SimulationTime Class Reference

#include <SimulationTime.hpp>

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 IsFinished () const

unsigned GetTotalNumberOfTimeSteps () const

void SetStartTime (double startTime)

Static Public Member Functions

static SimulationTime * Instance ()

static void Destroy ()

Protected Member Functions

SimulationTime ()

SimulationTime (const SimulationTime &)

SimulationTime & operator= (const SimulationTime &)

Private Member Functions

template<class Archive>

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

Private Attributes

double mDurationOfSimulation

unsigned mTotalTimeStepsInSimulation

unsigned mTimeStepsElapsed

bool mEndTimeAndNumberOfTimeStepsSet

double mCurrentTime

double mEndTime

double mStartTime

bool mStartTimeSet

Static Private Attributes

static SimulationTime * mpInstance = NULL

Friends

class boost::serialization::access

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 45 of file SimulationTime.hpp.

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 46 of file SimulationTime.cpp.

References mCurrentTime, mEndTimeAndNumberOfTimeStepsSet, mpInstance, mStartTime, mStartTimeSet, and mTimeStepsElapsed.

SimulationTime::SimulationTime ( const SimulationTime & ) [protected]

Copy constructor.

Member Function Documentation

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 36 of file SimulationTime.cpp.

References mpInstance.

Referenced by TissueSimulation< DIM >::AfterSolve(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), AbstractCellCycleModel::GetAge(), IngeWntSwatCellCycleModel::IngeWntSwatCellCycleModel(), TissueCell::IsDead(), TissueSimulationArchiver< DIM, SIM >::Load(), CryptSimulation2d::PostSolve(), AbstractSimpleCellCycleModel::ResetForDivision(), TissueSimulationArchiver< DIM, SIM >::Save(), AbstractCellCycleModel::serialize(), AbstractCancerTestSuite::setUp(), CryptSimulation2d::SetupSolve(), TissueSimulation< DIM >::Solve(), WntCellCycleModel::SolveOdeToTime(), IngeWntSwatCellCycleModel::SolveOdeToTime(), TissueCell::StartApoptosis(), TissueCell::TimeUntilDeath(), TissueCell::TissueCell(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), AbstractWntOdeBasedCellCycleModel::UpdateCellType(), WntCellCycleModel::WntCellCycleModel(), MeshBasedTissue< DIM >::WriteResultsToFiles(), AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

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 dvided

Definition at line 116 of file SimulationTime.cpp.

References mCurrentTime, mDurationOfSimulation, mEndTime, mEndTimeAndNumberOfTimeStepsSet, mStartTimeSet, and mTotalTimeStepsInSimulation.

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

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 (now extended) note that 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 to split the next run into.

Definition at line 132 of file SimulationTime.cpp.

References mCurrentTime, mDurationOfSimulation, mEndTime, mEndTimeAndNumberOfTimeStepsSet, mStartTime, mStartTimeSet, mTimeStepsElapsed, and mTotalTimeStepsInSimulation.

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

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 78 of file SimulationTime.cpp.

References mDurationOfSimulation, mEndTimeAndNumberOfTimeStepsSet, mStartTimeSet, and mTotalTimeStepsInSimulation.

Referenced by GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), CryptSimulation2d::PostSolve(), WntCellCycleModel::SolveOdeToTime(), and IngeWntSwatCellCycleModel::SolveOdeToTime().

void SimulationTime::IncrementTimeOneStep ( )

Increment the simulation time by one time step.

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

Definition at line 86 of file SimulationTime.cpp.

References mCurrentTime, mDurationOfSimulation, mEndTimeAndNumberOfTimeStepsSet, mStartTime, mStartTimeSet, mTimeStepsElapsed, and mTotalTimeStepsInSimulation.

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

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 97 of file SimulationTime.cpp.

References mEndTimeAndNumberOfTimeStepsSet, and mTimeStepsElapsed.

Referenced by CryptSimulation2d::PostSolve(), and TissueSimulation< DIM >::Solve().

double SimulationTime::GetTime ( ) const

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

Returns:: simulation time

Definition at line 104 of file SimulationTime.cpp.

References mCurrentTime, and mStartTimeSet.

Referenced by AbstractCellCycleModel::GetAge(), CryptSimulation2d::PostSolve(), AbstractSimpleCellCycleModel::ResetForDivision(), TissueSimulationArchiver< DIM, SIM >::Save(), CryptSimulation2d::SetupSolve(), TissueSimulation< DIM >::Solve(), TissueCell::StartApoptosis(), TissueCell::TimeUntilDeath(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), MeshBasedTissue< DIM >::WriteResultsToFiles(), AbstractTissue< DIM >::WriteTimeAndNodeResultsToFiles(), MeshBasedTissue< DIM >::WriteTissueAreaResultsToFile(), and MeshBasedTissue< DIM >::WriteVoronoiResultsToFile().

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 59 of file SimulationTime.cpp.

References mpInstance.

Referenced by AbstractCancerTestSuite::tearDown().

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 152 of file SimulationTime.cpp.

References mStartTimeSet.

Referenced by TissueSimulationArchiver< DIM, SIM >::Load(), and TissueSimulationArchiver< DIM, SIM >::Save().

bool SimulationTime::IsFinished ( ) const

Returns:: whether the simulation has finished.

Definition at line 158 of file SimulationTime.cpp.

References mCurrentTime, and mEndTime.

unsigned SimulationTime::GetTotalNumberOfTimeSteps ( ) const

Returns:: the total number of time steps to be taken in this run.

Definition at line 164 of file SimulationTime.cpp.

References mTotalTimeStepsInSimulation.

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 69 of file SimulationTime.cpp.

References mCurrentTime, mStartTime, and mStartTimeSet.

Referenced by AbstractCancerTestSuite::setUp().

SimulationTime& SimulationTime::operator= ( const SimulationTime & ) [protected]

Overloaded assignement operator.

template<class Archive>

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

Serialization of a SimulationTime object must be done with care. Before the object is serialized via a pointer, it *MUST* be serialized directly, or an assertion will trip when a second instance of the class is created on de-serialization.

Parameters:

	archive
	version

Definition at line 221 of file SimulationTime.hpp.

References mCurrentTime, mDurationOfSimulation, mEndTime, mEndTimeAndNumberOfTimeStepsSet, mStartTime, mStartTimeSet, mTimeStepsElapsed, and mTotalTimeStepsInSimulation.

Friends And Related Function Documentation

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

Needed for serialization.

Definition at line 210 of file SimulationTime.hpp.

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 165 of file SimulationTime.hpp.

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

double SimulationTime::mDurationOfSimulation [private]

The duration of the simulation (cancer time units are in hours).

Definition at line 170 of file SimulationTime.hpp.

Referenced by GetTimeStep(), IncrementTimeOneStep(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), and SetEndTimeAndNumberOfTimeSteps().

unsigned SimulationTime::mTotalTimeStepsInSimulation [private]

The total number of steps for this simualation.

Definition at line 175 of file SimulationTime.hpp.

Referenced by GetTimeStep(), GetTotalNumberOfTimeSteps(), IncrementTimeOneStep(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), and SetEndTimeAndNumberOfTimeSteps().

unsigned SimulationTime::mTimeStepsElapsed [private]

The number of time steps which have been taken to date.

Definition at line 180 of file SimulationTime.hpp.

Referenced by GetTimeStepsElapsed(), IncrementTimeOneStep(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), and SimulationTime().

bool SimulationTime::mEndTimeAndNumberOfTimeStepsSet [private]

A flag allowing us to determine whether the simulation time is ready to be used.

Definition at line 186 of file SimulationTime.hpp.

Referenced by GetTimeStep(), GetTimeStepsElapsed(), IncrementTimeOneStep(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), SetEndTimeAndNumberOfTimeSteps(), and SimulationTime().

double SimulationTime::mCurrentTime [private]

The current time (in hours)

Definition at line 191 of file SimulationTime.hpp.

Referenced by GetTime(), IncrementTimeOneStep(), IsFinished(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), SetEndTimeAndNumberOfTimeSteps(), SetStartTime(), and SimulationTime().

double SimulationTime::mEndTime [private]

The time at which the simulation should stop

Definition at line 196 of file SimulationTime.hpp.

Referenced by IsFinished(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), and SetEndTimeAndNumberOfTimeSteps().

double SimulationTime::mStartTime [private]

Stores the time at which the simulation started

Definition at line 201 of file SimulationTime.hpp.

Referenced by IncrementTimeOneStep(), ResetEndTimeAndNumberOfTimeSteps(), serialize(), SetStartTime(), and SimulationTime().

bool SimulationTime::mStartTimeSet [private]

A flag allowing us to determine whether the start time of the simulation has been set.

Definition at line 207 of file SimulationTime.hpp.

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

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

/tmp/release_1/cancer/src/common/SimulationTime.hpp
/tmp/release_1/cancer/src/common/SimulationTime.cpp


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	IsFinished () const
unsigned	GetTotalNumberOfTimeSteps () const
void	SetStartTime (double startTime)
Static Public Member Functions
static SimulationTime *	Instance ()
static void	Destroy ()
Protected Member Functions
	SimulationTime ()
	SimulationTime (const SimulationTime &)
SimulationTime &	operator= (const SimulationTime &)
Private Member Functions
template<class Archive>
void	serialize (Archive &archive, const unsigned int version)
Private Attributes
double	mDurationOfSimulation
unsigned	mTotalTimeStepsInSimulation
unsigned	mTimeStepsElapsed
bool	mEndTimeAndNumberOfTimeStepsSet
double	mCurrentTime
double	mEndTime
double	mStartTime
bool	mStartTimeSet
Static Private Attributes
static SimulationTime *	mpInstance = NULL
Friends
class	boost::serialization::access