#include <CryptSimulation2d.hpp>

Inheritance diagram for CryptSimulation2d:

Collaboration diagram for CryptSimulation2d:

Public Member Functions
	CryptSimulation2d (AbstractCellPopulation< 2 > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

virtual	~CryptSimulation2d ()

void	UseJiggledBottomCells ()

void	SetBottomCellAncestors ()

void	OutputSimulationParameters (out_stream &rParamsFile)

Public Member Functions inherited from OffLatticeSimulation< 2 >
	OffLatticeSimulation (AbstractCellPopulation< ELEMENT_DIM, ELEMENT_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

void	AddForce (boost::shared_ptr< AbstractForce< ELEMENT_DIM, ELEMENT_DIM > > pForce)

void	RemoveAllForces ()

void	AddCellPopulationBoundaryCondition (boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, ELEMENT_DIM > > pBoundaryCondition)

void	RemoveAllCellPopulationBoundaryConditions ()

void	SetNumericalMethod (boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, ELEMENT_DIM > > pNumericalMethod)

const boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, ELEMENT_DIM > >	GetNumericalMethod () const

void	OutputAdditionalSimulationSetup (out_stream &rParamsFile)

const std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, ELEMENT_DIM > > > &	rGetForceCollection () const

Public Member Functions inherited from AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >
	AbstractCellBasedSimulation (AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

virtual	~AbstractCellBasedSimulation ()

std::vector< double >	GetNodeLocation (const unsigned &rNodeIndex)

double	GetDt ()

unsigned	GetNumBirths ()

unsigned	GetNumDeaths ()

std::string	GetOutputDirectory ()

void	SetDt (double dt)

void	SetEndTime (double endTime)

void	SetOutputDirectory (std::string outputDirectory)

void	SetSamplingTimestepMultiple (unsigned samplingTimestepMultiple)

void	SetNoBirth (bool noBirth)

void	SetUpdateCellPopulationRule (bool updateCellPopulation)

bool	GetUpdateCellPopulationRule ()

void	AddCellKiller (boost::shared_ptr< AbstractCellKiller< SPACE_DIM > > pCellKiller)

void	RemoveAllCellKillers ()

void	AddSimulationModifier (boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > pSimulationModifier)

std::vector< boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > > *	GetSimulationModifiers ()

void	Solve ()

AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &	rGetCellPopulation ()

const AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &	rGetCellPopulation () const

bool	GetOutputDivisionLocations ()

void	SetOutputDivisionLocations (bool outputDivisionLocations)

bool	GetOutputCellVelocities ()

void	SetOutputCellVelocities (bool outputCellVelocities)

Public Member Functions inherited from Identifiable
virtual	~Identifiable ()

std::string	GetIdentifier () const

Protected Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)

void	SetupSolve ()

Protected Member Functions inherited from OffLatticeSimulation< 2 >
virtual void	UpdateCellLocationsAndTopology ()

void	RevertToOldLocations (std::map< Node< ELEMENT_DIM > *, c_vector< double, ELEMENT_DIM > > oldNodeLoctions)

void	ApplyBoundaries (std::map< Node< ELEMENT_DIM > *, c_vector< double, ELEMENT_DIM > > oldNodeLoctions)

virtual void	WriteVisualizerSetupFile ()

Protected Member Functions inherited from AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >
virtual unsigned	DoCellBirth ()

unsigned	DoCellRemoval ()

virtual bool	StoppingEventHasOccurred ()

virtual void	UpdateCellPopulation ()

void	OutputSimulationSetup ()

Protected Attributes
bool	mUsingMeshBasedCellPopulation

Protected Attributes inherited from OffLatticeSimulation< 2 >
std::vector< boost::shared_ptr< AbstractForce< ELEMENT_DIM, ELEMENT_DIM > > >	mForceCollection

std::vector< boost::shared_ptr< AbstractCellPopulationBoundaryCondition< ELEMENT_DIM, ELEMENT_DIM > > >	mBoundaryConditions

boost::shared_ptr< AbstractNumericalMethod< ELEMENT_DIM, ELEMENT_DIM > >	mpNumericalMethod

Protected Attributes inherited from AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >
double	mDt

double	mEndTime

AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM > &	mrCellPopulation

bool	mDeleteCellPopulationInDestructor

bool	mInitialiseCells

bool	mNoBirth

bool	mUpdateCellPopulation

std::string	mOutputDirectory

std::string	mSimulationOutputDirectory

out_stream	mpVizSetupFile

unsigned	mNumBirths

unsigned	mNumDeaths

bool	mOutputDivisionLocations

out_stream	mpDivisionLocationFile

bool	mOutputCellVelocities

out_stream	mpCellVelocitiesFile

std::vector< boost::shared_ptr< AbstractCellKiller< SPACE_DIM > > >	mCellKillers

std::vector< boost::shared_ptr< AbstractCellBasedSimulationModifier< ELEMENT_DIM, SPACE_DIM > > >	mSimulationModifiers

unsigned	mSamplingTimestepMultiple

Friends
class	TestCryptSimulation2dWithMeshBasedCellPopulation

class	TestCryptSimulation2dWithVertexBasedCellPopulation

class	boost::serialization::access

Detailed Description

A 2D crypt simulation object. For more details on the crypt geometry, see the papers by van Leeuwen et al (2009) [doi:10.1111/j.1365-2184.2009.00627.x] and Osborne et al (2010) [doi:10.1098/rsta.2010.0173].

Definition at line 54 of file CryptSimulation2d.hpp.

Constructor & Destructor Documentation

CryptSimulation2d::CryptSimulation2d	(	AbstractCellPopulation< 2 > &	rCellPopulation,
		bool	deleteCellPopulationInDestructor = `false`,
		bool	initialiseCells = `true`
	)

Constructor.

Parameters

rCellPopulation	A cell population object
deleteCellPopulationInDestructor	Whether to delete the cell population on destruction to free up memory (defaults to false)
initialiseCells	whether to initialise cells (defaults to true, set to false when loading from an archive)

Definition at line 46 of file CryptSimulation2d.cpp.

References OffLatticeSimulation< 2 >::AddCellPopulationBoundaryCondition(), EXCEPTION, MAKE_PTR, MAKE_PTR_ARGS, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mDeleteCellPopulationInDestructor, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and mUsingMeshBasedCellPopulation.

CryptSimulation2d::~CryptSimulation2d ( )

virtual

Destructor.

This frees the CryptSimulationBoundaryCondition.

Definition at line 85 of file CryptSimulation2d.cpp.

Member Function Documentation

void CryptSimulation2d::OutputSimulationParameters ( out_stream & rParamsFile )

virtual

Outputs simulation 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

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 146 of file CryptSimulation2d.cpp.

References CHASTE_CLASS_EXPORT, OffLatticeSimulation< 2 >::mBoundaryConditions, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationParameters().

template<class Archive >

void CryptSimulation2d::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprotected

Archive the simulation and member variable.

Parameters

archive	the archive
version	the current version of this class

Definition at line 71 of file CryptSimulation2d.hpp.

References SerializableSingleton< SINGLETON_CLASS >::GetSerializationWrapper(), and WntConcentration< DIM >::Instance().

void CryptSimulation2d::SetBottomCellAncestors ( )

Sets the Ancestor index of all the cells at the bottom in order, can be used to trace clonal populations.

Definition at line 117 of file CryptSimulation2d.cpp.

References MAKE_PTR_ARGS, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and mUsingMeshBasedCellPopulation.

void CryptSimulation2d::SetupSolve ( )

protectedvirtual

Overridden SetupSolve() method.

Write initial beta catenin results to file if required.

Reimplemented from OffLatticeSimulation< 2 >.

Definition at line 89 of file CryptSimulation2d.cpp.

References AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mpVizSetupFile, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::SetupSolve().

void CryptSimulation2d::UseJiggledBottomCells ( )

Set method for mUseJiggledBottomCells.

Definition at line 111 of file CryptSimulation2d.cpp.

References OffLatticeSimulation< 2 >::mBoundaryConditions.

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 63 of file CryptSimulation2d.hpp.

Member Data Documentation

bool CryptSimulation2d::mUsingMeshBasedCellPopulation

protected

Helper member that stores whether we are using a MeshBasedCellPopulationWithGhostNodes (if not, then we are assumed to be using a VertexBasedCellPopulation).

Definition at line 83 of file CryptSimulation2d.hpp.

Referenced by CryptSimulation2d(), and SetBottomCellAncestors().

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

crypt/src/simulation/CryptSimulation2d.hpp
crypt/src/simulation/CryptSimulation2d.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation