#include <OnLatticeSimulation.hpp>

Inheritance diagram for OnLatticeSimulation< DIM >:

Collaboration diagram for OnLatticeSimulation< DIM >:

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

void	AddCaUpdateRule (boost::shared_ptr< AbstractCaUpdateRule< DIM > > pUpdateRule)

void	RemoveAllCaUpdateRules ()

void	AddCaSwitchingUpdateRule (boost::shared_ptr< AbstractCaSwitchingUpdateRule< DIM > > pUpdateRule)

void	RemoveAllCaSwitchingUpdateRules ()

void	AddPottsUpdateRule (boost::shared_ptr< AbstractPottsUpdateRule< DIM > > pUpdateRule)

void	RemoveAllPottsUpdateRules ()

void	OutputAdditionalSimulationSetup (out_stream &rParamsFile)

void	OutputSimulationParameters (out_stream &rParamsFile)

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

virtual	~AbstractCellBasedSimulation ()

void	SetCellBasedPdeHandler (CellBasedPdeHandler< ELEMENT_DIM > *pCellBasedPdeHandler)

CellBasedPdeHandler < ELEMENT_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< ELEMENT_DIM > > pCellKiller)

void	RemoveAllCellKillers ()

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

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

void	Solve ()

AbstractCellPopulation < ELEMENT_DIM, ELEMENT_DIM > &	rGetCellPopulation ()

const AbstractCellPopulation < ELEMENT_DIM, ELEMENT_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
void	UpdateCellPopulation ()

void	UpdateCellLocationsAndTopology ()

virtual c_vector< double, DIM >	CalculateCellDivisionVector (CellPtr pParentCell)

virtual void	WriteVisualizerSetupFile ()

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

unsigned	DoCellRemoval ()

virtual void	SetupSolve ()

virtual bool	StoppingEventHasOccurred ()

void	OutputSimulationSetup ()

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

Friends
class	boost::serialization::access

Additional Inherited Members
Protected Attributes inherited from AbstractCellBasedSimulation< DIM >
double	mDt

double	mEndTime

AbstractCellPopulation < ELEMENT_DIM, ELEMENT_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 < ELEMENT_DIM > > >	mCellKillers

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

unsigned	mSamplingTimestepMultiple

CellBasedPdeHandler < ELEMENT_DIM > *	mpCellBasedPdeHandler

Detailed Description

template<unsigned DIM>
class OnLatticeSimulation< DIM >

Run an on-lattice 2D or 3D cell-based simulation.

The OnLatticeSimulation is constructed with a CellPopulation, which updates the correspondence between each Cell and its spatial representation and handles cell division (governed by the CellCycleModel associated with each cell). Once constructed, one or more Update rules may be passed to the OnLatticeSimulation object, to define the processes which update cells in the CellPopulation. Similarly, one or more CellKillers may be passed to the OnLatticeSimulation object to specify conditions in which Cells may die.

Definition at line 59 of file OnLatticeSimulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

OnLatticeSimulation< DIM >::OnLatticeSimulation	(	AbstractCellPopulation< DIM > &	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 45 of file OnLatticeSimulation.cpp.

References EXCEPTION, and AbstractCellBasedSimulation< DIM >::mDt.

Member Function Documentation

template<unsigned DIM>

void OnLatticeSimulation< DIM >::AddCaSwitchingUpdateRule ( boost::shared_ptr< AbstractCaSwitchingUpdateRule< DIM > > pUpdateRule )

Add a switching update rule to be used in this simulation.

Parameters

pUpdateRule shared pointer to a CA switching update rule law

Definition at line 80 of file OnLatticeSimulation.cpp.

References CaBasedCellPopulation< DIM >::AddSwitchingUpdateRule().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::AddCaUpdateRule ( boost::shared_ptr< AbstractCaUpdateRule< DIM > > pUpdateRule )

Add an update rule to be used in this simulation.

Parameters

pUpdateRule shared pointer to a CA update rule law

Definition at line 61 of file OnLatticeSimulation.cpp.

References CaBasedCellPopulation< DIM >::AddUpdateRule().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::AddPottsUpdateRule ( boost::shared_ptr< AbstractPottsUpdateRule< DIM > > pUpdateRule )

Add an update rule to be used in this simulation (use this to set the Hamiltonian).

Parameters

pUpdateRule shared pointer to a Potts update rule law

Definition at line 98 of file OnLatticeSimulation.cpp.

References PottsBasedCellPopulation< DIM >::AddUpdateRule().

template<unsigned DIM>

c_vector< double, DIM > OnLatticeSimulation< DIM >::CalculateCellDivisionVector ( CellPtr pParentCell )

protectedvirtual

Overridden CalculateCellDivisionVector() method for determining how cell division occurs. This method returns a vector which is then passed into the CellPopulation method AddCell(). This method may be overridden by subclasses.

Parameters

pParentCell the parent cell

Returns: a vector containing information on cell division.

Todo:: do something for Potts models here

Implements AbstractCellBasedSimulation< DIM >.

Definition at line 116 of file OnLatticeSimulation.cpp.

template<unsigned DIM>

void OnLatticeSimulation< DIM >::OutputAdditionalSimulationSetup ( out_stream & rParamsFile )

virtual

Overridden OutputAdditionalSimulationSetup() method to output the force and cell population boundary condition information.

Parameters

rParamsFile the file stream to which the parameters are output

Reimplemented from AbstractCellBasedSimulation< DIM >.

Definition at line 170 of file OnLatticeSimulation.cpp.

References NEVER_REACHED, CaBasedCellPopulation< DIM >::rGetSwitchingUpdateRuleCollection(), PottsBasedCellPopulation< DIM >::rGetUpdateRuleCollection(), and CaBasedCellPopulation< DIM >::rGetUpdateRuleCollection().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::OutputSimulationParameters ( out_stream & rParamsFile )

virtual

Overridden OutputSimulationParameters() method.

Parameters

rParamsFile the file stream to which the parameters are output

Implements AbstractCellBasedSimulation< DIM >.

Definition at line 217 of file OnLatticeSimulation.cpp.

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

template<unsigned DIM>

void OnLatticeSimulation< DIM >::RemoveAllCaSwitchingUpdateRules ( )

Method to remove all the CaSwitchingUpdateRules

Definition at line 89 of file OnLatticeSimulation.cpp.

References CaBasedCellPopulation< DIM >::RemoveAllSwitchingUpdateRules().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::RemoveAllCaUpdateRules ( )

Method to remove all the CaUpdateRules

Definition at line 70 of file OnLatticeSimulation.cpp.

References CaBasedCellPopulation< DIM >::RemoveAllUpdateRules().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::RemoveAllPottsUpdateRules ( )

Method to remove all the PottsUpdateRules

Definition at line 107 of file OnLatticeSimulation.cpp.

References PottsBasedCellPopulation< DIM >::RemoveAllUpdateRules().

template<unsigned DIM>

template<class Archive >

void OnLatticeSimulation< DIM >::serialize	(	Archive &	archive,
		const unsigned int	version
	)

inlineprivate

Serialize the object and any member variables.

Parameters

archive	the archive
version	the current version of this class

Definition at line 72 of file OnLatticeSimulation.hpp.

template<unsigned DIM>

void OnLatticeSimulation< DIM >::UpdateCellLocationsAndTopology ( )

protectedvirtual

Overridden UpdateCellLocationsAndTopology() method.

If using a PottsBasedCellPopulation, this method performs Monte Carlo sampling.

Implements AbstractCellBasedSimulation< DIM >.

Definition at line 132 of file OnLatticeSimulation.cpp.

References GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), GenericEventHandler< 11, CellBasedEventHandler >::EndEvent(), and AbstractOnLatticeCellPopulation< DIM >::UpdateCellLocations().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::UpdateCellPopulation ( )

protectedvirtual

Overridden UpdateCellPopulation() method.

If using a CaBasedCellPopulation, this method does nothing if at the start of a simulation that has just been loaded, to ensure consistency in random number generation.

Todo:: #2066 This code should be covered by cell_based/test/simulation/TestOnLatticeSimulationWithCaBasedCellPopulation.hpp TestLoad

Reimplemented from AbstractCellBasedSimulation< DIM >.

Definition at line 141 of file OnLatticeSimulation.cpp.

References SimulationTime::Instance(), NEVER_REACHED, and AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateCellPopulation().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::WriteVisualizerSetupFile ( )

protectedvirtual

Overridden WriteVisualizerSetupFile() method.

Reimplemented from AbstractCellBasedSimulation< DIM >.

Definition at line 123 of file OnLatticeSimulation.cpp.

Friends And Related Function Documentation

template<unsigned DIM>

friend class boost::serialization::access

friend

Needed for serialization.

Definition at line 64 of file OnLatticeSimulation.hpp.

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

cell_based/src/simulation/OnLatticeSimulation.hpp
cell_based/src/simulation/OnLatticeSimulation.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

template<unsigned DIM> class OnLatticeSimulation< DIM >

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

template<unsigned DIM>
class OnLatticeSimulation< DIM >