#include <CHybridMethodODE45.h>

Inheritance diagram for CHybridMethodODE45:

Classes
struct	Data

Public Member Functions
	CHybridMethodODE45 (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::hybridODE45, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)

	CHybridMethodODE45 (const CHybridMethodODE45 &src, const CDataContainer *pParent)

virtual bool	elevateChildren ()

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

virtual void	start ()

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

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

	~CHybridMethodODE45 ()

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

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 ()

Protected Types
enum	IntergrationType { DETERMINISTIC , HYBRID }

enum	PartitioningStrategyType { AllDeterministic = 0 , UserSpecified , AllStochastic }

enum	RootMasking { NONE = 0 , ALL , DISCRETE }

Protected Member Functions
C_INT32	checkModel (CModel *model)

bool	checkRoots ()

	CHybridMethodODE45 ()

void	determineIntegrationType ()

C_FLOAT64	doSingleStep (C_FLOAT64 endTime)

void	evalF (const C_FLOAT64 t, const C_FLOAT64 y, C_FLOAT64 *ydot)

void	evalR (const C_FLOAT64 t, const C_FLOAT64 y, const size_t nr, C_FLOAT64 r)

void	fireReaction ()

CMathReaction *	getReactionToFire ()

void	integrateDeterministicPart (C_FLOAT64 ds)

void	partitionSystem ()

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)

Static Protected Member Functions
static void	EvalF (const size_t n, const C_FLOAT64 t, const C_FLOAT64 y, C_FLOAT64 ydot)

static void	EvalR (const size_t n, const C_FLOAT64 t, const C_FLOAT64 y, const size_t nr, C_FLOAT64 *r)

Protected Attributes
RootMasking	mRootMasking

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
static std::string	PartitioningStrategy []

Static Protected Attributes inherited from CTrajectoryMethod
static const bool	ReducedModel

Private Member Functions
void	createRootMask ()

void	destroyRootMask ()

void	initializeParameter ()

void	maskRoots (CVectorCore< C_FLOAT64 > &rootValues)

Private Attributes
C_FLOAT64	mA0

CVector< C_FLOAT64 * >	mAmuPointers

CVectorCore< C_FLOAT64 >	mAmuVariables

CVectorCore< C_FLOAT64 >	mContainerFluxes

size_t	mCountContainerVariables

size_t	mCountReactionSpecies

Data	mData

CVectorCore< bool >	mDiscreteRoots

bool	mEventProcessing

bool	mFireReaction

size_t	mFirstReactionSpeciesIndex

CVector< C_FLOAT64 * >	mFluxPointers

bool	mHasDetermReaction

bool	mHasStoiReaction

IntergrationType	mIntegrationType

CVector< C_FLOAT64 >	mLastSuccessState

size_t	mMaxBalance

bool	mMaxStepsReached

CVector< C_INT >	mMethodRootsFound

CRungeKutta	mODE45

bool	mODEInitalized

size_t	mOutputCounter

std::ofstream	mOutputFile

std::string	mOutputFileName

C_FLOAT64 *	mpAbsoluteTolerance

CCopasiParameterGroup *	mpFastReactions

C_INT *	mpHybridRoot

unsigned C_INT32 *	mpMaxInternalSteps

std::string *	mpPartitioningStrategy

CRandom *	mpRandomGenerator

unsigned C_INT32 *	mpRandomSeed

C_FLOAT64 *	mpRelativeTolerance

CCore::CUpdateSequence	mPropensitiesUpdateSequence

bool *	mpUseRandomSeed

const C_FLOAT64 *	mpYdot

CRungeKutta::RKMethodStatus	mRKMethodStatus

size_t	mRootCounter

CVector< bool >	mRootMask

CVector< C_FLOAT64 >	mRootsNonZero

CVector< C_FLOAT64 >	mRootValuesLeft

CVectorCore< C_FLOAT64 >	mRootValuesRight

CVector< C_FLOAT64 >	mSavedFluxes

CVector< CMathReaction * >	mSlowReactions

CCore::CUpdateSequence	mSpeciesRateUpdateSequence

C_FLOAT64	mTargetTime

CVector< C_FLOAT64 >	mY

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

Detailed Description

A class to record whether a metab is slow or fast

Parameters

fastReactions	is applied to store which reactions this metab participates
flag,if	set is empty -> false, else, -> true

Member Enumeration Documentation

◆ IntergrationType

enum CHybridMethodODE45::IntergrationType

protected

Enumerator
DETERMINISTIC
HYBRID

◆ PartitioningStrategyType

enum CHybridMethodODE45::PartitioningStrategyType

protected

Enumerator
AllDeterministic
UserSpecified
AllStochastic

◆ RootMasking

enum CHybridMethodODE45::RootMasking

protected

Enumerator
NONE
ALL
DISCRETE

Constructor & Destructor Documentation

◆ CHybridMethodODE45() [1/3]

CHybridMethodODE45::CHybridMethodODE45 ( )

protected

Default Constructor

◆ CHybridMethodODE45() [2/3]

CHybridMethodODE45::CHybridMethodODE45	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType = `CTaskEnum::Method::hybridODE45`,
		const CTaskEnum::Task &	taskType = `CTaskEnum::Task::timeCourse`
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Method & methodType (default: hybridODE45)
const	CTaskEnum::Task & taskType (default: timeCourse)

Default constructor.

References CHybridMethodODE45::Data::dim, initializeParameter(), mData, and CHybridMethodODE45::Data::pMethod.

◆ CHybridMethodODE45() [3/3]

CHybridMethodODE45::CHybridMethodODE45	(	const CHybridMethodODE45 &	src,
		const CDataContainer *	pParent
	)

Copy constructor

Parameters

const	CHybridMethodODE45 & src
const	CDataContainer * pParent (default: NULL)

Copy Constructor

References CHybridMethodODE45::Data::dim, initializeParameter(), mData, and CHybridMethodODE45::Data::pMethod.

◆ ~CHybridMethodODE45()

CHybridMethodODE45::~CHybridMethodODE45 ( )

Destructor.

References CVectorCore< CType >::array(), and CTrajectoryMethod::mRootsFound.

Member Function Documentation

◆ checkModel()

C_INT32 CHybridMethodODE45::checkModel ( CModel * model )

protected

Test the model if it is proper to perform stochastic simulations on. Several properties are tested (e.g. integer stoichometry, all reactions take place in one compartment only, irreversibility...).

Returns: 0, if everything is ok; <0, if an error occured.

References C_FLOAT64, C_INT32, CModel::getReactions(), CModel::getStoi(), INT_EPSILON, CMatrix< CType >::numRows(), and CDataVector< CType >::size().

◆ checkRoots()

bool CHybridMethodODE45::checkRoots ( )

protected

Check whether a root has been found

References CVectorCore< CType >::array(), C_FLOAT64, C_INT, CMathContainer::getRootIsDiscrete(), CMathContainer::getRootIsTimeDependent(), CCopasiMethod::mpContainer, CTrajectoryMethod::mRootsFound, mRootsNonZero, mRootValuesLeft, mRootValuesRight, CMath::NoToggle, CVectorCore< CType >::size(), CMath::ToggleBoth, CMath::ToggleEquality, and CMath::ToggleInequality.

Referenced by fireReaction().

◆ createRootMask()

void CHybridMethodODE45::createRootMask ( )

private

References ALL, CVectorCore< CType >::array(), C_FLOAT64, CMathContainer::calculateRootDerivatives(), CMathContainer::getRoots(), min, CCopasiMethod::mpContainer, mRootMask, mRootMasking, CTrajectoryMethod::mRootsFound, CVector< CType >::resize(), CVectorCore< CType >::size(), and CMathContainer::updateRootValues().

Referenced by integrateDeterministicPart().

◆ destroyRootMask()

void CHybridMethodODE45::destroyRootMask ( )

private

References mRootMask, mRootMasking, NONE, and CVector< CType >::resize().

Referenced by fireReaction(), integrateDeterministicPart(), and stateChange().

◆ determineIntegrationType()

void CHybridMethodODE45::determineIntegrationType ( )

protected

Setup mMethod, switching between Deterministic Method and Hybrid Method

References DETERMINISTIC, HYBRID, mHasStoiReaction, and mIntegrationType.

Referenced by start().

◆ doSingleStep()

C_FLOAT64 CHybridMethodODE45::doSingleStep ( C_FLOAT64 endTime )

protected

Simulates the system over the next interval of time. The current time and the end time of the current step() are given as arguments.

Parameters

endTime A C_FLOAT64 specifying the end time of the step()

Returns: A C_FLOAT giving the new time

Simulates the system over the next interval of time. The new time after this step is returned.

Parameters

endTime A C_FLOAT64 specifying the endTime of the current step()

Returns: A C_FLOAT giving the new time

References C_FLOAT64, CRungeKutta::ERROR, fireReaction(), integrateDeterministicPart(), mEventProcessing, mFireReaction, CTrajectoryMethod::mpContainerStateTime, and mRKMethodStatus.

Referenced by step().

◆ elevateChildren()

bool CHybridMethodODE45::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().

◆ evalF()

void CHybridMethodODE45::evalF	(	const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		C_FLOAT64 *	ydot
	)

protected

This evaluates the derivatives for the complete model

Derivative Calculation Function

References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::array(), C_FLOAT64, CHybridMethodODE45::Data::dim, HYBRID, mAmuPointers, mContainerFluxes, mCountContainerVariables, mCountReactionSpecies, mData, mFirstReactionSpeciesIndex, mFluxPointers, mIntegrationType, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mPropensitiesUpdateSequence, mpYdot, mSavedFluxes, mSpeciesRateUpdateSequence, CVectorCore< CType >::size(), and CMathContainer::updateSimulatedValues().

Referenced by EvalF().

◆ EvalF()

void CHybridMethodODE45::EvalF	(	const size_t *	n,
		const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		C_FLOAT64 *	ydot
	)

staticprotected

Dummy Function for calculating derivative of ODE systems

Dummy f function for calculating derivative of y

References evalF(), and CHybridMethodODE45::Data::pMethod.

Referenced by integrateDeterministicPart().

◆ evalR()

void CHybridMethodODE45::evalR	(	const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		const size_t *	nr,
		C_FLOAT64 *	r
	)

protected

This evaluates the roots value of the system

Dummy Function for calculating roots value

References C_FLOAT64, CHybridMethodODE45::Data::dim, CMathContainer::getRoots(), HYBRID, CVectorCore< CType >::initialize(), mA0, mAmuPointers, maskRoots(), mCountContainerVariables, mData, mIntegrationType, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mRootMasking, NONE, CVectorCore< CType >::size(), and CMathContainer::updateRootValues().

Referenced by EvalR().

◆ EvalR()

void CHybridMethodODE45::EvalR	(	const size_t *	n,
		const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		const size_t *	nr,
		C_FLOAT64 *	r
	)

staticprotected

Dummy Function for calculating roots value

Dummy f function for calculating roots value

References evalR(), and CHybridMethodODE45::Data::pMethod.

Referenced by integrateDeterministicPart().

◆ fireReaction()

void CHybridMethodODE45::fireReaction ( )

protected

Fire slow reaction and update populations and propensities when Hybrid Method is used

References checkRoots(), destroyRootMask(), CMathReaction::fire(), CRandom::getRandomOO(), getReactionToFire(), mA0, mAmuVariables, mEventProcessing, mFireReaction, CCopasiMethod::mpContainer, mpRandomGenerator, mRKMethodStatus, mRootValuesLeft, mRootValuesRight, CRungeKutta::RESTART, CMathContainer::updateRootValues(), and CMathContainer::updateSimulatedValues().

Referenced by doSingleStep().

◆ getReactionToFire()

CMathReaction * CHybridMethodODE45::getReactionToFire ( )

protected

Function return a reaction index which is a slow reaction firing at the event time.

Returns: CMathReaction * pReaction

Calculate which slow reaction fires

References CVectorCore< CType >::array(), C_FLOAT64, CRandom::getRandomOO(), mA0, mAmuVariables, mpRandomGenerator, mSlowReactions, and CVectorCore< CType >::size().

Referenced by fireReaction().

◆ initializeParameter()

void CHybridMethodODE45::initializeParameter ( )

private

Intialize the method parameter

Initialize the method parameter

References CCopasiParameterGroup::addParameter(), CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::CN, CCopasiParameterGroup::getElementTemplates(), CCopasiParameterGroup::getParameter(), mpAbsoluteTolerance, mpFastReactions, mpMaxInternalSteps, mpPartitioningStrategy, mpRandomSeed, mpRelativeTolerance, mpUseRandomSeed, PartitioningStrategy, RANDOM_SEED, CCopasiParameter::setValidValues(), CCopasiParameter::STRING, CCopasiParameter::UDOUBLE, CCopasiParameter::UINT, and USE_RANDOM_SEED.

Referenced by CHybridMethodODE45(), and elevateChildren().

◆ integrateDeterministicPart()

void CHybridMethodODE45::integrateDeterministicPart ( C_FLOAT64 endTime )

protected

Integrates the deterministic reactions of the system over the specified time interval.

Parameters

ds	A C_FLOAT64 specifying the stepsize.

References ALL, CVectorCore< CType >::array(), C_FLOAT64, C_INT, CRungeKutta::CONTINUE, createRootMask(), destroyRootMask(), CHybridMethodODE45::Data::dim, DISCRETE, CRungeKutta::ERROR, EvalF(), EvalR(), CCopasiMessage::EXCEPTION, fatalError, CTrajectoryProblem::getAutomaticStepSize(), CRungeKutta::getErrorMesssage(), CRungeKutta::INITIALIZE, max, CTrajectoryMethod::mContainerState, mCountContainerVariables, MCTrajectoryMethod, mData, mDiscreteRoots, mEventProcessing, mFireReaction, mLastSuccessState, mMethodRootsFound, mODE45, mpAbsoluteTolerance, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mpHybridRoot, mpMaxInternalSteps, CTrajectoryMethod::mpProblem, mpRelativeTolerance, mRKMethodStatus, mRootCounter, mRootMask, mRootMasking, CTrajectoryMethod::mRootsFound, mY, NONE, CRungeKutta::RESTART, CRungeKutta::ROOTFOUND, CVectorCore< CType >::size(), and CMathContainer::updateSimulatedValues().

Referenced by doSingleStep().

◆ isValidProblem()

bool CHybridMethodODE45::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CTrajectoryMethod.

References CCopasiMessage::ERROR, CTrajectoryProblem::getDuration(), CTrajectoryMethod::isValidProblem(), and MCTrajectoryMethod.

◆ maskRoots()

void CHybridMethodODE45::maskRoots ( CVectorCore< C_FLOAT64 > & rootValues )

private

References CVectorCore< CType >::array(), C_FLOAT64, mRootMask, and CVectorCore< CType >::size().

Referenced by evalR().

◆ partitionSystem()

void CHybridMethodODE45::partitionSystem ( )

protected

Check whether a function is fast or not.

References AllDeterministic, AllStochastic, CVectorCore< CType >::array(), CCopasiParameterGroup::beginIndex(), C_FLOAT64, CCore::Default, CMath::Dependent, CCopasiParameterGroup::endIndex(), fatalError, CMathContainer::getFluxes(), CMathContainer::getMathReaction(), CDataObject::getObjectFromCN(), CMathReaction::getPropensityObject(), CMathContainer::getReactions(), CMathObject::getSimulationType(), CMathContainer::getSimulationUpToDateObjects(), CMathContainer::getTransientDependencies(), CMathDependencyGraph::getUpdateSequence(), CMathObject::getValuePointer(), CMathObject::getValueType(), CMath::Independent, CVectorCore< CType >::initialize(), mAmuPointers, mContainerFluxes, mFluxPointers, mHasDetermReaction, mHasStoiReaction, CCopasiMethod::mpContainer, mpFastReactions, mpPartitioningStrategy, mPropensitiesUpdateSequence, mSlowReactions, mSpeciesRateUpdateSequence, PartitioningStrategy, CMath::Rate, CVector< CType >::resize(), CVectorCore< CType >::size(), CCopasiParameterGroup::size(), and UserSpecified.

Referenced by start().

◆ start()

void CHybridMethodODE45::start ( )

virtual

This instructs the method to prepare for integration starting with the initialState given.

Parameters

const CState * initialState

Reimplemented from CTrajectoryMethod.

◆ stateChange()

void CHybridMethodODE45::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(), CMath::EventSimulation, CRungeKutta::INITIALIZE, mRKMethodStatus, CRungeKutta::RESTART, and CMath::State.

◆ step()

CTrajectoryMethod::Status CHybridMethodODE45::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

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

Returns: Status status

Reimplemented from CTrajectoryMethod.

References C_FLOAT64, doSingleStep(), CRungeKutta::ERROR, CTrajectoryMethod::FAILURE, CTrajectoryProblem::getAutomaticStepSize(), CTrajectoryMethod::mContainerState, mEventProcessing, min, mLastSuccessState, mMaxStepsReached, CTrajectoryMethod::mpContainerStateTime, mpMaxInternalSteps, CTrajectoryMethod::mpProblem, mRKMethodStatus, mRootCounter, mTargetTime, CTrajectoryMethod::NORMAL, CTrajectoryMethod::ROOT, and CCopasiMessage::WARNING.

Member Data Documentation

◆ mA0

C_FLOAT64 CHybridMethodODE45::mA0

private

Referenced by evalR(), fireReaction(), getReactionToFire(), and start().

◆ mAmuPointers

CVector< C_FLOAT64 * > CHybridMethodODE45::mAmuPointers

private

Referenced by evalF(), evalR(), and partitionSystem().

◆ mAmuVariables

CVectorCore< C_FLOAT64 > CHybridMethodODE45::mAmuVariables

private

The variables handling the integrated propensities of the stochastic reactions.

Referenced by fireReaction(), getReactionToFire(), and start().

◆ mContainerFluxes

CVectorCore< C_FLOAT64 > CHybridMethodODE45::mContainerFluxes

private

Referenced by evalF(), and partitionSystem().

◆ mCountContainerVariables

size_t CHybridMethodODE45::mCountContainerVariables

private

Referenced by evalF(), evalR(), integrateDeterministicPart(), and start().

◆ mCountReactionSpecies

size_t CHybridMethodODE45::mCountReactionSpecies

private

Referenced by evalF(), and start().

◆ mData

Data CHybridMethodODE45::mData

private

mData.dim is the dimension of the ODE system. mData.pMethod contains CLsodaMethod * this to be used in the static method EvalF

Referenced by CHybridMethodODE45(), evalF(), evalR(), integrateDeterministicPart(), and start().

◆ mDiscreteRoots

CVectorCore< bool > CHybridMethodODE45::mDiscreteRoots

private

A which indicates whether roots change only discretely.

Referenced by integrateDeterministicPart(), and start().

◆ mEventProcessing

bool CHybridMethodODE45::mEventProcessing

private

Status of Root and Slow Event

Referenced by doSingleStep(), fireReaction(), integrateDeterministicPart(), and step().

◆ mFireReaction

bool CHybridMethodODE45::mFireReaction

private

Referenced by doSingleStep(), fireReaction(), and integrateDeterministicPart().

◆ mFirstReactionSpeciesIndex

size_t CHybridMethodODE45::mFirstReactionSpeciesIndex

private

Referenced by evalF(), and start().

◆ mFluxPointers

CVector< C_FLOAT64 * > CHybridMethodODE45::mFluxPointers

private

Referenced by evalF(), and partitionSystem().

◆ mHasDetermReaction

bool CHybridMethodODE45::mHasDetermReaction

private

Referenced by partitionSystem().

◆ mHasStoiReaction

bool CHybridMethodODE45::mHasStoiReaction

private

Bool value

Referenced by determineIntegrationType(), and partitionSystem().

◆ mIntegrationType

IntergrationType CHybridMethodODE45::mIntegrationType

private

An Integer showes the method now CHybridMethod used 0 == Stochastic 1 == Deterministic 2 == Hybrid

Referenced by determineIntegrationType(), evalF(), evalR(), and start().

◆ mLastSuccessState

CVector< C_FLOAT64 > CHybridMethodODE45::mLastSuccessState

private

A pointer to the current state in complete model view.

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

◆ mMaxBalance

size_t CHybridMethodODE45::mMaxBalance

private

maximal increase of a particle number in one step.

◆ mMaxStepsReached

bool CHybridMethodODE45::mMaxStepsReached

private

Referenced by start(), and step().

◆ mMethodRootsFound

CVector< C_INT > CHybridMethodODE45::mMethodRootsFound

private

Referenced by integrateDeterministicPart(), and start().

◆ mODE45

CRungeKutta CHybridMethodODE45::mODE45

private

mODE45

Referenced by integrateDeterministicPart().

◆ mODEInitalized

bool CHybridMethodODE45::mODEInitalized

private

Record whether ODE solver has been initialized

◆ mOutputCounter

size_t CHybridMethodODE45::mOutputCounter

private

Output counter.

◆ mOutputFile

std::ofstream CHybridMethodODE45::mOutputFile

private

File output stream to write data.

◆ mOutputFileName

std::string CHybridMethodODE45::mOutputFileName

private

Output filename.

◆ mpAbsoluteTolerance

C_FLOAT64* CHybridMethodODE45::mpAbsoluteTolerance

private

Referenced by initializeParameter(), and integrateDeterministicPart().

◆ mpFastReactions

CCopasiParameterGroup* CHybridMethodODE45::mpFastReactions

private

Referenced by initializeParameter(), and partitionSystem().

◆ mpHybridRoot

C_INT* CHybridMethodODE45::mpHybridRoot

private

Referenced by integrateDeterministicPart(), and start().

◆ mpMaxInternalSteps

unsigned C_INT32* CHybridMethodODE45::mpMaxInternalSteps

private

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

◆ mpPartitioningStrategy

std::string* CHybridMethodODE45::mpPartitioningStrategy

private

Referenced by initializeParameter(), and partitionSystem().

◆ mpRandomGenerator

CRandom* CHybridMethodODE45::mpRandomGenerator

private

The random number generator.

Referenced by fireReaction(), getReactionToFire(), and start().

◆ mpRandomSeed

unsigned C_INT32* CHybridMethodODE45::mpRandomSeed

private

Referenced by initializeParameter(), and start().

◆ mpRelativeTolerance

C_FLOAT64* CHybridMethodODE45::mpRelativeTolerance

private

Referenced by initializeParameter(), and integrateDeterministicPart().

◆ mPropensitiesUpdateSequence

CCore::CUpdateSequence CHybridMethodODE45::mPropensitiesUpdateSequence

private

Referenced by evalF(), and partitionSystem().

◆ mpUseRandomSeed

bool* CHybridMethodODE45::mpUseRandomSeed

private

Referenced by initializeParameter(), and start().

◆ mpYdot

const C_FLOAT64* CHybridMethodODE45::mpYdot

private

Referenced by evalF(), and start().

◆ mRKMethodStatus

CRungeKutta::RKMethodStatus CHybridMethodODE45::mRKMethodStatus

private

Referenced by doSingleStep(), fireReaction(), integrateDeterministicPart(), start(), stateChange(), and step().

◆ mRootCounter

size_t CHybridMethodODE45::mRootCounter

private

Max number of doSingleStep() per step()

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

◆ mRootMask

CVector< bool > CHybridMethodODE45::mRootMask

private

A mask which hides all roots being constant and zero.

Referenced by createRootMask(), destroyRootMask(), integrateDeterministicPart(), and maskRoots().

◆ mRootMasking

RootMasking CHybridMethodODE45::mRootMasking

protected

Root counter to determine whether the internal step limit is exceeded. A Boolean flag indicating whether we should try masking roots

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

◆ mRootsNonZero

CVector< C_FLOAT64 > CHybridMethodODE45::mRootsNonZero

private

2 Vector for storing root value

Referenced by checkRoots(), and start().

◆ mRootValuesLeft

CVector< C_FLOAT64 > CHybridMethodODE45::mRootValuesLeft

private

Value of Roots before a reaction event

Referenced by checkRoots(), fireReaction(), and start().

◆ mRootValuesRight

CVectorCore< C_FLOAT64 > CHybridMethodODE45::mRootValuesRight

private

Value of Roots after a reaction event

Referenced by checkRoots(), fireReaction(), and start().

◆ mSavedFluxes

CVector< C_FLOAT64 > CHybridMethodODE45::mSavedFluxes

private

Referenced by evalF().

◆ mSlowReactions

CVector< CMathReaction * > CHybridMethodODE45::mSlowReactions

private

Vector containing pointers to the slow of the model.

Referenced by getReactionToFire(), partitionSystem(), and start().

◆ mSpeciesRateUpdateSequence

CCore::CUpdateSequence CHybridMethodODE45::mSpeciesRateUpdateSequence

private

Referenced by evalF(), and partitionSystem().

◆ mTargetTime

C_FLOAT64 CHybridMethodODE45::mTargetTime

private

Time Record

Referenced by start(), and step().

◆ mY

CVector< C_FLOAT64 > CHybridMethodODE45::mY

private

Vector of integration variables

Referenced by integrateDeterministicPart(), and start().

◆ PartitioningStrategy

std::string CHybridMethodODE45::PartitioningStrategy

staticprotected

Initial value:

=
{
  "All Reactions Deterministic",
  "User specified Partition",
  "All Reactions Stochastic",
  ""
}

CHybridMethodODE45

This class implements an hybrid algorithm for the simulation of a biochemical system over time.

File name: CHybridMethodODE45.cpp Author: Shuo Wang Email: shuow.nosp@m.ang..nosp@m.learn.nosp@m.er@g.nosp@m.mail..nosp@m.com

Last change: 11, Aug 2014

Referenced by initializeParameter(), and partitionSystem().

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

Classes

Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Static Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ IntergrationType

◆ PartitioningStrategyType

◆ RootMasking

Constructor & Destructor Documentation

◆ CHybridMethodODE45() [1/3]

◆ CHybridMethodODE45() [2/3]

◆ CHybridMethodODE45() [3/3]

◆ ~CHybridMethodODE45()

Member Function Documentation

◆ checkModel()

◆ checkRoots()

◆ createRootMask()

◆ destroyRootMask()

◆ determineIntegrationType()

◆ doSingleStep()

◆ elevateChildren()

◆ evalF()

◆ EvalF()

◆ evalR()

◆ EvalR()

◆ fireReaction()

◆ getReactionToFire()

◆ initializeParameter()

◆ integrateDeterministicPart()

◆ isValidProblem()

◆ maskRoots()

◆ partitionSystem()

◆ start()

◆ stateChange()

◆ step()

Member Data Documentation

◆ mA0

◆ mAmuPointers

◆ mAmuVariables

◆ mContainerFluxes

◆ mCountContainerVariables

◆ mCountReactionSpecies

◆ mData

◆ mDiscreteRoots

◆ mEventProcessing

◆ mFireReaction

◆ mFirstReactionSpeciesIndex

◆ mFluxPointers

◆ mHasDetermReaction

◆ mHasStoiReaction

◆ mIntegrationType

◆ mLastSuccessState

◆ mMaxBalance

◆ mMaxStepsReached

◆ mMethodRootsFound

◆ mODE45

◆ mODEInitalized

◆ mOutputCounter

◆ mOutputFile

◆ mOutputFileName

◆ mpAbsoluteTolerance

◆ mpFastReactions

◆ mpHybridRoot

◆ mpMaxInternalSteps

◆ mpPartitioningStrategy

◆ mpRandomGenerator

◆ mpRandomSeed

◆ mpRelativeTolerance

◆ mPropensitiesUpdateSequence

◆ mpUseRandomSeed

◆ mpYdot

◆ mRKMethodStatus

◆ mRootCounter