#include <RandomNumberGenerator.hpp>

Inheritance diagram for RandomNumberGenerator:

Collaboration diagram for RandomNumberGenerator:

Public Member Functions
double	StandardNormalRandomDeviate ()
double	NormalRandomDeviate (double mean, double sd)
double	ranf ()
unsigned	randMod (unsigned base)
template<class T >
void	Shuffle (std::vector< boost::shared_ptr< T > > &rValues)
void	Shuffle (unsigned num, std::vector< unsigned > &rValues)
void	Reseed (int seed)
Static Public Member Functions
static RandomNumberGenerator *	Instance ()
static void	Destroy ()
Protected Member Functions
	RandomNumberGenerator ()
Private Member Functions
template<class Archive >
void	save (Archive &archive, const unsigned int version) const
template<class Archive >
void	load (Archive &archive, const unsigned int version)
Private Attributes
int	mSeed
long unsigned	mTimesCalled
double	mWorkingMem1
double	mWorkingMem2
double	mWorkingMemW
double	mRandNum2
bool	mUseLastNum
Static Private Attributes
static RandomNumberGenerator *	mpInstance = NULL
Friends
class	boost::serialization::access

Detailed Description

A special singleton class allowing one to generate different types of random number in a globally consistent way.

Definition at line 49 of file RandomNumberGenerator.hpp.

Constructor & Destructor Documentation

RandomNumberGenerator::RandomNumberGenerator ( ) [protected]

Protected constructor. Use Instance() to access the random number generator.

Definition at line 47 of file RandomNumberGenerator.cpp.

References mpInstance, and mSeed.

Referenced by Instance().

Member Function Documentation

void RandomNumberGenerator::Destroy ( ) [static]

Destroy the current instance of the random number generator. The next call to Instance will create a new instance and re-seed. This method *must* be called before program exit, to avoid a memory leak.

Definition at line 69 of file RandomNumberGenerator.cpp.

References mpInstance.

Referenced by AbstractCellBasedTestSuite::tearDown().

RandomNumberGenerator * RandomNumberGenerator::Instance ( ) [static]

Return a pointer to the random number generator object. The object is created the first time this method is called.

Definition at line 60 of file RandomNumberGenerator.cpp.

References mpInstance, and RandomNumberGenerator().

Referenced by AbstractCellBasedSimulation< ELEMENT_DIM, SPACE_DIM >::AbstractCellBasedSimulation(), MultipleCaBasedCellPopulation< DIM >::AddCell(), DiffusionForce< DIM >::AddForceContribution(), CryptSimulation2d::CalculateCellDivisionVector(), CryptSimulation1d::CalculateCellDivisionVector(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector(), RandomCellKiller< DIM >::CheckAndLabelSingleCellForApoptosis(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), CellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateBasicRandom(), StochasticWntCellCycleModel::GenerateStochasticG2Duration(), StochasticOxygenBasedCellCycleModel::GenerateStochasticG2Duration(), HoneycombMeshGenerator::GetCircularMesh(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetShortAxisOfElement(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), StochasticWntCellCycleModel::serialize(), SimpleWntCellCycleModel::serialize(), AbstractCellBasedSimulation< DIM >::serialize(), RandomCellKiller< DIM >::serialize(), StochasticOxygenBasedCellCycleModel::serialize(), StochasticDurationGenerationBasedCellCycleModel::serialize(), StochasticDurationCellCycleModel::serialize(), SimpleWntCellCycleModel::SetG1Duration(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), AbstractCellBasedTestSuite::setUp(), Shuffle(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), MultipleCaBasedCellPopulation< DIM >::UpdateCellLocations(), SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration(), and MultipleCaBasedCellPopulation< DIM >::WriteVtkResultsToFile().

template<class Archive >

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

Load the RandomNumberGenerator and its member variables.

Note:: do not serialize this singleton directly. Instead, serialize the object returned by GetSerializationWrapper().

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from SerializableSingleton< RandomNumberGenerator >.

Definition at line 106 of file RandomNumberGenerator.hpp.

References mRandNum2, mSeed, mTimesCalled, and mUseLastNum.

double RandomNumberGenerator::NormalRandomDeviate	(	double	mean,
		double	sd
	)

Generate a random number from a normal distribution with given mean and standard deviation.

Parameters:

mean	the mean of the normal distribution from which the random number is drawn
sd	the standard deviation of the normal distribution from which the random number is drawn

Definition at line 90 of file RandomNumberGenerator.cpp.

References StandardNormalRandomDeviate().

Referenced by StochasticWntCellCycleModel::GenerateStochasticG2Duration(), StochasticOxygenBasedCellCycleModel::GenerateStochasticG2Duration(), and SimpleWntCellCycleModel::SetG1Duration().

unsigned RandomNumberGenerator::randMod ( unsigned base )

Generate a random number modulo base (i.e. an integer within the range 0,..,base-1),

Parameters:

base	the order of the field of positive integers from which the random number is drawn

Definition at line 78 of file RandomNumberGenerator.cpp.

References mTimesCalled.

Referenced by MultipleCaBasedCellPopulation< DIM >::AddCell(), Shuffle(), and PottsBasedCellPopulation< DIM >::UpdateCellLocations().

double RandomNumberGenerator::ranf ( )

Generate a uniform random number in (0,1).

Definition at line 84 of file RandomNumberGenerator.cpp.

References mTimesCalled.

Referenced by CryptSimulation2d::CalculateCellDivisionVector(), CryptSimulation1d::CalculateCellDivisionVector(), OffLatticeSimulation< ELEMENT_DIM, SPACE_DIM >::CalculateCellDivisionVector(), RandomCellKiller< DIM >::CheckAndLabelSingleCellForApoptosis(), CryptCellsGenerator< CELL_CYCLE_MODEL >::Generate(), CellsGenerator< CELL_CYCLE_MODEL, DIM >::GenerateBasicRandom(), HoneycombMeshGenerator::GetCircularMesh(), CryptStatistics::GetCryptSection(), CryptProjectionStatistics::GetCryptSection(), VertexMesh< ELEMENT_DIM, SPACE_DIM >::GetShortAxisOfElement(), CryptSimulationBoundaryCondition< DIM >::ImposeBoundaryCondition(), StochasticDurationGenerationBasedCellCycleModel::SetG1Duration(), StochasticDurationCellCycleModel::SetG1Duration(), StandardNormalRandomDeviate(), PottsBasedCellPopulation< DIM >::UpdateCellLocations(), MultipleCaBasedCellPopulation< DIM >::UpdateCellLocations(), SimpleOxygenBasedCellCycleModel::UpdateHypoxicDuration(), and MultipleCaBasedCellPopulation< DIM >::WriteVtkResultsToFile().

void RandomNumberGenerator::Reseed ( int seed )

Reseed the random number generator.

Parameters:

seed	the new seed

Definition at line 95 of file RandomNumberGenerator.cpp.

References mSeed, and mTimesCalled.

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), and AbstractCellBasedTestSuite::setUp().

template<class Archive >

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

Save the RandomNumberGenerator and its member variables.

Note:: do not serialize this singleton directly. Instead, serialize the object returned by GetSerializationWrapper().

Parameters:

archive	the archive
version	the current version of this class

Reimplemented from SerializableSingleton< RandomNumberGenerator >.

Definition at line 88 of file RandomNumberGenerator.hpp.

References mRandNum2, mSeed, mTimesCalled, and mUseLastNum.

template<class T >

void RandomNumberGenerator::Shuffle ( std::vector< boost::shared_ptr< T > > & rValues ) [inline]

Produce a permutation of the integers and non-empty std::vector, using the Knuth-algorithm (also called the Fisher-Yates algorithm), a linear time unbiased method. The values are shuffled in place.

Parameters:

rValues the intial values and the output permutation of shuffled values. Must be non-empty

Definition at line 180 of file RandomNumberGenerator.hpp.

References Instance(), and randMod().

Referenced by DistributedTetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::ParMetisLibraryNodeAndElementPartitioning(), TetrahedralMesh< ELEMENT_DIM, SPACE_DIM >::PermuteNodes(), and PottsBasedCellPopulation< DIM >::UpdateCellLocations().

void RandomNumberGenerator::Shuffle	(	unsigned	num,
		std::vector< unsigned > &	rValues
	)

Produce a permutation of the integers 0,1,..,num-1, using the Knuth-algorithm (also called the Fisher-Yates algorithm), a linear time unbiased method. The shuffled values are returned in rValues, which doesn't need to be correctly-sized when passed in.

Parameters:

num	the number of integers to shuffle
rValues	the output permutation of shuffled values (any initial values ignored)

Definition at line 102 of file RandomNumberGenerator.cpp.

References Instance(), and randMod().

double RandomNumberGenerator::StandardNormalRandomDeviate ( )

Uses a ranf() call and an approximation to the inverse PDF of the normal distribution to generate an accurate estimate of a normally distributed random number. Adapted from the algorithm outlined at http://home.online.no/~pjacklam/notes/invnorm/#Pseudo_code_for_rational_approximation

Returns:: a random number from the normal distribution with mean 0 and standard distribution 1.

This little method implements the Box-Mueller/Marsaglia polar method for getting normally distributed variables from uniform ones.

G.E.P. Box and Mervin E. Muller, A Note on the Generation of Random Normal Deviates, The Annals of Mathematical Statistics (1958), Vol. 29, No. 2 pp. 610–611

doi:10.1214/aoms/1177706645

as given on http://en.wikipedia.org/wiki/Marsaglia_polar_method on 29/11/10

Definition at line 120 of file RandomNumberGenerator.cpp.

References mRandNum2, mUseLastNum, mWorkingMem1, mWorkingMem2, mWorkingMemW, and ranf().

Referenced by DiffusionForce< DIM >::AddForceContribution(), and NormalRandomDeviate().