Cylindrical2dMesh Class Reference

#include <Cylindrical2dMesh.hpp>

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List of all members.

Public Member Functions

 Cylindrical2dMesh (double width)
 Cylindrical2dMesh (double width, std::vector< Node< 2 > * > nodes)
 ~Cylindrical2dMesh ()
void ReMesh (NodeMap &rMap)
c_vector< double, 2 > GetVectorFromAtoB (const c_vector< double, 2 > &rLocation1, const c_vector< double, 2 > &rLocation2)
void SetNode (unsigned index, ChastePoint< 2 > point, bool concreteMove)
double GetWidth (const unsigned &rDimension) const
unsigned AddNode (Node< 2 > *pNewNode)

Private Member Functions

void UpdateTopAndBottom ()
void CreateHaloNodes ()
void CreateMirrorNodes ()
void ReconstructCylindricalMesh ()
void DeleteHaloNodes ()
void CorrectNonPeriodicMesh ()
void GenerateVectorsOfElementsStraddlingPeriodicBoundaries ()
unsigned GetCorrespondingNodeIndex (unsigned nodeIndex)
void UseTheseElementsToDecideMeshing (std::set< unsigned > &rMainSideElements)
template<class Archive>
void serialize (Archive &archive, const unsigned int version)

Private Attributes

double mWidth
double mTop
double mBottom
std::vector< unsigned > mLeftOriginals
std::vector< unsigned > mLeftImages
std::map< unsigned, unsigned > mImageToLeftOriginalNodeMap
std::vector< unsigned > mRightOriginals
std::vector< unsigned > mRightImages
std::map< unsigned, unsigned > mImageToRightOriginalNodeMap
std::set< unsigned > mLeftPeriodicBoundaryElementIndices
std::set< unsigned > mRightPeriodicBoundaryElementIndices
std::vector< unsigned > mTopHaloNodes
std::vector< unsigned > mBottomHaloNodes

Friends

class TestCylindrical2dMesh
class boost::serialization::access


Detailed Description

A subclass of MutableMesh<2,2> for a rectangular mesh with periodic left and right boundaries, representing a cylindrical 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 48 of file Cylindrical2dMesh.hpp.


Constructor & Destructor Documentation

Cylindrical2dMesh::Cylindrical2dMesh ( double  width  ) 

Constructor.

Parameters:
width the width of the mesh (circumference)

Definition at line 38 of file Cylindrical2dMesh.cpp.

Cylindrical2dMesh::Cylindrical2dMesh ( double  width,
std::vector< Node< 2 > * >  nodes 
)

A constructor which reads in a width and collection of nodes, then calls a ReMesh() command to create the elements of the mesh.

Parameters:
width the periodic length scale
nodes a collection of nodes to construct the mesh with

Definition at line 49 of file Cylindrical2dMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, MutableMesh< 2, 2 >::ReMesh(), and Node< SPACE_DIM >::rGetLocation().

Cylindrical2dMesh::~Cylindrical2dMesh (  ) 

Destructor.

Definition at line 45 of file Cylindrical2dMesh.cpp.


Member Function Documentation

void Cylindrical2dMesh::UpdateTopAndBottom (  )  [private]

Calls AbstractMesh<2,2>::CalculateBoundingBox() to calculate mTop and mBottom for the cylindrical mesh.

This method should only ever be called by the public ReMesh() method.

Definition at line 67 of file Cylindrical2dMesh.cpp.

References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::CalculateBoundingBox(), mBottom, mTop, ChasteCuboid< SPACE_DIM >::rGetLowerCorner(), and ChasteCuboid< SPACE_DIM >::rGetUpperCorner().

Referenced by CreateHaloNodes().

void Cylindrical2dMesh::CreateHaloNodes (  )  [private]

This method creates a compressed row of nodes, just above and below the main mesh at a constant height (a 'halo'). These will mesh to a known configuration (each one on the boundary), this avoids boundary elements of lengths over half the mesh width, which prevent the process of cylindrical meshing.

The nodes which are created are later removed by DeleteHaloNodes().

Definition at line 138 of file Cylindrical2dMesh.cpp.

References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), mBottom, mBottomHaloNodes, mTop, mTopHaloNodes, mWidth, and UpdateTopAndBottom().

Referenced by ReMesh().

void Cylindrical2dMesh::CreateMirrorNodes (  )  [private]

void Cylindrical2dMesh::ReconstructCylindricalMesh (  )  [private]

After any corrections have been made to the boundary elements (see UseTheseElementsToDecideMeshing()) this method deletes the mirror image nodes, elements and boundary elements created for a cylindrical remesh by cycling through the elements and changing elements with partly real and partly imaginary elements to be real with periodic real nodes instead of mirror image nodes. We end up with very strangely shaped elements which cross the whole mesh but specify the correct connections between nodes.

This method should only ever be called by the public ReMesh() method.

Definition at line 312 of file Cylindrical2dMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetBoundaryElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllBoundaryElements(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::IsDeleted(), BoundaryElement< ELEMENT_DIM, SPACE_DIM >::MarkAsDeleted(), MutableMesh< 2, 2 >::mDeletedBoundaryElementIndices, MutableMesh< 2, 2 >::mDeletedElementIndices, MutableMesh< 2, 2 >::mDeletedNodeIndices, mImageToLeftOriginalNodeMap, mImageToRightOriginalNodeMap, mLeftImages, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, mRightImages, and AbstractElement< ELEMENT_DIM, SPACE_DIM >::ReplaceNode().

Referenced by ReMesh().

void Cylindrical2dMesh::DeleteHaloNodes (  )  [private]

This method should only ever be called by the public ReMesh method.

This method removes the nodes which were added by CreateHaloNodes() before the remeshing algorithm was called.

Definition at line 446 of file Cylindrical2dMesh.cpp.

References MutableMesh< 2, 2 >::DeleteBoundaryNodeAt(), mBottomHaloNodes, and mTopHaloNodes.

Referenced by ReMesh().

void Cylindrical2dMesh::CorrectNonPeriodicMesh (  )  [private]

This method should only ever be called by the public ReMesh() method.

Uses mLeftPeriodicBoundaryElementIndices and mRightPeriodicBoundaryElementIndices and compares the nodes in each to ensure that both boundaries have been meshed identically. If they have not it calls UseTheseElementsToDecideMeshing() to sort out the troublesome elements which have been meshed differently on each side and uses the meshing of the elements on the right hand boundary to decide on how to mesh the left hand side.

Definition at line 527 of file Cylindrical2dMesh.cpp.

References GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), GetCorrespondingNodeIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), mLeftPeriodicBoundaryElementIndices, mRightPeriodicBoundaryElementIndices, NEVER_REACHED, and UseTheseElementsToDecideMeshing().

Referenced by ReMesh().

void Cylindrical2dMesh::GenerateVectorsOfElementsStraddlingPeriodicBoundaries (  )  [private]

This method should only ever be called by the public ReMesh method.

The elements which straddle the periodic boundaries need to be identified in order to compare the list on the right with the list on the left and reconstruct a cylindrical mesh.

Empties and repopulates the member variables mLeftPeriodicBoundaryElementIndices and mRightPeriodicBoundaryElementIndices

Definition at line 708 of file Cylindrical2dMesh.cpp.

References AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), mImageToLeftOriginalNodeMap, mImageToRightOriginalNodeMap, mLeftPeriodicBoundaryElementIndices, and mRightPeriodicBoundaryElementIndices.

Referenced by CorrectNonPeriodicMesh().

unsigned Cylindrical2dMesh::GetCorrespondingNodeIndex ( unsigned  nodeIndex  )  [private]

This method should only ever be called by the public ReMesh() method.

Parameters:
nodeIndex The index of an original/mirrored node
Returns:
the index of the corresponding mirror image of that node (can be either an original or mirror node)

Definition at line 750 of file Cylindrical2dMesh.cpp.

References mLeftImages, mLeftOriginals, mRightImages, and mRightOriginals.

Referenced by CorrectNonPeriodicMesh(), and UseTheseElementsToDecideMeshing().

void Cylindrical2dMesh::UseTheseElementsToDecideMeshing ( std::set< unsigned > &  rMainSideElements  )  [private]

template<class Archive>
void Cylindrical2dMesh::serialize ( Archive &  archive,
const unsigned int  version 
) [inline, private]

Archives the member variables of the Cylindrical2dMesh class which have to be preserved during the lifetime of the mesh.

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

Parameters:
archive the archive
version the current version of this class the current version of this class

Reimplemented from MutableMesh< 2, 2 >.

Definition at line 199 of file Cylindrical2dMesh.hpp.

References mBottom, mTop, and mWidth.

void Cylindrical2dMesh::ReMesh ( NodeMap rMap  )  [virtual]

Overridden ReMesh() method.

Conduct a cylindrical remesh by calling CreateMirrorNodes() to create mirror image nodes, then calling ReMesh() on the parent class, then mapping the new node indices and calling ReconstructCylindricalMesh() to remove surplus nodes, leaving a fully periodic mesh.

Parameters:
rMap a reference to a nodemap which should be created with the required number of nodes.

Reimplemented from MutableMesh< 2, 2 >.

Definition at line 167 of file Cylindrical2dMesh.cpp.

References CorrectNonPeriodicMesh(), CreateHaloNodes(), CreateMirrorNodes(), DeleteHaloNodes(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), NodeMap::GetNewIndex(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), NodeMap::IsDeleted(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::IsDeleted(), NodeMap::IsIdentityMap(), mBottomHaloNodes, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementJacobianDeterminants, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElements, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mBoundaryElementWeightedDirections, mImageToLeftOriginalNodeMap, mImageToRightOriginalNodeMap, mLeftImages, mLeftOriginals, mLeftPeriodicBoundaryElementIndices, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, mRightImages, mRightOriginals, mRightPeriodicBoundaryElementIndices, mTopHaloNodes, ReconstructCylindricalMesh(), BoundaryElement< ELEMENT_DIM, SPACE_DIM >::RegisterWithNodes(), MutableMesh< 2, 2 >::ReIndex(), MutableMesh< ELEMENT_DIM, SPACE_DIM >::ReMesh(), NodeMap::ResetToIdentity(), NodeMap::Resize(), NodeMap::SetDeleted(), NodeMap::SetNewIndex(), and NodeMap::Size().

c_vector< double, 2 > Cylindrical2dMesh::GetVectorFromAtoB ( const c_vector< double, 2 > &  rLocation1,
const c_vector< double, 2 > &  rLocation2 
)

Overridden GetVectorFromAtoB() method.

Evaluates the (surface) distance between two points in a 2D cylindrical geometry.

Parameters:
rLocation1 the x and y co-ordinates of point 1
rLocation2 the x and y co-ordinates of point 2
Returns:
the vector from location1 to location2

Definition at line 456 of file Cylindrical2dMesh.cpp.

References mWidth.

void Cylindrical2dMesh::SetNode ( unsigned  index,
ChastePoint< 2 >  point,
bool  concreteMove 
)

Overridden SetNode() method.

If the location should be set outside a cylindrical boundary, it is moved back onto the cylinder.

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

Definition at line 483 of file Cylindrical2dMesh.cpp.

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

Referenced by AddNode().

double Cylindrical2dMesh::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 or 1)
Returns:
The maximum distance between any nodes in this dimension.

Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.

Definition at line 501 of file Cylindrical2dMesh.cpp.

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

unsigned Cylindrical2dMesh::AddNode ( Node< 2 > *  pNewNode  ) 

Overridden AddNode() method.

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

Definition at line 516 of file Cylindrical2dMesh.cpp.

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


Friends And Related Function Documentation

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

Needed for serialization.

Reimplemented from MutableMesh< 2, 2 >.

Definition at line 186 of file Cylindrical2dMesh.hpp.


Member Data Documentation

double Cylindrical2dMesh::mWidth [private]

The circumference of the cylinder.

Definition at line 54 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), CreateMirrorNodes(), GetVectorFromAtoB(), GetWidth(), serialize(), and SetNode().

double Cylindrical2dMesh::mTop [private]

The top of the cylinder (y coordinate).

Definition at line 57 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), serialize(), and UpdateTopAndBottom().

double Cylindrical2dMesh::mBottom [private]

The bottom of the cylinder (y coordinate).

Definition at line 60 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), serialize(), and UpdateTopAndBottom().

std::vector<unsigned> Cylindrical2dMesh::mLeftOriginals [private]

The left nodes which have been mirrored during the remesh.

Definition at line 63 of file Cylindrical2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetCorrespondingNodeIndex(), and ReMesh().

std::vector<unsigned> Cylindrical2dMesh::mLeftImages [private]

The image nodes corresponding to these left nodes (on right of mesh).

Definition at line 66 of file Cylindrical2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetCorrespondingNodeIndex(), ReconstructCylindricalMesh(), and ReMesh().

std::map<unsigned, unsigned> Cylindrical2dMesh::mImageToLeftOriginalNodeMap [private]

A map from image node index (on right of mesh) to original node index (on left of mesh).

Definition at line 69 of file Cylindrical2dMesh.hpp.

Referenced by CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), ReconstructCylindricalMesh(), and ReMesh().

std::vector<unsigned> Cylindrical2dMesh::mRightOriginals [private]

The right nodes which have been mirrored during the remesh.

Definition at line 72 of file Cylindrical2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetCorrespondingNodeIndex(), and ReMesh().

std::vector<unsigned> Cylindrical2dMesh::mRightImages [private]

The image nodes corresponding to these right nodes (on left of mesh).

Definition at line 75 of file Cylindrical2dMesh.hpp.

Referenced by CreateMirrorNodes(), GetCorrespondingNodeIndex(), ReconstructCylindricalMesh(), and ReMesh().

std::map<unsigned, unsigned> Cylindrical2dMesh::mImageToRightOriginalNodeMap [private]

A map from image node index (on left of mesh) to original node index (on right of mesh).

Definition at line 78 of file Cylindrical2dMesh.hpp.

Referenced by CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), ReconstructCylindricalMesh(), and ReMesh().

The indices of elements which straddle the left periodic boundary.

Definition at line 81 of file Cylindrical2dMesh.hpp.

Referenced by CorrectNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), and ReMesh().

The indices of elements which straddle the right periodic boundary.

Definition at line 84 of file Cylindrical2dMesh.hpp.

Referenced by CorrectNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), and ReMesh().

std::vector<unsigned > Cylindrical2dMesh::mTopHaloNodes [private]

The indices of nodes on the top boundary.

Definition at line 87 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), DeleteHaloNodes(), and ReMesh().

std::vector<unsigned > Cylindrical2dMesh::mBottomHaloNodes [private]

The indices of nodes on the bottom boundary.

Definition at line 90 of file Cylindrical2dMesh.hpp.

Referenced by CreateHaloNodes(), DeleteHaloNodes(), and ReMesh().


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

Generated on Tue May 31 14:33:17 2011 for Chaste by  doxygen 1.5.5