Chaste Commit::baa90ac2819b962188b7562f2326be23c47859a7
DeltaNotchEdgeTrackingModifier< DIM > Class Template Reference

#include <DeltaNotchEdgeTrackingModifier.hpp>

+ Inheritance diagram for DeltaNotchEdgeTrackingModifier< DIM >:
+ Collaboration diagram for DeltaNotchEdgeTrackingModifier< DIM >:

Public Member Functions

 DeltaNotchEdgeTrackingModifier ()
 
virtual ~DeltaNotchEdgeTrackingModifier ()
 
virtual void UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation)
 
virtual void SetupSolve (AbstractCellPopulation< DIM, DIM > &rCellPopulation, std::string outputDirectory)
 
void UpdateCellData (AbstractCellPopulation< DIM, DIM > &rCellPopulation)
 
void OutputSimulationModifierParameters (out_stream &rParamsFile)
 
- Public Member Functions inherited from AbstractCellBasedSimulationModifier< DIM, DIM >
 AbstractCellBasedSimulationModifier ()
 
virtual ~AbstractCellBasedSimulationModifier ()
 
virtual void UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)=0
 
virtual void UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
 
virtual void SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)=0
 
virtual void UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
 
void OutputSimulationModifierInfo (out_stream &rParamsFile)
 
- Public Member Functions inherited from Identifiable
virtual ~Identifiable ()
 
std::string GetIdentifier () const
 

Private Member Functions

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

Friends

class boost::serialization::access
 

Detailed Description

template<unsigned DIM>
class DeltaNotchEdgeTrackingModifier< DIM >

A modifier class in which the mean levels of Delta in neighbouring cells are computed and stored in CellData. To be used in conjunction with Delta Notch cell cycle models.

Definition at line 51 of file DeltaNotchEdgeTrackingModifier.hpp.

Constructor & Destructor Documentation

◆ DeltaNotchEdgeTrackingModifier()

Default constructor.

Definition at line 42 of file DeltaNotchEdgeTrackingModifier.cpp.

◆ ~DeltaNotchEdgeTrackingModifier()

Destructor.

Definition at line 48 of file DeltaNotchEdgeTrackingModifier.cpp.

Member Function Documentation

◆ OutputSimulationModifierParameters()

template<unsigned DIM>
void DeltaNotchEdgeTrackingModifier< DIM >::OutputSimulationModifierParameters ( out_stream &  rParamsFile)
virtual

Overridden OutputSimulationModifierParameters() method. Output any simulation modifier parameters to file.

Parameters
rParamsFilethe file stream to which the parameters are output

Implements AbstractCellBasedSimulationModifier< DIM, DIM >.

Definition at line 134 of file DeltaNotchEdgeTrackingModifier.cpp.

References AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters().

◆ serialize()

template<unsigned DIM>
template<class Archive >
void DeltaNotchEdgeTrackingModifier< DIM >::serialize ( Archive &  archive,
const unsigned int  version 
)
inlineprivate

Boost Serialization method for archiving/checkpointing. Archives the object and its member variables.

Parameters
archiveThe boost archive.
versionThe current version of this class.

Definition at line 64 of file DeltaNotchEdgeTrackingModifier.hpp.

◆ SetupSolve()

template<unsigned DIM>
void DeltaNotchEdgeTrackingModifier< DIM >::SetupSolve ( AbstractCellPopulation< DIM, DIM > &  rCellPopulation,
std::string  outputDirectory 
)
virtual

Overridden SetupSolve() method.

Specifies what to do in the simulation before the start of the time loop.

Parameters
rCellPopulationreference to the cell population
outputDirectorythe output directory, relative to where Chaste output is stored

Definition at line 60 of file DeltaNotchEdgeTrackingModifier.cpp.

◆ UpdateAtEndOfTimeStep()

template<unsigned DIM>
void DeltaNotchEdgeTrackingModifier< DIM >::UpdateAtEndOfTimeStep ( AbstractCellPopulation< DIM, DIM > &  rCellPopulation)
virtual

Overridden UpdateAtEndOfTimeStep() method.

Specifies what to do in the simulation at the end of each time step.

Parameters
rCellPopulationreference to the cell population

Definition at line 53 of file DeltaNotchEdgeTrackingModifier.cpp.

◆ UpdateCellData()

template<unsigned DIM>
void DeltaNotchEdgeTrackingModifier< DIM >::UpdateCellData ( AbstractCellPopulation< DIM, DIM > &  rCellPopulation)

Helper method to compute the mean level of Delta in each cell's neighbours and store these in the CellData.

Note: If using a CaBasedCellPopulation, we assume a Moore neighbourhood and unit carrying capacity. If a cell has no neighbours (such as an isolated cell in a CaBasedCellPopulation), we store the value -1 in the CellData.

Parameters
rCellPopulationreference to the cell population

Definition at line 70 of file DeltaNotchEdgeTrackingModifier.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::End(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetCellUsingLocationIndex(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetNeighbouringEdgeIndices(), and CellSrnModel::GetNumEdgeSrn().

Friends And Related Symbol Documentation

◆ boost::serialization::access

template<unsigned DIM>
friend class boost::serialization::access
friend

Needed for serialization.

Definition at line 55 of file DeltaNotchEdgeTrackingModifier.hpp.


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