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Chaste Commit::333233612e3dcc941d260418acd7b5ccdc30390e
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#include <Cylindrical2dVertexMesh.hpp>
Public Member Functions | |
Cylindrical2dVertexMesh (double width, std::vector< Node< 2 > * > nodes, std::vector< VertexElement< 2, 2 > * > vertexElements, double cellRearrangementThreshold=0.01, double t2Threshold=0.001) | |
Cylindrical2dVertexMesh (Cylindrical2dMesh &rMesh, bool isBounded=false) | |
~Cylindrical2dVertexMesh () | |
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) |
void | CheckNodeLocation (Node< 2 > *pNode) |
void | Scale (const double xScale=1.0, const double yScale=1.0, const double zScale=1.0) |
VertexMesh< 2, 2 > * | GetMeshForVtk () |
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void | PerformNodeMerge (Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB) |
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) |
void | SetCheckForT3Swaps (bool checkForT3Swaps) |
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 |
bool | GetCheckForT3Swaps () const |
std::vector< c_vector< double, SPACE_DIM > > | GetLocationsOfT1Swaps () |
c_vector< double, SPACE_DIM > | GetLastT2SwapLocation () |
std::vector< c_vector< double, SPACE_DIM > > | GetLocationsOfT3Swaps () |
std::vector< c_vector< double, SPACE_DIM > > | GetLocationsOfIntersectionSwaps () |
void | ClearLocationsOfT1Swaps () |
void | ClearLocationsOfT3Swaps () |
void | ClearLocationsOfIntersectionSwaps () |
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 () |
void | SetMeshOperationTracking (const bool track) |
VertexMeshOperationRecorder< ELEMENT_DIM, SPACE_DIM > * | GetOperationRecorder () |
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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, bool isBounded=false, bool scaleBoundByEdgeLength=true, double maxDelaunayEdgeLength=DBL_MAX, bool offsetNewBoundaryNodes=false) | |
Alternative 2D 'Voronoi' constructor. | |
VertexMesh (TetrahedralMesh< 3, 3 > &rMesh) | |
VertexMesh () | |
virtual | ~VertexMesh () |
unsigned | GetNumEdges () const |
Edge< SPACE_DIM > * | GetEdge (unsigned index) const |
const EdgeHelper< SPACE_DIM > & | rGetEdgeHelper () const |
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< unsigned > | GetNeighbouringNodeIndices (unsigned nodeIndex) |
std::set< unsigned > | GetNeighbouringNodeNotAlsoInElement (unsigned nodeIndex, unsigned elemIndex) |
std::set< unsigned > | GetNeighbouringElementIndices (unsigned elementIndex) |
bool | IsNearExistingNodes (c_vector< double, SPACE_DIM > newNodeLocation, std::vector< Node< SPACE_DIM > * > nodesToCheck, double minClearance) |
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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 DistributedVectorFactory * | GetDistributedVectorFactory () |
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 | 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) |
Cylindrical2dVertexMesh () | |
Private Attributes | |
double | mWidth |
VertexMesh< 2, 2 > * | mpMeshForVtk |
Friends | |
class | TestCylindrical2dVertexMesh |
class | boost::serialization::access |
A subclass of MutableVertexMesh<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 53 of file Cylindrical2dVertexMesh.hpp.
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Constructor - used for serialization only.
Definition at line 334 of file Cylindrical2dVertexMesh.cpp.
Cylindrical2dVertexMesh::Cylindrical2dVertexMesh | ( | double | width, |
std::vector< Node< 2 > * > | nodes, | ||
std::vector< VertexElement< 2, 2 > * > | vertexElements, | ||
double | cellRearrangementThreshold = 0.01 , |
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double | t2Threshold = 0.001 |
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Default constructor.
width | the width (circumference) of the mesh |
nodes | vector of pointers to nodes |
vertexElements | vector of pointers to VertexElements |
cellRearrangementThreshold | the minimum threshold distance for element rearrangement (defaults to 0.01) |
t2Threshold | the maximum threshold distance for Type 2 swaps (defaults to 0.001) |
Definition at line 39 of file Cylindrical2dVertexMesh.cpp.
References MutableVertexMesh< 2, 2 >::ReMesh().
Cylindrical2dVertexMesh::Cylindrical2dVertexMesh | ( | Cylindrical2dMesh & | rMesh, |
bool | isBounded = false |
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) |
Alternative constructor. Creates a Voronoi tessellation of a given Cylindrical2dMesh, which must be Delaunay (see TetrahedralMesh::CheckIsVoronoi).
rMesh | a Cylindrical2dMesh |
isBounded | a boolean to indicate whether to bound the voronoi tesselation. Defaults to false. |
Create a std::vector of pairs, where each pair comprises the angle between the centre of the Voronoi element and each node with that node's global index in the Voronoi mesh.
Definition at line 52 of file Cylindrical2dVertexMesh.cpp.
References MutableElement< ELEMENT_DIM, SPACE_DIM >::AddNode(), CheckNodeLocation(), MutableVertexMesh< 2, 2 >::Clear(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GenerateVerticesFromElementCircumcentres(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetElement(), AbstractTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::GetNumAllElements(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::IsNearExistingNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::mElements, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mMeshChangesDuringSimulation, AbstractMesh< ELEMENT_DIM, SPACE_DIM >::mNodes, VertexMesh< ELEMENT_DIM, SPACE_DIM >::mpDelaunayMesh, Node< SPACE_DIM >::rGetContainingElementIndices(), and Node< SPACE_DIM >::rGetLocation().
Cylindrical2dVertexMesh::~Cylindrical2dVertexMesh | ( | ) |
Overridden AddNode() method.
pNewNode | the node to be added to the mesh |
Definition at line 401 of file Cylindrical2dVertexMesh.cpp.
References MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::AddNode(), and CheckNodeLocation().
void Cylindrical2dVertexMesh::CheckNodeLocation | ( | Node< 2 > * | pNode | ) |
Helper method to check if a node is within, x in [0,mWidth) and move back into the domain if needed.
pNode | the node to be checked |
Definition at line 410 of file Cylindrical2dVertexMesh.cpp.
References mWidth, Node< SPACE_DIM >::rGetLocation(), and Node< SPACE_DIM >::rGetModifiableLocation().
Referenced by Cylindrical2dVertexMesh(), and AddNode().
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Overridden GetMeshForVtk() method.
Return a pointer to an extended mesh that is a 'non-periodic' version of our mesh. This can then be used when writing to VTK.
Reimplemented from VertexMesh< ELEMENT_DIM, SPACE_DIM >.
Definition at line 433 of file Cylindrical2dVertexMesh.cpp.
References VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorBegin(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetElementIteratorEnd(), Node< SPACE_DIM >::GetIndex(), AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetNode(), MutableVertexMesh< 2, 2 >::GetNumNodes(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::mpDelaunayMesh, mpMeshForVtk, and mWidth.
c_vector< double, 2 > Cylindrical2dVertexMesh::GetVectorFromAtoB | ( | const c_vector< double, 2 > & | rLocation1, |
const c_vector< double, 2 > & | rLocation2 | ||
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Overridden GetVectorFromAtoB() method. This 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 347 of file Cylindrical2dVertexMesh.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 386 of file Cylindrical2dVertexMesh.cpp.
References AbstractMesh< ELEMENT_DIM, SPACE_DIM >::GetWidth(), and mWidth.
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Overridden Scale method to also scale the width (mWidth) of the mesh
xScale | is the scale in the x-direction (defaults to 1.0) |
yScale | is the scale in the y-direction (defaults to 1.0) |
zScale | is the scale in the z-direction (defaults to 1.0) note this has to be 1.0 as only a 2d Mesh |
Reimplemented from AbstractMesh< ELEMENT_DIM, SPACE_DIM >.
Definition at line 423 of file Cylindrical2dVertexMesh.cpp.
References mWidth, and AbstractMesh< ELEMENT_DIM, SPACE_DIM >::Scale().
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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.
archive | the archive |
version | the current version of this class |
Definition at line 81 of file Cylindrical2dVertexMesh.hpp.
References mWidth.
void Cylindrical2dVertexMesh::SetNode | ( | unsigned | nodeIndex, |
ChastePoint< 2 > | point | ||
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Overridden SetNode() method.
If the location should be set outside a cylindrical boundary move it back onto the cylinder.
nodeIndex | is the index of the node to be moved |
point | is the new target location of the node |
Definition at line 366 of file Cylindrical2dVertexMesh.cpp.
References mWidth, ChastePoint< DIM >::rGetLocation(), ChastePoint< DIM >::SetCoordinate(), and MutableVertexMesh< ELEMENT_DIM, SPACE_DIM >::SetNode().
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Needed for serialization.
Definition at line 69 of file Cylindrical2dVertexMesh.hpp.
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friend |
Definition at line 55 of file Cylindrical2dVertexMesh.hpp.
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private |
Auxiliary mesh pointer, created/updated when GetMeshForVtk() is called and stored so that it may be deleted by the destructor.
Definition at line 66 of file Cylindrical2dVertexMesh.hpp.
Referenced by ~Cylindrical2dVertexMesh(), and GetMeshForVtk().
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private |
The circumference of the cylinder.
Definition at line 60 of file Cylindrical2dVertexMesh.hpp.
Referenced by CheckNodeLocation(), GetMeshForVtk(), GetVectorFromAtoB(), GetWidth(), Scale(), serialize(), and SetNode().