SimulationTime Class Reference

#include <SimulationTime.hpp>

Inheritance diagram for SimulationTime:

Collaboration diagram for SimulationTime:

List of all members.

Public Member Functions
void	SetEndTimeAndNumberOfTimeSteps (double endTime, unsigned totalTimeStepsInSimulation)
void	ResetEndTimeAndNumberOfTimeSteps (const double &rEndTime, const unsigned &rNumberOfTimeStepsInThisRun)
double	GetTimeStep () const
void	IncrementTimeOneStep ()
unsigned	GetTimeStepsElapsed () const
double	GetTime () const
bool	IsStartTimeSetUp () const
bool	IsEndTimeAndNumberOfTimeStepsSetUp () const
bool	IsFinished () const
void	SetStartTime (double startTime)
Static Public Member Functions
static SimulationTime *	Instance ()
static void	Destroy ()
Protected Member Functions
	SimulationTime ()
Private Member Functions
template<class Archive >
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
double	mStartTime
Static Private Attributes
static SimulationTime *	mpInstance = NULL
static boost::shared_ptr < TimeStepper >	mpTimeStepper
Friends
class	boost::serialization::access

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Detailed Description

Simulation time object stores the simulation time. It uses the singleton pattern to provide a globally consistent time.

Note that the start time, end time and number of time steps must be set before time can be incremented and returned.

You should generally use the calls IncrementTimeOneStep() and GetTime() when using this class.

Definition at line 55 of file SimulationTime.hpp.

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Constructor & Destructor Documentation

SimulationTime::SimulationTime

(

)

[protected]

Default simulation time constructor

Sets up time, you must set the start time, end time and number of time steps before using the object.

Definition at line 57 of file SimulationTime.cpp.

References mpInstance.

Referenced by Instance().

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Member Function Documentation

void SimulationTime::Destroy

(

)

[static]

Destroy the current SimulationTime instance. The next call to Instance will create a new instance, on which SetEndTimeAndNumberOfTimeSteps must be called again to reset time.

This method *must* be called before program exit, to avoid a memory leak.

Definition at line 65 of file SimulationTime.cpp.

References mpInstance.

Referenced by Instance(), and AbstractCellBasedTestSuite::tearDown().

double SimulationTime::GetTime

(

)

const

Get the simulation time (in hours), should not have rounding errors.

Returns:

simulation time

Definition at line 92 of file SimulationTime.cpp.

References DOUBLE_UNSET, mpTimeStepper, and mStartTime.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::DoCellBirth(), AbstractCellCycleModel::GetAge(), NagaiHondaForce< DIM >::GetTargetAreaOfCell(), Cell::GetTimeUntilDeath(), CellBasedPdeHandler< DIM >::OpenResultsFiles(), AbstractSimpleCellCycleModel::ResetForDivision(), CellBasedSimulationArchiver< DIM, SIM >::Save(), CryptSimulation2d::SetupSolve(), SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), Cell::StartApoptosis(), CryptSimulation2d::UpdateAtEndOfTimeStep(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), OnLatticeSimulation< DIM >::UpdateCellLocationsAndTopology(), SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodePositions(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteCellIdDataToFile(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteCellPopulationVolumeResultsToFile(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), PottsBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), NodeBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), MultipleCaBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteCellVolumeResultsToFile(), DiscreteSystemForceCalculator::WriteResultsToFile(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), PottsBasedCellPopulation< DIM >::WriteResultsToFiles(), MultipleCaBasedCellPopulation< DIM >::WriteResultsToFiles(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteTimeAndNodeResultsToFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteTimeAndNodeResultsToFiles(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVoronoiResultsToFile().

double SimulationTime::GetTimeStep

(

)

const

Get the simulation time step, set in earlier calls.

Warning: Use of this method may result in round errors; generally use GetTime() instead.

Returns:

time step for this run of the simulation

Definition at line 74 of file SimulationTime.cpp.

References mpTimeStepper.

Referenced by DiffusionForce< DIM >::AddForceContribution(), CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), CellCycleModelOdeHandler::GetDt(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), CryptSimulation2d::UpdateAtEndOfTimeStep(), SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase(), and ContactInhibitionCellCycleModel::UpdateCellCyclePhase().

unsigned SimulationTime::GetTimeStepsElapsed

(

)

const

Get the number of time steps that have elapsed.

Returns:

number of time steps which have been taken

Definition at line 86 of file SimulationTime.cpp.

References mpTimeStepper.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), CryptSimulation2d::UpdateAtEndOfTimeStep(), OnLatticeSimulation< DIM >::UpdateCellLocationsAndTopology(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MultipleCaBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

void SimulationTime::IncrementTimeOneStep

(

)

Increment the simulation time by one time step.

GetTime() will return an updated current time after this call.

Definition at line 80 of file SimulationTime.cpp.

References mpTimeStepper.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve().

SimulationTime * SimulationTime::Instance

(

)

[static]

Return a pointer to the simulation time object. The first time this is called the simulation time object is created.

Definition at line 46 of file SimulationTime.cpp.

References Destroy(), mpInstance, mpTimeStepper, and SimulationTime().

Referenced by DiffusionForce< DIM >::AddForceContribution(), CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< ELEMENT_DIM, SPACE_DIM >::CalculateForceBetweenNodes(), Cell::Cell(), RandomCellKiller< DIM >::CheckAndLabelSingleCellForApoptosis(), CellBasedPdeHandler< DIM >::CloseResultsFiles(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::DoCellBirth(), AbstractCellCycleModel::GetAge(), CellCycleModelOdeHandler::GetDt(), NagaiHondaForce< DIM >::GetTargetAreaOfCell(), Cell::GetTimeUntilDeath(), Cell::IsDead(), CellBasedPdeHandler< DIM >::OpenResultsFiles(), AbstractSimpleCellCycleModel::ResetForDivision(), CellBasedSimulationArchiver< DIM, SIM >::Save(), AbstractCellBasedSimulation< DIM >::serialize(), AbstractCellCycleModel::serialize(), AbstractCellBasedTestSuite::setUp(), CryptSimulation2d::SetupSolve(), SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel(), AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve(), CellBasedPdeHandler< DIM >::SolvePdeAndWriteResultsToFile(), Cell::StartApoptosis(), CryptSimulation2d::UpdateAtEndOfTimeStep(), SingleOdeWntCellCycleModel::UpdateCellCyclePhase(), AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase(), SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase(), DeltaNotchCellCycleModel::UpdateCellCyclePhase(), ContactInhibitionCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), OnLatticeSimulation< DIM >::UpdateCellLocationsAndTopology(), OnLatticeSimulation< DIM >::UpdateCellPopulation(), SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::UpdateNodePositions(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteCellIdDataToFile(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteCellPopulationVolumeResultsToFile(), VertexBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), PottsBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), NodeBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), MultipleCaBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteCellVolumeResultsToFile(), DiscreteSystemForceCalculator::WriteResultsToFile(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), PottsBasedCellPopulation< DIM >::WriteResultsToFiles(), MultipleCaBasedCellPopulation< DIM >::WriteResultsToFiles(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteResultsToFiles(), AbstractCentreBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteTimeAndNodeResultsToFiles(), AbstractCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteTimeAndNodeResultsToFiles(), MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVoronoiResultsToFile(), VertexBasedCellPopulation< DIM >::WriteVtkResultsToFile(), PottsBasedCellPopulation< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulationWithParticles< DIM >::WriteVtkResultsToFile(), NodeBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MultipleCaBasedCellPopulation< DIM >::WriteVtkResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< ELEMENT_DIM, SPACE_DIM >::WriteVtkResultsToFile().

bool SimulationTime::IsEndTimeAndNumberOfTimeStepsSetUp

(

)

const

Allows lower classes to check whether the simulation time class has been set up before using it

Returns:

whether the end time of the simulation and the number of timesteps has been set.

Definition at line 140 of file SimulationTime.cpp.

References mpTimeStepper.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve().

bool SimulationTime::IsFinished

(

)

const

Returns:

whether the simulation has finished.

Definition at line 152 of file SimulationTime.cpp.

References mpTimeStepper.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve().

bool SimulationTime::IsStartTimeSetUp

(

)

const

Allows lower classes to check whether the simulation time class has been set up before using it

Returns:

whether the start time of the simulation has been set.

Definition at line 135 of file SimulationTime.cpp.

References DOUBLE_UNSET, and mStartTime.

Referenced by CellBasedSimulationArchiver< DIM, SIM >::Save().

void SimulationTime::ResetEndTimeAndNumberOfTimeSteps	(	const double &	rEndTime,
		const unsigned &	rNumberOfTimeStepsInThisRun
	)

Reset method for the end time and the number of time steps, to run the simulation further after a first initial run.

Parameters:

rEndTime	the new end time for this simulation (the simulation will run from the current time to this new end time, NOT from 0 to this end time)
rNumberOfTimeStepsInThisRun	the number of time steps into which the next run is split

Definition at line 121 of file SimulationTime.cpp.

References DOUBLE_UNSET, mpTimeStepper, and mStartTime.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve().

template<class Archive >

void SimulationTime::serialize	(	Archive &	archive,
		const unsigned int	version
	)		[inline, private]

Serialization of a SimulationTime object must be done with care. Do not serialize this singleton directly. Instead, serialize the object returned by GetSerializationWrapper.

Parameters:

archive	the archive
version	the current version of this class

Definition at line 190 of file SimulationTime.hpp.

References mpTimeStepper, and mStartTime.

void SimulationTime::SetEndTimeAndNumberOfTimeSteps	(	double	endTime,
		unsigned	totalTimeStepsInSimulation
	)

Sets the end time and the number of time steps. This must be called after SetStartTime() but before using any other methods.

Parameters:

endTime	time at which to end this run of the simulation
totalTimeStepsInSimulation	the number of time steps into which the above will be divided

Definition at line 111 of file SimulationTime.cpp.

References DOUBLE_UNSET, mpTimeStepper, and mStartTime.

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::Solve().

void SimulationTime::SetStartTime

(

double

startTime

)

Set the start time of the simulation

Parameters:

startTime

the time at which the simulation begins (usually 0.0 hours)

Definition at line 105 of file SimulationTime.cpp.

References DOUBLE_UNSET, and mStartTime.

Referenced by AbstractCellBasedTestSuite::setUp().

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Friends And Related Function Documentation

friend class boost::serialization::access [friend]

Needed for serialization.

Reimplemented from SerializableSingleton< SimulationTime >.

Definition at line 179 of file SimulationTime.hpp.

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Member Data Documentation

SimulationTime * SimulationTime::mpInstance = NULL [static, private]

A pointer to the singleton instance of this class.

Pointer to the single instance

Definition at line 164 of file SimulationTime.hpp.

Referenced by Destroy(), Instance(), and SimulationTime().

boost::shared_ptr< TimeStepper > SimulationTime::mpTimeStepper [static, private]

Delegate all time stepping to a TimeStepper class

Shared pointer to the delegated class

Definition at line 170 of file SimulationTime.hpp.

Referenced by GetTime(), GetTimeStep(), GetTimeStepsElapsed(), IncrementTimeOneStep(), Instance(), IsEndTimeAndNumberOfTimeStepsSetUp(), IsFinished(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), and SetEndTimeAndNumberOfTimeSteps().

double SimulationTime::mStartTime [private]

Stores the time at which the simulation started

Definition at line 175 of file SimulationTime.hpp.

Referenced by GetTime(), IsStartTimeSetUp(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), SetEndTimeAndNumberOfTimeSteps(), and SetStartTime().

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

• cell_based/src/common/SimulationTime.hpp
• cell_based/src/common/SimulationTime.cpp