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

#include <DeltaNotchEdgeInteriorTrackingModifier.hpp>

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

Public Member Functions

 DeltaNotchEdgeInteriorTrackingModifier ()
 
virtual ~DeltaNotchEdgeInteriorTrackingModifier ()
 
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 DeltaNotchEdgeInteriorTrackingModifier< 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 DeltaNotchEdgeInteriorTrackingModifier.hpp.

Constructor & Destructor Documentation

◆ DeltaNotchEdgeInteriorTrackingModifier()

◆ ~DeltaNotchEdgeInteriorTrackingModifier()

Member Function Documentation

◆ OutputSimulationModifierParameters()

template<unsigned DIM>
void DeltaNotchEdgeInteriorTrackingModifier< 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 157 of file DeltaNotchEdgeInteriorTrackingModifier.cpp.

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

◆ serialize()

template<unsigned DIM>
template<class Archive >
void DeltaNotchEdgeInteriorTrackingModifier< 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 63 of file DeltaNotchEdgeInteriorTrackingModifier.hpp.

◆ SetupSolve()

template<unsigned DIM>
void DeltaNotchEdgeInteriorTrackingModifier< 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 59 of file DeltaNotchEdgeInteriorTrackingModifier.cpp.

◆ UpdateAtEndOfTimeStep()

template<unsigned DIM>
void DeltaNotchEdgeInteriorTrackingModifier< 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 DeltaNotchEdgeInteriorTrackingModifier.cpp.

◆ UpdateCellData()

template<unsigned DIM>
void DeltaNotchEdgeInteriorTrackingModifier< 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 69 of file DeltaNotchEdgeInteriorTrackingModifier.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 54 of file DeltaNotchEdgeInteriorTrackingModifier.hpp.


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