#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	AddMultipleCaUpdateRule (boost::shared_ptr< AbstractMultipleCaUpdateRule< DIM > > pUpdateRule)
void	RemoveAllMultipleCaUpdateRules ()
void	AddPottsUpdateRule (boost::shared_ptr< AbstractPottsUpdateRule< DIM > > pUpdateRule)
void	RemoveAllPottsUpdateRules ()
bool	GetOutputCellVelocities ()
void	SetOutputCellVelocities (bool outputCellVelocities)
virtual void	SetupSolve ()
virtual void	UpdateAtEndOfSolve ()
void	OutputAdditionalSimulationSetup (out_stream &rParamsFile)
void	OutputSimulationParameters (out_stream &rParamsFile)
Protected Member Functions
void	UpdateCellPopulation ()
void	UpdateCellLocationsAndTopology ()
virtual c_vector< double, DIM >	CalculateCellDivisionVector (CellPtr pParentCell)
virtual void	WriteVisualizerSetupFile ()
Protected Attributes
bool	mOutputCellVelocities
out_stream	mpCellVelocitiesFile
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	boost::serialization::access

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 >::AddMultipleCaUpdateRule ( boost::shared_ptr< AbstractMultipleCaUpdateRule< DIM > > pUpdateRule )

Add an update rule to be used in this simulation.

Parameters:

pUpdateRule shared pointer to a multiple CA update rule law

Definition at line 62 of file OnLatticeSimulation.cpp.

References MultipleCaBasedCellPopulation< 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 80 of file OnLatticeSimulation.cpp.

References PottsBasedCellPopulation< DIM >::AddUpdateRule().

template<unsigned DIM>

c_vector< double, DIM > OnLatticeSimulation< DIM >::CalculateCellDivisionVector ( CellPtr pParentCell ) [protected, virtual]

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 98 of file OnLatticeSimulation.cpp.

template<unsigned DIM>

bool OnLatticeSimulation< DIM >::GetOutputCellVelocities ( )

Overridden OutputAdditionalSimulationSetup() method. Outputs the update rule information.

Definition at line 192 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 233 of file OnLatticeSimulation.cpp.

References MultipleCaBasedCellPopulation< DIM >::rGetUpdateRuleCollection(), and PottsBasedCellPopulation< 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 269 of file OnLatticeSimulation.cpp.

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

template<unsigned DIM>

void OnLatticeSimulation< DIM >::RemoveAllMultipleCaUpdateRules ( )

Method to remove all the MultipleCaUpdateRules

Definition at line 71 of file OnLatticeSimulation.cpp.

References MultipleCaBasedCellPopulation< DIM >::RemoveAllUpdateRules().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::RemoveAllPottsUpdateRules ( )

Method to remove all the PottsUpdateRules

Definition at line 89 of file OnLatticeSimulation.cpp.

References PottsBasedCellPopulation< DIM >::RemoveAllUpdateRules().

template<unsigned DIM>

template<class Archive >

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

Serialize the object and any member variables.

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from AbstractCellBasedSimulation< DIM >.

Definition at line 72 of file OnLatticeSimulation.hpp.

References OnLatticeSimulation< DIM >::mOutputCellVelocities.

template<unsigned DIM>

void OnLatticeSimulation< DIM >::SetOutputCellVelocities ( bool outputCellVelocities )

Set mOutputCellVelocities.

Parameters:

outputCellVelocities the new value of mOutputCellVelocities

Definition at line 198 of file OnLatticeSimulation.cpp.

template<unsigned DIM>

void OnLatticeSimulation< DIM >::SetupSolve ( ) [virtual]

Overridden SetupSolve() method to setup the cell velocities file.

Reimplemented from AbstractCellBasedSimulation< DIM >.

Definition at line 173 of file OnLatticeSimulation.cpp.

References OutputFileHandler::OpenOutputFile().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::UpdateAtEndOfSolve ( ) [virtual]

Overridden UpdateAtEndOfSolve() method to close the cell velocities file.

Reimplemented from AbstractCellBasedSimulation< DIM >.

Definition at line 183 of file OnLatticeSimulation.cpp.

template<unsigned DIM>

void OnLatticeSimulation< DIM >::UpdateCellLocationsAndTopology ( ) [protected, virtual]

Overridden UpdateCellLocationsAndTopology() method.

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

Implements AbstractCellBasedSimulation< DIM >.

Definition at line 114 of file OnLatticeSimulation.cpp.

References AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::Begin(), GenericEventHandler< 11, CellBasedEventHandler >::BeginEvent(), GenericEventHandler< 11, CellBasedEventHandler >::EndEvent(), SimulationTime::GetTime(), SimulationTime::GetTimeStepsElapsed(), SimulationTime::Instance(), and AbstractOnLatticeCellPopulation< DIM >::UpdateCellLocations().

template<unsigned DIM>

void OnLatticeSimulation< DIM >::UpdateCellPopulation ( ) [protected, virtual]

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.