, including all inherited members.
| AbstractCellPopulation() | AbstractCellPopulation< DIM > | [inline, protected] |
| AbstractCellPopulation(std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | AbstractCellPopulation< DIM > | [inline] |
| AbstractCentreBasedCellPopulation() | AbstractCentreBasedCellPopulation< DIM > | [inline, protected] |
| AbstractCentreBasedCellPopulation(std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | AbstractCentreBasedCellPopulation< DIM > | [inline] |
| AddCell(CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, virtual] |
| AddNode(Node< DIM > *pNewNode) | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| Begin() | AbstractCellPopulation< DIM > | [inline] |
| boost::serialization::access class | MeshBasedCellPopulationWithGhostNodes< DIM > | [friend] |
| CalculateForceBetweenGhostNodes(const unsigned &rNodeAGlobalIndex, const unsigned &rNodeBGlobalIndex) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline] |
| CheckCellPointers() | MeshBasedCellPopulation< DIM > | [inline] |
| CloseOutputFiles() | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| CreateCellPair(CellPtr pCell1, CellPtr pCell2) | MeshBasedCellPopulation< DIM > | [inline] |
| CreateOutputFiles(const std::string &rDirectory, bool cleanOutputDirectory) | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| CreateVoronoiTessellation() | MeshBasedCellPopulation< DIM > | |
| CreateVoronoiTessellation() | MeshBasedCellPopulation< DIM > | [inline] |
| End() | AbstractCellPopulation< DIM > | [inline] |
| GenerateCellResults(unsigned locationIndex, std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter) | AbstractCentreBasedCellPopulation< DIM > | [inline, virtual] |
| GenerateCellResultsAndWriteToFiles() | AbstractCentreBasedCellPopulation< DIM > | [inline, virtual] |
| GetAreaBasedDampingConstantParameter() | MeshBasedCellPopulation< DIM > | [inline] |
| GetCellAncestors() | AbstractCellPopulation< DIM > | [inline] |
| GetCellMutationStateCount() | AbstractCellPopulation< DIM > | [inline] |
| GetCellPropertyRegistry() | AbstractCellPopulation< DIM > | [inline] |
| GetCellUsingLocationIndex(unsigned index) | AbstractCellPopulation< DIM > | [inline] |
| GetDampingConstant(unsigned nodeIndex) | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| GetDampingConstantMutant() | AbstractCellPopulation< DIM > | [inline] |
| GetDampingConstantNormal() | AbstractCellPopulation< DIM > | [inline] |
| GetGhostNodeIndices() | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline] |
| GetIdentifier() const | Identifiable | |
| GetLocationIndexUsingCell(CellPtr pCell) | AbstractCellPopulation< DIM > | [inline] |
| GetLocationOfCellCentre(CellPtr pCell) | AbstractCentreBasedCellPopulation< DIM > | [inline, virtual] |
| GetMeinekeDivisionSeparation() | AbstractCentreBasedCellPopulation< DIM > | [inline] |
| GetNode(unsigned index) | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| GetNodeCorrespondingToCell(CellPtr pCell) | AbstractCentreBasedCellPopulation< DIM > | [inline] |
| GetNumNodes() | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| GetNumRealCells() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputCellAges() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputCellAncestors() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputCellCyclePhases() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputCellIdData() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputCellMutationStates() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputCellPopulationVolumes() | MeshBasedCellPopulation< DIM > | [inline] |
| GetOutputCellProliferativeTypes() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputCellVariables() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputCellVolumes() | AbstractCellPopulation< DIM > | [inline] |
| GetOutputVoronoiData() | MeshBasedCellPopulation< DIM > | [inline] |
| GetSurfaceAreaOfVoronoiElement(unsigned index) | MeshBasedCellPopulation< DIM > | [inline] |
| GetVolumeOfVoronoiElement(unsigned index) | MeshBasedCellPopulation< DIM > | [inline] |
| GetVoronoiEdgeLength(unsigned index1, unsigned index2) | MeshBasedCellPopulation< DIM > | [inline] |
| GetVoronoiTessellation() | MeshBasedCellPopulation< DIM > | [inline] |
| GetWidth(const unsigned &rDimension) | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| InitialiseCells() | AbstractCellPopulation< DIM > | [inline] |
| IsCellAssociatedWithADeletedLocation(CellPtr pCell) | AbstractCentreBasedCellPopulation< DIM > | [inline, virtual] |
| IsGhostNode(unsigned index) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, virtual] |
| IsMarkedSpring(const std::pair< CellPtr, CellPtr > &rCellPair) | MeshBasedCellPopulation< DIM > | [inline] |
| IsMeshBasedCellPopulation() | AbstractCellPopulation< DIM > | [inline] |
| mAreaBasedDampingConstantParameter | MeshBasedCellPopulation< DIM > | [protected] |
| MarkSpring(std::pair< CellPtr, CellPtr > &rCellPair) | MeshBasedCellPopulation< DIM > | [inline] |
| mCellCyclePhaseCount | AbstractCellPopulation< DIM > | [protected] |
| mCellLocationMap | AbstractCellPopulation< DIM > | [protected] |
| mCellPopulationContainsMesh | AbstractCellPopulation< DIM > | [protected] |
| mCellProliferativeTypeCount | AbstractCellPopulation< DIM > | [protected] |
| mCells | AbstractCellPopulation< DIM > | [protected] |
| mDampingConstantMutant | AbstractCellPopulation< DIM > | [protected] |
| mDampingConstantNormal | AbstractCellPopulation< DIM > | [protected] |
| mDeleteMesh | MeshBasedCellPopulation< DIM > | [protected] |
| mDirPath | MeshBasedCellPopulation< DIM > | [protected] |
| MeshBasedCellPopulation(MutableMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true) | MeshBasedCellPopulation< DIM > | [inline] |
| MeshBasedCellPopulation(MutableMesh< DIM, DIM > &rMesh) | MeshBasedCellPopulation< DIM > | [inline] |
| MeshBasedCellPopulationWithGhostNodes(MutableMesh< DIM, DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, double ghostSpringStiffness=15.0) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline] |
| MeshBasedCellPopulationWithGhostNodes(MutableMesh< DIM, DIM > &rMesh, double ghostSpringStiffness=15.0) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline] |
| mGhostSpringStiffness | MeshBasedCellPopulationWithGhostNodes< DIM > | [private] |
| mIsGhostNode | MeshBasedCellPopulationWithGhostNodes< DIM > | [private] |
| mLocationCellMap | AbstractCellPopulation< DIM > | [protected] |
| mMarkedSprings | MeshBasedCellPopulation< DIM > | [protected] |
| mMeinekeDivisionSeparation | AbstractCentreBasedCellPopulation< DIM > | [protected] |
| mOutputCellAges | AbstractCellPopulation< DIM > | [protected] |
| mOutputCellAncestors | AbstractCellPopulation< DIM > | [protected] |
| mOutputCellCyclePhases | AbstractCellPopulation< DIM > | [protected] |
| mOutputCellIdData | AbstractCellPopulation< DIM > | [protected] |
| mOutputCellMutationStates | AbstractCellPopulation< DIM > | [protected] |
| mOutputCellPopulationVolumes | MeshBasedCellPopulation< DIM > | [protected] |
| mOutputCellProliferativeTypes | AbstractCellPopulation< DIM > | [protected] |
| mOutputCellVariables | AbstractCellPopulation< DIM > | [protected] |
| mOutputCellVolumes | AbstractCellPopulation< DIM > | [protected] |
| mOutputVoronoiData | MeshBasedCellPopulation< DIM > | [protected] |
| mpCellAgesFile | AbstractCellPopulation< DIM > | [protected] |
| mpCellCyclePhasesFile | AbstractCellPopulation< DIM > | [protected] |
| mpCellIdFile | AbstractCellPopulation< DIM > | [protected] |
| mpCellMutationStatesFile | AbstractCellPopulation< DIM > | [protected] |
| mpCellPopulationVolumesFile | MeshBasedCellPopulation< DIM > | [protected] |
| mpCellProliferativeTypesFile | AbstractCellPopulation< DIM > | [protected] |
| mpCellPropertyRegistry | AbstractCellPopulation< DIM > | [protected] |
| mpCellVariablesFile | AbstractCellPopulation< DIM > | [protected] |
| mpCellVolumesFile | MeshBasedCellPopulation< DIM > | [protected] |
| mpVizBoundaryNodesFile | AbstractCellPopulation< DIM > | [protected] |
| mpVizCellAncestorsFile | AbstractCellPopulation< DIM > | [protected] |
| mpVizCellProliferativeTypesFile | AbstractCellPopulation< DIM > | [protected] |
| mpVizElementsFile | MeshBasedCellPopulation< DIM > | [protected] |
| mpVizNodesFile | AbstractCellPopulation< DIM > | [protected] |
| mpVoronoiFile | MeshBasedCellPopulation< DIM > | [protected] |
| mpVoronoiTessellation | MeshBasedCellPopulation< DIM > | [protected] |
| mpVtkMetaFile | MeshBasedCellPopulation< DIM > | [protected] |
| mrMesh | MeshBasedCellPopulation< DIM > | [protected] |
| mUseAreaBasedDampingConstant | MeshBasedCellPopulation< DIM > | [protected] |
| OutputCellPopulationInfo(out_stream &rParamsFile) | AbstractCellPopulation< DIM > | [inline] |
| OutputCellPopulationParameters(out_stream &rParamsFile) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, virtual] |
| RemoveDeadCells() | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| rGetCellCyclePhaseCount() const | AbstractCellPopulation< DIM > | [inline] |
| rGetCellProliferativeTypeCount() const | AbstractCellPopulation< DIM > | [inline] |
| rGetCells() | AbstractCellPopulation< DIM > | [inline] |
| rGetGhostNodes() | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline] |
| rGetMesh() | MeshBasedCellPopulation< DIM > | [inline] |
| rGetMesh() const | MeshBasedCellPopulation< DIM > | [inline] |
| serialize(Archive &archive, const unsigned int version) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, private] |
| SetAreaBasedDampingConstant(bool useAreaBasedDampingConstant) | MeshBasedCellPopulation< DIM > | [inline] |
| SetAreaBasedDampingConstantParameter(double areaBasedDampingConstantParameter) | MeshBasedCellPopulation< DIM > | [inline] |
| SetCellAncestorsToLocationIndices() | AbstractCellPopulation< DIM > | [inline] |
| SetDampingConstantMutant(double dampingConstantMutant) | AbstractCellPopulation< DIM > | [inline] |
| SetDampingConstantNormal(double dampingConstantNormal) | AbstractCellPopulation< DIM > | [inline] |
| SetDefaultMutationStateOrdering() | AbstractCellPopulation< DIM > | [inline] |
| SetGhostNodes(const std::set< unsigned > &rGhostNodeIndices) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, private] |
| SetMeinekeDivisionSeparation(double divisionSeparation) | AbstractCentreBasedCellPopulation< DIM > | [inline] |
| SetNode(unsigned nodeIndex, ChastePoint< DIM > &rNewLocation) | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| SetOutputCellAges(bool outputCellAges) | AbstractCellPopulation< DIM > | [inline] |
| SetOutputCellAncestors(bool outputCellAncestors) | AbstractCellPopulation< DIM > | [inline] |
| SetOutputCellCyclePhases(bool outputCellCyclePhases) | AbstractCellPopulation< DIM > | [inline] |
| SetOutputCellIdData(bool outputCellIdData) | AbstractCellPopulation< DIM > | [inline] |
| SetOutputCellMutationStates(bool outputCellMutationStates) | AbstractCellPopulation< DIM > | [inline] |
| SetOutputCellPopulationVolumes(bool outputCellPopulationVolumes) | MeshBasedCellPopulation< DIM > | [inline] |
| SetOutputCellProliferativeTypes(bool outputCellProliferativeTypes) | AbstractCellPopulation< DIM > | [inline] |
| SetOutputCellVariables(bool outputCellVariables) | AbstractCellPopulation< DIM > | [inline] |
| SetOutputCellVolumes(bool outputCellVolumes) | AbstractCellPopulation< DIM > | [inline] |
| SetOutputVoronoiData(bool outputVoronoiData) | MeshBasedCellPopulation< DIM > | [inline] |
| SpringsBegin() | MeshBasedCellPopulation< DIM > | [inline] |
| SpringsEnd() | MeshBasedCellPopulation< DIM > | [inline] |
| TestMeshBasedCellPopulationWithGhostNodes class | MeshBasedCellPopulationWithGhostNodes< DIM > | [friend] |
| UnmarkSpring(std::pair< CellPtr, CellPtr > &rCellPair) | MeshBasedCellPopulation< DIM > | [inline] |
| Update(bool hasHadBirthsOrDeaths=true) | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| UpdateGhostNodesAfterReMesh(NodeMap &rMap) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, virtual] |
| UpdateGhostPositions(double dt) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline] |
| UpdateNodeLocations(const std::vector< c_vector< double, DIM > > &rNodeForces, double dt) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, virtual] |
| UseAreaBasedDampingConstant() | MeshBasedCellPopulation< DIM > | [inline] |
| Validate() | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, private, virtual] |
| WriteCellIdDataToFile() | AbstractCellPopulation< DIM > | [inline] |
| WriteCellPopulationVolumeResultsToFile() | MeshBasedCellPopulation< DIM > | [inline] |
| WriteCellResultsToFiles(std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter) | AbstractCellPopulation< DIM > | [inline] |
| WriteCellVolumeResultsToFile() | MeshBasedCellPopulation< DIM > | [inline] |
| WriteResultsToFiles() | MeshBasedCellPopulation< DIM > | [inline, virtual] |
| WriteTimeAndNodeResultsToFiles() | AbstractCentreBasedCellPopulation< DIM > | [inline, virtual] |
| WriteVoronoiResultsToFile() | MeshBasedCellPopulation< DIM > | [inline] |
| WriteVtkResultsToFile() | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, virtual] |
| ~AbstractCellPopulation() | AbstractCellPopulation< DIM > | [inline, virtual] |
| ~Identifiable() | Identifiable | [virtual] |
| ~MeshBasedCellPopulation() | MeshBasedCellPopulation< DIM > | [inline] |
