AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > Class Template Reference

#include <AbstractCellBasedSimulationModifier.hpp>

Inheritance diagram for AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >:

Collaboration diagram for AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >:

Public Member Functions
	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)
virtual void	OutputSimulationModifierParameters (out_stream &rParamsFile)=0
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 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

AbstractCellBasedSimulationModifier()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedSimulationModifier

(

)

Default constructor.

Definition at line 39 of file AbstractCellBasedSimulationModifier.cpp.

~AbstractCellBasedSimulationModifier()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::~AbstractCellBasedSimulationModifier ( )

virtual

Destructor.

Definition at line 44 of file AbstractCellBasedSimulationModifier.cpp.

Member Function Documentation

OutputSimulationModifierInfo()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierInfo

(

out_stream &

rParamsFile

)

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.

OutputSimulationModifierParameters()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM>

void AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM >::OutputSimulationModifierParameters ( out_stream &  rParamsFile )

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 AbstractBoxDomainPdeModifier< DIM >, AbstractGrowingDomainPdeModifier< DIM >, AbstractPdeModifier< DIM >, EllipticBoxDomainPdeModifier< DIM >, EllipticGrowingDomainPdeModifier< DIM >, ParabolicBoxDomainPdeModifier< DIM >, ParabolicGrowingDomainPdeModifier< DIM >, AbstractTargetAreaModifier< DIM >, DeltaNotchEdgeInteriorTrackingModifier< DIM >, DeltaNotchEdgeTrackingModifier< DIM >, DeltaNotchTrackingModifier< DIM >, DivisionBiasTrackingModifier< DIM >, ExtrinsicPullModifier< DIM >, ImmersedBoundarySimulationModifier< DIM >, ImmersedBoundarySvgWriter< DIM >, NormallyDistributedTargetAreaModifier< DIM >, SimpleTargetAreaModifier< DIM >, TargetAreaLinearGrowthModifier< DIM >, and VolumeTrackingModifier< DIM >.

Definition at line 58 of file AbstractCellBasedSimulationModifier.cpp.

Referenced by AbstractPdeModifier< DIM >::OutputSimulationModifierParameters(), AbstractTargetAreaModifier< DIM >::OutputSimulationModifierParameters(), DeltaNotchEdgeInteriorTrackingModifier< DIM >::OutputSimulationModifierParameters(), DeltaNotchEdgeTrackingModifier< DIM >::OutputSimulationModifierParameters(), DeltaNotchTrackingModifier< DIM >::OutputSimulationModifierParameters(), DivisionBiasTrackingModifier< DIM >::OutputSimulationModifierParameters(), ExtrinsicPullModifier< DIM >::OutputSimulationModifierParameters(), ImmersedBoundarySimulationModifier< DIM >::OutputSimulationModifierParameters(), ImmersedBoundarySvgWriter< DIM >::OutputSimulationModifierParameters(), and VolumeTrackingModifier< DIM >::OutputSimulationModifierParameters().

serialize()

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  )

inlineprivate

Serialize the object.

Parameters

archive	the archive
version	the current version of this class

Definition at line 59 of file AbstractCellBasedSimulationModifier.hpp.

SetupSolve()

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  )

pure virtual

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

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

Parameters

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

UpdateAtEndOfOutputTimeStep()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

inlinevirtual

Specify what to do in the simulation at the end of each output timestep, after UpdateAtEndOfTimeStep() has been called.

Parameters

rCellPopulation

reference to the cell population

Definition at line 91 of file AbstractCellBasedSimulationModifier.hpp.

UpdateAtEndOfSolve()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

inlinevirtual

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

Parameters

rCellPopulation

reference to the cell population

Definition at line 111 of file AbstractCellBasedSimulationModifier.hpp.

UpdateAtEndOfTimeStep()

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

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

pure virtual

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

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

Parameters

rCellPopulation

reference to the cell population

Friends And Related Symbol Documentation

boost::serialization::access

template<unsigned ELEMENT_DIM, unsigned SPACE_DIM = ELEMENT_DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 51 of file AbstractCellBasedSimulationModifier.hpp.

---

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

• cell_based/src/simulation/modifiers/AbstractCellBasedSimulationModifier.hpp
• cell_based/src/simulation/modifiers/AbstractCellBasedSimulationModifier.cpp