#include <CStochasticRungeKuttaRI5.h>

Inheritance diagram for CStochasticRungeKuttaRI5:

Public Member Functions
	CStochasticRungeKuttaRI5 (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::stochasticRunkeKuttaRI5, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)

	CStochasticRungeKuttaRI5 (const CStochasticRungeKuttaRI5 &src, const CDataContainer *pParent)

virtual bool	elevateChildren ()

void	evalRoot (const double &time, CVectorCore< C_FLOAT64 > &rootValues)

virtual void	start ()

virtual void	stateChange (const CMath::StateChange &change)

virtual Status	step (const double &deltaT, const bool &final=false)

	~CStochasticRungeKuttaRI5 ()

Public Member Functions inherited from CTrajectoryMethod
	CTrajectoryMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)

	CTrajectoryMethod (const CTrajectoryMethod &src, const CDataContainer *pParent)

const CVectorCore< C_INT > &	getRoots () const

const bool &	integrateReducedModel () const

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

void	setProblem (CTrajectoryProblem *problem)

	~CTrajectoryMethod ()

Public Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent)

virtual void	clearCallBack ()

const CProcessReportLevel &	getCallBack () const

CMathContainer *	getMathContainer () const

const CTaskEnum::Method &	getSubType () const

const CTaskEnum::Task &	getType () const

virtual void	load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)

CCopasiMethod &	operator= (const CCopasiMethod &rhs)

virtual void	print (std::ostream *ostream) const

virtual void	printResult (std::ostream *ostream) const

virtual bool	setCallBack (CProcessReportLevel callBack)

void	setMathContainer (CMathContainer *pContainer)

virtual	~CCopasiMethod ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

void	addParameter (CCopasiParameter *pParameter)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

CCopasiParameterGroup *	assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
CType *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

index_iterator	beginIndex () const

const_name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")

void	clear ()

virtual void	createUndoData (CUndoData &undoData, const CUndoData::Type &type, const CData &oldData=CData(), const CCore::Framework &framework=CCore::Framework::ParticleNumbers) const

index_iterator	endIndex () const

const_name_iterator	endName () const

CCopasiParameterGroup &	getElementTemplates ()

const CCopasiParameterGroup &	getElementTemplates () const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

virtual size_t	getIndex (const CDataObject *pObject) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const size_t &index) const

std::string	getKey (const std::string &name) const

virtual const std::string &	getName (const size_t &index) const

virtual const CObjectInterface *	getObject (const CCommonName &cn) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter *	getParameter (std::string name)

const CCopasiParameter *	getParameter (std::string name) const

CCopasiParameter::Type	getType (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

template<class CType >
CType &	getValue (const size_t &index)

template<class CType >
const CType &	getValue (const size_t &index) const

template<class CType >
CType &	getValue (const std::string &name)

template<class CType >
const CType &	getValue (const std::string &name) const

bool	haveTemplate () const

virtual CUndoObjectInterface *	insert (const CData &data)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

virtual bool	remove (CDataObject *pObject)

bool	removeParameter (CCopasiParameter *pParameter)

bool	removeParameter (const size_t &index)

bool	removeParameter (const std::string &name)

virtual void	setUserInterfaceFlag (const UserInterfaceFlag &flag)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

size_t	size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual CData	toData () const

virtual void	updateIndex (const size_t &index, const CUndoObjectInterface *pUndoObject)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CDataContainer pParent=NO_PARENT, const std::string &objectType="Parameter")

virtual CCommonName	getCN () const override

template<class CType >
const CType &	getDefault () const

virtual const std::string &	getKey () const override

virtual std::string	getObjectDisplayName () const override

const CCopasiParameter::Type &	getType () const

const UserInterfaceFlag &	getUserInterfaceFlag () const

template<class CType >
std::vector< std::pair< CType, CType > > &	getValidValues ()

template<class CType >
const std::vector< std::pair< CType, CType > > &	getValidValues () const

void *	getValidValuesPointer () const

template<class CType >
CType &	getValue ()

template<class CType >
const CType &	getValue () const

virtual void *	getValuePointer () const override

CDataObject *	getValueReference () const

bool	hasValidValues () const

bool	isBasic () const

bool	isDefault () const

bool	isEditable () const

bool	isUnsupported () const

bool	isValidValue (const bool &value) const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const CCommonName &value) const

template<class CType >
bool	isValidValue (const CType &) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setDefault (const CType &defaultValue)

bool	setDefault (const std::vector< CCopasiParameter * > &defaultValue)

virtual bool	setObjectParent (const CDataContainer *pParent) override

template<class CType , class Enum >
bool	setValidValues (const CEnumAnnotation< CType, Enum > &validValues)

template<class CType >
bool	setValidValues (const std::vector< std::pair< CType, CType > > &validValues)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

Public Member Functions inherited from CDataContainer
virtual bool	add (CDataObject *pObject, const bool &adopt=true)

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

	CDataContainer (const CDataContainer &src, const CDataContainer *pParent)

	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

virtual std::string	getChildObjectUnits (const CDataObject *pObject) const

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

void	objectRenamed (CDataObject *pObject, const std::string &oldName)

virtual	~CDataContainer ()

Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)

void	addReference (const CDataContainer *pReference)

virtual void	calculateValue () override

	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)

virtual void	destruct () override

virtual const CDataObject *	getDataObject () const override

CDataContainer *	getObjectAncestor (const std::string &type) const

CDataModel *	getObjectDataModel () const

const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const

const std::string &	getObjectName () const

CDataContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override

virtual const CValidity &	getValidity () const override

bool	hasFlag (const Flag &flag) const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override

bool	prerequisitsContains (const DataObjectSet &objects) const

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

void	validityChanged (const CValidity &changedValidity) override

void	validityRemoved (const CValidity &changedValidity)

virtual	~CDataObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

	CObjectInterface (const CObjectInterface &src)

virtual	~CObjectInterface ()

Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()

	CUndoObjectInterface (const CUndoObjectInterface &src)

bool	generateUuid ()

const xg::Guid &	getUuid () const

bool	setUuid (const std::string &uuid)

bool	setUuid (const xg::Guid &uuid)

virtual	~CUndoObjectInterface ()

Private Member Functions
void	buildStage1 ()

void	buildStage2 ()

void	buildStage3 ()

C_FLOAT64	calculateSmallestPhysicalValue () const

void	calculateStateVariables (const double &time)

void	createRootMask ()

	CStochasticRungeKuttaRI5 ()

void	destroyRootMask ()

void	evalNoise (C_FLOAT64 *pNoise, const size_t &noiseDimension)

void	evalRate (C_FLOAT64 *rates)

void	generateRandomNumbers ()

void	initializeParameter ()

CTrajectoryMethod::Status	internalStep ()

C_FLOAT64	randomIHat ()

C_FLOAT64	randomITilde ()

Private Attributes
CMatrix< C_FLOAT64 >	mA

CVector< C_FLOAT64 >	mAtol

CVector< CMatrix< C_FLOAT64 > >	mB

CVector< CMatrix< C_FLOAT64 > >	mBB

CVectorCore< C_FLOAT64 >	mContainerNoise

CVectorCore< C_FLOAT64 >	mContainerRates

CVectorCore< C_FLOAT64 >	mContainerRoots

CVectorCore< C_FLOAT64 >	mContainerVariables

CVector< C_FLOAT64 >	mH10

CVector< C_FLOAT64 >	mH20

CMatrix< C_FLOAT64 >	mH2k

CVector< C_FLOAT64 >	mH30

CMatrix< C_FLOAT64 >	mH3k

CMatrix< C_FLOAT64 >	mHH2k

CMatrix< C_FLOAT64 >	mHH3k

size_t	mInternalSteps

C_FLOAT64	mLastCalculatedTime

CVector< C_FLOAT64 >	mLastCalculatedVariables

CVector< C_FLOAT64 * >	mNoiseInputValues

CVector< CCore::CUpdateSequence >	mNoiseUpdateSequences

size_t	mNumNoise

size_t	mNumRoots

size_t	mNumVariables

C_FLOAT64 *	mpAbsoluteTolerance

bool *	mpForcePhysicalCorrectness

CVector< bool >	mPhysicalValues

C_FLOAT64 *	mpInternalStepSize

unsigned C_INT32 *	mpMaxInternalSteps

C_INT *	mpPhysicalCorrectnessRootFound

CRandom *	mpRandom

C_FLOAT64 *	mpRootRelativeTolerance

CRootFinder::Eval *	mpRootValueCalculator

CVector< C_FLOAT64 >	mRandomIHat

CMatrix< C_FLOAT64 >	mRandomIMatrix

CVector< C_FLOAT64 >	mRandomITilde

size_t	mRootCounter

CRootFinder	mRootFinder

CVector< C_INT >	mRootMask

CRootFinder::RootMasking	mRootMasking

CVectorCore< C_FLOAT64 >	mRoots

C_FLOAT64	mSqrtStepSize

C_FLOAT64	mStepSize

CVector< C_FLOAT64 >	mSumAll1

CVector< C_FLOAT64 >	mSumAll2

CMatrix< C_FLOAT64 >	mSumPartial1

CMatrix< C_FLOAT64 >	mSumPartial2

C_FLOAT64	mTargetDelta

C_FLOAT64	mTargetTime

C_FLOAT64	mTime

Additional Inherited Members
Public Types inherited from CTrajectoryMethod
enum	Status { FAILURE = -1 , NORMAL = 0 , ROOT = 1 }

Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameter >	const_name_iterator

typedef std::vector< CCopasiParameter * >	elements

typedef elements::iterator	index_iterator

typedef CDataObjectMap::type_iterator< CCopasiParameter >	name_iterator

Public Types inherited from CCopasiParameter
enum class	eUserInterfaceFlag { editable , basic , unsupported , __SIZE }

enum class	Type { DOUBLE = 0 , UDOUBLE , INT , UINT , BOOL , GROUP , STRING , CN , KEY , FILE , EXPRESSION , INVALID , __SIZE }

typedef CFlags< eUserInterfaceFlag >	UserInterfaceFlag

Public Types inherited from CDataContainer
typedef CDataObjectMap	objectMap

Public Types inherited from CDataObject
typedef std::set< const CDataObject * >	DataObjectSet

enum	Flag { Container , Vector , Matrix , NameVector , Reference , ValueBool , ValueInt , ValueInt64 , ValueDbl , NonUniqueName , StaticString , ValueString , Separator , DisplayName , ModelEntity , Array , DataModel , Root , Gui , __SIZE }

Public Types inherited from CObjectInterface
typedef std::vector< const CDataContainer * >	ContainerList

typedef std::set< const CObjectInterface * >	ObjectSet

Static Public Member Functions inherited from CCopasiParameter
static void	allocateValidValues (const Type &type, void *&pValidValues)

static void	allocateValue (const Type &type, void *&pValue)

static void	assignValue (const Type &type, void &pValue, const void pNewValue)

static void	deleteValidValues (const Type &type, void *&pValidValues)

static void	deleteValue (const Type &type, void *&pValue)

static CCopasiParameter *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataContainer
static CDataContainer *	fromData (const CData &data, CUndoObjectInterface *pParent)

Static Public Member Functions inherited from CDataObject
static CDataObject *	fromData (const CData &data, CUndoObjectInterface *pParent)

static void	sanitizeObjectName (std::string &name)

Static Public Member Functions inherited from CObjectInterface
static const CDataObject *	DataObject (const CObjectInterface *pInterface)

static CObjectInterface *	GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName)

Static Public Member Functions inherited from CUndoObjectInterface
template<class CType >
static CType *	fromData (const CData &, CUndoObjectInterface *)

Static Public Attributes inherited from CCopasiParameter
static const CEnumAnnotation< std::string, Type >	TypeName

static const CEnumAnnotation< std::string, Type >	XMLType

Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList	EmptyList

Protected Member Functions inherited from CTrajectoryMethod
void	output (const bool &useMoieties)

virtual void	signalMathContainerChanged ()

Protected Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiMethod &src)

	CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src)

Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > *	addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataObjectReference< CType > *	addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

template<class CType >
CDataVectorReference< CType > *	addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)

	CDataContainer (const CDataContainer &src)

void	initObjects ()

Protected Member Functions inherited from CDataObject
	CDataObject ()

	CDataObject (const std::string &name, const CDataContainer pParent=static_cast< CDataContainer >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

Protected Attributes inherited from CTrajectoryMethod
CVectorCore< C_FLOAT64 >	mContainerState

C_FLOAT64 *	mpContainerStateTime

CTrajectoryProblem *	mpProblem

const bool *	mpReducedModel

CTrajectoryTask *	mpTask

CVectorCore< C_INT >	mRootsFound

Protected Attributes inherited from CCopasiMethod
CMathContainer *	mpContainer

CProcessReportLevel	mProcessReport

Protected Attributes inherited from CCopasiParameter
std::string	mKey

void *	mpDefault

void *	mpValidValues

void *	mpValue

CDataObject *	mpValueReference

UserInterfaceFlag	mUserInterfaceFlag

Protected Attributes inherited from CDataContainer
objectMap	mObjects

Protected Attributes inherited from CDataObject
ObjectSet	mPrerequisits

std::set< CDataContainer * >	mReferences

Protected Attributes inherited from CObjectInterface
CValidity	mValidity

Static Protected Attributes inherited from CTrajectoryMethod
static const bool	ReducedModel

Constructor & Destructor Documentation

◆ CStochasticRungeKuttaRI5() [1/3]

CStochasticRungeKuttaRI5::CStochasticRungeKuttaRI5 ( )

private

Constructor.

◆ CStochasticRungeKuttaRI5() [2/3]

CStochasticRungeKuttaRI5::CStochasticRungeKuttaRI5	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType = `CTaskEnum::Method::stochasticRunkeKuttaRI5`,
		const CTaskEnum::Task &	taskType = `CTaskEnum::Task::timeCourse`
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Method & methodType (default: deterministic)
const	CTaskEnum::Task & taskType (default: timeCourse)

References evalRoot(), initializeParameter(), and mpRootValueCalculator.

◆ CStochasticRungeKuttaRI5() [3/3]

CStochasticRungeKuttaRI5::CStochasticRungeKuttaRI5	(	const CStochasticRungeKuttaRI5 &	src,
		const CDataContainer *	pParent
	)

Copy constructor.

Parameters

const CStochasticRungeKuttaRI5 &	src
const	CDataContainer * pParent (default: NULL)

References CVectorCore< CType >::initialize(), initializeParameter(), mContainerNoise, mContainerRates, mContainerRoots, mContainerVariables, and mRoots.

◆ ~CStochasticRungeKuttaRI5()

CStochasticRungeKuttaRI5::~CStochasticRungeKuttaRI5 ( )

Destructor.

Member Function Documentation

◆ buildStage1()

void CStochasticRungeKuttaRI5::buildStage1 ( )

private

References CMatrix< CType >::array(), CVectorCore< CType >::begin(), c01, c11, c21, C_FLOAT64, evalNoise(), evalRate(), mA, mB, mBB, mContainerVariables, mH10, mNumNoise, mNumVariables, CTrajectoryMethod::mpContainerStateTime, mRandomIHat, mRandomIMatrix, mStepSize, mSumAll1, mSumPartial1, and mTime.

Referenced by calculateStateVariables().

◆ buildStage2()

void CStochasticRungeKuttaRI5::buildStage2 ( )

private

References A021, A121, A221, CMatrix< CType >::array(), B021, B121, B221, CVectorCore< CType >::begin(), c02, c12, c22, C_FLOAT64, CVectorCore< CType >::end(), evalNoise(), evalRate(), mA, mB, mBB, mContainerVariables, mH10, mH20, mH2k, mHH2k, mNumNoise, mNumVariables, CTrajectoryMethod::mpContainerStateTime, mRandomIHat, mRandomIMatrix, mSqrtStepSize, mStepSize, mSumAll1, mSumAll2, mSumPartial1, mSumPartial2, and mTime.

Referenced by calculateStateVariables().

◆ buildStage3()

void CStochasticRungeKuttaRI5::buildStage3 ( )

private

References A031, A032, A131, A132, A231, A232, B031, B032, B131, B132, B231, B232, CVectorCore< CType >::begin(), c03, c13, c23, C_FLOAT64, CVectorCore< CType >::end(), evalNoise(), evalRate(), mA, mB, mBB, mContainerVariables, mH10, mH30, mH3k, mHH3k, mNumNoise, mNumVariables, CTrajectoryMethod::mpContainerStateTime, mSqrtStepSize, mStepSize, mSumAll1, mSumAll2, mSumPartial1, mSumPartial2, and mTime.

Referenced by calculateStateVariables().

◆ calculateSmallestPhysicalValue()

C_FLOAT64 CStochasticRungeKuttaRI5::calculateSmallestPhysicalValue ( ) const

private

References CVectorCore< CType >::begin(), C_FLOAT64, CVectorCore< CType >::end(), mAtol, mContainerVariables, mpForcePhysicalCorrectness, and mPhysicalValues.

Referenced by evalRoot(), and internalStep().

◆ calculateStateVariables()

void CStochasticRungeKuttaRI5::calculateStateVariables ( const double & time )

private

◆ createRootMask()

void CStochasticRungeKuttaRI5::createRootMask ( )

private

References CRootFinder::ALL, CVectorCore< CType >::array(), CVectorCore< CType >::begin(), C_FLOAT64, C_INT, CMathContainer::calculateRootDerivatives(), CRootFinder::CONTINUOUS, CRootFinder::DISCRETE, CVectorCore< CType >::end(), CMathContainer::getRootIsDiscrete(), mContainerRoots, min, mNumRoots, CCopasiMethod::mpContainer, mRootMask, mRootMasking, CVector< CType >::resize(), and CMathContainer::updateSimulatedValues().

Referenced by internalStep().

◆ destroyRootMask()

void CStochasticRungeKuttaRI5::destroyRootMask ( )

private

References CVectorCore< CType >::begin(), C_FLOAT64, C_INT, CRootFinder::DISCRETE, CVectorCore< CType >::end(), CRootFinder::getRootError(), mContainerRoots, min, CCopasiMethod::mpContainer, mRootFinder, mRootMask, mRootMasking, CRootFinder::NONE, and CMathContainer::updateSimulatedValues().

Referenced by stateChange().

◆ elevateChildren()

bool CStochasticRungeKuttaRI5::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

References initializeParameter().

◆ evalNoise()

void CStochasticRungeKuttaRI5::evalNoise	(	C_FLOAT64 *	pNoise,
		const size_t &	noiseDimension
	)

private

This evaluates the noise

References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::begin(), C_FLOAT64, mContainerNoise, mNoiseUpdateSequences, mNumVariables, CCopasiMethod::mpContainer, and CMathContainer::resetNoise().

Referenced by buildStage1(), buildStage2(), and buildStage3().

◆ evalRate()

void CStochasticRungeKuttaRI5::evalRate ( C_FLOAT64 * rates )

private

This evaluates the derivatives

References CVectorCore< CType >::begin(), C_FLOAT64, mContainerRates, mNumVariables, CCopasiMethod::mpContainer, and CMathContainer::updateSimulatedValues().

Referenced by buildStage1(), buildStage2(), and buildStage3().

◆ evalRoot()

void CStochasticRungeKuttaRI5::evalRoot	(	const double &	time,
		CVectorCore< C_FLOAT64 > &	rootValues
	)

This evaluates the roots

References CVectorCore< CType >::begin(), C_FLOAT64, calculateSmallestPhysicalValue(), calculateStateVariables(), mContainerRoots, mNumRoots, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, CVectorCore< CType >::size(), and CMathContainer::updateRootValues().

Referenced by CStochasticRungeKuttaRI5().

◆ generateRandomNumbers()

void CStochasticRungeKuttaRI5::generateRandomNumbers ( )

private

References CMatrix< CType >::array(), CVectorCore< CType >::begin(), C_FLOAT64, mInternalSteps, mLastCalculatedTime, mNumNoise, mRandomIHat, mRandomIMatrix, mRandomITilde, randomIHat(), and randomITilde().

Referenced by internalStep().

◆ initializeParameter()

void CStochasticRungeKuttaRI5::initializeParameter ( )

private

Initialize the method parameter

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, mpAbsoluteTolerance, mpForcePhysicalCorrectness, mpInternalStepSize, mpMaxInternalSteps, mpRootRelativeTolerance, CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.

Referenced by CStochasticRungeKuttaRI5(), and elevateChildren().

◆ internalStep()

CTrajectoryMethod::Status CStochasticRungeKuttaRI5::internalStep ( )

private

References CRootFinder::ALL, CVectorCore< CType >::begin(), C_FLOAT64, C_INT, calculateSmallestPhysicalValue(), calculateStateVariables(), CRootFinder::checkRoots(), createRootMask(), CRootFinder::DISCRETE, CVectorCore< CType >::end(), CCopasiMessage::EXCEPTION, CTrajectoryMethod::FAILURE, fatalError, generateRandomNumbers(), CRootFinder::getRootTime(), CRootFinder::InvalidInterval, CMathContainer::isStateValid(), max, mContainerVariables, MCTrajectoryMethod, mH10, min, mInternalSteps, mNumRoots, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mpForcePhysicalCorrectness, mpInternalStepSize, mpMaxInternalSteps, mpPhysicalCorrectnessRootFound, mpRootRelativeTolerance, mRootFinder, mRootMasking, CTrajectoryMethod::mRootsFound, mTargetTime, mTime, CTrajectoryMethod::NORMAL, CRootFinder::NotAdvanced, CRootFinder::NotFound, CMath::NoToggle, CRootFinder::restart(), CTrajectoryMethod::ROOT, and CRootFinder::RootFound.

Referenced by step().

◆ randomIHat()

C_FLOAT64 CStochasticRungeKuttaRI5::randomIHat ( )

private

References CRandom::getRandomU(), and mpRandom.

Referenced by generateRandomNumbers().

◆ randomITilde()

C_FLOAT64 CStochasticRungeKuttaRI5::randomITilde ( )

private

References CRandom::getRandomU(), and mpRandom.

Referenced by generateRandomNumbers().

◆ start()

void CStochasticRungeKuttaRI5::start ( )

virtual

This instructs the method to prepare for integration

Reimplemented from CTrajectoryMethod.

References CVectorCore< CType >::begin(), CMathUpdateSequence::begin(), C_FLOAT64, C_INT, CMath::Compartment, CCore::Default, CRootFinder::DISCRETE, CMathUpdateSequence::empty(), CVectorCore< CType >::end(), CMathUpdateSequence::end(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getCountNoise(), CMathObject::getEntityType(), CMathContainer::getMathObject(), CMathContainer::getNoise(), CMathContainer::getNoiseInputObjects(), CMathContainer::getRandomGenerator(), CMathContainer::getRate(), CMathContainer::getRootIsDiscrete(), CMathContainer::getRoots(), CRootFinder::getRootValues(), CMathContainer::getStateObjects(), CRootFinder::getToggledRoots(), CMathContainer::getTransientDependencies(), CMathDependencyGraph::getUpdateSequence(), CVectorCore< CType >::initialize(), CRootFinder::initialize(), CMathContainer::initializeAtolVector(), CMathUpdateSequence::insert(), mA, mAtol, mB, mBB, mContainerNoise, mContainerRates, mContainerRoots, CTrajectoryMethod::mContainerState, mContainerVariables, mH10, mH20, mH2k, mH30, mH3k, mHH2k, mHH3k, mLastCalculatedTime, mNoiseInputValues, mNoiseUpdateSequences, mNumNoise, mNumRoots, mNumVariables, mpAbsoluteTolerance, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mPhysicalValues, mpInternalStepSize, mpPhysicalCorrectnessRootFound, mpRandom, mpRootRelativeTolerance, mpRootValueCalculator, mRandomIHat, mRandomIMatrix, mRandomITilde, mRootFinder, mRootMask, mRoots, CTrajectoryMethod::mRootsFound, mSqrtStepSize, mStepSize, mSumAll1, mSumAll2, mSumPartial1, mSumPartial2, mTargetTime, mTime, CRootFinder::NONE, CMatrix< CType >::resize(), CVector< CType >::resize(), CVectorCore< CType >::size(), CMath::Species, and CTrajectoryMethod::start().

◆ stateChange()

void CStochasticRungeKuttaRI5::stateChange ( const CMath::StateChange & change )

virtual

Inform the trajectory method that the state has changed outside its control

Parameters

const CMath::StateChange & change

Reimplemented from CTrajectoryMethod.

References CMath::ContinuousSimulation, destroyRootMask(), CFlags< Enum >::isSet(), mContainerVariables, mH10, mLastCalculatedTime, mRootFinder, CRootFinder::restart(), and CMath::State.

◆ step()

CTrajectoryMethod::Status CStochasticRungeKuttaRI5::step	(	const double &	deltaT,
		const bool &	final = `false`
	)

virtual

This instructs the method to calculate a time step of deltaT starting with the current state, i.e., the result of the previous step. The new state (after deltaT) is expected in the current state. The return value is the actual timestep taken.

Parameters

const	double & deltaT
const	bool & final (default: false)

Returns: Status status

Reimplemented from CTrajectoryMethod.

References CTrajectoryMethod::FAILURE, CTrajectoryProblem::getAutomaticStepSize(), internalStep(), mInternalSteps, mpInternalStepSize, mpMaxInternalSteps, CTrajectoryMethod::mpProblem, mRootCounter, mTargetDelta, mTargetTime, mTime, and CTrajectoryMethod::NORMAL.

Member Data Documentation

◆ mA

CMatrix< C_FLOAT64 > CStochasticRungeKuttaRI5::mA

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), and start().

◆ mAtol

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mAtol

private

Referenced by calculateSmallestPhysicalValue(), and start().

◆ mB

CVector< CMatrix< C_FLOAT64 > > CStochasticRungeKuttaRI5::mB

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), and start().

◆ mBB

CVector< CMatrix< C_FLOAT64 > > CStochasticRungeKuttaRI5::mBB

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), and start().

◆ mContainerNoise

CVectorCore< C_FLOAT64 > CStochasticRungeKuttaRI5::mContainerNoise

private

Referenced by CStochasticRungeKuttaRI5(), evalNoise(), and start().

◆ mContainerRates

CVectorCore< C_FLOAT64 > CStochasticRungeKuttaRI5::mContainerRates

private

Referenced by CStochasticRungeKuttaRI5(), evalRate(), and start().

◆ mContainerRoots

CVectorCore< C_FLOAT64 > CStochasticRungeKuttaRI5::mContainerRoots

private

Referenced by createRootMask(), CStochasticRungeKuttaRI5(), destroyRootMask(), evalRoot(), and start().

◆ mContainerVariables

CVectorCore< C_FLOAT64 > CStochasticRungeKuttaRI5::mContainerVariables

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateSmallestPhysicalValue(), calculateStateVariables(), CStochasticRungeKuttaRI5(), internalStep(), start(), and stateChange().

◆ mH10

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mH10

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), internalStep(), start(), and stateChange().

◆ mH20

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mH20

private

Referenced by buildStage2(), and start().

◆ mH2k

CMatrix< C_FLOAT64 > CStochasticRungeKuttaRI5::mH2k

private

Referenced by buildStage2(), and start().

◆ mH30

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mH30

private

Referenced by buildStage3(), and start().

◆ mH3k

CMatrix< C_FLOAT64 > CStochasticRungeKuttaRI5::mH3k

private

Referenced by buildStage3(), and start().

◆ mHH2k

CMatrix< C_FLOAT64 > CStochasticRungeKuttaRI5::mHH2k

private

Referenced by buildStage2(), and start().

◆ mHH3k

CMatrix< C_FLOAT64 > CStochasticRungeKuttaRI5::mHH3k

private

Referenced by buildStage3(), and start().

◆ mInternalSteps

size_t CStochasticRungeKuttaRI5::mInternalSteps

private

Referenced by generateRandomNumbers(), internalStep(), and step().

◆ mLastCalculatedTime

C_FLOAT64 CStochasticRungeKuttaRI5::mLastCalculatedTime

private

Referenced by calculateStateVariables(), generateRandomNumbers(), start(), and stateChange().

◆ mLastCalculatedVariables

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mLastCalculatedVariables

private

Referenced by calculateStateVariables().

◆ mNoiseInputValues

CVector< C_FLOAT64 * > CStochasticRungeKuttaRI5::mNoiseInputValues

private

Referenced by start().

◆ mNoiseUpdateSequences

CVector< CCore::CUpdateSequence > CStochasticRungeKuttaRI5::mNoiseUpdateSequences

private

Referenced by evalNoise(), and start().

◆ mNumNoise

size_t CStochasticRungeKuttaRI5::mNumNoise

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), generateRandomNumbers(), and start().

◆ mNumRoots

size_t CStochasticRungeKuttaRI5::mNumRoots

private

Referenced by createRootMask(), evalRoot(), internalStep(), and start().

◆ mNumVariables

size_t CStochasticRungeKuttaRI5::mNumVariables

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), evalNoise(), evalRate(), and start().

◆ mpAbsoluteTolerance

C_FLOAT64* CStochasticRungeKuttaRI5::mpAbsoluteTolerance

private

A pointer to to the value "Absolute Tolerance"

Referenced by initializeParameter(), and start().

◆ mpForcePhysicalCorrectness

bool* CStochasticRungeKuttaRI5::mpForcePhysicalCorrectness

private

A pointer to the value "Force Physical Correctness"

Referenced by calculateSmallestPhysicalValue(), initializeParameter(), and internalStep().

◆ mPhysicalValues

CVector< bool > CStochasticRungeKuttaRI5::mPhysicalValues

private

Referenced by calculateSmallestPhysicalValue(), and start().

◆ mpInternalStepSize

C_FLOAT64* CStochasticRungeKuttaRI5::mpInternalStepSize

private

A pointer to the value of "Internal Steps Size"

Referenced by calculateStateVariables(), initializeParameter(), internalStep(), start(), and step().

◆ mpMaxInternalSteps

unsigned C_INT32* CStochasticRungeKuttaRI5::mpMaxInternalSteps

private

A pointer to the value of "Max Internal Steps"

Referenced by initializeParameter(), internalStep(), and step().

◆ mpPhysicalCorrectnessRootFound

C_INT* CStochasticRungeKuttaRI5::mpPhysicalCorrectnessRootFound

private

A pointer to the value which indicate the physical correctness root was found.

Referenced by internalStep(), and start().

◆ mpRandom

CRandom* CStochasticRungeKuttaRI5::mpRandom

private

A pointer to the random number generator

Referenced by randomIHat(), randomITilde(), and start().

◆ mpRootRelativeTolerance

C_FLOAT64* CStochasticRungeKuttaRI5::mpRootRelativeTolerance

private

A pointer to the value of "Tolerance for Root Finder"

Referenced by initializeParameter(), internalStep(), and start().

◆ mpRootValueCalculator

CRootFinder::Eval* CStochasticRungeKuttaRI5::mpRootValueCalculator

private

Referenced by CStochasticRungeKuttaRI5(), and start().

◆ mRandomIHat

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mRandomIHat

private

Referenced by buildStage1(), buildStage2(), calculateStateVariables(), generateRandomNumbers(), and start().

◆ mRandomIMatrix

CMatrix< C_FLOAT64 > CStochasticRungeKuttaRI5::mRandomIMatrix

private

Referenced by buildStage1(), buildStage2(), calculateStateVariables(), generateRandomNumbers(), and start().

◆ mRandomITilde

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mRandomITilde

private

Referenced by generateRandomNumbers(), and start().

◆ mRootCounter

size_t CStochasticRungeKuttaRI5::mRootCounter

private

Referenced by step().

◆ mRootFinder

CRootFinder CStochasticRungeKuttaRI5::mRootFinder

private

Referenced by destroyRootMask(), internalStep(), start(), and stateChange().

◆ mRootMask

CVector< C_INT > CStochasticRungeKuttaRI5::mRootMask

private

Referenced by createRootMask(), destroyRootMask(), and start().

◆ mRootMasking

CRootFinder::RootMasking CStochasticRungeKuttaRI5::mRootMasking

private

Referenced by createRootMask(), destroyRootMask(), and internalStep().

◆ mRoots

CVectorCore< C_FLOAT64 > CStochasticRungeKuttaRI5::mRoots

private

Referenced by CStochasticRungeKuttaRI5(), and start().

◆ mSqrtStepSize

C_FLOAT64 CStochasticRungeKuttaRI5::mSqrtStepSize

private

Referenced by buildStage2(), buildStage3(), calculateStateVariables(), and start().

◆ mStepSize

C_FLOAT64 CStochasticRungeKuttaRI5::mStepSize

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), and start().

◆ mSumAll1

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mSumAll1

private

Referenced by buildStage1(), buildStage2(), buildStage3(), and start().

◆ mSumAll2

CVector< C_FLOAT64 > CStochasticRungeKuttaRI5::mSumAll2

private

Referenced by buildStage2(), buildStage3(), and start().

◆ mSumPartial1

CMatrix< C_FLOAT64 > CStochasticRungeKuttaRI5::mSumPartial1

private

Referenced by buildStage1(), buildStage2(), buildStage3(), and start().

◆ mSumPartial2

CMatrix< C_FLOAT64 > CStochasticRungeKuttaRI5::mSumPartial2

private

Referenced by buildStage2(), buildStage3(), and start().

◆ mTargetDelta

C_FLOAT64 CStochasticRungeKuttaRI5::mTargetDelta

private

Referenced by step().

◆ mTargetTime

C_FLOAT64 CStochasticRungeKuttaRI5::mTargetTime

private

Referenced by internalStep(), start(), and step().

◆ mTime

C_FLOAT64 CStochasticRungeKuttaRI5::mTime

private

Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), internalStep(), start(), and step().

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CStochasticRungeKuttaRI5() [1/3]

◆ CStochasticRungeKuttaRI5() [2/3]

◆ CStochasticRungeKuttaRI5() [3/3]

◆ ~CStochasticRungeKuttaRI5()

Member Function Documentation

◆ buildStage1()

◆ buildStage2()

◆ buildStage3()

◆ calculateSmallestPhysicalValue()

◆ calculateStateVariables()

◆ createRootMask()

◆ destroyRootMask()

◆ elevateChildren()

◆ evalNoise()

◆ evalRate()

◆ evalRoot()

◆ generateRandomNumbers()

◆ initializeParameter()

◆ internalStep()

◆ randomIHat()

◆ randomITilde()

◆ start()

◆ stateChange()

◆ step()

Member Data Documentation

◆ mA

◆ mAtol

◆ mB

◆ mBB

◆ mContainerNoise

◆ mContainerRates

◆ mContainerRoots

◆ mContainerVariables

◆ mH10

◆ mH20

◆ mH2k

◆ mH30

◆ mH3k

◆ mHH2k

◆ mHH3k

◆ mInternalSteps

◆ mLastCalculatedTime

◆ mLastCalculatedVariables

◆ mNoiseInputValues

◆ mNoiseUpdateSequences

◆ mNumNoise

◆ mNumRoots

◆ mNumVariables

◆ mpAbsoluteTolerance

◆ mpForcePhysicalCorrectness

◆ mPhysicalValues

◆ mpInternalStepSize

◆ mpMaxInternalSteps

◆ mpPhysicalCorrectnessRootFound

◆ mpRandom

◆ mpRootRelativeTolerance

◆ mpRootValueCalculator

◆ mRandomIHat

◆ mRandomIMatrix

◆ mRandomITilde

◆ mRootCounter

◆ mRootFinder

◆ mRootMask

◆ mRootMasking

◆ mRoots

◆ mSqrtStepSize

◆ mStepSize

◆ mSumAll1

◆ mSumAll2

◆ mSumPartial1

◆ mSumPartial2

◆ mTargetDelta

◆ mTargetTime

◆ mTime