AbstractTargetAreaModifier< DIM > Class Template Reference

#include <AbstractTargetAreaModifier.hpp>

Inherits AbstractCellBasedSimulationModifier< DIM, DIM >.

Inherited by FarhadifarTypeModifier< DIM >, and SimpleTargetAreaModifier< DIM >.

Collaboration diagram for AbstractTargetAreaModifier< DIM >:

[legend]

List of all members.

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)
Protected Attributes
double	mReferenceTargetArea
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

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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 49 of file AbstractTargetAreaModifier.hpp.

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Constructor & Destructor Documentation

template<unsigned DIM>

AbstractTargetAreaModifier< DIM >::AbstractTargetAreaModifier

(

)

[inline]

Default constructor.

Definition at line 39 of file AbstractTargetAreaModifier.cpp.

template<unsigned DIM>

AbstractTargetAreaModifier< DIM >::~AbstractTargetAreaModifier

(

)

[inline, virtual]

Destructor.

Definition at line 46 of file AbstractTargetAreaModifier.cpp.

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Member Function Documentation

template<unsigned DIM>

double AbstractTargetAreaModifier< DIM >::GetReferenceTargetArea

(

)

[inline]

Get the reference target area.

Returns:

the reference target area.

Definition at line 86 of file AbstractTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::mReferenceTargetArea.

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters

(

out_stream &

rParamsFile

)

[inline, 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 FarhadifarTypeModifier< DIM >, and SimpleTargetAreaModifier< DIM >.

Definition at line 99 of file AbstractTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::mReferenceTargetArea.

template<unsigned DIM>

template<class Archive >

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

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.

Reimplemented from AbstractCellBasedSimulationModifier< DIM, DIM >.

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

Definition at line 61 of file AbstractTargetAreaModifier.hpp.

References AbstractTargetAreaModifier< DIM >::mReferenceTargetArea.

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::SetReferenceTargetArea

(

double

referenceTargetArea

)

[inline]

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

Parameters:

referenceTargetArea

the new value of mReferenceTargetArea

Definition at line 92 of file AbstractTargetAreaModifier.cpp.

References AbstractTargetAreaModifier< DIM >::mReferenceTargetArea.

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::SetupSolve	(	AbstractCellPopulation< DIM, DIM > &	rCellPopulation,
		std::string	outputDirectory
	)			[inline, 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 EXCEPTION, and AbstractTargetAreaModifier< DIM >::UpdateTargetAreas().

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::UpdateAtEndOfTimeStep

(

AbstractCellPopulation< DIM, DIM > &

rCellPopulation

)

[inline, 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. This method has to be overwritten in child classes.

Parameters:

pCell

pointer to the cell

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

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

template<unsigned DIM>

void AbstractTargetAreaModifier< DIM >::UpdateTargetAreas

(

AbstractCellPopulation< DIM, DIM > &

rCellPopulation

)

[inline]

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

Parameters:

rCellPopulation

reference to the cell population

Definition at line 72 of file AbstractTargetAreaModifier.cpp.

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

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

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Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from AbstractCellBasedSimulationModifier< DIM, DIM >.

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

Definition at line 52 of file AbstractTargetAreaModifier.hpp.

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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 72 of file AbstractTargetAreaModifier.hpp.

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

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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