AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractCellBasedSimulationModifier.hpp>

Collaboration diagram for AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	AbstractCellBasedSimulationModifier ()
virtual	~AbstractCellBasedSimulationModifier ()
virtual void	UpdateAtEndOfTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
virtual void	UpdateAtEndOfOutputTimeStep (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
virtual void	SetupSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, std::string outputDirectory)
virtual void	UpdateAtEndOfSolve (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation)
void	OutputSimulationModifierInfo (out_stream &rParamsFile)
virtual void	OutputSimulationModifierParameters (out_stream &rParamsFile)=0
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

Detailed Description

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>
class AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >

An abstract modifier class (to implement setup, update and finalise methods), for use in cell-based simulations.

Definition at line 48 of file AbstractCellBasedSimulationModifier.hpp.

Constructor & Destructor Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedSimulationModifier ( ) [inline]

Default constructor.

Definition at line 39 of file AbstractCellBasedSimulationModifier.cpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::~AbstractCellBasedSimulationModifier ( ) [inline, virtual]

Destructor.

Definition at line 44 of file AbstractCellBasedSimulationModifier.cpp.

Member Function Documentation

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierInfo ( out_stream & rParamsFile ) [inline]

Output the modifier type used in the simulation to file and then call OutputSimulationModifierParameters() to output all relevant parameters.

Parameters:

rParamsFile

the file stream to which the parameters are output

Definition at line 49 of file AbstractCellBasedSimulationModifier.cpp.

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

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters ( out_stream & rParamsFile ) [inline, pure virtual]

Output any simulation modifier parameters to file.

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

Parameters:

rParamsFile

the file stream to which the parameters are output

Implemented in AbstractTargetAreaModifier< DIM >, DeltaNotchTrackingModifier< DIM >, FarhadifarTypeModifier< DIM >, SimpleTargetAreaModifier< DIM >, and VolumeTrackingModifier< DIM >.

Definition at line 58 of file AbstractCellBasedSimulationModifier.cpp.

Referenced by AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierInfo().

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

template<class Archive >

void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)			`[inline, private]`

Serialize the object.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented in AbstractTargetAreaModifier< DIM >, DeltaNotchTrackingModifier< DIM >, FarhadifarTypeModifier< DIM >, SimpleTargetAreaModifier< DIM >, and VolumeTrackingModifier< DIM >.

Definition at line 59 of file AbstractCellBasedSimulationModifier.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::SetupSolve	(	AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &	rCellPopulation,
		std::string	outputDirectory
	)			`[inline, virtual]`

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 99 of file AbstractCellBasedSimulationModifier.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::UpdateAtEndOfOutputTimeStep ( AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > & rCellPopulation ) [inline, virtual]

Specify what to do in the simulation at the end of each output timestep.

Parameters:

rCellPopulation

reference to the cell population

Definition at line 89 of file AbstractCellBasedSimulationModifier.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::UpdateAtEndOfSolve ( AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > & rCellPopulation ) [inline, virtual]

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

Parameters:

rCellPopulation

reference to the cell population

Definition at line 108 of file AbstractCellBasedSimulationModifier.hpp.

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

virtual void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::UpdateAtEndOfTimeStep ( AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > & rCellPopulation ) [inline, virtual]