#include <CSteadyStateMethod.h>

Inheritance diagram for CSteadyStateMethod:

Public Types
enum	ReturnCode { notFound = 0 , found , foundEquilibrium , foundNegative }

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

Public Member Functions
	CSteadyStateMethod (const CSteadyStateMethod &src, const CDataContainer *pParent)

void	doJacobian (CMatrix< C_FLOAT64 > &jacobian, CMatrix< C_FLOAT64 > &jacobianX)

bool	elevateChildren ()

std::string	getMethodLog () const

C_FLOAT64	getStabilityResolution ()

virtual bool	initialize (const CSteadyStateProblem *pProblem)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

CSteadyStateMethod::ReturnCode	process (CVectorCore< C_FLOAT64 > &State, CMatrix< C_FLOAT64 > &jacobianX, CProcessReportLevel handler)

	~CSteadyStateMethod ()

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 Member Functions
bool	allPositive ()

void	calculateJacobian (const C_FLOAT64 &oldMaxRate, const bool &reduced)

	CSteadyStateMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::steadyState)

	CSteadyStateMethod (CTaskEnum::Method subType, const CDataContainer *pParent=NO_PARENT)

void	initializeParameter ()

bool	isEquilibrium (const C_FLOAT64 &resolution) const

virtual CSteadyStateMethod::ReturnCode	processInternal ()

virtual CSteadyStateMethod::ReturnCode	returnProcess (bool steadyStateFound)

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

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

virtual void	signalMathContainerChanged ()

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
CVector< C_FLOAT64 >	mAtol

CVector< C_FLOAT64 * >	mCompartmentVolumes

CVectorCore< C_FLOAT64 >	mContainerState

CVectorCore< C_FLOAT64 >	mContainerStateReduced

std::ostringstream	mMethodLog

C_FLOAT64 *	mpContainerStateTime

C_FLOAT64 *	mpDerivationFactor

C_FLOAT64 *	mpDerivationResolution

CMatrix< C_FLOAT64 > *	mpJacobian

CSteadyStateTask *	mpParentTask

const CSteadyStateProblem *	mpProblem

C_FLOAT64 *	mpSSResolution

CVector< C_FLOAT64 >	mStartState

CVectorCore< C_FLOAT64 >	mSteadyState

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

Private Member Functions
	CSteadyStateMethod ()

Additional Inherited Members
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

Member Enumeration Documentation

◆ ReturnCode

enum CSteadyStateMethod::ReturnCode

Enumerator
notFound
found
foundEquilibrium
foundNegative

Constructor & Destructor Documentation

◆ CSteadyStateMethod() [1/4]

CSteadyStateMethod::CSteadyStateMethod ( )

private

Default constructor.

◆ CSteadyStateMethod() [2/4]

CSteadyStateMethod::CSteadyStateMethod	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType,
		const CTaskEnum::Task &	taskType = `CTaskEnum::Task::steadyState`
	)

protected

Specific constructor

Parameters

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

CSteadyStateMethod class. This class describes the interface to all steady state methods. The various method like Newton have to be derived from this class.

Created for COPASI by Stefan Hoops 2002 Default constructor.

References CONSTRUCTOR_TRACE, and initializeParameter().

◆ CSteadyStateMethod() [3/4]

CSteadyStateMethod::CSteadyStateMethod	(	CTaskEnum::Method	subType,
		const CDataContainer *	pParent = `NO_PARENT`
	)

protected

Specific constructor.

Parameters

CTaskEnum::Method	subType
const	CDataContainer * pParent (default: NULL)

◆ CSteadyStateMethod() [4/4]

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

Copy constructor.

Parameters

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

Copy constructor.

Parameters

const CSteadyStateMethod & src

References CONSTRUCTOR_TRACE, and initializeParameter().

◆ ~CSteadyStateMethod()

CSteadyStateMethod::~CSteadyStateMethod ( )

Destructor.

References DESTRUCTOR_TRACE.

Member Function Documentation

◆ allPositive()

bool CSteadyStateMethod::allPositive ( )

protected

Check whether all values make physically sence, i.e., volumes and particle number are positive

Returns: bool allPositive

References CVectorCore< CType >::array(), C_FLOAT64, CMath::Compartment, CMathContainer::getCountFixedEventTargets(), CMathObject::getEntityType(), CMathContainer::getMathObject(), CMathContainer::getModel(), CModel::getQuantity2NumberFactor(), mCompartmentVolumes, mContainerState, CCopasiMethod::mpContainer, mpDerivationResolution, CVectorCore< CType >::size(), CMath::Species, and CMathContainer::updateSimulatedValues().

Referenced by CNewtonMethod::doIntegration(), CNewtonMethod::doNewtonStep(), and returnProcess().

◆ calculateJacobian()

void CSteadyStateMethod::calculateJacobian	(	const C_FLOAT64 &	oldMaxRate,
		const bool &	reduced
	)

protected

References CMathContainer::calculateJacobian(), mContainerState, mContainerStateReduced, CCopasiMethod::mpContainer, mpDerivationFactor, mpJacobian, and CMathContainer::setState().

Referenced by CNewtonMethod::doNewtonStep(), and CNewtonMethod::targetFunction().

◆ doJacobian()

void CSteadyStateMethod::doJacobian	(	CMatrix< C_FLOAT64 > &	jacobian,
		CMatrix< C_FLOAT64 > &	jacobianX
	)

calls the CModel methods to calculate the jacobians (at the steady state). This trivial method is implemented in the method because it may need to know about some method parameters

References CMathContainer::calculateJacobian(), CCopasiMethod::mpContainer, mpDerivationFactor, mSteadyState, and CMathContainer::setState().

Referenced by CSteadyStateTask::process().

◆ elevateChildren()

bool CSteadyStateMethod::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().

◆ getMethodLog()

std::string CSteadyStateMethod::getMethodLog ( ) const

References mMethodLog.

◆ getStabilityResolution()

C_FLOAT64 CSteadyStateMethod::getStabilityResolution ( )

returns the resolution for stability analysis

References C_FLOAT64.

Referenced by CSteadyStateTask::process().

◆ initialize()

bool CSteadyStateMethod::initialize ( const CSteadyStateProblem * pProblem )

virtual

Initialize the method must be called before process

Parameters

const CSteadyStateProblem * pProblem

Returns: bool success

Reimplemented in CNewtonMethod.

References CVectorCore< CType >::array(), CVectorCore< CType >::begin(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getState(), CVectorCore< CType >::initialize(), CMathContainer::initializeAtolVector(), mAtol, mContainerState, mContainerStateReduced, CCopasiMethod::mpContainer, mpContainerStateTime, mpProblem, mpSSResolution, and CVectorCore< CType >::size().

Referenced by CNewtonMethod::initialize(), and CSteadyStateTask::initialize().

◆ initializeParameter()

void CSteadyStateMethod::initializeParameter ( )

protected

initialize parameters and handle parameters of old COPASI files

References CCopasiParameterGroup::assertParameter(), C_FLOAT64, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), mpDerivationFactor, mpDerivationResolution, mpSSResolution, CCopasiParameterGroup::removeParameter(), CCopasiParameterGroup::setValue(), and CCopasiParameter::UDOUBLE.

Referenced by CSteadyStateMethod(), CNewtonMethod::elevateChildren(), and elevateChildren().

◆ isEquilibrium()

bool CSteadyStateMethod::isEquilibrium ( const C_FLOAT64 & resolution ) const

protected

Check whether the steady state is chemical equilibrium

Parameters

const C_FLOAT64 & resolution @retrun bool isEquilibrium

References CVectorCore< CType >::begin(), C_FLOAT64, CVectorCore< CType >::end(), CMathReaction::getNumberBalance(), CMathReaction::getParticleFluxObject(), CMathContainer::getReactions(), CMathObject::getValue(), mAtol, max, CCopasiMethod::mpContainer, mpContainerStateTime, and CMathContainer::updateTransientDataValues().

Referenced by returnProcess().

◆ isValidProblem()

bool CSteadyStateMethod::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CCopasiMethod.

Reimplemented in CNewtonMethod.

References CCopasiMessage::EXCEPTION, and CCopasiMethod::isValidProblem().

Referenced by CSteadyStateTask::initialize(), and CNewtonMethod::isValidProblem().

◆ process()

CSteadyStateMethod::ReturnCode CSteadyStateMethod::process	(	CVectorCore< C_FLOAT64 > &	State,
		CMatrix< C_FLOAT64 > &	jacobianX,
		CProcessReportLevel	handler
	)

This instructs the method to calculate a the steady state starting with the initialState given. The steady state is returned in the object pointed to by steadyState.

Parameters

CVectorCore<	C_FLOAT64 > & State
CMatrix<	C_FLOAT64 > & jacobianX
CProcessReport	* handler

Returns: CSteadyStateMethod::ReturnCode returnCode

This instructs the method to calculate a the steady state starting with the initialState given. The steady state is returned in the object pointed to by steadyState.

Parameters

CState	* steadyState
const	CState * initialState
C_FLOAT64	* jacobian
CEigen	* eigenValues

Returns: CSteadyStateMethod::ReturnCode returnCode

References CDataObject::getObjectParent(), CVectorCore< CType >::initialize(), mpJacobian, mpParentTask, CCopasiMethod::mProcessReport, mStartState, mSteadyState, and processInternal().

Referenced by CSteadyStateTask::process().

◆ processInternal()

CSteadyStateMethod::ReturnCode CSteadyStateMethod::processInternal ( )

protectedvirtual

This instructs the method to calculate a the steady state starting with the initialState given. The steady state is returned in the object pointed to by steadyState.

Returns: CSteadyStateMethod::ReturnCode returnCode

This instructs the method to calculate a the steady state

Returns: CSteadyStateMethod::ReturnCode returnCode

Reimplemented in CNewtonMethod.

References notFound.

Referenced by process().

◆ returnProcess()

CSteadyStateMethod::ReturnCode CSteadyStateMethod::returnProcess ( bool steadyStateFound )

protectedvirtual

This function has to be called at the return of any implementation of the protected function process()

Returns: CSteadyStateMethod::ReturnCode returnCode

This function has to be called at the return of any implementation of the protected function process

Parameters

bool	success
const	C_FLOAT64 & factor
const	C_FLOAT64 & resolution

Returns: CSteadyStateMethod::ReturnCode returnCode

References allPositive(), found, foundEquilibrium, foundNegative, CMathContainer::getState(), isEquilibrium(), CCopasiMethod::mpContainer, mpSSResolution, mStartState, mSteadyState, and notFound.

Referenced by CNewtonMethod::processInternal().

Member Data Documentation

◆ mAtol

CVector< C_FLOAT64 > CSteadyStateMethod::mAtol

protected

Referenced by initialize(), isEquilibrium(), CNewtonMethod::targetFunctionDistance(), and CNewtonMethod::targetFunctionRate().

◆ mCompartmentVolumes

CVector< C_FLOAT64 * > CSteadyStateMethod::mCompartmentVolumes

protected

Referenced by allPositive(), CNewtonMethod::initialize(), CNewtonMethod::targetFunctionDistance(), and CNewtonMethod::targetFunctionRate().

◆ mContainerState

CVectorCore< C_FLOAT64 > CSteadyStateMethod::mContainerState

protected

Referenced by allPositive(), calculateJacobian(), initialize(), and CNewtonMethod::processInternal().

◆ mContainerStateReduced

CVectorCore< C_FLOAT64 > CSteadyStateMethod::mContainerStateReduced

protected

Referenced by calculateJacobian(), CNewtonMethod::initialize(), and initialize().

◆ mMethodLog

std::ostringstream CSteadyStateMethod::mMethodLog

protected

Referenced by CNewtonMethod::doIntegration(), CNewtonMethod::doNewtonStep(), getMethodLog(), CNewtonMethod::processInternal(), and CNewtonMethod::processNewton().

◆ mpContainerStateTime

C_FLOAT64* CSteadyStateMethod::mpContainerStateTime

protected

Referenced by initialize(), and isEquilibrium().

◆ mpDerivationFactor

C_FLOAT64* CSteadyStateMethod::mpDerivationFactor

protected

The factor for numerical derivation

Referenced by calculateJacobian(), doJacobian(), initializeParameter(), and CNewtonMethod::targetFunctionDistance().

◆ mpDerivationResolution

C_FLOAT64* CSteadyStateMethod::mpDerivationResolution

protected

The resolution of the variable of numerical derivation

Referenced by allPositive(), and initializeParameter().

◆ mpJacobian

CMatrix< C_FLOAT64 >* CSteadyStateMethod::mpJacobian

protected

The jacobian of the steadystate

Referenced by calculateJacobian(), CNewtonMethod::doNewtonStep(), and process().

◆ mpParentTask

CSteadyStateTask* CSteadyStateMethod::mpParentTask

protected

A pointer to the task.

Referenced by process().

◆ mpProblem

const CSteadyStateProblem* CSteadyStateMethod::mpProblem

protected

A pointer to the problem.

Referenced by initialize().

◆ mpSSResolution

C_FLOAT64* CSteadyStateMethod::mpSSResolution

protected

The concentration rate that is considered zero

Referenced by initialize(), initializeParameter(), CNewtonMethod::isSteadyState(), and returnProcess().

◆ mStartState

CVector< C_FLOAT64 > CSteadyStateMethod::mStartState

protected

The state from where the method started

Referenced by process(), and returnProcess().

◆ mSteadyState

CVectorCore< C_FLOAT64 > CSteadyStateMethod::mSteadyState

protected

A pointer to the steady state

Referenced by doJacobian(), process(), and returnProcess().

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

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Member Enumeration Documentation

◆ ReturnCode

Constructor & Destructor Documentation

◆ CSteadyStateMethod() [1/4]

◆ CSteadyStateMethod() [2/4]

◆ CSteadyStateMethod() [3/4]

◆ CSteadyStateMethod() [4/4]

◆ ~CSteadyStateMethod()

Member Function Documentation

◆ allPositive()

◆ calculateJacobian()

◆ doJacobian()

◆ elevateChildren()

◆ getMethodLog()

◆ getStabilityResolution()

◆ initialize()

◆ initializeParameter()

◆ isEquilibrium()

◆ isValidProblem()

◆ process()

◆ processInternal()

◆ returnProcess()

Member Data Documentation

◆ mAtol

◆ mCompartmentVolumes

◆ mContainerState

◆ mContainerStateReduced

◆ mMethodLog

◆ mpContainerStateTime

◆ mpDerivationFactor

◆ mpDerivationResolution

◆ mpJacobian

◆ mpParentTask

◆ mpProblem

◆ mpSSResolution

◆ mStartState

◆ mSteadyState