VolumeTrackingModifier< DIM > Class Template Reference

#include <VolumeTrackingModifier.hpp>

Inherits AbstractCellBasedSimulationModifier< DIM, DIM >.

Collaboration diagram for VolumeTrackingModifier< DIM >:

Public Member Functions
	VolumeTrackingModifier ()
virtual	~VolumeTrackingModifier ()
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)
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 VolumeTrackingModifier< DIM >

A modifier class which at each simulation time step calculates the volume of each cell and stores it in in the CellData property as "volume". To be used in conjunction with contact inhibition cell cycle models.

Definition at line 50 of file VolumeTrackingModifier.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

VolumeTrackingModifier< DIM >::VolumeTrackingModifier ( ) [inline]

Default constructor.

Definition at line 40 of file VolumeTrackingModifier.cpp.

template<unsigned DIM>

VolumeTrackingModifier< DIM >::~VolumeTrackingModifier ( ) [inline, virtual]

Destructor.

Definition at line 46 of file VolumeTrackingModifier.cpp.

Member Function Documentation

template<unsigned DIM>

void VolumeTrackingModifier< 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 >.

Definition at line 100 of file VolumeTrackingModifier.cpp.

template<unsigned DIM>

template<class Archive >

void VolumeTrackingModifier< 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 >.

Definition at line 62 of file VolumeTrackingModifier.hpp.

template<unsigned DIM>

void VolumeTrackingModifier< 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 VolumeTrackingModifier.cpp.

References VolumeTrackingModifier< DIM >::UpdateCellData().

template<unsigned DIM>

void VolumeTrackingModifier< 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 VolumeTrackingModifier.cpp.

References VolumeTrackingModifier< DIM >::UpdateCellData().

template<unsigned DIM>

void VolumeTrackingModifier< DIM >::UpdateCellData ( AbstractCellPopulation< DIM, DIM > & rCellPopulation ) [inline]

Helper method to compute the volume of each cell in the population and store these in the CellData.

Parameters:

rCellPopulation

reference to the cell population

This hack is needed because in the case of a MeshBasedCellPopulation in which multiple cell divisions have occurred over one time step, the Voronoi tessellation (while existing) is out-of-date. Thus, if we did not regenerate the Voronoi tessellation here, an assertion may trip as we try to access a Voronoi element whose index exceeds the number of elements in the out-of-date tessellation.