Chaste Commit::1fd4e48e3990e67db148bc1bc4cf6991a0049d0c
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > Class Template Referenceabstract

#include <AbstractCellPopulation.hpp>

+ Inheritance diagram for AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >:
+ Collaboration diagram for AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >:

Classes

class  Iterator
 

Public Member Functions

 AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh, std::vector< CellPtr > &rCells, const std::vector< unsigned > locationIndices=std::vector< unsigned >())
 
virtual ~AbstractCellPopulation ()
 
void InitialiseCells ()
 
void SetDataOnAllCells (const std::string &rDataName, double dataValue)
 
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & rGetMesh ()
 
virtual TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * GetTetrahedralMeshForPdeModifier ()=0
 
virtual bool IsPdeNodeAssociatedWithNonApoptoticCell (unsigned pdeNodeIndex)
 
virtual double GetCellDataItemAtPdeNode (unsigned pdeNodeIndex, std::string &rVariableName, bool dirichletBoundaryConditionApplies=false, double dirichletBoundaryValue=0.0)=0
 
std::list< CellPtr > & rGetCells ()
 
virtual unsigned GetNumNodes ()=0
 
virtual c_vector< double, SPACE_DIM > GetLocationOfCellCentre (CellPtr pCell)=0
 
virtual Node< SPACE_DIM > * GetNode (unsigned index)=0
 
virtual void SetNode (unsigned nodeIndex, ChastePoint< SPACE_DIM > &rNewLocation)=0
 
virtual bool IsCellAssociatedWithADeletedLocation (CellPtr pCell)=0
 
virtual void WriteDataToVisualizerSetupFile (out_stream &pVizSetupFile)
 
virtual CellPtr AddCell (CellPtr pNewCell, CellPtr pParentCell=CellPtr())=0
 
virtual double GetDefaultTimeStep ()=0
 
virtual unsigned RemoveDeadCells ()=0
 
virtual void Update (bool hasHadBirthsOrDeaths=true)=0
 
std::vector< unsignedGetCellMutationStateCount ()
 
std::vector< unsignedGetCellProliferativeTypeCount ()
 
std::vector< unsignedGetCellCyclePhaseCount ()
 
unsigned GetNumRealCells ()
 
unsigned GetNumAllCells ()
 
void SetCellAncestorsToLocationIndices ()
 
std::set< unsignedGetCellAncestors ()
 
virtual CellPtr GetCellUsingLocationIndex (unsigned index)
 
std::set< CellPtr > GetCellsUsingLocationIndex (unsigned index)
 
virtual bool IsCellAttachedToLocationIndex (unsigned index)
 
void SetCellUsingLocationIndex (unsigned index, CellPtr pCell)
 
virtual void AddCellUsingLocationIndex (unsigned index, CellPtr pCell)
 
virtual void RemoveCellUsingLocationIndex (unsigned index, CellPtr pCell)
 
void MoveCellInLocationMap (CellPtr pCell, unsigned old_index, unsigned new_index)
 
unsigned GetLocationIndexUsingCell (CellPtr pCell)
 
boost::shared_ptr< CellPropertyRegistryGetCellPropertyRegistry ()
 
void SetDefaultCellMutationStateAndProliferativeTypeOrdering ()
 
virtual double GetWidth (const unsigned &rDimension)=0
 
virtual double GetVolumeOfCell (CellPtr pCell)=0
 
virtual std::set< unsignedGetNeighbouringNodeIndices (unsigned index)=0
 
virtual std::set< unsignedGetNeighbouringLocationIndices (CellPtr pCell)=0
 
virtual std::set< std::pair< unsigned, unsigned > > GetNeighbouringEdgeIndices (CellPtr pCell, unsigned pEdgeIndex)
 
c_vector< double, SPACE_DIM > GetCentroidOfCellPopulation ()
 
virtual void UpdateCellProcessLocation ()
 
virtual void OpenWritersFiles (OutputFileHandler &rOutputFileHandler)
 
virtual void CloseWritersFiles ()
 
virtual void WriteResultsToFiles (const std::string &rDirectory)
 
virtual void AcceptPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter)=0
 
virtual void AcceptPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationCountWriter)=0
 
virtual void AcceptPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationEventWriter)=0
 
virtual void AcceptCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter, CellPtr pCell)=0
 
std::vector< std::string > GetDivisionsInformation ()
 
void AddDivisionInformation (std::string divisionInformation)
 
void ClearDivisionsInformation ()
 
std::vector< std::string > GetRemovalsInformation ()
 
void AddRemovalInformation (std::string removalInformation)
 
void ClearRemovalsInformation ()
 
void GenerateRemovalInformation (CellPtr pCell, std::string killerInfo)
 
void KillCell (CellPtr pCell, std::string killerInfo)
 
void StartApoptosisOnCell (CellPtr pCell, std::string killerInfo)
 
void OutputCellPopulationInfo (out_stream &rParamsFile)
 
virtual void OutputCellPopulationParameters (out_stream &rParamsFile)=0
 
virtual void SimulationSetupHook (AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM > *pSimulation)
 
bool GetOutputResultsForChasteVisualizer ()
 
template<template< unsigned, unsigned > class T>
void AddPopulationWriter ()
 
template<template< unsigned, unsigned > class T>
void AddCellWriter ()
 
template<template< unsigned, unsigned > class T>
void AddCellPopulationCountWriter ()
 
template<template< unsigned, unsigned > class T>
void AddCellPopulationEventWriter ()
 
void AddPopulationWriter (boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > pPopulationWriter)
 
void AddCellWriter (boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > pCellWriter)
 
void AddCellPopulationCountWriter (boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationCountWriter)
 
void AddCellPopulationEventWriter (boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > pCellPopulationEventWriter)
 
template<template< unsigned, unsigned > class T>
bool HasWriter () const
 
void SetOutputResultsForChasteVisualizer (bool outputResultsForChasteVisualizer)
 
c_vector< double, SPACE_DIM > GetSizeOfCellPopulation ()
 
virtual bool IsRoomToDivide (CellPtr pCell)
 
std::pair< unsigned, unsignedCreateOrderedPair (unsigned index1, unsigned index2)
 
Iterator Begin ()
 
Iterator End ()
 
- Public Member Functions inherited from Identifiable
virtual ~Identifiable ()
 
std::string GetIdentifier () const
 

Protected Member Functions

virtual void Validate ()=0
 
virtual void WriteVtkResultsToFile (const std::string &rDirectory)=0
 
 AbstractCellPopulation (AbstractMesh< ELEMENT_DIM, SPACE_DIM > &rMesh)
 
virtual void AcceptCellWritersAcrossPopulation ()
 

Protected Attributes

std::map< unsigned, std::set< CellPtr > > mLocationCellMap
 
std::map< Cell *, unsignedmCellLocationMap
 
AbstractMesh< ELEMENT_DIM, SPACE_DIM > & mrMesh
 
std::list< CellPtr > mCells
 
c_vector< double, SPACE_DIM > mCentroid
 
out_stream mpVtkMetaFile
 
boost::shared_ptr< CellPropertyRegistrympCellPropertyRegistry
 
bool mOutputResultsForChasteVisualizer
 
std::vector< boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > > > mCellWriters
 
std::vector< boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > > > mCellPopulationWriters
 
std::vector< boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > > > mCellPopulationCountWriters
 
std::vector< boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > > > mCellPopulationEventWriters
 
std::vector< std::string > mDivisionsInformation
 
std::vector< std::string > mRemovalsInformation
 

Private Member Functions

template<class Archive >
void serialize (Archive &archive, const unsigned int version)
 
void OpenRoundRobinWritersFilesForAppend (OutputFileHandler &rOutputFileHandler)
 
void CloseRoundRobinWritersFiles ()
 

Friends

class boost::serialization::access
 

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
class AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >

An abstract facade class encapsulating a cell population.

Contains a group of cells and associated methods.

Template Parameters
ELEMENT_DIMDimension of the elements.
SPACE_DIMDimension of the space. If not specified, it defaults to ELEMENT_DIM.

Definition at line 82 of file AbstractCellPopulation.hpp.

Constructor & Destructor Documentation

◆ AbstractCellPopulation() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation ( AbstractMesh< ELEMENT_DIM, SPACE_DIM > &  rMesh)
protected

Constructor that just takes in a mesh.

Parameters
rMeshthe mesh for the population.

Definition at line 110 of file AbstractCellPopulation.cpp.

◆ AbstractCellPopulation() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellPopulation ( AbstractMesh< ELEMENT_DIM, SPACE_DIM > &  rMesh,
std::vector< CellPtr > &  rCells,
const std::vector< unsigned locationIndices = std::vector<unsigned>() 
)

AbstractCellPopulation Constructor.

Note
Warning: the passed-in vector of cells will be emptied, even if the constructor throws an exception!
Parameters
rMesha reference to the mesh underlying the cell population
rCellsa vector of cells. Copies of the cells will be stored in the cell population, and the passed-in vector cleared.
locationIndicesan optional vector of location indices that correspond to real cells

Definition at line 68 of file AbstractCellPopulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::ClearDivisionsInformation(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::ClearRemovalsInformation(), EXCEPTION, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCells, AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap, and AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPropertyRegistry.

◆ ~AbstractCellPopulation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::~AbstractCellPopulation ( )
virtual

Base class with virtual methods needs a virtual destructor.

Definition at line 116 of file AbstractCellPopulation.cpp.

Member Function Documentation

◆ AcceptCellWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWriter ( boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > >  pCellWriter,
CellPtr  pCell 
)
pure virtual

Accept a cell writer so it can write data from this object to file.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
pCellWriterthe population writer.
pCellthe cell whose data are being written.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulation< DIM >.

◆ AcceptCellWritersAcrossPopulation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptCellWritersAcrossPopulation ( )
protectedvirtual

Call AcceptCellWriter across the whole population.

By default the implementation here iterates over the cell population, but this is overridden in some classes that need to go over nodes.

Reimplemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, and NodeBasedCellPopulationWithParticles< DIM >.

Definition at line 715 of file AbstractCellPopulation.cpp.

◆ AcceptPopulationCountWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationCountWriter ( boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > >  pPopulationCountWriter)
pure virtual

Accept a cell population count writer so it can write data from this object to file.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
pPopulationCountWriterthe population count writer.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulation< DIM >.

◆ AcceptPopulationEventWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationEventWriter ( boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > >  pPopulationEventWriter)
pure virtual

Accept a cell population event writer so it can write data from this object to file.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
pPopulationEventWriterthe population event writer.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulation< DIM >.

◆ AcceptPopulationWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AcceptPopulationWriter ( boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > >  pPopulationWriter)
pure virtual

Accept a cell population writer so it can write data from this object to file.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
pPopulationWriterthe population writer.

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, and MeshBasedCellPopulation< DIM >.

◆ AddCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual CellPtr AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCell ( CellPtr  pNewCell,
CellPtr  pParentCell = CellPtr() 
)
pure virtual

Add a new cell to the cell population.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
pNewCellthe cell to add
pParentCellpointer to a parent cell (if required)
Returns
address of cell as it appears in the cell list (internal of this method uses a copy constructor along the way).

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, NodeBasedCellPopulation< DIM >, NodeBasedCellPopulationWithParticles< DIM >, AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

◆ AddCellPopulationCountWriter() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<template< unsigned, unsigned > class T>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationCountWriter ( )
inline

Add a cell population count writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.

Definition at line 821 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationCountWriters.

◆ AddCellPopulationCountWriter() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationCountWriter ( boost::shared_ptr< AbstractCellPopulationCountWriter< ELEMENT_DIM, SPACE_DIM > >  pCellPopulationCountWriter)
inline

Add a cell population count writer through an input argument. This alternative to the templated AddCellPopulationCountWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.

Parameters
pCellPopulationCountWritershared pointer to a cell population count writer

Definition at line 871 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationCountWriters.

◆ AddCellPopulationEventWriter() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<template< unsigned, unsigned > class T>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationEventWriter ( )
inline

Add a cell population event writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.

Definition at line 832 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationEventWriters.

◆ AddCellPopulationEventWriter() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellPopulationEventWriter ( boost::shared_ptr< AbstractCellPopulationEventWriter< ELEMENT_DIM, SPACE_DIM > >  pCellPopulationEventWriter)
inline

Add a cell population count writer through an input argument. This alternative to the templated AddCellPopulationEventWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.

Parameters
pCellPopulationEventWritershared pointer to a cell population event writer

Definition at line 884 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationEventWriters.

◆ AddCellUsingLocationIndex()

◆ AddCellWriter() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<template< unsigned, unsigned > class T>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellWriter ( )
inline

Add a cell writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.

Definition at line 810 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters.

◆ AddCellWriter() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddCellWriter ( boost::shared_ptr< AbstractCellWriter< ELEMENT_DIM, SPACE_DIM > >  pCellWriter)
inline

Add a cell writer through an input argument. This alternative to the templated AddCellWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.

Parameters
pCellWritershared pointer to a cell writer

Definition at line 858 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters.

◆ AddDivisionInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddDivisionInformation ( std::string  divisionInformation)

Add information for a division event.

Division Time, Location of Parent Cell (x,y,z), Age on Division, Parent Cell ID, New Cell ID.

Parameters
divisionInformationdivision information string

Definition at line 831 of file AbstractCellPopulation.cpp.

◆ AddPopulationWriter() [1/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<template< unsigned, unsigned > class T>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddPopulationWriter ( )
inline

Add a cell population writer based on its type. Template parameters are inferred from the population. The implementation of this function must be available in the header file.

Definition at line 799 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters.

◆ AddPopulationWriter() [2/2]

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddPopulationWriter ( boost::shared_ptr< AbstractCellPopulationWriter< ELEMENT_DIM, SPACE_DIM > >  pPopulationWriter)
inline

Add a cell population writer through an input argument. This alternative to the templated AddPopulationWriter() method allows the user to, for example, add a writer with a non-default value for its member mFileName.

Parameters
pPopulationWritershared pointer to a cell population writer

Definition at line 845 of file AbstractCellPopulation.hpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters.

◆ AddRemovalInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::AddRemovalInformation ( std::string  removalInformation)

Add information for a division event.

Parameters
removalInformationremoval information string

Definition at line 849 of file AbstractCellPopulation.cpp.

◆ Begin()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin ( )
Returns
iterator pointing to the first cell in the cell population

Definition at line 1119 of file AbstractCellPopulation.hpp.

Referenced by CryptProjectionForce::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath(), EllipticBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), CryptProjectionStatistics::GetCryptSection(), CryptStatistics::GetCryptSection(), AbstractBoxDomainPdeModifier< DIM >::InitialiseCellPdeElementMap(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), CellwiseDataGradient< DIM >::SetupGradients(), ParabolicBoxDomainPdeModifier< DIM >::SetupInitialSolutionVector(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellData(), AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), DeltaNotchEdgeInteriorTrackingModifier< DIM >::UpdateCellData(), DeltaNotchEdgeTrackingModifier< DIM >::UpdateCellData(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), DivisionBiasTrackingModifier< DIM >::UpdateCellData(), VolumeTrackingModifier< DIM >::UpdateCellData(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellPdeElementMap(), CryptProjectionForce::UpdateNode3dLocationMap(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), and RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ ClearDivisionsInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::ClearDivisionsInformation ( )

◆ ClearRemovalsInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::ClearRemovalsInformation ( )

◆ CloseRoundRobinWritersFiles()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseRoundRobinWritersFiles ( )
private

Close all files in mCellPopulationWriters and mCellWriters.

Files in mCellPopulationCountWriters are NOT closed in this call since they are not written in a round-robin fashion

Definition at line 481 of file AbstractCellPopulation.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::CloseFile().

◆ CloseWritersFiles()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CloseWritersFiles ( )
virtual

Close output files associated with any writers in the members mCellPopulationCountWriters, mCellPopulationWriters and mCellWriters.

The method also closes the .pvd output file if VTK is available.

Definition at line 497 of file AbstractCellPopulation.cpp.

◆ CreateOrderedPair()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::pair< unsigned, unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::CreateOrderedPair ( unsigned  index1,
unsigned  index2 
)
Returns
a pair of indices ordered by node index. Used by the rest length routines.
Parameters
index1a node index
index2a node index

Definition at line 936 of file AbstractCellPopulation.cpp.

Referenced by MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CalculateRestLengths(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRestLength(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetRestLength().

◆ End()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Iterator AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End ( )
Returns
iterator pointing to one past the last cell in the cell population

Definition at line 1125 of file AbstractCellPopulation.hpp.

Referenced by CryptProjectionForce::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath(), EllipticBoxDomainPdeModifier< DIM >::ConstructBoundaryConditionsContainer(), CryptProjectionStatistics::GetCryptSection(), CryptStatistics::GetCryptSection(), AbstractBoxDomainPdeModifier< DIM >::InitialiseCellPdeElementMap(), AbstractCryptStatistics::LabelAllCellsAsHealthy(), AbstractCryptStatistics::LabelSPhaseCells(), CellwiseDataGradient< DIM >::SetupGradients(), ParabolicBoxDomainPdeModifier< DIM >::SetupInitialSolutionVector(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellData(), AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), DeltaNotchEdgeInteriorTrackingModifier< DIM >::UpdateCellData(), DeltaNotchEdgeTrackingModifier< DIM >::UpdateCellData(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), DivisionBiasTrackingModifier< DIM >::UpdateCellData(), VolumeTrackingModifier< DIM >::UpdateCellData(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellPdeElementMap(), CryptProjectionForce::UpdateNode3dLocationMap(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), and RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ GenerateRemovalInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GenerateRemovalInformation ( CellPtr  pCell,
std::string  killerInfo 
)

Helper method to store information about the removal in mRemovalInformation

Parameters
pCellthe cell
killerInfoadditional information the killer wants output i.e. the type of killer.

Definition at line 861 of file AbstractCellPopulation.cpp.

References SimulationTime::GetTime(), and SimulationTime::Instance().

◆ GetCellAncestors()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::set< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellAncestors ( )

Loops over cells and makes a list of the ancestors that are part of the cell population.

Returns
remaining_ancestors The size of this set tells you how many clonal populations remain.

Definition at line 185 of file AbstractCellPopulation.cpp.

◆ GetCellCyclePhaseCount()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellCyclePhaseCount ( )

Find out how many cells in each cell cycle phase there are.

Returns
The number of cells of each phase (evaluated at each visualizer output) [0] = G_ZERO_PHASE [1] = G_ONE_PHASE [2] = S_PHASE [3] = G_TWO_PHASE [4] = M_PHASE

Definition at line 265 of file AbstractCellPopulation.cpp.

Referenced by CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellProliferativePhasesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ GetCellDataItemAtPdeNode()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellDataItemAtPdeNode ( unsigned  pdeNodeIndex,
std::string &  rVariableName,
bool  dirichletBoundaryConditionApplies = false,
double  dirichletBoundaryValue = 0.0 
)
pure virtual
Parameters
pdeNodeIndexindex of a node in a tetrahedral mesh for use with a PDE modifier
rVariableNamethe name of the cell data item to get
dirichletBoundaryConditionApplieswhere a Dirichlet boundary condition is used (optional; defaults to false)
dirichletBoundaryValuethe value of the Dirichlet boundary condition, if used (optional; defaults to 0.0)
Returns
the value of a CellData item (interpolated if necessary) at a node, specified by its index in a tetrahedral mesh for use with a PDE modifier. This method can be called by PDE modifier classes.

As this method is pure virtual, it must be overridden in subclasses.

Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Referenced by ParabolicGrowingDomainPdeModifier< DIM >::UpdateSolutionVector().

◆ GetCellMutationStateCount()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellMutationStateCount ( )

Find out how many cells of each mutation state there are

Returns
The number of cells of each mutation state (evaluated at each visualizer output), with default ordering [0] = healthy count [1] = APC one hit [2] = APC two hit [3] = beta catenin one hit

Definition at line 196 of file AbstractCellPopulation.cpp.

Referenced by CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ GetCellProliferativeTypeCount()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellProliferativeTypeCount ( )

Find out how many cells of each type there are.

Returns
The number of cells of each type (evaluated at each visualizer output), with default ordering [0] = STEM [1] = TRANSIT [2] = DIFFERENTIATED [3] = DEFAULT

Definition at line 230 of file AbstractCellPopulation.cpp.

Referenced by CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellProliferativeTypesCountWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ GetCellPropertyRegistry()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
boost::shared_ptr< CellPropertyRegistry > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellPropertyRegistry ( )

◆ GetCellsUsingLocationIndex()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::set< CellPtr > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellsUsingLocationIndex ( unsigned  index)

Get the set of cells corresponding to a given location index.

Note that the set may be empty.

Parameters
indexthe location index
Returns
the set of cells.

Definition at line 345 of file AbstractCellPopulation.cpp.

◆ GetCellUsingLocationIndex()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
CellPtr AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex ( unsigned  index)
virtual

Get the cell corresponding to a given location index.

This method assumes that there is at most one cell attached to a location index and an assertion fails if not.

Todo:
should be an exception?
Parameters
indexthe location index
Returns
the cell.

Reimplemented in NodeBasedCellPopulation< DIM >.

Definition at line 324 of file AbstractCellPopulation.cpp.

References EXCEPTION.

Referenced by FarhadifarForce< DIM >::AddForceContribution(), NagaiHondaForce< DIM >::AddForceContribution(), ImmersedBoundaryLinearDifferentialAdhesionForce< DIM >::AddImmersedBoundaryForceContribution(), CryptShovingCaBasedDivisionRule::CalculateDaughterNodeIndex(), ShovingCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), CryptProjectionForce::CalculateForceBetweenNodes(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers(), AdhesionPottsUpdateRule< DIM >::EvaluateHamiltonianContribution(), NagaiHondaDifferentialAdhesionForce< DIM >::GetAdhesionParameter(), NodeBasedCellPopulation< DIM >::GetCellUsingLocationIndex(), CellwiseDataGradient< DIM >::SetupGradients(), DeltaNotchEdgeInteriorTrackingModifier< DIM >::UpdateCellData(), DeltaNotchEdgeTrackingModifier< DIM >::UpdateCellData(), DeltaNotchTrackingModifier< DIM >::UpdateCellData(), LinearSpringWithVariableSpringConstantsForce< DIM >::VariableSpringConstantMultiplicationFactor(), DifferentialAdhesionGeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::VariableSpringConstantMultiplicationFactor(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), NodeVelocityWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ GetCentroidOfCellPopulation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector< double, SPACE_DIM > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCentroidOfCellPopulation ( )

◆ GetDefaultTimeStep()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDefaultTimeStep ( )
pure virtual
Returns
a default value for the time step to use when simulating the cell population.

As this method is pure virtual, it must be overridden in subclasses.

Note that the time step can be reset by calling SetDt() on the simulation object used to simulate the cell population.

Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, AbstractOnLatticeCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedSimulation().

◆ GetDivisionsInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector< std::string > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetDivisionsInformation ( )

Return details of all divisions since the last sampling time step.

Returns
mDivisionsInformation

Definition at line 826 of file AbstractCellPopulation.cpp.

Referenced by CellDivisionLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellDivisionLocationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ GetLocationIndexUsingCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell ( CellPtr  pCell)

Get the location index corresponding to a given cell.

Assumes there is one location index for each cell and an assertion fails if not.

Parameters
pCellthe cell
Returns
the location index.

Definition at line 414 of file AbstractCellPopulation.cpp.

Referenced by CryptProjectionForce::AddForceContribution(), BuskeCompressionForce< DIM >::AddForceContribution(), ChemotacticForce< DIM >::AddForceContribution(), ShortAxisImmersedBoundaryDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), ShortAxisVertexBasedDivisionRule< SPACE_DIM >::CalculateCellDivisionVector(), CryptShovingCaBasedDivisionRule::CalculateDaughterNodeIndex(), ExclusionCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), ShovingCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::CheckCellPointers(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::GetCellDataForVtkOutput(), CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >::GetVectorCellDataForVtkOutput(), ExclusionCaBasedDivisionRule< SPACE_DIM >::IsRoomToDivide(), CellwiseDataGradient< DIM >::SetupGradients(), AbstractGrowingDomainPdeModifier< DIM >::UpdateCellData(), CryptProjectionForce::UpdateNode3dLocationMap(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationElementWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), HeterotypicBoundaryLengthWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), CellAgesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellCycleModelProteinConcentrationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellDataItemWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellIdWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellLabelWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellLocationIndexWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellRosetteRankWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), ImmersedBoundaryBoundaryCellWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), ImmersedBoundaryNeighbourNumberWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

◆ GetLocationOfCellCentre()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual c_vector< double, SPACE_DIM > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre ( CellPtr  pCell)
pure virtual

Find where a given cell is in space.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
pCellthe cell
Returns
the location of the cell

Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Referenced by RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath(), AbstractBoxDomainPdeModifier< DIM >::InitialiseCellPdeElementMap(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellData(), DivisionBiasTrackingModifier< DIM >::UpdateCellData(), AbstractBoxDomainPdeModifier< DIM >::UpdateCellPdeElementMap(), CryptProjectionForce::UpdateNode3dLocationMap(), RadialCellDataDistributionWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation(), CellAgesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellAppliedForceWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellDataItemWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellDeltaNotchWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellIdWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellLabelWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellRadiusWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellRosetteRankWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), CellVolumesWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), ImmersedBoundaryBoundaryCellWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), ImmersedBoundaryNeighbourNumberWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell(), and CellBetaCateninWriter< ELEMENT_DIM, SPACE_DIM >::VisitCell().

◆ GetNeighbouringEdgeIndices()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::set< std::pair< unsigned, unsigned > > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringEdgeIndices ( CellPtr  pCell,
unsigned  pEdgeIndex 
)
virtual

Gets the local edge index of the neighbouring element

Parameters
pCellCell pointer
pEdgeIndexLocal edge index
Returns
pair of element location and local edge index

Reimplemented in VertexBasedCellPopulation< DIM >.

Definition at line 454 of file AbstractCellPopulation.cpp.

Referenced by DeltaNotchEdgeInteriorTrackingModifier< DIM >::UpdateCellData(), and DeltaNotchEdgeTrackingModifier< DIM >::UpdateCellData().

◆ GetNeighbouringLocationIndices()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual std::set< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringLocationIndices ( CellPtr  pCell)
pure virtual

◆ GetNeighbouringNodeIndices()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual std::set< unsigned > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringNodeIndices ( unsigned  index)
pure virtual

Given a node index, returns the set of neighbouring node indices.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
indexthe node index
Returns
the set of neighbouring node indices.

Implemented in AbstractOnLatticeCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

◆ GetNode()

◆ GetNumAllCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumAllCells ( )

This returns the number of cells that are present in the internal mCells vector. It also includes dead cells and cells that are associated with a deleted location in the mesh.

Returns
the number of real cells.

Definition at line 169 of file AbstractCellPopulation.cpp.

◆ GetNumNodes()

◆ GetNumRealCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNumRealCells ( )

This counts the number of cells that the cell iterator covers. It does not include dead cells or cells that are associated with a deleted location in the mesh.

Returns
the number of real cells.

Definition at line 156 of file AbstractCellPopulation.cpp.

Referenced by CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ GetOutputResultsForChasteVisualizer()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetOutputResultsForChasteVisualizer ( )
Returns
mOutputResultsForChasteVisualizer

Definition at line 814 of file AbstractCellPopulation.cpp.

◆ GetRemovalsInformation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector< std::string > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetRemovalsInformation ( )

Return details of all cell removals since the last sampling time step.

Returns
mRemovalsInformation

Definition at line 843 of file AbstractCellPopulation.cpp.

Referenced by CellRemovalLocationsWriter< ELEMENT_DIM, SPACE_DIM >::Visit(), and CellRemovalLocationsWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ GetSizeOfCellPopulation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector< double, SPACE_DIM > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetSizeOfCellPopulation ( )
Returns
The width (maximum distance to centroid) of the cell population in each dimension

Definition at line 906 of file AbstractCellPopulation.cpp.

Referenced by NodeBasedCellPopulation< DIM >::GetSizeOfCellPopulation().

◆ GetTetrahedralMeshForPdeModifier()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual TetrahedralMesh< ELEMENT_DIM, SPACE_DIM > * AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetTetrahedralMeshForPdeModifier ( )
pure virtual

◆ GetVolumeOfCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetVolumeOfCell ( CellPtr  pCell)
pure virtual

◆ GetWidth()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual double AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetWidth ( const unsigned rDimension)
pure virtual

Calculate the 'width' of any dimension of the cell population.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
rDimensiona dimension (0,1 or 2)
Returns
The maximum distance between any nodes in this dimension.

Implemented in CaBasedCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

◆ HasWriter()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
template<template< unsigned, unsigned > class T>
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::HasWriter ( ) const
inline

◆ InitialiseCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::InitialiseCells ( )

Initialise each cell's cell-cycle model.

Definition at line 121 of file AbstractCellPopulation.cpp.

◆ IsCellAssociatedWithADeletedLocation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAssociatedWithADeletedLocation ( CellPtr  pCell)
pure virtual

Helper method for establishing if a cell is real.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
pCellthe cell
Returns
whether a given cell is associated with a deleted node (cell-centre models) or element (vertex models).

Implemented in AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractCentreBasedCellPopulation< DIM >, CaBasedCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

◆ IsCellAttachedToLocationIndex()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsCellAttachedToLocationIndex ( unsigned  index)
virtual

◆ IsPdeNodeAssociatedWithNonApoptoticCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsPdeNodeAssociatedWithNonApoptoticCell ( unsigned  pdeNodeIndex)
virtual
Parameters
pdeNodeIndexindex of a node in a tetrahedral mesh for use with a PDE modifier
Returns
if a node, specified by its index in a tetrahedral mesh for use with a PDE modifier, is associated with a non-apoptotic cell. This method can be called by PDE classes.

As this method is pure virtual, it must be overridden in subclasses.

Reimplemented in CaBasedCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Definition at line 955 of file AbstractCellPopulation.cpp.

◆ IsRoomToDivide()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::IsRoomToDivide ( CellPtr  pCell)
virtual
Returns
whether there is room into which a given cell may divide. Returns true by default, but may be overridden in subclasses.
Parameters
pCellpointer to a cell

Reimplemented in CaBasedCellPopulation< DIM >.

Definition at line 900 of file AbstractCellPopulation.cpp.

◆ KillCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::KillCell ( CellPtr  pCell,
std::string  killerInfo 
)

Helper method to mark a cell as killed and store information about the removal.

Parameters
pCellthe cell
killerInfoadditional information the killer wants output i.e. the type of killer.

Definition at line 880 of file AbstractCellPopulation.cpp.

Referenced by RadialSloughingCellKiller::CheckAndLabelCellsForApoptosisOrDeath().

◆ MoveCellInLocationMap()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::MoveCellInLocationMap ( CellPtr  pCell,
unsigned  old_index,
unsigned  new_index 
)

Change the location index of a cell in mLocationCellMap and mCellLocationMap

Parameters
pCellthe cell to move
old_indexthe old location index
new_indexthe new location index

Definition at line 404 of file AbstractCellPopulation.cpp.

Referenced by CryptShovingCaBasedDivisionRule::CalculateDaughterNodeIndex(), and ShovingCaBasedDivisionRule< SPACE_DIM >::CalculateDaughterNodeIndex().

◆ OpenRoundRobinWritersFilesForAppend()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenRoundRobinWritersFilesForAppend ( OutputFileHandler rOutputFileHandler)
private

Open all files in mCellPopulationWriters and mCellWriters in append mode for writing.

Files in mCellPopulationCountWriters are NOT opened in this call since they are not written in a round-robin fashion.

Parameters
rOutputFileHandlerhandler for the directory in which to open this file.

Definition at line 581 of file AbstractCellPopulation.cpp.

References AbstractCellBasedWriter< ELEMENT_DIM, SPACE_DIM >::OpenOutputFileForAppend().

◆ OpenWritersFiles()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OpenWritersFiles ( OutputFileHandler rOutputFileHandler)
virtual

Open output files (and, if required, write headers) for any writers in the members mCellPopulationCountWriters, mCellPopulationWriters and mCellWriters.

The method also writes the header for the .pvd output file if VTK is available.

Before doing this, the method also creates appropriate writer objects if mOutputResultsForChasteVisualizer is set to true.

This method is public because it is called by the simulation class at the start of the Solve() call.

Parameters
rOutputFileHandlerhandler for the directory in which to open this file.

Reimplemented in CaBasedCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulation< DIM >, MeshBasedCellPopulationWithGhostNodes< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Definition at line 519 of file AbstractCellPopulation.cpp.

Referenced by CaBasedCellPopulation< DIM >::OpenWritersFiles(), ImmersedBoundaryCellPopulation< DIM >::OpenWritersFiles(), PottsBasedCellPopulation< DIM >::OpenWritersFiles(), and VertexBasedCellPopulation< DIM >::OpenWritersFiles().

◆ OutputCellPopulationInfo()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::OutputCellPopulationInfo ( out_stream &  rParamsFile)

Outputs CellPopulation used in the simulation to file and then calls OutputCellPopulationParameters to output all relevant parameters.

Parameters
rParamsFilethe file stream to which the parameters are output

Loop over cells and generate a set of cell-cycle model classes that are present in the population.

Todo:
this currently ignores different parameter regimes (#1453)

Loop over cells and generate a set of SRN model classes that are present in the population.

Todo:
this currently ignores different parameter regimes (#1453)

Definition at line 731 of file AbstractCellPopulation.cpp.

◆ OutputCellPopulationParameters()

◆ RemoveCellUsingLocationIndex()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveCellUsingLocationIndex ( unsigned  index,
CellPtr  pCell 
)
virtual

Removes a cell from a given location index.

Parameters
indexthe location index
pCellthe cell.

Reimplemented in CaBasedCellPopulation< DIM >.

Definition at line 388 of file AbstractCellPopulation.cpp.

References EXCEPTION.

Referenced by CaBasedCellPopulation< DIM >::RemoveCellUsingLocationIndex().

◆ RemoveDeadCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual unsigned AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::RemoveDeadCells ( )
pure virtual

◆ rGetCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::list< CellPtr > & AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetCells ( )

◆ rGetMesh()

◆ serialize()

◆ SetCellAncestorsToLocationIndices()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellAncestorsToLocationIndices ( )

Sets the Ancestor index of all the cells at this time to be the same as their location index, can be used to trace clonal populations.

Definition at line 175 of file AbstractCellPopulation.cpp.

References MAKE_PTR_ARGS.

◆ SetCellUsingLocationIndex()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetCellUsingLocationIndex ( unsigned  index,
CellPtr  pCell 
)

Set the cell corresponding to a given location index.

Assumes there is one cell for each location index and replaces any existing cell attached to the location index. If you wish to attach an additional cell to a location index use AddCellUsingLocaitonIndex as SetCellUsingLocation Index will overwrite cells attached to this index.

Parameters
indexthe location index
pCellthe cell.

Definition at line 367 of file AbstractCellPopulation.cpp.

◆ SetDataOnAllCells()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDataOnAllCells ( const std::string &  rDataName,
double  dataValue 
)

Add an item of cell data to every cell in the population

Parameters
rDataNameis the name associated with the data
dataValueis the value of the data, initially the same for each cell

Definition at line 133 of file AbstractCellPopulation.cpp.

◆ SetDefaultCellMutationStateAndProliferativeTypeOrdering()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetDefaultCellMutationStateAndProliferativeTypeOrdering ( )

Set a default ordering on cell mutation states and cell proliferative types, so that existing tests don't need to specify the old ordering explicitly.

Definition at line 429 of file AbstractCellPopulation.cpp.

Referenced by CellMutationStatesCountWriter< ELEMENT_DIM, SPACE_DIM >::WriteHeader().

◆ SetNode()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetNode ( unsigned  nodeIndex,
ChastePoint< SPACE_DIM > &  rNewLocation 
)
pure virtual

Move the node with a given index to a new point in space.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
nodeIndexthe index of the node to be moved
rNewLocationthe new target location of the node

Implemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulation< DIM >, AbstractOffLatticeCellPopulation< ELEMENT_DIM, SPACE_DIM >, AbstractOffLatticeCellPopulation< DIM >, and AbstractOffLatticeCellPopulation< ELEMENT_DIM, ELEMENT_DIM >.

◆ SetOutputResultsForChasteVisualizer()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SetOutputResultsForChasteVisualizer ( bool  outputResultsForChasteVisualizer)

Set mOutputResultsForChasteVisualizer.

Parameters
outputResultsForChasteVisualizerthe new value of mOutputResultsForChasteVisualizer

Definition at line 820 of file AbstractCellPopulation.cpp.

◆ SimulationSetupHook()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::SimulationSetupHook ( AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM > *  pSimulation)
virtual

Empty hook method to provide the ability to specify some additional property of a cell-based simulation object.

This method is called immediately prior to calling SetupSolve() within the Solve() method in AbstractCellBasedSimulation.

This method can be overridden, for example, to add a T2SwapCellKiller to the simulation object in the case of a VertexBasedCellPopulation. This functionality avoids the need for static or dynamic casts to specific cell population types within simulation methods.

Parameters
pSimulationpointer to a cell-based simulation object

Definition at line 809 of file AbstractCellPopulation.cpp.

◆ StartApoptosisOnCell()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::StartApoptosisOnCell ( CellPtr  pCell,
std::string  killerInfo 
)

Helper method to mark a cell as starting apoptosis and store information about the removal.

Parameters
pCellthe cell
killerInfoadditional information the killer wants output i.e. the type of killer.

Definition at line 890 of file AbstractCellPopulation.cpp.

◆ Update()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Update ( bool  hasHadBirthsOrDeaths = true)
pure virtual

Remove the Nodes (for cell-centre) or VertexElements (for cell-vertex) which have been marked as deleted and update the correspondence with Cells.

As this method is pure virtual, it must be overridden in subclasses.

Parameters
hasHadBirthsOrDeaths- a bool saying whether cell population has had Births Or Deaths

Implemented in CaBasedCellPopulation< DIM >, ImmersedBoundaryCellPopulation< DIM >, MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulation< DIM >, NodeBasedCellPopulation< DIM >, PottsBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Referenced by DeltaNotchTrackingModifier< DIM >::UpdateCellData(), DivisionBiasTrackingModifier< DIM >::UpdateCellData(), VolumeTrackingModifier< DIM >::UpdateCellData(), and CellPopulationAdjacencyMatrixWriter< ELEMENT_DIM, SPACE_DIM >::VisitAnyPopulation().

◆ UpdateCellProcessLocation()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellProcessLocation ( )
virtual

Update the ownership of cell in a parallel cell-based simulation.

Reimplemented in NodeBasedCellPopulation< DIM >.

Definition at line 476 of file AbstractCellPopulation.cpp.

◆ Validate()

◆ WriteDataToVisualizerSetupFile()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteDataToVisualizerSetupFile ( out_stream &  pVizSetupFile)
virtual

Write any data necessary to a visualization setup file. Used by AbstractCellBasedSimulation::WriteVisualizerSetupFile().

Parameters
pVizSetupFilea visualization setup file

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulation< DIM >, and VertexBasedCellPopulation< DIM >.

Definition at line 362 of file AbstractCellPopulation.cpp.

◆ WriteResultsToFiles()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles ( const std::string &  rDirectory)
virtual

Write results from the current cell population state to output files.

Parameters
rDirectorypathname of the output directory, relative to where Chaste output is stored

Reimplemented in MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >, MeshBasedCellPopulation< 1 >, MeshBasedCellPopulation< 2 >, MeshBasedCellPopulation< DIM >, and PottsBasedCellPopulation< DIM >.

Definition at line 596 of file AbstractCellPopulation.cpp.

References PetscTools::BeginRoundRobin().

Referenced by PottsBasedCellPopulation< DIM >::WriteResultsToFiles().

◆ WriteVtkResultsToFile()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
virtual void AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile ( const std::string &  rDirectory)
protectedpure virtual

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 87 of file AbstractCellPopulation.hpp.

Member Data Documentation

◆ mCellLocationMap

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::map<Cell*, unsigned> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellLocationMap
protected

◆ mCellPopulationCountWriters

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<boost::shared_ptr<AbstractCellPopulationCountWriter<ELEMENT_DIM, SPACE_DIM> > > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationCountWriters
protected

◆ mCellPopulationEventWriters

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<boost::shared_ptr<AbstractCellPopulationEventWriter<ELEMENT_DIM, SPACE_DIM> > > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationEventWriters
protected

◆ mCellPopulationWriters

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<boost::shared_ptr<AbstractCellPopulationWriter<ELEMENT_DIM, SPACE_DIM> > > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellPopulationWriters
protected

◆ mCells

◆ mCellWriters

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<boost::shared_ptr<AbstractCellWriter<ELEMENT_DIM, SPACE_DIM> > > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCellWriters
protected

◆ mCentroid

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
c_vector<double, SPACE_DIM> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mCentroid
protected

Population centroid.

Definition at line 142 of file AbstractCellPopulation.hpp.

◆ mDivisionsInformation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<std::string> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mDivisionsInformation
protected

Details of cell divisions, to be used by CellDivisionLocationsWriter The locations are stored until they are cleared by ClearDivisionsInformation().

Definition at line 169 of file AbstractCellPopulation.hpp.

◆ mLocationCellMap

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::map<unsigned, std::set<CellPtr> > AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mLocationCellMap
protected

◆ mOutputResultsForChasteVisualizer

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
bool AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mOutputResultsForChasteVisualizer
protected

Whether to write results to file for visualization using the Chaste java visualizer (defaults to true).

Definition at line 151 of file AbstractCellPopulation.hpp.

Referenced by AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::serialize().

◆ mpCellPropertyRegistry

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
boost::shared_ptr<CellPropertyRegistry> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpCellPropertyRegistry
protected

◆ mpVtkMetaFile

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
out_stream AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mpVtkMetaFile
protected

Meta results file for VTK.

Definition at line 145 of file AbstractCellPopulation.hpp.

◆ mRemovalsInformation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>
std::vector<std::string> AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::mRemovalsInformation
protected

Details of cell removals, to be used by CellRemovalLocationsWriter The locations are stored until they are cleared by ClearRemovalsInformation().

Definition at line 175 of file AbstractCellPopulation.hpp.

◆ mrMesh


The documentation for this class was generated from the following files: