#include <CSteadyStateTask.h>

Inheritance diagram for CSteadyStateTask:

Public Member Functions
	CSteadyStateTask (const CDataContainer *pParent, const CTaskEnum::Task &type=CTaskEnum::Task::steadyState)

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

const CEigen &	getEigenValues () const

const CEigen &	getEigenValuesReduced () const

const CMatrix< C_FLOAT64 > &	getJacobian () const

const CDataArray *	getJacobianAnnotated () const

const CMatrix< C_FLOAT64 > &	getJacobianReduced () const

const CDataArray *	getJacobianXAnnotated () const

const CSteadyStateMethod::ReturnCode &	getResult () const

const CVectorCore< C_FLOAT64 > &	getState () const

virtual const CTaskEnum::Method *	getValidMethods () const override

virtual bool	initialize (const OutputFlag &of, COutputHandler pOutputHandler, std::ostream pOstream) override

void	load (CReadConfig &configBuffer)

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

virtual bool	process (const bool &useInitialValues) override

virtual bool	restore (const bool &updateModel=true) override

virtual bool	updateMatrices () override

virtual	~CSteadyStateTask ()

Public Member Functions inherited from CCopasiTask
virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

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

	CCopasiTask (const CDataContainer *pParent, const CTaskEnum::Task &taskType, const std::string &type="Task")

void	cleanup ()

virtual void	clearCallBack ()

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

const CProcessReportLevel &	getCallBack () const

const CDescription &	getDescription () const

virtual const std::string &	getKey () const

CMathContainer *	getMathContainer () const

CCopasiMethod *	getMethod ()

const CCopasiMethod *	getMethod () const

COutputHandler *	getOutputHandler () const

const OutputFlag &	getOutputMode () const

CCopasiProblem *	getProblem ()

const CCopasiProblem *	getProblem () const

CReport &	getReport ()

const CReport &	getReport () const

const CResult &	getResult () const

CCopasiParameterGroup *	getSliders ()

CTaskEnum::Task	getType () const

const bool &	isScheduled () const

const bool &	isUpdateModel () const

virtual void	output (const COutputInterface::Activity &activity)

virtual void	separate (const COutputInterface::Activity &activity)

virtual bool	setCallBack (CProcessReportLevel callBack)

void	setIgnoreProblemData (const bool &ignoreProblemData)

void	setMathContainer (CMathContainer *pContainer)

bool	setMethodType (const CTaskEnum::Method &type)

void	setScheduled (const bool &scheduled)

void	setType (const CTaskEnum::Task &type)

virtual void	setUpdateModel (const bool &updateModel)

virtual CData	toData () const

virtual	~CCopasiTask ()

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 size_t	getIndex (const CDataObject *pObject) const

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

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

virtual CUndoObjectInterface *	insert (const CData &data) override

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

virtual bool	remove (CDataObject *pObject)

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 CCommonName	getCN () const override

virtual const CDataObject *	getDataObject () const override

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

CDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName () const override

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

virtual void *	getValuePointer () 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)

virtual bool	setObjectParent (const CDataContainer *pParent)

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

virtual	~CUndoObjectInterface ()

Private Member Functions
void	cleanup ()

	CSteadyStateTask ()

void	initObjects ()

Friends
std::ostream &	operator<< (std::ostream &os, const CSteadyStateTask &A)

Additional Inherited Members
Public Types inherited from CCopasiTask
enum	eOutputFlagBase { INITIALIZE = 0x01 , STREAM = 0x02 , FINISH = 0x04 , REPORT = 0x10 , PLOT = 0x20 , TIME_SERIES = 0x40 }

enum	OutputFlag { NO_OUTPUT = 0 , OUTPUT_BEFORE = INITIALIZE , OUTPUT_DURING = STREAM , OUTPUT_AFTER = FINISH , OUTPUT = REPORT \| PLOT \| STREAM , OUTPUT_SE = REPORT \| PLOT \| INITIALIZE \| STREAM \| FINISH , OUTPUT_UI = REPORT \| PLOT \| TIME_SERIES \| INITIALIZE \| STREAM \| FINISH , ONLY_TIME_SERIES = TIME_SERIES \| INITIALIZE \| STREAM \| FINISH }

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

static bool	isValidMethod (const CTaskEnum::Method &method, const CTaskEnum::Method *validMethods)

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 *)

Public Attributes inherited from CCopasiTask
std::string	Error

std::string	Warning

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

Protected Member Functions inherited from CCopasiTask
bool	isTaskValid () const

virtual void	signalMathContainerChanged ()

virtual void	signalMethodChanged ()

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 CCopasiTask
CDescription	mDescription

OutputFlag	mDoOutput

bool	mIgnoreProblemData

CVector< C_FLOAT64 >	mInitialState

std::string	mKey

unsigned C_INT32	mOutputCounter

CMathContainer *	mpContainer

CCopasiMethod *	mpMethod

COutputHandler *	mpOutputHandler

CCopasiProblem *	mpProblem

CProcessReportLevel	mProcessReport

CCopasiParameterGroup *	mpSliders

CReport	mReport

CResult	mResult

bool	mScheduled

CTaskEnum::Task	mType

bool	mUpdateModel

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

Constructor & Destructor Documentation

◆ CSteadyStateTask() [1/3]

CSteadyStateTask::CSteadyStateTask ( )

private

Default constructor

◆ CSteadyStateTask() [2/3]

CSteadyStateTask::CSteadyStateTask	(	const CDataContainer *	pParent,
		const CTaskEnum::Task &	type = `CTaskEnum::Task::steadyState`
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Task & type (default: steadyState)

References CMethodFactory::create(), CCopasiTask::getType(), initObjects(), CCopasiTask::mpMethod, and CTaskEnum::Newton.

◆ CSteadyStateTask() [3/3]

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

Copy constructor

Parameters

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

References initObjects().

◆ ~CSteadyStateTask()

CSteadyStateTask::~CSteadyStateTask ( )

virtual

Destructor

Member Function Documentation

◆ cleanup()

void CSteadyStateTask::cleanup ( )

private

cleanup()

◆ getEigenValues()

const CEigen & CSteadyStateTask::getEigenValues ( ) const

Retrieves a the eigenvalues of the steady state.

Returns: const CEigen & eigenValues

References mEigenValues.

◆ getEigenValuesReduced()

const CEigen & CSteadyStateTask::getEigenValuesReduced ( ) const

Retrieves a the eigenvalues of the steady state.

Returns: const CEigen & eigenValues

References mEigenValuesX.

Referenced by CLNATask::process().

◆ getJacobian()

const CMatrix< C_FLOAT64 > & CSteadyStateTask::getJacobian ( ) const

Retrieves a the jacobian of the steady state.

Returns: const CMatrix< C_FLOAT64 > jacobian

References mJacobian.

Referenced by CMCAMethod::createLinkMatrix().

◆ getJacobianAnnotated()

const CDataArray * CSteadyStateTask::getJacobianAnnotated ( ) const

References mpJacobianAnn.

◆ getJacobianReduced()

const CMatrix< C_FLOAT64 > & CSteadyStateTask::getJacobianReduced ( ) const

Retrieves a the jacobian of the steady state.

Returns: const CMatrix< C_FLOAT64 > jacobian

References mJacobianReduced.

◆ getJacobianXAnnotated()

const CDataArray * CSteadyStateTask::getJacobianXAnnotated ( ) const

References mpJacobianXAnn.

◆ getResult()

const CSteadyStateMethod::ReturnCode& CSteadyStateTask::getResult ( ) const

inline

Converts the eigenvalues vector to matrix

Parameters

CEigen &eigenvalues

Returns: CMatrix<C_FLOAT64> &matrix

References mResult.

Referenced by CLNATask::process(), and CMCAMethod::setSteadyStateTask().

◆ getState()

const CVectorCore< C_FLOAT64 > & CSteadyStateTask::getState ( ) const

Retrieves a pointer to steady state.

Returns: const CVectorCore< C_FLOAT64 > & steadyState

References mSteadyState.

◆ getValidMethods()

const CTaskEnum::Method * CSteadyStateTask::getValidMethods ( ) const

overridevirtual

Retrieve the list of valid methods

Returns: const CTaskEnum::Method * pValidMethods

Reimplemented from CCopasiTask.

References CTaskEnum::Newton, and CTaskEnum::UnsetMethod.

◆ initialize()

bool CSteadyStateTask::initialize	(	const OutputFlag &	of,
		COutputHandler *	pOutputHandler,
		std::ostream *	pOstream
	)

overridevirtual

Initialize the task. If an ostream is given this ostream is used instead of the target specified in the report. This allows nested tasks to share the same output device.

Parameters

const	OutputFlag & of
COutputHandler	* pOutputHandler
std::ostream	* pOstream (default: NULL)

Returns: bool success

Reimplemented from CCopasiTask.

References CMathContainer::getState(), CSteadyStateProblem::initialize(), CSteadyStateMethod::initialize(), CCopasiTask::initialize(), CSteadyStateMethod::isValidProblem(), CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mSteadyState, and updateMatrices().

Referenced by CFitProblem::initialize(), CTimeSensTask::initialize(), and CTrajectoryTask::initialize().

◆ initObjects()

void CSteadyStateTask::initObjects ( )

private

References mEigenvaluesMatrix, mEigenvaluesXMatrix, mJacobian, mJacobianReduced, mpEigenvaluesJacobianAnn, mpEigenvaluesJacobianXAnn, mpJacobianAnn, mpJacobianXAnn, CDataArray::Objects, CDataArray::setDescription(), CDataArray::setDimensionDescription(), CDataArray::setMode(), and CDataArray::Vector.

Referenced by CSteadyStateTask().

◆ load()

void CSteadyStateTask::load ( CReadConfig & configBuffer )

Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)

Parameters

configbuffer reference to a CReadConfig object.

References CReadConfig::getVariable(), CReadConfig::LOOP, CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiTask::mScheduled.

Referenced by CDataModel::loadModel().

◆ print()

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

overridevirtual

This is the output method for any object. The default implementation provided with CDataObject uses the ostream operator<< of the object to print the object.To override this default behavior one needs to reimplement the virtual print function.

Parameters

std::ostream * ostream

Reimplemented from CDataObject.

◆ process()

bool CSteadyStateTask::process ( const bool & useInitialValues )

overridevirtual

Process the task with or without initializing to the initial state.

Parameters

const bool & useInitialValues

Returns: bool success

Reimplemented from CCopasiTask.

References COutputInterface::AFTER, CMathContainer::applyInitialValues(), CMatrix< CType >::array(), COutputInterface::BEFORE, C_FLOAT64, C_INT32, CEigen::calcEigenValues(), CSteadyStateMethod::doJacobian(), CMathContainer::getCountFixedEventTargets(), CEigen::getI(), CEigen::getR(), CSteadyStateMethod::getStabilityResolution(), CMathContainer::getState(), CMathContainer::isAutonomous(), CSteadyStateProblem::isJacobianRequested(), CSteadyStateProblem::isStabilityAnalysisRequested(), CMathContainer::isStateValid(), mEigenValues, mEigenvaluesMatrix, mEigenValuesX, mEigenvaluesXMatrix, mJacobian, mJacobianReduced, CCopasiTask::mpContainer, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mProcessReport, mResult, mSteadyState, CSteadyStateMethod::notFound, CCopasiTask::output(), CSteadyStateMethod::process(), CMathContainer::pushAllTransientValues(), CMathContainer::setState(), CMatrix< CType >::size(), CVectorCore< CType >::size(), CEigen::stabilityAnalysis(), CMathContainer::updateSimulatedValues(), and CMathContainer::updateTransientDataValues().

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), CLNATask::process(), CMCATask::process(), CTimeSensTask::processStart(), and CTrajectoryTask::processStart().

◆ restore()

bool CSteadyStateTask::restore ( const bool & updateModel = true )

overridevirtual

Perform necessary cleanup procedures

Reimplemented from CCopasiTask.

References CMathContainer::getState(), CMathContainer::isStateValid(), CCopasiTask::mInitialState, CCopasiTask::mpContainer, mResult, mSteadyState, CCopasiTask::mUpdateModel, CSteadyStateMethod::notFound, CCore::ParticleNumbers, CMathContainer::pushInitialState(), CCopasiTask::setCallBack(), CMathContainer::setInitialState(), CMathContainer::setState(), CMathContainer::updateInitialValues(), and CMathContainer::updateSimulatedValues().

Referenced by CFitProblem::restore().

◆ updateMatrices()

bool CSteadyStateTask::updateMatrices ( )

overridevirtual

Resizes result matrices and updates array annotations for a specific task. This is used when we need to know about the data structures of a task result without actually performing the task, e.g. when selecting objects for output. For now we assume that this functionality is also performed when initialize() is called.

Reimplemented from CCopasiTask.

References CVectorCore< CType >::array(), CMathContainer::getCountFixedEventTargets(), CMathObject::getDataObject(), CMathContainer::getMathObject(), CDataObject::getObjectParent(), CMathContainer::getState(), mEigenvaluesMatrix, mEigenvaluesXMatrix, mJacobian, mJacobianReduced, CCopasiTask::mpContainer, mpJacobianAnn, mpJacobianXAnn, CDataArray::resize(), CMatrix< CType >::resize(), CDataArray::setAnnotation(), and CVectorCore< CType >::size().

Referenced by initialize().

Friends And Related Function Documentation

◆ operator<<

std::ostream& operator<<	(	std::ostream &	os,
		const CSteadyStateTask &	A
	)

friend

Member Data Documentation

◆ mEigenValues

CEigen CSteadyStateTask::mEigenValues

private

The Eigenvalues of the Jacobian of the system

Referenced by getEigenValues(), and process().

◆ mEigenvaluesMatrix

CMatrix<C_FLOAT64> CSteadyStateTask::mEigenvaluesMatrix

private

The Eigenvalues matrix of the Jacobian of the system

Referenced by initObjects(), process(), and updateMatrices().

◆ mEigenValuesX

CEigen CSteadyStateTask::mEigenValuesX

private

The Eigenvalues of the Jacobian of the reduced system

Referenced by getEigenValuesReduced(), and process().

◆ mEigenvaluesXMatrix

CMatrix<C_FLOAT64> CSteadyStateTask::mEigenvaluesXMatrix

private

The Eigenvalues matrix of the Jacobian of the reduced system

Referenced by initObjects(), process(), and updateMatrices().

◆ mJacobian

CMatrix< C_FLOAT64 > CSteadyStateTask::mJacobian

private

The jacobian of the steady state.

Referenced by getJacobian(), initObjects(), process(), and updateMatrices().

◆ mJacobianReduced

CMatrix< C_FLOAT64 > CSteadyStateTask::mJacobianReduced

private

The jacobian of the steady state.

Referenced by getJacobianReduced(), initObjects(), process(), and updateMatrices().

◆ mpEigenvaluesJacobianAnn

CDataArray* CSteadyStateTask::mpEigenvaluesJacobianAnn

private

Referenced by initObjects().

◆ mpEigenvaluesJacobianXAnn

CDataArray* CSteadyStateTask::mpEigenvaluesJacobianXAnn

private

Referenced by initObjects().

◆ mpJacobianAnn

CDataArray* CSteadyStateTask::mpJacobianAnn

private

Referenced by getJacobianAnnotated(), initObjects(), and updateMatrices().

◆ mpJacobianXAnn

CDataArray* CSteadyStateTask::mpJacobianXAnn

private

Referenced by getJacobianXAnnotated(), initObjects(), and updateMatrices().

◆ mResult

CSteadyStateMethod::ReturnCode CSteadyStateTask::mResult

private

The result of the steady state analysis.

Referenced by getResult(), process(), and restore().

◆ mSteadyState

CVector< C_FLOAT64 > CSteadyStateTask::mSteadyState

private

A pointer to the found steady state.

Referenced by getState(), initialize(), process(), and restore().

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

Private Attributes
CEigen	mEigenValues

CMatrix< C_FLOAT64 >	mEigenvaluesMatrix

CEigen	mEigenValuesX

CMatrix< C_FLOAT64 >	mEigenvaluesXMatrix

CMatrix< C_FLOAT64 >	mJacobian

CMatrix< C_FLOAT64 >	mJacobianReduced

CDataArray *	mpEigenvaluesJacobianAnn

CDataArray *	mpEigenvaluesJacobianXAnn

CDataArray *	mpJacobianAnn

CDataArray *	mpJacobianXAnn

CSteadyStateMethod::ReturnCode	mResult

CVector< C_FLOAT64 >	mSteadyState

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ CSteadyStateTask() [1/3]

◆ CSteadyStateTask() [2/3]

◆ CSteadyStateTask() [3/3]

◆ ~CSteadyStateTask()

Member Function Documentation

◆ cleanup()

◆ getEigenValues()

◆ getEigenValuesReduced()

◆ getJacobian()

◆ getJacobianAnnotated()

◆ getJacobianReduced()

◆ getJacobianXAnnotated()

◆ getResult()

◆ getState()

◆ getValidMethods()

◆ initialize()

◆ initObjects()

◆ load()

◆ print()

◆ process()

◆ restore()

◆ updateMatrices()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ mEigenValues

◆ mEigenvaluesMatrix

◆ mEigenValuesX

◆ mEigenvaluesXMatrix

◆ mJacobian

◆ mJacobianReduced

◆ mpEigenvaluesJacobianAnn

◆ mpEigenvaluesJacobianXAnn

◆ mpJacobianAnn

◆ mpJacobianXAnn

◆ mResult

◆ mSteadyState