AbstractCellBasedSimulation< DIM > Class Template Reference

#include <AbstractCellBasedSimulation.hpp>

Inherited by OffLatticeSimulation< DIM >, OffLatticeSimulation< 1 >, OffLatticeSimulation< 2 >, and OnLatticeSimulation< DIM >.

Collaboration diagram for AbstractCellBasedSimulation< DIM >:

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List of all members.

Public Member Functions
	AbstractCellBasedSimulation (AbstractCellPopulation< DIM > &rCellPopulation, bool deleteCellPopulationInDestructor=false, bool initialiseCells=true)
virtual	~AbstractCellBasedSimulation ()
void	SetCellBasedPdeHandler (CellBasedPdeHandler< DIM > *pCellBasedPdeHandler)
CellBasedPdeHandler< 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)
void	AddCellKiller (boost::shared_ptr< AbstractCellKiller< DIM > > pCellKiller)
void	Solve ()
AbstractCellPopulation< DIM > &	rGetCellPopulation ()
const AbstractCellPopulation < DIM > &	rGetCellPopulation () const
virtual void	OutputSimulationParameters (out_stream &rParamsFile)=0
Protected Member Functions
virtual void	WriteVisualizerSetupFile ()
virtual unsigned	DoCellBirth ()
virtual c_vector< double, DIM >	CalculateCellDivisionVector (CellPtr pParentCell)=0
unsigned	DoCellRemoval ()
virtual void	PostSolve ()
virtual void	SetupSolve ()
virtual void	AfterSolve ()
virtual bool	StoppingEventHasOccurred ()
virtual void	UpdateCellPopulation ()
virtual void	UpdateCellLocationsAndTopology ()=0
void	OutputSimulationSetup ()
virtual void	OutputAdditionalSimulationSetup (out_stream &rParamsFile)
Protected Attributes
double	mDt
double	mEndTime
AbstractCellPopulation< DIM > &	mrCellPopulation
bool	mDeleteCellPopulationInDestructor
bool	mInitialiseCells
bool	mNoBirth
bool	mUpdateCellPopulation
std::string	mOutputDirectory
std::string	mSimulationOutputDirectory
out_stream	mpVizSetupFile
unsigned	mNumBirths
unsigned	mNumDeaths
std::vector< boost::shared_ptr < AbstractCellKiller< DIM > > >	mCellKillers
unsigned	mSamplingTimestepMultiple
CellBasedPdeHandler< DIM > *	mpCellBasedPdeHandler
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Friends
class	TestCryptSimulation2d
class	TestOffLatticeSimulation3d
class	TestOffLatticeSimulation
class	boost::serialization::access

Detailed Description

template<unsigned DIM>
class AbstractCellBasedSimulation< DIM >

An abstract cell-based simulation class. This class contains common functionality from off lattice and on lattice simulations.

The AbstractCellBasedSimulation 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 CellKillers may be passed to the AbstractCellBasedSimulation object to specify conditions in which Cells may die,

Subclasses use one or more Force laws or update rules (Which are passed to the child class object) to define the mechanical properties of the CellPopulation.

Definition at line 58 of file AbstractCellBasedSimulation.hpp.

Constructor & Destructor Documentation

template<unsigned DIM>

AbstractCellBasedSimulation< DIM >::AbstractCellBasedSimulation	(	AbstractCellPopulation< DIM > &	rCellPopulation,
		bool	deleteCellPopulationInDestructor = `false`,
		bool	initialiseCells = `true`
	)			`[inline]`

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 AbstractCellBasedSimulation.cpp.

References RandomNumberGenerator::Instance(), AbstractCellBasedSimulation< DIM >::mInitialiseCells, and AbstractCellBasedSimulation< DIM >::mrCellPopulation.

template<unsigned DIM>

AbstractCellBasedSimulation< DIM >::~AbstractCellBasedSimulation ( ) [inline, virtual]

Destructor.

This frees the cell population if it was created by de-serialization.

Definition at line 72 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mDeleteCellPopulationInDestructor, AbstractCellBasedSimulation< DIM >::mpCellBasedPdeHandler, and AbstractCellBasedSimulation< DIM >::mrCellPopulation.

Member Function Documentation

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::AddCellKiller ( boost::shared_ptr< AbstractCellKiller< DIM > > pCellKiller ) [inline]

Add a cell killer to be used in this simulation.

Parameters:

pCellKiller

pointer to a cell killer

Definition at line 228 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mCellKillers.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::AfterSolve ( ) [inline, protected, virtual]

This method may be overridden in subclasses to do something at the end of each time loop.

Reimplemented in OffLatticeSimulation< DIM >, OnLatticeSimulation< DIM >, CryptSimulation2d, OffLatticeSimulation< 1 >, and OffLatticeSimulation< 2 >.

Definition at line 266 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mpCellBasedPdeHandler.

Referenced by AbstractCellBasedSimulation< DIM >::Solve().

template<unsigned DIM>

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

Method for determining how cell division occurs. This method returns a vector which is then passed into the CellPopulation method AddCell().

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

Parameters:

pParentCell

the parent cell

Returns:: a vector containing information on cell division.

Implemented in OffLatticeSimulation< DIM >, OnLatticeSimulation< DIM >, CryptSimulation1d, CryptSimulation2d, OffLatticeSimulation< 1 >, and OffLatticeSimulation< 2 >.

Referenced by AbstractCellBasedSimulation< DIM >::DoCellBirth().

template<unsigned DIM>

unsigned AbstractCellBasedSimulation< DIM >::DoCellBirth ( ) [inline, protected, virtual]

During a simulation time step, process any cell divisions that need to occur. If the simulation includes cell birth, causes (almost) all cells that are ready to divide to produce daughter cells.

Returns:: the number of births that occurred.

Definition at line 94 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::CalculateCellDivisionVector(), AbstractCellBasedSimulation< DIM >::mNoBirth, and AbstractCellBasedSimulation< DIM >::mrCellPopulation.

Referenced by AbstractCellBasedSimulation< DIM >::UpdateCellPopulation().

template<unsigned DIM>

unsigned AbstractCellBasedSimulation< DIM >::DoCellRemoval ( ) [inline, protected]

During a simulation time step, process any cell sloughing or death

This uses the cell killers to remove cells and associated nodes from the facade class.

Returns:: the number of deaths that occurred.

Definition at line 131 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mCellKillers, and AbstractCellBasedSimulation< DIM >::mrCellPopulation.

Referenced by AbstractCellBasedSimulation< DIM >::UpdateCellPopulation().

template<unsigned DIM>

CellBasedPdeHandler< DIM > * AbstractCellBasedSimulation< DIM >::GetCellBasedPdeHandler ( ) [inline]

Returns:: mpCellBasedPdeHandler

Definition at line 88 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mpCellBasedPdeHandler.

template<unsigned DIM>

double AbstractCellBasedSimulation< DIM >::GetDt ( ) [inline]

Returns:: the timestep of the simulation

Definition at line 159 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mDt.

template<unsigned DIM>

std::vector< double > AbstractCellBasedSimulation< DIM >::GetNodeLocation ( const unsigned & rNodeIndex ) [inline]

Get a node's location (ONLY FOR TESTING).

Parameters:

rNodeIndex

the node index

Returns:: the co-ordinates of this node.

Definition at line 234 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mrCellPopulation.

template<unsigned DIM>

unsigned AbstractCellBasedSimulation< DIM >::GetNumBirths ( ) [inline]

Returns:: the number of births that have occurred in the entire simulation (since t=0)

Definition at line 165 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mNumBirths.

template<unsigned DIM>

unsigned AbstractCellBasedSimulation< DIM >::GetNumDeaths ( ) [inline]

Returns:: the number of deaths that have occurred in the entire simulation (since t=0).

Definition at line 171 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mNumDeaths.

template<unsigned DIM>

std::string AbstractCellBasedSimulation< DIM >::GetOutputDirectory ( ) [inline]

Get the output directory of the simulation.

Definition at line 191 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mOutputDirectory.

template<unsigned DIM>

virtual void AbstractCellBasedSimulation< DIM >::OutputAdditionalSimulationSetup ( out_stream & rParamsFile ) [inline, protected, virtual]

Helper method to output additional simulations parameters and information defined in subclasses to file.

Parameters:

rParamsFile

the file stream to which the parameters are output

Reimplemented in OffLatticeSimulation< DIM >, OnLatticeSimulation< DIM >, OffLatticeSimulation< 1 >, and OffLatticeSimulation< 2 >.

Definition at line 237 of file AbstractCellBasedSimulation.hpp.

Referenced by AbstractCellBasedSimulation< DIM >::OutputSimulationSetup().

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::OutputSimulationParameters ( out_stream & rParamsFile ) [inline, pure 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

Implemented in OffLatticeSimulation< DIM >, OnLatticeSimulation< DIM >, CryptSimulation1d, CryptSimulation2d, OffLatticeSimulation< 1 >, and OffLatticeSimulation< 2 >.

Definition at line 483 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mDt, AbstractCellBasedSimulation< DIM >::mEndTime, AbstractCellBasedSimulation< DIM >::mpCellBasedPdeHandler, and AbstractCellBasedSimulation< DIM >::mSamplingTimestepMultiple.

Referenced by AbstractCellBasedSimulation< DIM >::OutputSimulationSetup().

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::OutputSimulationSetup ( ) [inline, protected]

Helper method to output all the simulations parameters and information to file.

Definition at line 437 of file AbstractCellBasedSimulation.cpp.

References Identifiable::GetIdentifier(), AbstractCellBasedSimulation< DIM >::mCellKillers, AbstractCellBasedSimulation< DIM >::mrCellPopulation, AbstractCellBasedSimulation< DIM >::mSimulationOutputDirectory, OutputFileHandler::OpenOutputFile(), AbstractCellBasedSimulation< DIM >::OutputAdditionalSimulationSetup(), AbstractCellBasedSimulation< DIM >::OutputSimulationParameters(), ExecutableSupport::WriteLibraryInfo(), and ExecutableSupport::WriteMachineInfoFile().

Referenced by AbstractCellBasedSimulation< DIM >::Solve().

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::PostSolve ( ) [inline, protected, virtual]

A method for subclasses to do something at the end of each timestep

Reimplemented in DeltaNotchOffLatticeSimulation< DIM >, VolumeTrackedOffLatticeSimulation< DIM >, and CryptSimulation2d.

Definition at line 255 of file AbstractCellBasedSimulation.cpp.

References GenericEventHandler< 10, CellBasedEventHandler >::BeginEvent(), GenericEventHandler< 10, CellBasedEventHandler >::EndEvent(), AbstractCellBasedSimulation< DIM >::mpCellBasedPdeHandler, and AbstractCellBasedSimulation< DIM >::mSamplingTimestepMultiple.

Referenced by AbstractCellBasedSimulation< DIM >::Solve().

template<unsigned DIM>

const AbstractCellPopulation< DIM > & AbstractCellBasedSimulation< DIM >::rGetCellPopulation ( ) const [inline]

Returns:: const reference to the cell population (used in archiving).

Definition at line 210 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mrCellPopulation.

template<unsigned DIM>

AbstractCellPopulation< DIM > & AbstractCellBasedSimulation< DIM >::rGetCellPopulation ( ) [inline]

Returns:: reference to the cell population.

Definition at line 204 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mrCellPopulation.

template<unsigned DIM>

template<class Archive >

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

Save or restore the simulation.

Parameters:

	archive	the archive
	version	the current version of this class

Reimplemented in DeltaNotchOffLatticeSimulation< DIM >, OffLatticeSimulation< DIM >, OnLatticeSimulation< DIM >, VolumeTrackedOffLatticeSimulation< DIM >, CryptSimulation1d, CryptSimulation2d, OffLatticeSimulation< 1 >, and OffLatticeSimulation< 2 >.

Definition at line 77 of file AbstractCellBasedSimulation.hpp.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::SetCellBasedPdeHandler ( CellBasedPdeHandler< DIM > * pCellBasedPdeHandler ) [inline]

Set mpCellBasedPdeHandler

Parameters:

pCellBasedPdeHandler

pointer to a CellBasedPdeHandler object

Definition at line 82 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mpCellBasedPdeHandler.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::SetDt ( double dt ) [inline]

Set the timestep of the simulation.

Parameters:

dt

the timestep to use

Definition at line 152 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mDt.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::SetEndTime ( double endTime ) [inline]

Set the end time and resets the timestep to be endtime/100.

Parameters:

endTime

the end time to use

Definition at line 177 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mEndTime.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::SetNoBirth ( bool noBirth ) [inline]

Set the simulation to run with no birth.

Parameters:

noBirth

whether to run with no birth

Definition at line 222 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mNoBirth.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::SetOutputDirectory ( std::string outputDirectory ) [inline]

Set the output directory of the simulation.

Parameters:

outputDirectory

the output directory to use

Definition at line 184 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mOutputDirectory, and AbstractCellBasedSimulation< DIM >::mSimulationOutputDirectory.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::SetSamplingTimestepMultiple ( unsigned samplingTimestepMultiple ) [inline]

Set the ratio of the number of actual timesteps to the number of timesteps at which results are written to file. Default value is set to 1 by the constructor.

Parameters:

samplingTimestepMultiple

the ratio to use

Definition at line 197 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mSamplingTimestepMultiple.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::SetUpdateCellPopulationRule ( bool updateCellPopulation ) [inline]

Set whether to update the topology of the cell population at each time step.

Parameters:

updateCellPopulation

whether to update the cell population each time step

Definition at line 216 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mUpdateCellPopulation.

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::SetupSolve ( ) [inline, protected, virtual]

A method for subclasses to do something at before the start of the time loop.

Reimplemented in OffLatticeSimulation< DIM >, OnLatticeSimulation< DIM >, CryptSimulation2d, OffLatticeSimulation< 1 >, and OffLatticeSimulation< 2 >.

Definition at line 245 of file AbstractCellBasedSimulation.cpp.

References AbstractCellBasedSimulation< DIM >::mpCellBasedPdeHandler, AbstractCellBasedSimulation< DIM >::mpVizSetupFile, and AbstractCellBasedSimulation< DIM >::mSimulationOutputDirectory.

Referenced by AbstractCellBasedSimulation< DIM >::Solve().

template<unsigned DIM>

void AbstractCellBasedSimulation< DIM >::Solve ( ) [inline]

Main solve method.

This method sets up the simulation time, creates output files, and initialises the cell population. It then iterates through a time loop. At each time step, first any cell death or birth is implemented, then the cell population topology is updated, then the forces are recalculated and the cell population evolved according to whatever force laws are present in the simulation, and finally the results for that time step are output to file. At the end of the time loop, the method closes any output files.

Definition at line 275 of file AbstractCellBasedSimulation.cpp.

template<unsigned DIM>

bool AbstractCellBasedSimulation< DIM >::StoppingEventHasOccurred ( ) [inline, protected, virtual]

A child class can overload this if they want the simulation to stop based on certain conditions before the specified end time (for example, run until a crypt becomes monoclonal).

Definition at line 396 of file AbstractCellBasedSimulation.cpp.

Referenced by AbstractCellBasedSimulation< DIM >::Solve().

template<unsigned DIM>

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

Updates the locations and topology of cells, must be defined in subclasses.

For example this calculates forces and updates node positions in off lattice simulations.

Implemented in OffLatticeSimulation< DIM >, OnLatticeSimulation< DIM >, OffLatticeSimulation< 1 >, and OffLatticeSimulation< 2 >.

Referenced by AbstractCellBasedSimulation< DIM >::Solve().

template<unsigned DIM>

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

Calls the deaths, births and (if mUpdateCellPopulation is true) CellPopulation::Update() methods.

Reimplemented in OnLatticeSimulation< DIM >.