, including all inherited members.
AbstractCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
AbstractCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
AbstractCentreBasedCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [protected] |
AbstractCentreBasedCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | |
AbstractOffLatticeCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh) | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
AbstractOffLatticeCellPopulation(AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >()) | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
AddCell(CellPtr pNewCell, const c_vector< double, DIM > &rCellDivisionVector, CellPtr pParentCell) | MeshBasedCellPopulationWithGhostNodes< DIM > | |
MeshBasedCellPopulation< DIM >::AddCell(CellPtr pNewCell, const c_vector< double, ELEMENT_DIM > &rCellDivisionVector, CellPtr pParentCell) | MeshBasedCellPopulation< DIM > | [virtual] |
AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::AddCell(CellPtr pNewCell, const c_vector< double, SPACE_DIM > &rCellDivisionVector, CellPtr pParentCell=CellPtr()) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [virtual] |
AddCellUsingLocationIndex(unsigned index, CellPtr pCell) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [virtual] |
AddNode(Node< ELEMENT_DIM > *pNewNode) | MeshBasedCellPopulation< DIM > | |
AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::AddNode(Node< SPACE_DIM > *pNewNode)=0 | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | [pure virtual] |
Begin() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
boost::serialization::access class | MeshBasedCellPopulationWithGhostNodes< DIM > | [friend] |
CalculateForceBetweenGhostNodes(const unsigned &rNodeAGlobalIndex, const unsigned &rNodeBGlobalIndex) | MeshBasedCellPopulationWithGhostNodes< DIM > | |
CalculateRestLengths() | MeshBasedCellPopulation< DIM > | |
CheckCellPointers() | MeshBasedCellPopulation< DIM > | |
CloseOutputFiles() | MeshBasedCellPopulation< DIM > | [virtual] |
CreateCellPair(CellPtr pCell1, CellPtr pCell2) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | |
CreateOutputFiles(const std::string &rDirectory, bool cleanOutputDirectory) | MeshBasedCellPopulation< DIM > | [virtual] |
CreateVoronoiTessellation() | MeshBasedCellPopulation< DIM > | |
End() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GenerateCellResults(CellPtr pCell, std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [virtual] |
GenerateCellResultsAndWriteToFiles() | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [virtual] |
GetAbsoluteMovementThreshold() | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetAreaBasedDampingConstantParameter() | MeshBasedCellPopulation< DIM > | |
GetCellAncestors() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetCellMutationStateCount() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetCellPropertyRegistry() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetCellsUsingLocationIndex(unsigned index) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetCellUsingLocationIndex(unsigned index) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetCentroidOfCellPopulation() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetDampingConstant(unsigned nodeIndex) | MeshBasedCellPopulation< DIM > | [virtual] |
GetDampingConstantMutant() | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetDampingConstantNormal() | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetGhostNodeIndices() | MeshBasedCellPopulationWithGhostNodes< DIM > | |
GetIdentifier() const | Identifiable | |
GetLocationIndexUsingCell(CellPtr pCell) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetLocationOfCellCentre(CellPtr pCell) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [virtual] |
GetMeinekeDivisionSeparation() | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | |
GetNeighbouringNodeIndices(unsigned index) | MeshBasedCellPopulation< DIM > | [virtual] |
GetNode(unsigned index) | MeshBasedCellPopulation< DIM > | [virtual] |
GetNodeCorrespondingToCell(CellPtr pCell) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | |
GetNumNodes() | MeshBasedCellPopulation< DIM > | [virtual] |
GetNumRealCells() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputCellAges() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputCellAncestors() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputCellCyclePhases() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputCellIdData() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputCellMutationStates() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputCellPopulationVolumes() | MeshBasedCellPopulation< DIM > | |
GetOutputCellProliferativeTypes() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputCellVariables() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputCellVolumes() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetOutputVoronoiData() | MeshBasedCellPopulation< DIM > | |
GetRestLength(unsigned indexA, unsigned indexB) | MeshBasedCellPopulation< DIM > | |
GetSizeOfCellPopulation() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
GetSurfaceAreaOfVoronoiElement(unsigned index) | MeshBasedCellPopulation< DIM > | |
GetVolumeOfCell(CellPtr pCell) | MeshBasedCellPopulation< DIM > | [virtual] |
GetVolumeOfVoronoiElement(unsigned index) | MeshBasedCellPopulation< DIM > | |
GetVoronoiEdgeLength(unsigned index1, unsigned index2) | MeshBasedCellPopulation< DIM > | |
GetVoronoiTessellation() | MeshBasedCellPopulation< DIM > | |
GetWidth(const unsigned &rDimension) | MeshBasedCellPopulation< DIM > | [virtual] |
GetWriteVtkAsPoints() | MeshBasedCellPopulation< DIM > | |
InitialiseCells() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
IsCellAssociatedWithADeletedLocation(CellPtr pCell) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [virtual] |
IsCellAttachedToLocationIndex(unsigned index) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
IsGhostNode(unsigned index) | MeshBasedCellPopulationWithGhostNodes< DIM > | [virtual] |
IsMarkedSpring(const std::pair< CellPtr, CellPtr > &rCellPair) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | |
IsParticle(unsigned index) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [virtual] |
mAbsoluteMovementThreshold | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mAreaBasedDampingConstantParameter | MeshBasedCellPopulation< DIM > | [protected] |
MarkSpring(std::pair< CellPtr, CellPtr > &rCellPair) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | |
mCellCyclePhaseCount | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mCellLocationMap | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mCellProliferativeTypeCount | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mCells | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mCentroid | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mDampingConstantMutant | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mDampingConstantNormal | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mDeleteMesh | MeshBasedCellPopulation< DIM > | [protected] |
mDirPath | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
MeshBasedCellPopulation(MutableMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >(), bool deleteMesh=false, bool validate=true) | MeshBasedCellPopulation< DIM > | |
MeshBasedCellPopulation(MutableMesh< ELEMENT_DIM, ELEMENT_DIM > &rMesh) | MeshBasedCellPopulation< DIM > | |
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 > | |
MeshBasedCellPopulationWithGhostNodes(MutableMesh< DIM, DIM > &rMesh, double ghostSpringStiffness=15.0) | MeshBasedCellPopulationWithGhostNodes< DIM > | |
mGhostSpringStiffness | MeshBasedCellPopulationWithGhostNodes< DIM > | [private] |
mHasVariableRestLength | MeshBasedCellPopulation< DIM > | [protected] |
mIsGhostNode | MeshBasedCellPopulationWithGhostNodes< DIM > | [private] |
mLocationCellMap | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mMarkedSprings | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [protected] |
mMeinekeDivisionSeparation | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [protected] |
mNodePairs | MeshBasedCellPopulation< DIM > | [protected] |
mOutputCellAges | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mOutputCellAncestors | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mOutputCellCyclePhases | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mOutputCellIdData | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mOutputCellMutationStates | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mOutputCellPopulationVolumes | MeshBasedCellPopulation< DIM > | [protected] |
mOutputCellProliferativeTypes | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mOutputCellVariables | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mOutputCellVolumes | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mOutputVoronoiData | MeshBasedCellPopulation< DIM > | [protected] |
MoveCellInLocationMap(CellPtr pCell, unsigned old_index, unsigned new_index) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
mpCellAgesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpCellCyclePhasesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpCellIdFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpCellMutationStatesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpCellPopulationVolumesFile | MeshBasedCellPopulation< DIM > | [protected] |
mpCellProliferativeTypesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpCellPropertyRegistry | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpCellVariablesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpCellVolumesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpMutableMesh | MeshBasedCellPopulation< DIM > | [protected] |
mpVizBoundaryNodesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpVizCellAncestorsFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpVizCellProliferativePhasesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpVizCellProliferativeTypesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpVizElementsFile | MeshBasedCellPopulation< DIM > | [protected] |
mpVizNodesFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mpVoronoiFile | MeshBasedCellPopulation< DIM > | [protected] |
mpVoronoiTessellation | MeshBasedCellPopulation< DIM > | [protected] |
mpVtkMetaFile | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mrMesh | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [protected] |
mSpringRestLengths | MeshBasedCellPopulation< DIM > | [protected] |
mUseAreaBasedDampingConstant | MeshBasedCellPopulation< DIM > | [protected] |
mWriteVtkAsPoints | MeshBasedCellPopulation< DIM > | [protected] |
OutputCellPopulationInfo(out_stream &rParamsFile) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
OutputCellPopulationParameters(out_stream &rParamsFile) | MeshBasedCellPopulationWithGhostNodes< DIM > | [virtual] |
RemoveCellUsingLocationIndex(unsigned index, CellPtr pCell) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [virtual] |
RemoveDeadCells() | MeshBasedCellPopulation< DIM > | [virtual] |
rGetCellCyclePhaseCount() const | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
rGetCellProliferativeTypeCount() const | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
rGetCells() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
rGetGhostNodes() | MeshBasedCellPopulationWithGhostNodes< DIM > | |
rGetMesh() | MeshBasedCellPopulation< DIM > | |
rGetMesh() const | MeshBasedCellPopulation< DIM > | |
rGetNodePairs() | MeshBasedCellPopulation< DIM > | [virtual] |
serialize(Archive &archive, const unsigned int version) | MeshBasedCellPopulationWithGhostNodes< DIM > | [inline, private] |
SetAbsoluteMovementThreshold(double absoluteMovementThreshold) | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetAreaBasedDampingConstant(bool useAreaBasedDampingConstant) | MeshBasedCellPopulation< DIM > | |
SetAreaBasedDampingConstantParameter(double areaBasedDampingConstantParameter) | MeshBasedCellPopulation< DIM > | |
SetCellAncestorsToLocationIndices() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetCellUsingLocationIndex(unsigned index, CellPtr pCell) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetDampingConstantMutant(double dampingConstantMutant) | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetDampingConstantNormal(double dampingConstantNormal) | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetDataOnAllCells(const std::string &dataName, double dataValue) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetDefaultMutationStateOrdering() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetGhostNodes(const std::set< unsigned > &rGhostNodeIndices) | MeshBasedCellPopulationWithGhostNodes< DIM > | [private] |
SetMeinekeDivisionSeparation(double divisionSeparation) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | |
SetNode(unsigned nodeIndex, ChastePoint< ELEMENT_DIM > &rNewLocation) | MeshBasedCellPopulation< DIM > | |
AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM >::SetNode(unsigned nodeIndex, ChastePoint< SPACE_DIM > &rNewLocation)=0 | AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM > | [pure virtual] |
SetOutputCellAges(bool outputCellAges) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetOutputCellAncestors(bool outputCellAncestors) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetOutputCellCyclePhases(bool outputCellCyclePhases) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetOutputCellIdData(bool outputCellIdData) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetOutputCellMutationStates(bool outputCellMutationStates) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetOutputCellPopulationVolumes(bool outputCellPopulationVolumes) | MeshBasedCellPopulation< DIM > | |
SetOutputCellProliferativeTypes(bool outputCellProliferativeTypes) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetOutputCellVariables(bool outputCellVariables) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetOutputCellVolumes(bool outputCellVolumes) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
SetOutputVoronoiData(bool outputVoronoiData) | MeshBasedCellPopulation< DIM > | |
SetWriteVtkAsPoints(bool writeVtkAsPoints) | MeshBasedCellPopulation< DIM > | |
SpringsBegin() | MeshBasedCellPopulation< DIM > | |
SpringsEnd() | MeshBasedCellPopulation< DIM > | |
TessellateIfNeeded() | MeshBasedCellPopulation< DIM > | |
TestMeshBasedCellPopulationWithGhostNodes class | MeshBasedCellPopulationWithGhostNodes< DIM > | [friend] |
UnmarkSpring(std::pair< CellPtr, CellPtr > &rCellPair) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | |
Update(bool hasHadBirthsOrDeaths=true) | MeshBasedCellPopulation< DIM > | [virtual] |
UpdateGhostNodesAfterReMesh(NodeMap &rMap) | MeshBasedCellPopulationWithGhostNodes< DIM > | [virtual] |
UpdateGhostPositions(double dt) | MeshBasedCellPopulationWithGhostNodes< DIM > | |
UpdateNodeLocations(const std::vector< c_vector< double, DIM > > &rNodeForces, double dt) | MeshBasedCellPopulationWithGhostNodes< DIM > | |
MeshBasedCellPopulation< DIM >::UpdateNodeLocations(const std::vector< c_vector< double, SPACE_DIM > > &rNodeForces, double dt) | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [virtual] |
UseAreaBasedDampingConstant() | MeshBasedCellPopulation< DIM > | |
Validate() | MeshBasedCellPopulationWithGhostNodes< DIM > | [private, virtual] |
WriteCellIdDataToFile() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
WriteCellPopulationVolumeResultsToFile() | MeshBasedCellPopulation< DIM > | |
WriteCellResultsToFiles(std::vector< unsigned > &rCellProliferativeTypeCounter, std::vector< unsigned > &rCellCyclePhaseCounter) | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | |
WriteCellVolumeResultsToFile() | MeshBasedCellPopulation< DIM > | [virtual] |
WriteResultsToFiles() | MeshBasedCellPopulation< DIM > | [virtual] |
WriteTimeAndNodeResultsToFiles() | AbstractCentreBasedCellPopulation< ELEMENT_DIM, ELEMENT_DIM > | [virtual] |
WriteVoronoiResultsToFile() | MeshBasedCellPopulation< DIM > | |
WriteVtkResultsToFile() | MeshBasedCellPopulationWithGhostNodes< DIM > | [virtual] |
~AbstractCellPopulation() | AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > | [virtual] |
~Identifiable() | Identifiable | [virtual] |
~MeshBasedCellPopulation() | MeshBasedCellPopulation< DIM > | [virtual] |