AbstractMesh() | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
AddElement(VertexElement< ELEMENT_DIM, SPACE_DIM > *pNewElement) | MutableVertexMesh< 2, 2 > | |
AddNode(Node< 2 > *pNewNode) | Toroidal2dVertexMesh | |
MutableVertexMesh< 2, 2 >::AddNode(Node< SPACE_DIM > *pNewNode) | MutableVertexMesh< 2, 2 > | |
boost::serialization::access | Toroidal2dVertexMesh | friend |
BoundaryNodeIterator typedef | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
CalculateAreaOfFace(VertexElement< ELEMENT_DIM - 1, SPACE_DIM > *pFace) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
CalculateBoundingBox(const std::vector< Node< SPACE_DIM > * > &rNodes) const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | protected |
CalculateBoundingBox() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
CalculateMaximumContainingElementsPerProcess() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
CalculateMomentsOfElement(unsigned index) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
CalculateUnitNormalToFaceWithArea(VertexElement< ELEMENT_DIM - 1, SPACE_DIM > *pFace, c_vector< double, SPACE_DIM > &rNormal) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
CheckForIntersections() | MutableVertexMesh< 2, 2 > | protected |
CheckForRosettes() | MutableVertexMesh< 2, 2 > | private |
CheckForSwapsFromShortEdges() | MutableVertexMesh< 2, 2 > | protectedvirtual |
CheckForT2Swaps(VertexElementMap &rElementMap) | MutableVertexMesh< 2, 2 > | |
CheckNodeLocation(Node< 2 > *pNode) | Toroidal2dVertexMesh | |
Clear() | MutableVertexMesh< 2, 2 > | virtual |
ClearLocationsOfIntersectionSwaps() | MutableVertexMesh< 2, 2 > | |
ClearLocationsOfT1Swaps() | MutableVertexMesh< 2, 2 > | |
ClearLocationsOfT3Swaps() | MutableVertexMesh< 2, 2 > | |
ConstructFromMeshReader(AbstractMeshReader< 2, 2 > &rMeshReader, double width, double height) | Toroidal2dVertexMesh | |
MutableVertexMesh< 2, 2 >::ConstructFromMeshReader(AbstractMeshReader< ELEMENT_DIM, SPACE_DIM > &rMeshReader) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
DeleteElementPriorToReMesh(unsigned index) | MutableVertexMesh< 2, 2 > | |
DeleteNodePriorToReMesh(unsigned index) | MutableVertexMesh< 2, 2 > | |
DivideEdge(Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB) | MutableVertexMesh< 2, 2 > | |
DivideElement(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned nodeAIndex, unsigned nodeBIndex, bool placeOriginalElementBelow=false) | MutableVertexMesh< 2, 2 > | protected |
DivideElementAlongGivenAxis(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, c_vector< double, SPACE_DIM > axisOfDivision, bool placeOriginalElementBelow=false) | MutableVertexMesh< 2, 2 > | |
DivideElementAlongShortAxis(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, bool placeOriginalElementBelow=false) | MutableVertexMesh< 2, 2 > | |
ElementIncludesPoint(const c_vector< double, SPACE_DIM > &rTestPoint, unsigned elementIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
GenerateEdgesFromElements(std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > &rElements) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
GenerateVerticesFromElementCircumcentres(TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
GetAreaGradientOfElementAtNode(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetBoundaryNodeIteratorBegin() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
GetBoundaryNodeIteratorEnd() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
GetCellRearrangementRatio() const | MutableVertexMesh< 2, 2 > | |
GetCellRearrangementThreshold() const | MutableVertexMesh< 2, 2 > | |
GetCentroidOfElement(unsigned index) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetCheckForInternalIntersections() const | MutableVertexMesh< 2, 2 > | |
GetCheckForT3Swaps() const | MutableVertexMesh< 2, 2 > | |
GetDelaunayNodeIndexCorrespondingToVoronoiElementIndex(unsigned elementIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetDistanceBetweenNodes(unsigned indexA, unsigned indexB) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
GetDistanceForT3SwapChecking() const | MutableVertexMesh< 2, 2 > | |
GetDistributedVectorFactory() | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetEdge(unsigned index) const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetEdgeLength(unsigned elementIndex1, unsigned elementIndex2) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetElement(unsigned index) const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetElementIteratorBegin(bool skipDeletedElements=true) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | inline |
GetElementIteratorEnd() | VertexMesh< ELEMENT_DIM, SPACE_DIM > | inline |
GetElongationShapeFactorOfElement(unsigned elementIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetFace(unsigned index) const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetLastT2SwapLocation() | MutableVertexMesh< 2, 2 > | |
GetLocalIndexForElementEdgeClosestToPoint(const c_vector< double, SPACE_DIM > &rTestPoint, unsigned elementIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
GetLocationsOfIntersectionSwaps() | MutableVertexMesh< 2, 2 > | |
GetLocationsOfT1Swaps() | MutableVertexMesh< 2, 2 > | |
GetLocationsOfT3Swaps() | MutableVertexMesh< 2, 2 > | |
GetMeshFileBaseName() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
GetMeshForVtk() | Toroidal2dVertexMesh | virtual |
GetNearestNodeIndex(const ChastePoint< SPACE_DIM > &rTestPoint) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetNeighbouringElementIndices(unsigned elementIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNeighbouringNodeIndices(unsigned nodeIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNeighbouringNodeNotAlsoInElement(unsigned nodeIndex, unsigned elemIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNextEdgeGradientOfElementAtNode(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNode(unsigned index) const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNodeFromPrePermutationIndex(unsigned index) const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNodeIteratorBegin(bool skipDeletedNodes=true) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | inline |
GetNodeIteratorEnd() | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | inline |
GetNodeOrHaloNode(unsigned index) const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetNumAllElements() const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNumAllNodes() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetNumBoundaryNodes() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNumEdges() const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNumElements() const | MutableVertexMesh< 2, 2 > | virtual |
GetNumFaces() const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetNumNodeAttributes() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
GetNumNodes() const | MutableVertexMesh< 2, 2 > | virtual |
GetOperationRecorder() | MutableVertexMesh< 2, 2 > | |
GetPerimeterGradientOfElementAtNode(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetPreviousEdgeGradientOfElementAtNode(VertexElement< ELEMENT_DIM, SPACE_DIM > *pElement, unsigned localIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetProtorosetteFormationProbability() const | MutableVertexMesh< 2, 2 > | |
GetProtorosetteResolutionProbabilityPerTimestep() const | MutableVertexMesh< 2, 2 > | |
GetRosetteRankOfElement(unsigned index) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetRosetteResolutionProbabilityPerTimestep() const | MutableVertexMesh< 2, 2 > | |
GetShortAxisOfElement(unsigned index) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetSurfaceAreaOfElement(unsigned index) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetT2Threshold() const | MutableVertexMesh< 2, 2 > | |
GetVectorFromAtoB(const c_vector< double, 2 > &rLocation1, const c_vector< double, 2 > &rLocation2) | Toroidal2dVertexMesh | |
MutableVertexMesh< 2, 2 >::GetVectorFromAtoB(const c_vector< double, SPACE_DIM > &rLocationA, const c_vector< double, SPACE_DIM > &rLocationB) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetVolumeOfElement(unsigned index) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
GetVoronoiElementIndexCorrespondingToDelaunayNodeIndex(unsigned nodeIndex) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
GetWidth(const unsigned &rDimension) const | Toroidal2dVertexMesh | virtual |
HandleHighOrderJunctions(Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB) | MutableVertexMesh< 2, 2 > | privatevirtual |
IdentifySwapType(Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB) | MutableVertexMesh< 2, 2 > | protectedvirtual |
IsMeshChanging() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
IsMeshOnDisk() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
IsNearExistingNodes(c_vector< double, SPACE_DIM > newNodeLocation, std::vector< Node< SPACE_DIM > * > nodesToCheck, double minClearance) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
load(Archive &archive, const unsigned int version) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | inlineprotected |
mBoundaryNodes | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mCellRearrangementRatio | MutableVertexMesh< 2, 2 > | protected |
mCellRearrangementThreshold | MutableVertexMesh< 2, 2 > | protected |
mCheckForInternalIntersections | MutableVertexMesh< 2, 2 > | protected |
mCheckForT3Swaps | MutableVertexMesh< 2, 2 > | protected |
mDeletedElementIndices | MutableVertexMesh< 2, 2 > | protected |
mDeletedNodeIndices | MutableVertexMesh< 2, 2 > | protected |
mDistanceForT3SwapChecking | MutableVertexMesh< 2, 2 > | protected |
mEdgeHelper | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mElements | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mFaces | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mHeight | Toroidal2dVertexMesh | private |
mLastT2SwapLocation | MutableVertexMesh< 2, 2 > | protected |
mLocationsOfIntersectionSwaps | MutableVertexMesh< 2, 2 > | protected |
mMeshChangesDuringSimulation | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mMeshFileBaseName | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mNodePermutation | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mNodes | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mOperationRecorder | MutableVertexMesh< 2, 2 > | protected |
mpDelaunayMesh | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mpDistributedVectorFactory | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mpMeshForVtk | Toroidal2dVertexMesh | private |
mProtorosetteFormationProbability | MutableVertexMesh< 2, 2 > | protected |
mProtorosetteResolutionProbabilityPerTimestep | MutableVertexMesh< 2, 2 > | protected |
mRosetteResolutionProbabilityPerTimestep | MutableVertexMesh< 2, 2 > | protected |
mT2Threshold | MutableVertexMesh< 2, 2 > | protected |
mTrackMeshOperations | MutableVertexMesh< 2, 2 > | protected |
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< 2, 2 > | |
MutableVertexMesh() | MutableVertexMesh< 2, 2 > | |
mVoronoiElementIndexMap | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
mWidth | Toroidal2dVertexMesh | private |
PerformIntersectionSwap(Node< SPACE_DIM > *pNode, unsigned elementIndex) | MutableVertexMesh< 2, 2 > | private |
PerformNodeMerge(Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB) | MutableVertexMesh< 2, 2 > | |
PerformProtorosetteResolution(Node< SPACE_DIM > *pProtorosetteNode) | MutableVertexMesh< 2, 2 > | private |
PerformRosetteRankDecrease(Node< SPACE_DIM > *pRosetteNode) | MutableVertexMesh< 2, 2 > | private |
PerformRosetteRankIncrease(Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB) | MutableVertexMesh< 2, 2 > | private |
PerformT1Swap(Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB, std::set< unsigned > &rElementsContainingNodes) | MutableVertexMesh< 2, 2 > | private |
PerformT2Swap(VertexElement< ELEMENT_DIM, SPACE_DIM > &rElement) | MutableVertexMesh< 2, 2 > | private |
PerformT3Swap(Node< SPACE_DIM > *pNode, unsigned elementIndex) | MutableVertexMesh< 2, 2 > | private |
PerformVoidRemoval(Node< SPACE_DIM > *pNodeA, Node< SPACE_DIM > *pNodeB, Node< SPACE_DIM > *pNodeC) | MutableVertexMesh< 2, 2 > | private |
PermuteNodes() | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
ReadNodesPerProcessorFile(const std::string &rNodesPerProcessorFile) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
RefreshMesh() | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
ReMesh(VertexElementMap &rElementMap) | MutableVertexMesh< 2, 2 > | virtual |
ReMesh() | MutableVertexMesh< 2, 2 > | |
RemoveDeletedNodes() | MutableVertexMesh< 2, 2 > | |
RemoveDeletedNodesAndElements(VertexElementMap &rElementMap) | MutableVertexMesh< 2, 2 > | |
rGetEdgeHelper() const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
rGetNodePermutation() const | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
Rotate(c_matrix< double, SPACE_DIM, SPACE_DIM > rotationMatrix) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
Rotate(c_vector< double, 3 > axis, double angle) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
Rotate(double theta) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
RotateX(const double theta) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
RotateY(const double theta) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
RotateZ(const double theta) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
save(Archive &archive, const unsigned int version) const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | inlineprotected |
Scale(const double xFactor=1.0, const double yFactor=1.0, const double zFactor=1.0) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
serialize(Archive &archive, const unsigned int version) | Toroidal2dVertexMesh | inlineprivate |
SetCellRearrangementRatio(double cellRearrangementRatio) | MutableVertexMesh< 2, 2 > | |
SetCellRearrangementThreshold(double cellRearrangementThreshold) | MutableVertexMesh< 2, 2 > | |
SetCheckForInternalIntersections(bool checkForInternalIntersections) | MutableVertexMesh< 2, 2 > | |
SetCheckForT3Swaps(bool checkForT3Swaps) | MutableVertexMesh< 2, 2 > | |
SetDistanceForT3SwapChecking(double distanceForT3SwapChecking) | MutableVertexMesh< 2, 2 > | |
SetDistributedVectorFactory(DistributedVectorFactory *pFactory) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
SetElementOwnerships() | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | protectedvirtual |
SetHeight(double height) | Toroidal2dVertexMesh | |
SetMeshHasChangedSinceLoading() | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
SetMeshOperationTracking(const bool track) | MutableVertexMesh< 2, 2 > | |
SetNode(unsigned nodeIndex, ChastePoint< 2 > point) | Toroidal2dVertexMesh | |
MutableVertexMesh< 2, 2 >::SetNode(unsigned nodeIndex, ChastePoint< SPACE_DIM > point) | MutableVertexMesh< 2, 2 > | virtual |
SetProtorosetteFormationProbability(double protorosetteFormationProbability) | MutableVertexMesh< 2, 2 > | |
SetProtorosetteResolutionProbabilityPerTimestep(double protorosetteResolutionProbabilityPerTimestep) | MutableVertexMesh< 2, 2 > | |
SetRosetteResolutionProbabilityPerTimestep(double rosetteResolutionProbabilityPerTimestep) | MutableVertexMesh< 2, 2 > | |
SetT2Threshold(double t2Threshold) | MutableVertexMesh< 2, 2 > | |
SetWidth(double width) | Toroidal2dVertexMesh | |
SolveBoundaryElementMapping(unsigned index) const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
SolveElementMapping(unsigned index) const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protected |
SolveNodeMapping(unsigned index) const | VertexMesh< ELEMENT_DIM, SPACE_DIM > | protectedvirtual |
TestToroidal2dVertexMesh (defined in Toroidal2dVertexMesh) | Toroidal2dVertexMesh | friend |
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() | Toroidal2dVertexMesh | |
Toroidal2dVertexMesh(Toroidal2dMesh &rMesh, bool isBounded=false) | Toroidal2dVertexMesh | |
Translate(const c_vector< double, SPACE_DIM > &rDisplacement) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
Translate(const double xMovement=0.0, const double yMovement=0.0, const double zMovement=0.0) | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | |
VertexMesh(std::vector< Node< SPACE_DIM > * > nodes, std::vector< VertexElement< ELEMENT_DIM, SPACE_DIM > * > vertexElements) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
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< ELEMENT_DIM, SPACE_DIM > | |
VertexMesh(TetrahedralMesh< 2, 2 > &rMesh, bool isPeriodic=false, bool isBounded=false, bool scaleBoundByEdgeLength=true, double maxDelaunayEdgeLength=DBL_MAX, bool offsetNewBoundaryNodes=false) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
VertexMesh(TetrahedralMesh< 3, 3 > &rMesh) | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
VertexMesh() | VertexMesh< ELEMENT_DIM, SPACE_DIM > | |
WidenEdgeOrCorrectIntersectionLocationIfNecessary(unsigned indexA, unsigned indexB, c_vector< double, 2 > intersection) | MutableVertexMesh< 2, 2 > | private |
~AbstractMesh() | AbstractMesh< ELEMENT_DIM, SPACE_DIM > | virtual |
~MutableVertexMesh() | MutableVertexMesh< 2, 2 > | virtual |
~Toroidal2dVertexMesh() | Toroidal2dVertexMesh | |
~VertexMesh() | VertexMesh< ELEMENT_DIM, SPACE_DIM > | virtual |