Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
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#include <Cylindrical2dMesh.hpp>
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 |
void | SetHaloScalingFactor (double haloScalingFactor) |
double | GetHaloScalingFactor () const |
void | SetHaloOffset (double haloOffset) |
double | GetHaloOffset () const |
unsigned | AddNode (Node< 2 > *pNewNode) |
bool | GetInstanceOfMismatchedBoundaryNodes () |
Public Member Functions inherited from MutableMesh< 2, 2 > | |
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) |
void | RescaleMeshFromBoundaryNode (ChastePoint< 1 > updatedPoint, unsigned boundaryNodeIndex) |
virtual unsigned | AddNode (Node< SPACE_DIM > *pNewNode) |
unsigned | AddElement (Element< ELEMENT_DIM, SPACE_DIM > *pNewElement) |
virtual void | SetNode (unsigned index, ChastePoint< SPACE_DIM > point, bool concreteMove=true) |
void | MoveMergeNode (unsigned index, unsigned targetIndex, bool concreteMove=true) |
virtual void | DeleteNode (unsigned index) |
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 |
virtual unsigned | GetMaximumNodeIndex () |
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 |
virtual Node< SPACE_DIM > * | GetNodeOrHaloNode (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 () |
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 |
double | mHaloScalingFactor |
double | mHaloOffset |
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 |
bool | mMismatchedBoundaryElements |
Friends | |
class | TestCylindrical2dMesh |
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 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< 2, 2 > | |
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 |
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 55 of file Cylindrical2dMesh.hpp.
Cylindrical2dMesh::Cylindrical2dMesh | ( | double | width | ) |
Constructor.
width | the width of the mesh (circumference) |
Definition at line 47 of file Cylindrical2dMesh.cpp.
A constructor which reads in a width and collection of nodes, then calls a ReMesh() command to create the elements of the mesh.
width | the periodic length scale |
nodes | a collection of nodes to construct the mesh with |
Definition at line 60 of file Cylindrical2dMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, MutableMesh< 2, 2 >::ReMesh(), Node< SPACE_DIM >::rGetLocation(), and UNUSED_OPT.
Cylindrical2dMesh::~Cylindrical2dMesh | ( | ) |
Destructor.
Definition at line 56 of file Cylindrical2dMesh.cpp.
Overridden AddNode() method.
pNewNode | the node to be added to the mesh |
Definition at line 532 of file Cylindrical2dMesh.cpp.
References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), Node< SPACE_DIM >::GetPoint(), and SetNode().
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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 543 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().
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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 159 of file Cylindrical2dMesh.cpp.
References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), mBottom, mBottomHaloNodes, mHaloOffset, mHaloScalingFactor, mTop, mTopHaloNodes, mWidth, and UpdateTopAndBottom().
Referenced by ReMesh().
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Creates a set of mirrored nodes for a cylindrical re-mesh. Updates mRightImages and mLeftImages. All mesh points should be 0 < x < mWidth.
This method should only ever be called by the public ReMesh() method.
Definition at line 92 of file Cylindrical2dMesh.cpp.
References MutableMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorBegin(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNodeIteratorEnd(), mImageToLeftOriginalNodeMap, mImageToRightOriginalNodeMap, mLeftImages, mLeftOriginals, mLeftPeriodicBoundaryElementIndices, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, mRightImages, mRightOriginals, mRightPeriodicBoundaryElementIndices, and mWidth.
Referenced by ReMesh().
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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 467 of file Cylindrical2dMesh.cpp.
References MutableMesh< 2, 2 >::DeleteBoundaryNodeAt(), mBottomHaloNodes, and mTopHaloNodes.
Referenced by ReMesh().
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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 735 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().
This method should only ever be called by the public ReMesh() method.
nodeIndex | The index of an original/mirrored node |
Definition at line 795 of file Cylindrical2dMesh.cpp.
References mLeftImages, mLeftOriginals, mRightImages, and mRightOriginals.
Referenced by CorrectNonPeriodicMesh(), and UseTheseElementsToDecideMeshing().
double Cylindrical2dMesh::GetHaloOffset | ( | ) | const |
double Cylindrical2dMesh::GetHaloScalingFactor | ( | ) | const |
Definition at line 838 of file Cylindrical2dMesh.cpp.
References mHaloScalingFactor.
bool Cylindrical2dMesh::GetInstanceOfMismatchedBoundaryNodes | ( | ) |
c_vector< double, 2 > Cylindrical2dMesh::GetVectorFromAtoB | ( | const c_vector< double, 2 > & | rLocation1, |
const c_vector< double, 2 > & | rLocation2 | ||
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Overridden GetVectorFromAtoB() method.
Evaluates the (surface) distance between two points in a 2D cylindrical geometry.
rLocation1 | the x and y co-ordinates of point 1 |
rLocation2 | the x and y co-ordinates of point 2 |
Definition at line 477 of file Cylindrical2dMesh.cpp.
References mWidth.
Overridden GetWidth() method.
Calculate the 'width' of any dimension of the mesh, taking periodicity into account.
rDimension | a dimension (0 or 1) |
Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.
Definition at line 517 of file Cylindrical2dMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and mWidth.
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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 333 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().
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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.
rMap | a reference to a nodemap which should be created with the required number of nodes. |
Reimplemented from MutableMesh< 2, 2 >.
Definition at line 188 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::GetSize(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::IsDeleted(), NodeMap::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(), and NodeMap::SetNewIndex().
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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.
archive | the archive |
version | the current version of this class the current version of this class |
Definition at line 215 of file Cylindrical2dMesh.hpp.
References mBottom, mHaloOffset, mHaloScalingFactor, mTop, and mWidth.
void Cylindrical2dMesh::SetHaloOffset | ( | double | haloOffset | ) |
Set mHaloOffset
haloOffset | the new value of mHaloOffset |
Definition at line 854 of file Cylindrical2dMesh.cpp.
References mHaloOffset.
void Cylindrical2dMesh::SetHaloScalingFactor | ( | double | haloScalingFactor | ) |
Set mHaloScalingFactor
haloScalingFactor | the new value of mHaloScalingFactor |
Definition at line 843 of file Cylindrical2dMesh.cpp.
References mHaloScalingFactor.
void Cylindrical2dMesh::SetNode | ( | unsigned | index, |
ChastePoint< 2 > | point, | ||
bool | concreteMove | ||
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Overridden SetNode() method.
If the location should be set outside a cylindrical boundary, it is moved back onto the cylinder.
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 499 of file Cylindrical2dMesh.cpp.
References mWidth, ChastePoint< DIM >::rGetLocation(), ChastePoint< DIM >::SetCoordinate(), and MutableMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().
Referenced by AddNode().
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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 85 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().
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This method takes in two elements which are not meshed in the same way on the opposite boundary. It deletes the corresponding two elements (connecting the same four nodes) and makes two new elements which are connected in the same way. We should then be able to reconstruct the cylindrical mesh properly.
rMainSideElements | two elements (usually in a square) which have been meshed differently on the opposite boundary |
Definition at line 653 of file Cylindrical2dMesh.cpp.
References GetCorrespondingNodeIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), AbstractElement< ELEMENT_DIM, SPACE_DIM >::GetNodeGlobalIndex(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllNodes(), MutableMesh< 2, 2 >::mDeletedElementIndices, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementInverseJacobians, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobianDeterminants, TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElementJacobians, AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::mElements, and MutableMesh< 2, 2 >::ReIndex().
Referenced by CorrectNonPeriodicMesh().
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Needed for serialization.
Definition at line 202 of file Cylindrical2dMesh.hpp.
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Definition at line 57 of file Cylindrical2dMesh.hpp.
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The bottom of the cylinder (y coordinate).
Definition at line 67 of file Cylindrical2dMesh.hpp.
Referenced by CreateHaloNodes(), serialize(), and UpdateTopAndBottom().
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The indices of nodes on the bottom boundary.
Definition at line 103 of file Cylindrical2dMesh.hpp.
Referenced by CreateHaloNodes(), DeleteHaloNodes(), and ReMesh().
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Scaling factor for offset of halo nodes
Definition at line 73 of file Cylindrical2dMesh.hpp.
Referenced by CreateHaloNodes(), GetHaloOffset(), serialize(), and SetHaloOffset().
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Scaling factor used to calculate numebr of halo nodes
Definition at line 70 of file Cylindrical2dMesh.hpp.
Referenced by CreateHaloNodes(), GetHaloScalingFactor(), serialize(), and SetHaloScalingFactor().
A map from image node index (on right of mesh) to original node index (on left of mesh).
Definition at line 82 of file Cylindrical2dMesh.hpp.
Referenced by CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), ReconstructCylindricalMesh(), and ReMesh().
A map from image node index (on left of mesh) to original node index (on right of mesh).
Definition at line 91 of file Cylindrical2dMesh.hpp.
Referenced by CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), ReconstructCylindricalMesh(), and ReMesh().
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The image nodes corresponding to these left nodes (on right of mesh).
Definition at line 79 of file Cylindrical2dMesh.hpp.
Referenced by CreateMirrorNodes(), GetCorrespondingNodeIndex(), ReconstructCylindricalMesh(), and ReMesh().
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The left nodes which have been mirrored during the remesh.
Definition at line 76 of file Cylindrical2dMesh.hpp.
Referenced by CreateMirrorNodes(), GetCorrespondingNodeIndex(), and ReMesh().
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The indices of elements which straddle the left periodic boundary.
Definition at line 94 of file Cylindrical2dMesh.hpp.
Referenced by CorrectNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), and ReMesh().
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Whether the number of left hand boundary nodes does not equal the number of right hand boundary nodes
Definition at line 106 of file Cylindrical2dMesh.hpp.
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The image nodes corresponding to these right nodes (on left of mesh).
Definition at line 88 of file Cylindrical2dMesh.hpp.
Referenced by CreateMirrorNodes(), GetCorrespondingNodeIndex(), ReconstructCylindricalMesh(), and ReMesh().
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The right nodes which have been mirrored during the remesh.
Definition at line 85 of file Cylindrical2dMesh.hpp.
Referenced by CreateMirrorNodes(), GetCorrespondingNodeIndex(), and ReMesh().
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The indices of elements which straddle the right periodic boundary.
Definition at line 97 of file Cylindrical2dMesh.hpp.
Referenced by CorrectNonPeriodicMesh(), CreateMirrorNodes(), GenerateVectorsOfElementsStraddlingPeriodicBoundaries(), and ReMesh().
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The top of the cylinder (y coordinate).
Definition at line 64 of file Cylindrical2dMesh.hpp.
Referenced by CreateHaloNodes(), serialize(), and UpdateTopAndBottom().
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The indices of nodes on the top boundary.
Definition at line 100 of file Cylindrical2dMesh.hpp.
Referenced by CreateHaloNodes(), DeleteHaloNodes(), and ReMesh().
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The circumference of the cylinder.
Definition at line 61 of file Cylindrical2dMesh.hpp.
Referenced by CreateHaloNodes(), CreateMirrorNodes(), GetVectorFromAtoB(), GetWidth(), serialize(), and SetNode().