#include <CryptSimulation1d.hpp>

Inheritance diagram for CryptSimulation1d:

Collaboration diagram for CryptSimulation1d:

Public Member Functions
	CryptSimulation1d (AbstractCellPopulation< 1 > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)

virtual	~CryptSimulation1d ()

void	OutputSimulationParameters (out_stream &rParamsFile)

Public Member Functions inherited from OffLatticeSimulation< 1 >
	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	OutputAdditionalSimulationSetup (out_stream &rParamsFile)

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 ()

void	SetCellBasedPdeHandler (CellBasedPdeHandler< SPACE_DIM > *pCellBasedPdeHandler)

CellBasedPdeHandler< SPACE_DIM > *	GetCellBasedPdeHandler ()

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

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

c_vector< double, 1 >	CalculateCellDivisionVector (CellPtr pParentCell)

Private Attributes
MeshBasedCellPopulation< 1 > *	mpStaticCastCellPopulation

Friends
class	TestCryptSimulation1d

class	boost::serialization::access

Additional Inherited Members
Protected Member Functions inherited from OffLatticeSimulation< 1 >
virtual void	UpdateCellLocationsAndTopology ()

virtual void	UpdateNodePositions ()

virtual void	SetupSolve ()

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 inherited from OffLatticeSimulation< 1 >
std::vector< boost::shared_ptr < AbstractForce< ELEMENT_DIM, ELEMENT_DIM > > >	mForceCollection

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

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

CellBasedPdeHandler< SPACE_DIM > *	mpCellBasedPdeHandler

Detailed Description

A 1D crypt simulation object. The model is a simplified version of a 2D crypt model developed by Meineke et al (doi:10.1046/j.0960-7722.2001.00216.x).

Definition at line 54 of file CryptSimulation1d.hpp.

Constructor & Destructor Documentation

CryptSimulation1d::CryptSimulation1d	(	AbstractCellPopulation< 1 > &	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 40 of file CryptSimulation1d.cpp.

References OffLatticeSimulation< 1 >::AddCellPopulationBoundaryCondition(), MAKE_PTR_ARGS, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mDeleteCellPopulationInDestructor, mpStaticCastCellPopulation, and AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation.

CryptSimulation1d::~CryptSimulation1d ( )

virtual

Destructor.

This frees the CryptSimulationBoundaryCondition.

Definition at line 57 of file CryptSimulation1d.cpp.

Member Function Documentation

c_vector< double, 1 > CryptSimulation1d::CalculateCellDivisionVector ( CellPtr pParentCell )

privatevirtual

Calculates the new locations of a dividing cell's cell centres. Moves the dividing node a bit and returns co-ordinates for the new node. It does this by picking a random direction (0->2PI) and placing the parent and daughter in opposing directions on this axis.

Parameters

pParentCell the parent cell

Returns: daughter_coords the coordinates for the daughter cell.

Reimplemented from OffLatticeSimulation< 1 >.

Definition at line 61 of file CryptSimulation1d.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationIndexUsingCell(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetLocationOfCellCentre(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::GetMeinekeDivisionSeparation(), RandomNumberGenerator::Instance(), mpStaticCastCellPopulation, AbstractCellBasedSimulation< ELEMENT_DIM, ELEMENT_DIM >::mrCellPopulation, and RandomNumberGenerator::ranf().

void CryptSimulation1d::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< 1 >.

Definition at line 115 of file CryptSimulation1d.cpp.

References OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::OutputSimulationParameters().

template<class Archive >

void CryptSimulation1d::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Archive the simulation and member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 70 of file CryptSimulation1d.hpp.

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

Friends And Related Function Documentation

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 62 of file CryptSimulation1d.hpp.

Member Data Documentation

MeshBasedCellPopulation<1>* CryptSimulation1d::mpStaticCastCellPopulation

private

Helper member that is a static cast of the cell population.

Definition at line 79 of file CryptSimulation1d.hpp.

Referenced by CalculateCellDivisionVector(), and CryptSimulation1d().

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

crypt/src/simulation/CryptSimulation1d.hpp
crypt/src/simulation/CryptSimulation1d.cpp

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation