Returns
the vector from location1 to location2

Definition at line 60 of file Toroidal2dVertexMesh.cpp.

References mHeight, and mWidth.

Referenced by serialize().

double Toroidal2dVertexMesh::GetWidth ( const unsigned rDimension) const
virtual

Overridden GetWidth() method.

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

Parameters
rDimensiona dimension (0 or 1)
Returns
The maximum distance between any nodes in this dimension.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 122 of file Toroidal2dVertexMesh.cpp.

References mHeight, and mWidth.

Referenced by serialize().

template<class Archive >
void Toroidal2dVertexMesh::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

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

The remaining member variables are re-initialised before being used by each ReMesh() call so they do not need to be archived.

Parameters
archivethe archive
versionthe current version of this class

Definition at line 78 of file Toroidal2dVertexMesh.hpp.

References AddNode(), CHASTE_CLASS_EXPORT, ConstructFromMeshReader(), GetMeshForVtk(), GetVectorFromAtoB(), GetWidth(), mHeight, mWidth, SetNode(), Toroidal2dVertexMesh(), and ~Toroidal2dVertexMesh().

void Toroidal2dVertexMesh::SetNode ( unsigned  nodeIndex,
ChastePoint< 2 >  point 
)

Overridden SetNode() method.

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

Parameters
nodeIndexis the index of the node to be moved
pointis the new target location of the node

Definition at line 91 of file Toroidal2dVertexMesh.cpp.

References mHeight, mWidth, ChastePoint< DIM >::rGetLocation(), ChastePoint< DIM >::SetCoordinate(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().

Referenced by AddNode(), and serialize().

Friends And Related Function Documentation

friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 66 of file Toroidal2dVertexMesh.hpp.

Member Data Documentation

double Toroidal2dVertexMesh::mHeight
private

The height of the mesh, taking account of top-bottom periodicity.

Definition at line 63 of file Toroidal2dVertexMesh.hpp.

Referenced by ConstructFromMeshReader(), GetMeshForVtk(), GetVectorFromAtoB(), GetWidth(), serialize(), and SetNode().

double Toroidal2dVertexMesh::mWidth
private

The width of the mesh, taking account of left-right periodicity.

Definition at line 60 of file Toroidal2dVertexMesh.hpp.

Referenced by ConstructFromMeshReader(), GetMeshForVtk(), GetVectorFromAtoB(), GetWidth(), serialize(), and SetNode().


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