SimulationTime Class Reference

#include <SimulationTime.hpp>

Collaboration diagram for SimulationTime:

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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 SimulationTimeInstance ()
static void Destroy ()

Protected Member Functions

 SimulationTime ()
 SimulationTime (const SimulationTime &)
SimulationTimeoperator= (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 SimulationTimempInstance = 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 mpInstance.

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 CellBasedSimulationWithPdes< DIM >::AfterSolve(), CryptProjectionForce::CalculateForceBetweenNodes(), GeneralisedLinearSpringForce< DIM >::CalculateForceBetweenNodes(), Cell::Cell(), AbstractCellCycleModel::GetAge(), CellCycleModelOdeHandler::GetDt(), NagaiHondaForce< DIM >::GetTargetAreaOfCell(), Cell::GetTimeUntilDeath(), Cell::IsDead(), CryptSimulationArchiver< DIM, SIM >::Load(), CellBasedSimulationArchiver< DIM, SIM >::Load(), VertexCryptSimulation2d::PostSolve(), CryptSimulation2d::PostSolve(), CellBasedSimulationWithPdes< DIM >::PostSolve(), AbstractSimpleCellCycleModel::ResetForDivision(), CryptSimulationArchiver< DIM, SIM >::Save(), CellBasedSimulationArchiver< DIM, SIM >::Save(), AbstractCellCycleModel::serialize(), AbstractCellBasedTestSuite::setUp(), VertexCryptSimulation2d::SetupSolve(), CryptSimulation2d::SetupSolve(), CellBasedSimulationWithPdes< DIM >::SetupSolve(), SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel(), CellBasedSimulation< DIM >::Solve(), Cell::StartApoptosis(), RandomCellKiller< DIM >::TestAndLabelSingleCellForApoptosis(), SingleOdeWntCellCycleModel::UpdateCellCyclePhase(), AbstractWntOdeBasedCellCycleModel::UpdateCellCyclePhase(), SimpleOxygenBasedCellCycleModel::UpdateCellCyclePhase(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration(), CellBasedSimulation< DIM >::UpdateNodePositions(), AbstractCellPopulation< DIM >::WriteCellIdDataToFile(), MeshBasedCellPopulation< DIM >::WriteCellPopulationVolumeResultsToFile(), MeshBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), DiscreteSystemForceCalculator::WriteResultsToFile(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), MeshBasedCellPopulation< DIM >::WriteResultsToFiles(), AbstractCellPopulation< DIM >::WriteResultsToFiles(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), MeshBasedCellPopulation< DIM >::WriteVoronoiResultsToFile(), MeshBasedCellPopulationWithGhostNodes< DIM >::WriteVtkResultsToFile(), and MeshBasedCellPopulation< DIM >::WriteVtkResultsToFile().

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 115 of file SimulationTime.cpp.

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

Referenced by CellBasedSimulation< 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 (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 131 of file SimulationTime.cpp.

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

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

double SimulationTime::GetTimeStep (  )  const

void SimulationTime::IncrementTimeOneStep (  ) 

Increment the simulation time by one time step.

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

Definition at line 85 of file SimulationTime.cpp.

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

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

unsigned SimulationTime::GetTimeStepsElapsed (  )  const

double SimulationTime::GetTime (  )  const

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

Returns:
simulation time

Definition at line 103 of file SimulationTime.cpp.

References mCurrentTime, and mStartTimeSet.

Referenced by AbstractCellCycleModel::GetAge(), NagaiHondaForce< DIM >::GetTargetAreaOfCell(), Cell::GetTimeUntilDeath(), VertexCryptSimulation2d::PostSolve(), CryptSimulation2d::PostSolve(), CellBasedSimulationWithPdes< DIM >::PostSolve(), AbstractSimpleCellCycleModel::ResetForDivision(), CryptSimulationArchiver< DIM, SIM >::Save(), CellBasedSimulationArchiver< DIM, SIM >::Save(), VertexCryptSimulation2d::SetupSolve(), CryptSimulation2d::SetupSolve(), CellBasedSimulationWithPdes< DIM >::SetupSolve(), SimpleOxygenBasedCellCycleModel::SimpleOxygenBasedCellCycleModel(), CellBasedSimulation< DIM >::Solve(), Cell::StartApoptosis(), AbstractOdeBasedCellCycleModel::UpdateCellCyclePhase(), SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration(), CellBasedSimulation< DIM >::UpdateNodePositions(), AbstractCellPopulation< DIM >::WriteCellIdDataToFile(), MeshBasedCellPopulation< DIM >::WriteCellPopulationVolumeResultsToFile(), MeshBasedCellPopulation< DIM >::WriteCellVolumeResultsToFile(), DiscreteSystemForceCalculator::WriteResultsToFile(), VertexBasedCellPopulation< DIM >::WriteResultsToFiles(), MeshBasedCellPopulation< DIM >::WriteResultsToFiles(), AbstractCellPopulation< DIM >::WriteResultsToFiles(), AbstractCentreBasedCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), AbstractCellPopulation< DIM >::WriteTimeAndNodeResultsToFiles(), and MeshBasedCellPopulation< 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 58 of file SimulationTime.cpp.

References mpInstance.

Referenced by AbstractCellBasedTestSuite::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 151 of file SimulationTime.cpp.

References mStartTimeSet.

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

bool SimulationTime::IsFinished (  )  const

Returns:
whether the simulation has finished.

Definition at line 157 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 163 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 68 of file SimulationTime.cpp.

References mCurrentTime, mStartTime, and mStartTimeSet.

Referenced by AbstractCellBasedTestSuite::setUp().

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

Overloaded assignment 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 the archive
version the current version of this class

Definition at line 219 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 208 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 163 of file SimulationTime.hpp.

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

The duration of the simulation (time is measured in units of hours).

Definition at line 168 of file SimulationTime.hpp.

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

The total number of steps for this simulation.

Definition at line 173 of file SimulationTime.hpp.

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

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

Definition at line 178 of file SimulationTime.hpp.

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

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

Definition at line 184 of file SimulationTime.hpp.

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

double SimulationTime::mCurrentTime [private]

double SimulationTime::mEndTime [private]

The time at which the simulation should stop

Definition at line 194 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 199 of file SimulationTime.hpp.

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

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

Definition at line 205 of file SimulationTime.hpp.

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


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

Generated on Mon Nov 1 12:37:22 2010 for Chaste by  doxygen 1.5.5