#include <AbstractTargetAreaModifier.hpp>

Inheritance diagram for AbstractTargetAreaModifier< DIM >:

Collaboration diagram for AbstractTargetAreaModifier< DIM >:

Public Member Functions
	AbstractTargetAreaModifier ()

virtual	~AbstractTargetAreaModifier ()

virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

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

double	GetReferenceTargetArea ()

void	SetReferenceTargetArea (double referenceTargetArea)

void	UpdateTargetAreas (AbstractCellPopulation< DIM, DIM > &rCellPopulation)

virtual void	UpdateTargetAreaOfCell (const CellPtr pCell)=0

virtual 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

Protected Attributes
double	mReferenceTargetArea

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 AbstractTargetAreaModifier< DIM >

A modifier class in which the target area property of each cell is updated. It is used to implement growth in vertex-based simulations.

Definition at line 48 of file AbstractTargetAreaModifier.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractTargetAreaModifier< DIM >::AbstractTargetAreaModifier ( )

Default constructor.

Definition at line 39 of file AbstractTargetAreaModifier.cpp.

template<unsigned DIM>

AbstractTargetAreaModifier< DIM >::~AbstractTargetAreaModifier ( )

virtual

Destructor.

Definition at line 46 of file AbstractTargetAreaModifier.cpp.

Member Function Documentation

template<unsigned DIM>

double AbstractTargetAreaModifier< DIM >::GetReferenceTargetArea ( )

Get the reference target area.

Returns: the reference target area.

Definition at line 79 of file AbstractTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::mReferenceTargetArea.

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile )

virtual

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

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellBasedSimulationModifier< DIM, DIM >.

Reimplemented in TargetAreaLinearGrowthModifier< DIM >, and SimpleTargetAreaModifier< DIM >.

Definition at line 92 of file AbstractTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::mReferenceTargetArea, and AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters().

Referenced by SimpleTargetAreaModifier< DIM >::OutputSimulationModifierParameters(), and TargetAreaLinearGrowthModifier< DIM >::OutputSimulationModifierParameters().

template<unsigned DIM>

template<class Archive >

void AbstractTargetAreaModifier< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

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

Parameters

archive	The boost archive.
version	The current version of this class.

Definition at line 60 of file AbstractTargetAreaModifier.hpp.

References AbstractTargetAreaModifier< DIM >::mReferenceTargetArea.

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::SetReferenceTargetArea ( double referenceTargetArea )

Set the reference target area. The standard value is 1.0.

Parameters

referenceTargetArea the new value of mReferenceTargetArea

Definition at line 85 of file AbstractTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::mReferenceTargetArea.

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::SetupSolve	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		std::string	outputDirectory
	)

virtual

Overridden SetupSolve() method.

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

Parameters

rCellPopulation	reference to the cell population
outputDirectory	the output directory, relative to where Chaste output is stored

Definition at line 57 of file AbstractTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::UpdateTargetAreas().

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::UpdateAtEndOfTimeStep ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

virtual

Overridden UpdateAtEndOfTimeStep() method.

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

Parameters

rCellPopulation reference to the cell population

Definition at line 51 of file AbstractTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::UpdateTargetAreas().

template<unsigned DIM>

virtual void AbstractTargetAreaModifier< DIM >::UpdateTargetAreaOfCell ( const CellPtr pCell )

pure virtual

Helper method to update the target area property of an individual cell.

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

Parameters

pCell pointer to the cell

Implemented in TargetAreaLinearGrowthModifier< DIM >, and SimpleTargetAreaModifier< DIM >.

Referenced by AbstractTargetAreaModifier< DIM >::UpdateTargetAreas().

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::UpdateTargetAreas ( AbstractCellPopulation< DIM, DIM > & rCellPopulation )

Helper method to update the target area property of all cells in the population.

Parameters

rCellPopulation reference to the cell population

Definition at line 67 of file AbstractTargetAreaModifier.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::rGetCells(), and AbstractTargetAreaModifier< DIM >::UpdateTargetAreaOfCell().

Referenced by AbstractTargetAreaModifier< DIM >::SetupSolve(), and AbstractTargetAreaModifier< DIM >::UpdateAtEndOfTimeStep().

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 51 of file AbstractTargetAreaModifier.hpp.

Member Data Documentation

template<unsigned DIM>

double AbstractTargetAreaModifier< DIM >::mReferenceTargetArea

protected

A reference area. Usually this is the target area of mature cells in the population.

Definition at line 71 of file AbstractTargetAreaModifier.hpp.

Referenced by AbstractTargetAreaModifier< DIM >::GetReferenceTargetArea(), AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters(), AbstractTargetAreaModifier< DIM >::serialize(), AbstractTargetAreaModifier< DIM >::SetReferenceTargetArea(), SimpleTargetAreaModifier< DIM >::UpdateTargetAreaOfCell(), and TargetAreaLinearGrowthModifier< DIM >::UpdateTargetAreaOfCell().

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

cell_based/src/simulation/modifiers/AbstractTargetAreaModifier.hpp
cell_based/src/simulation/modifiers/AbstractTargetAreaModifier.cpp

Public Member Functions

Protected Attributes

Private Member Functions

Friends

Detailed Description

template<unsigned DIM> class AbstractTargetAreaModifier< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

template<unsigned DIM>
class AbstractTargetAreaModifier< DIM >