#include <CSteadyStateTask.h>

Inheritance diagram for CSteadyStateTask:

Collaboration diagram for CSteadyStateTask:

Public Member Functions
virtual CCopasiMethod *	createMethod (const int &type) const

	CSteadyStateTask (const CCopasiContainer *pParent=NULL)

	CSteadyStateTask (const CSteadyStateTask &src, const CCopasiContainer *pParent=NULL)

const CEigen &	getEigenValues () const

const CEigen &	getEigenValuesReduced () const

const CMatrix< C_FLOAT64 > &	getJacobian () const

const CArrayAnnotation *	getJacobianAnnotated () const

const CMatrix< C_FLOAT64 > &	getJacobianReduced () const

const CArrayAnnotation *	getJacobianXAnnotated () const

const CSteadyStateMethod::ReturnCode &	getResult () const

const CState *	getState () const

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

void	load (CReadConfig &configBuffer)

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

virtual bool	process (const bool &useInitialValues)

virtual bool	restore ()

void	setInitialState ()

virtual bool	updateMatrices ()

virtual	~CSteadyStateTask ()

Public Member Functions inherited from CCopasiTask
	CCopasiTask (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="Task")

	CCopasiTask (const Type &taskType, const CCopasiContainer *pParent=NULL, const std::string &type="Task")

	CCopasiTask (const CCopasiTask &src, const CCopasiContainer *pParent=NULL)

void	cleanup ()

CProcessReport *	getCallBack () const

const CDescription &	getDescription () const

virtual const std::string &	getKey () const

CCopasiMethod *	getMethod ()

const CCopasiMethod *	getMethod () const

COutputHandler *	getOutputHandler () const

const OutputFlag &	getOutputMode () const

CCopasiProblem *	getProblem ()

const CCopasiProblem *	getProblem () const

CReport &	getReport ()

const CResult &	getResult () const

CCopasiParameterGroup *	getSliders ()

Type	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 (CProcessReport *pCallBack)

virtual bool	setMethodType (const int &type)

void	setScheduled (const bool &scheduled)

void	setType (const Type &type)

void	setUpdateModel (const bool &updateModel)

virtual	~CCopasiTask ()

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

	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)

	CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL)

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

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

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () const

virtual bool	remove (CCopasiObject *pObject)

virtual	~CCopasiContainer ()

Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)

	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)

void	clearDirectDependencies ()

void	clearRefresh ()

bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const

void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const

virtual CCopasiObjectName	getCN () const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

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

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () const

virtual void *	getValuePointer () const

bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const

bool	hasUpdateMethod () const

bool	isArray () const

bool	isContainer () const

bool	isDataModel () const

bool	isMatrix () const

bool	isNameVector () const

bool	isNonUniqueName () const

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

bool	isReference () const

bool	isRoot () const

bool	isSeparator () const

bool	isStaticString () const

bool	isValueBool () const

bool	isValueDbl () const

bool	isValueInt () const

bool	isValueInt64 () const

bool	isValueString () const

bool	isVector () const

virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const

void	removeDirectDependency (const CCopasiObject *pObject)

void	setDirectDependencies (const DataObjectSet &directDependencies)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CCopasiContainer *pParent)

void	setObjectValue (const C_FLOAT64 &value)

void	setObjectValue (const C_INT32 &value)

void	setObjectValue (const bool &value)

template<class CType >
void	setRefresh (CType pType, void(CType::method)(void))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_FLOAT64 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_INT32 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const bool &))

virtual	~CCopasiObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

Private Member Functions
void	cleanup ()

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_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 }

enum	Type { steadyState = 0, timeCourse, scan, fluxMode, optimization, parameterFitting, mca, lyap, tssAnalysis, sens, moieties, crosssection, lna, unset }

Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

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

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Static Public Member Functions inherited from CCopasiTask
static bool	isValidMethod (const unsigned int &method, const unsigned int *validMethods)

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Public Attributes inherited from CCopasiTask
std::string	Error

std::string	Warning

Static Public Attributes inherited from CCopasiTask
static const std::string	TypeName []

static const unsigned int	ValidMethods []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Types inherited from CCopasiObject
enum	Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 }

Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

void	initObjects ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Protected Attributes inherited from CCopasiTask
CDescription	mDescription

OutputFlag	mDoOutput

std::string	mKey

unsigned C_INT32	mOutputCounter

CProcessReport *	mpCallBack

CState *	mpInitialState

CCopasiMethod *	mpMethod

COutputHandler *	mpOutputHandler

CCopasiProblem *	mpProblem

CCopasiParameterGroup *	mpSliders

CReport	mReport

CResult	mResult

bool	mScheduled

Type	mType

bool	mUpdateModel

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 49 of file CSteadyStateTask.h.

Constructor & Destructor Documentation

CSteadyStateTask::CSteadyStateTask ( const CCopasiContainer * pParent = NULL )

Default constructor

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 40 of file CSteadyStateTask.cpp.

References CCopasiContainer::add(), createMethod(), initObjects(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiMethod::Newton.

                                                                   :
   CCopasiTask(CCopasiTask::steadyState, pParent),
   mpSteadyState(NULL),
   mJacobian(),
   mJacobianX(),
   mpJacobianAnn(NULL),
   mpJacobianXAnn(NULL),
   mEigenValues("Eigenvalues of Jacobian", this),
   mEigenValuesX("Eigenvalues of reduced system Jacobian", this)
 {
   mpProblem = new CSteadyStateProblem(this);
 
   mpMethod = createMethod(CCopasiMethod::Newton);
   this->add(mpMethod, true);
 
   initObjects();
 }

CSteadyStateTask::CSteadyStateTask	(	const CSteadyStateTask &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor

Parameters

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

Definition at line 58 of file CSteadyStateTask.cpp.

References CCopasiContainer::add(), createMethod(), CCopasiMethod::getSubType(), initObjects(), CCopasiTask::mpMethod, and CCopasiTask::mpProblem.

                                                                     :
   CCopasiTask(src, pParent),
   mpSteadyState(src.mpSteadyState),
   mJacobian(src.mJacobian),
   mJacobianX(src.mJacobianX),
   mpJacobianAnn(NULL),
   mpJacobianXAnn(NULL),
   mEigenValues(src.mEigenValues, this),
   mEigenValuesX(src.mEigenValuesX, this)
 {
   mpProblem =
     new CSteadyStateProblem(*(CSteadyStateProblem *) src.mpProblem, this);
 
   mpMethod = createMethod(src.mpMethod->getSubType());
   this->add(mpMethod, true);
 
   initObjects();
 }

CSteadyStateTask::~CSteadyStateTask ( )

virtual

Destructor

Definition at line 78 of file CSteadyStateTask.cpp.

References mpSteadyState, and pdelete.

 {
   pdelete(mpSteadyState);
 }

Member Function Documentation

void CSteadyStateTask::cleanup ( )

private

cleanup()

Definition at line 91 of file CSteadyStateTask.cpp.

92 {}

CCopasiMethod * CSteadyStateTask::createMethod ( const int & type ) const

virtual

Create a method of the specified type to solve the task. It is the duty of the caller to release the CCopasiMethod.

Parameters

const CCopasiMethod::SubType & type

Returns: CCopasiMethod *

Reimplemented from CCopasiTask.

Definition at line 84 of file CSteadyStateTask.cpp.

References CSteadyStateMethod::createMethod().

Referenced by CSteadyStateTask().

 {
   CCopasiMethod::SubType Type = (CCopasiMethod::SubType) type;
 
   return CSteadyStateMethod::createMethod(Type);
 }

const CEigen & CSteadyStateTask::getEigenValues ( ) const

Retrieves a the eigenvalues of the steady state.

Returns: const CEigen & eigenValues

Definition at line 156 of file CSteadyStateTask.cpp.

References mEigenValues.

Referenced by StateSubwidget::loadJacobian().

 {
   return mEigenValues;
 }

const CEigen & CSteadyStateTask::getEigenValuesReduced ( ) const

Retrieves a the eigenvalues of the steady state.

Returns: const CEigen & eigenValues

Definition at line 160 of file CSteadyStateTask.cpp.

References mEigenValuesX.

Referenced by StateSubwidget::loadJacobian(), and CLNATask::process().

 {
   return mEigenValuesX;
 }

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

Retrieves a the jacobian of the steady state.

Returns: const CMatrix< C_FLOAT64 > jacobian

Definition at line 141 of file CSteadyStateTask.cpp.

References mJacobian.

Referenced by CMCAMethod::createLinkMatrix().

142 {return mJacobian;}

CSteadyStateTask::mJacobian

CMatrix< C_FLOAT64 > mJacobian

Definition: CSteadyStateTask.h:61

const CArrayAnnotation * CSteadyStateTask::getJacobianAnnotated ( ) const

Definition at line 146 of file CSteadyStateTask.cpp.

References mpJacobianAnn.

Referenced by StateSubwidget::loadJacobian().

 {
   return mpJacobianAnn;
 }

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

Retrieves a the jacobian of the steady state.

Returns: const CMatrix< C_FLOAT64 > jacobian

Definition at line 143 of file CSteadyStateTask.cpp.

References mJacobianX.

144 {return mJacobianX;}

CSteadyStateTask::mJacobianX

CMatrix< C_FLOAT64 > mJacobianX

Definition: CSteadyStateTask.h:66

const CArrayAnnotation * CSteadyStateTask::getJacobianXAnnotated ( ) const

Definition at line 151 of file CSteadyStateTask.cpp.

References mpJacobianXAnn.

Referenced by StateSubwidget::loadJacobian().

 {
   return mpJacobianXAnn;
 }

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

inline

Converts the eigenvalues vector to matrix

Parameters

CEigen &eigenvalues

Returns: CMatrix<C_FLOAT64> &matrix

Definition at line 230 of file CSteadyStateTask.h.

References mResult.

Referenced by StateSubwidget::loadAll(), operator<<(), CLNATask::process(), CMCAMethod::setSteadyStateTask(), and SteadyStateWidget::taskFinishedEvent().

230 {return mResult;}

CSteadyStateTask::mResult

CSteadyStateMethod::ReturnCode mResult

Definition: CSteadyStateTask.h:103

const CState * CSteadyStateTask::getState ( ) const

Retrieves a pointer to steady state.

Returns: CState * pSteadyState

Definition at line 138 of file CSteadyStateTask.cpp.

References mpSteadyState.

Referenced by StateSubwidget::loadAll(), CQSteadyStateResult::loadResult(), operator<<(), and CQSteadyStateResult::slotUpdateModel().

139 {return mpSteadyState;}

CSteadyStateTask::mpSteadyState

CState * mpSteadyState

Definition: CSteadyStateTask.h:56

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

virtual

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.

Definition at line 220 of file CSteadyStateTask.cpp.

References CVectorCore< CType >::array(), CStateTemplate::beginIndependent(), CCopasiObject::getCN(), CStateTemplate::getEntities(), CModel::getInitialState(), CCopasiProblem::getModel(), CState::getNumDependent(), CModel::getNumDependentReactionMetabs(), CState::getNumIndependent(), CModel::getStateTemplate(), CModelEntity::getStatus(), CStateTemplate::getUserOrder(), CSteadyStateProblem::initialize(), CSteadyStateMethod::initialize(), CCopasiTask::initialize(), CCopasiMethod::isValidProblem(), mCalculateReducedSystem, mJacobian, mJacobianX, mpJacobianAnn, mpJacobianXAnn, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpSteadyState, CModelEntity::ODE, pdelete, CModelEntity::REACTIONS, CMatrix< CType >::resize(), CArrayAnnotation::resize(), CArrayAnnotation::setAnnotationCN(), CVectorCore< CType >::size(), and updateMatrices().

Referenced by CFitProblem::initialize(), CLNATask::initialize(), and CMCATask::initialize().

 {
   assert(mpProblem && mpMethod);
 
   if (!mpMethod->isValidProblem(mpProblem)) return false;
 
   bool success = true;
 
   if (!updateMatrices())
     return false;
 
   success &= CCopasiTask::initialize(of, pOutputHandler, pOstream);
 
   pdelete(mpSteadyState);
   mpSteadyState = new CState(mpProblem->getModel()->getInitialState());
 
   mCalculateReducedSystem = (mpProblem->getModel()->getNumDependentReactionMetabs() != 0);
 
 #ifdef xxxx
   // init Jacobians
   size_t sizeX = mpSteadyState->getNumIndependent();
   mJacobianX.resize(sizeX, sizeX);
   size_t size = sizeX + mpSteadyState->getNumDependent();
   mJacobian.resize(size, size);
 
   //jacobian annotations
   CStateTemplate & StateTemplate = mpProblem->getModel()->getStateTemplate();
 
   mpJacobianAnn->resize();
   CModelEntity **ppEntities = StateTemplate.getEntities();
   const size_t * pUserOrder = StateTemplate.getUserOrder().array();
   const size_t * pUserOrderEnd = pUserOrder + StateTemplate.getUserOrder().size();
 
   pUserOrder++; // We skip the time which is the first.
 
   size_t i, imax = size;
 
   for (i = 0; i < imax && pUserOrder != pUserOrderEnd; pUserOrder++)
     {
       const CModelEntity::Status & Status = ppEntities[*pUserOrder]->getStatus();
 
       if (Status == CModelEntity::ODE ||
           (Status == CModelEntity::REACTIONS && ppEntities[*pUserOrder]->isUsed()))
         {
           mpJacobianAnn->setAnnotationCN(0 , i, ppEntities[*pUserOrder]->getCN());
           mpJacobianAnn->setAnnotationCN(1 , i, ppEntities[*pUserOrder]->getCN());
 
           i++;
         }
     }
 
   mpJacobianXAnn->resize();
 
   ppEntities = StateTemplate.beginIndependent();
   imax = sizeX;
 
   for (i = 0; i < imax; ++i, ++ppEntities)
     {
       mpJacobianXAnn->setAnnotationCN(0 , i, (*ppEntities)->getCN());
       mpJacobianXAnn->setAnnotationCN(1 , i, (*ppEntities)->getCN());
     }
 
 #endif
 
   CSteadyStateProblem* pProblem =
     dynamic_cast<CSteadyStateProblem *>(mpProblem);
   assert(pProblem);
 
   success &= pProblem->initialize();
 
   CSteadyStateMethod* pMethod =
     dynamic_cast<CSteadyStateMethod *>(mpMethod);
   assert(pMethod);
 
   success &= pMethod->initialize(pProblem);
 
   return success;
 }

void CSteadyStateTask::initObjects ( )

private

Definition at line 94 of file CSteadyStateTask.cpp.

References mEigenvaluesMatrix, mEigenvaluesXMatrix, mJacobian, mJacobianX, mpEigenvaluesJacobianAnn, mpEigenvaluesJacobianXAnn, mpJacobianAnn, mpJacobianXAnn, CArrayAnnotation::OBJECTS, CArrayAnnotation::setDescription(), CArrayAnnotation::setDimensionDescription(), CArrayAnnotation::setMode(), and CArrayAnnotation::VECTOR.

Referenced by CSteadyStateTask().

 {
   mpJacobianAnn = new CArrayAnnotation("Jacobian (complete system)", this,
                                        new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mJacobian), true);
   mpJacobianAnn->setMode(CArrayAnnotation::OBJECTS);
   mpJacobianAnn->setDescription("");
   mpJacobianAnn->setDimensionDescription(0, "Variables of the system, including dependent species");
   mpJacobianAnn->setDimensionDescription(1, "Variables of the system, including dependent species");
 
   mpJacobianXAnn = new CArrayAnnotation("Jacobian (reduced system)", this,
                                         new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mJacobianX), true);
   mpJacobianXAnn->setMode(CArrayAnnotation::OBJECTS);
   mpJacobianXAnn->setDescription("");
   mpJacobianXAnn->setDimensionDescription(0, "Independent variables of the system");
   mpJacobianXAnn->setDimensionDescription(1, "Independent variables of the system");
 
   mpEigenvaluesJacobianAnn = new CArrayAnnotation("Eigenvalues of Jacobian", this,
       new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mEigenvaluesMatrix), true);
   mpEigenvaluesJacobianAnn->setMode(CArrayAnnotation::VECTOR);
   mpEigenvaluesJacobianAnn->setDescription("");
   mpEigenvaluesJacobianAnn->setDimensionDescription(0, "n-th value");
   mpEigenvaluesJacobianAnn->setDimensionDescription(1, "Real/Imaginary part");
 
   mpEigenvaluesJacobianXAnn = new CArrayAnnotation("Eigenvalues of reduced system Jacobian", this,
       new CCopasiMatrixInterface<CMatrix<C_FLOAT64> >(&mEigenvaluesXMatrix), true);
 //  mpEigenvaluesJacobianXAnn->setMode(CArrayAnnotation::VECTOR);
   mpEigenvaluesJacobianXAnn->setMode(CArrayAnnotation::OBJECTS);
   mpEigenvaluesJacobianXAnn->setDescription("");
   mpEigenvaluesJacobianXAnn->setDimensionDescription(0, "n-th value");
   mpEigenvaluesJacobianXAnn->setDimensionDescription(1, "Real/Imaginary part");
 }

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.

Definition at line 128 of file CSteadyStateTask.cpp.

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

Referenced by CCopasiDataModel::loadModel().

 {
   configBuffer.getVariable("SteadyState", "bool", &mScheduled,
                            CReadConfig::LOOP);
 
   ((CSteadyStateProblem *) mpProblem)->load(configBuffer);
 
   ((CSteadyStateMethod *) mpMethod)->load(configBuffer);
 }

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

virtual

This is the output method for any object. The default implementation provided with CCopasiObject 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 CCopasiObject.

Definition at line 126 of file CSteadyStateTask.cpp.

126 {(*ostream) << (*this);}

bool CSteadyStateTask::process ( const bool & useInitialValues )

virtual

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

Parameters

const bool & useInitialValues

Returns: bool success

Reimplemented from CCopasiTask.

Definition at line 301 of file CSteadyStateTask.cpp.

References COutputInterface::AFTER, CModel::applyInitialValues(), CMatrix< CType >::array(), COutputInterface::BEFORE, C_FLOAT64, C_INT32, CEigen::calcEigenValues(), CSteadyStateMethod::doJacobian(), CEigen::getI(), CCopasiProblem::getModel(), CEigen::getR(), CSteadyStateMethod::getStabilityResolution(), CModel::getState(), CState::getTime(), CSteadyStateProblem::isJacobianRequested(), CSteadyStateProblem::isStabilityAnalysisRequested(), CState::isValid(), mEigenValues, mEigenvaluesMatrix, mEigenValuesX, mEigenvaluesXMatrix, mJacobian, mJacobianX, CCopasiTask::mpCallBack, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mpSteadyState, mResult, CSteadyStateMethod::notFound, CCopasiTask::output(), CSteadyStateMethod::process(), restore(), CState::setTime(), CVectorCore< CType >::size(), CMatrix< CType >::size(), and CEigen::stabilityAnalysis().

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

 {
   if (useInitialValues)
     {
       mpProblem->getModel()->applyInitialValues();
     }
 
   *mpSteadyState = mpProblem->getModel()->getState();
 
   // A steady-state makes only sense in an autonomous model,
   // i.e., the time of the steady-state must not be changed
   // during simulation.
   C_FLOAT64 InitialTime = mpSteadyState->getTime();
 
   CSteadyStateMethod* pMethod =
     dynamic_cast<CSteadyStateMethod *>(mpMethod);
   assert(pMethod);
 
   CSteadyStateProblem* pProblem =
     dynamic_cast<CSteadyStateProblem *>(mpProblem);
   assert(pMethod);
 
   output(COutputInterface::BEFORE);
 
   //call the method
   mResult = pMethod->process(mpSteadyState,
                              mJacobianX,
                              mpCallBack);
 
   if (mResult == CSteadyStateMethod::notFound)
     restore();
 
   //update jacobian
   if (mpSteadyState->isValid())
     {
       if (pProblem->isJacobianRequested() ||
           pProblem->isStabilityAnalysisRequested())
         {
           pMethod->doJacobian(mJacobian, mJacobianX);
         }
 
       //mpProblem->getModel()->setState(mpSteadyState);
       //mpProblem->getModel()->updateRates();
 
       //calculate eigenvalues
       if (pProblem->isStabilityAnalysisRequested())
         {
           mEigenValues.calcEigenValues(mJacobian);
           mEigenValuesX.calcEigenValues(mJacobianX);
 
           mEigenValues.stabilityAnalysis(pMethod->getStabilityResolution());
           mEigenValuesX.stabilityAnalysis(pMethod->getStabilityResolution());
         }
     }
 
   // Reset the time.
   mpSteadyState->setTime(InitialTime);
 
   C_FLOAT64 * pTo;
   size_t i;
 
   // construct Eigenvalues of Jacobian
   CVector< C_FLOAT64 > vectorEigen_R = mEigenValues.getR();
   CVector< C_FLOAT64 > vectorEigen_I = mEigenValues.getI();
 
 #ifdef DEBUG_UI
   C_INT32 size = vectorEigen_R.size() + vectorEigen_I.size();
 
   std::cout << "vectorEigen_R.size() = " << vectorEigen_R.size() << " + vectorEigen_I.size() = " << vectorEigen_I.size() << " == " << size << std::endl;
   std::cout << "size = " << mEigenvaluesXMatrix.size() << std::endl;
 #endif
   assert(vectorEigen_R.size() == vectorEigen_I.size());
 
   pTo = mEigenvaluesMatrix.array();
 
   for (i = 0; i < vectorEigen_R.size(); ++i)
     {
       *pTo = vectorEigen_R[i]; ++pTo;
       *pTo = vectorEigen_I[i]; ++pTo;
     }
 
 #ifdef DEBUG_UI
   std::cout << mEigenvaluesMatrix << std::endl;
 #endif
 
   // construct Eigenvalues of Jacobian of reduced system
   CVector< C_FLOAT64 > vectorEigenX_R = mEigenValuesX.getR();
   CVector< C_FLOAT64 > vectorEigenX_I = mEigenValuesX.getI();
 
 #ifdef DEBUG_UI
   C_INT32 sizeX = vectorEigenX_R.size() + vectorEigenX_I.size();
 
   std::cout << "vectorEigenX_R.size() = " << vectorEigenX_R.size() << " + vectorEigenX_I.size() = " << vectorEigenX_I.size() << " == " << sizeX << std::endl;
   std::cout << "size = " << mEigenvaluesXMatrix.size() << std::endl;
 #endif
 
   assert(vectorEigenX_R.size() == vectorEigenX_I.size());
 
   pTo = mEigenvaluesXMatrix.array();
 
   for (i = 0; i < vectorEigenX_R.size(); ++i)
     {
       *pTo = vectorEigenX_R[i]; ++pTo;
       *pTo = vectorEigenX_I[i]; ++pTo;
     }
 
 #ifdef DEBUG_UI
   std::cout << mEigenvaluesXMatrix << std::endl;
 #endif
 
   output(COutputInterface::AFTER);
 
   return (mResult != CSteadyStateMethod::notFound);
 }

bool CSteadyStateTask::restore ( )

virtual

Perform necessary cleanup procedures

Reimplemented from CCopasiTask.

Definition at line 422 of file CSteadyStateTask.cpp.

References CCopasiProblem::getModel(), CModel::getState(), CCopasiTask::mpProblem, mpSteadyState, CCopasiTask::mUpdateModel, CCopasiTask::restore(), CModel::setInitialState(), CModel::setState(), CModel::updateInitialValues(), and CModel::updateSimulatedValues().

Referenced by process(), CFitProblem::restore(), CLNATask::restore(), CMCATask::restore(), and CQSteadyStateResult::slotUpdateModel().

 {
   bool success = CCopasiTask::restore();
 
   if (mUpdateModel)
     {
       CModel * pModel = mpProblem->getModel();
 
       pModel->setState(*mpSteadyState);
       pModel->updateSimulatedValues(true);
       pModel->setInitialState(pModel->getState());
       pModel->updateInitialValues();
     }
 
   return success;
 }

void CSteadyStateTask::setInitialState ( )

Set initial state by taking the current one.

Definition at line 416 of file CSteadyStateTask.cpp.

References CCopasiProblem::getModel(), CModel::getState(), CCopasiTask::mpProblem, and CModel::setInitialState().

 {
   CModel * pModel = mpProblem->getModel();
   pModel->setInitialState(pModel->getState());
 }

bool CSteadyStateTask::updateMatrices ( )

virtual

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.

Definition at line 165 of file CSteadyStateTask.cpp.

References CVectorCore< CType >::array(), CStateTemplate::beginIndependent(), CCopasiObject::getCN(), CStateTemplate::getEntities(), CCopasiProblem::getModel(), CStateTemplate::getNumDependent(), CStateTemplate::getNumIndependent(), CModel::getStateTemplate(), CModelEntity::getStatus(), CStateTemplate::getUserOrder(), mEigenvaluesMatrix, mEigenvaluesXMatrix, mJacobian, mJacobianX, mpJacobianAnn, mpJacobianXAnn, CCopasiTask::mpProblem, CModelEntity::ODE, CModelEntity::REACTIONS, CMatrix< CType >::resize(), CArrayAnnotation::resize(), CArrayAnnotation::setAnnotationCN(), and CVectorCore< CType >::size().

Referenced by initialize().

 {
   if (!mpProblem->getModel()) return false;
 
   const CStateTemplate & stateTemplate = mpProblem->getModel()->getStateTemplate();
 
   // init Jacobians
   size_t sizeX = stateTemplate.getNumIndependent();
   mJacobianX.resize(sizeX, sizeX);
   size_t size = sizeX + stateTemplate.getNumDependent();
   mJacobian.resize(size, size);
 
   // Jacobian Annotations
 
   mpJacobianAnn->resize();
   CModelEntity *const* ppEntities = stateTemplate.getEntities();
   const size_t * pUserOrder = stateTemplate.getUserOrder().array();
   const size_t * pUserOrderEnd = pUserOrder + stateTemplate.getUserOrder().size();
 
   pUserOrder++; // We skip the time which is the first.
 
   size_t i, imax = size;
 
   for (i = 0; i < imax && pUserOrder != pUserOrderEnd; pUserOrder++)
     {
       const CModelEntity::Status & Status = ppEntities[*pUserOrder]->getStatus();
 
       if (Status == CModelEntity::ODE ||
           (Status == CModelEntity::REACTIONS && ppEntities[*pUserOrder]->isUsed()))
         {
           mpJacobianAnn->setAnnotationCN(0 , i, ppEntities[*pUserOrder]->getCN());
           mpJacobianAnn->setAnnotationCN(1 , i, ppEntities[*pUserOrder]->getCN());
 
           i++;
         }
     }
 
   mpJacobianXAnn->resize();
 
   ppEntities = stateTemplate.beginIndependent();
   imax = sizeX;
 
   for (i = 0; i < imax; ++i, ++ppEntities)
     {
       mpJacobianXAnn->setAnnotationCN(0 , i, (*ppEntities)->getCN());
       mpJacobianXAnn->setAnnotationCN(1 , i, (*ppEntities)->getCN());
     }
 
   // initial dimension of Eigenvalues of Jacobian
   mEigenvaluesMatrix.resize(size, 2);
   mEigenvaluesXMatrix.resize(sizeX, 2);
 
   return true;
 }

Friends And Related Function Documentation

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

friend

Definition at line 439 of file CSteadyStateTask.cpp.

 {
   switch (A.getResult())
     {
       case CSteadyStateMethod::found:
         os << "A steady state with given resolution was found." << std::endl;
         break;
 
       case CSteadyStateMethod::notFound:
         os << "No steady state with given resolution was found!" << std::endl;
         os << "(below are the last unsuccessful trial values)" << std::endl;
         break;
 
       case CSteadyStateMethod::foundEquilibrium:
         os << "An equilibrium steady state (zero fluxes) was found." << std::endl;
         break;
 
       case CSteadyStateMethod::foundNegative:
         os << "An invalid steady state (negative concentrations) was found." << std::endl;
     }
 
   os << std::endl;
 
   // Update all necessary values.
   CState * pState = const_cast<CState *>(A.getState());
 
   if (!pState) return os;
 
   CModel * pModel = A.mpProblem->getModel();
 
   if (!pModel) return os;
 
   pModel->setState(*pState);
   pModel->updateSimulatedValues(true);
   pModel->updateNonSimulatedValues();
 
   // Metabolite Info: Name, Concentration, Concentration Rate, Particle Number, Particle Rate, Transition Time
   const CCopasiVector<CMetab> & Metabolites = pModel->getMetabolites();
   const CMetab * pMetab;
 
   size_t i, imax = Metabolites.size();
 
   os << "Species" << "\t";
   os << "Concentration";
 
   std::string Units = pModel->getConcentrationUnitsDisplayString();
 
   if (Units != "")
     os << " (" << Units << ")";
 
   os << "\t";
 
   os << "Concentration Rate";
   Units = pModel->getConcentrationRateUnitsDisplayString();
 
   if (Units != "")
     os << " (" << Units << ")";
 
   os << "\t";
 
   os << "Particle Number" << "\t";
 
   os << "Particle Number Rate";
   Units = pModel->getFrequencyUnitsDisplayString();
 
   if (Units != "")
     os << " (" << Units << ")";
 
   os << "\t";
 
   os << "Transition Time";
   Units = pModel->getTimeUnitsDisplayString();
 
   if (Units != "")
     os << " (" << Units << ")";
 
   os << std::endl;
 
   for (i = 0; i < imax; ++i)
     {
       pMetab = Metabolites[i];
       os << CMetabNameInterface::getDisplayName(pModel, *pMetab, false) << "\t";
       os << pMetab->getConcentration() << "\t";
       os << pMetab->getConcentrationRate() << "\t";
       os << pMetab->getValue() << "\t";
       os << pMetab->getRate() << "\t";
       os << pMetab->getTransitionTime() << std::endl;
     }
 
   os << std::endl;
 
   // Reaction Info: Name, Flux, Particle Flux
   const CCopasiVector<CReaction>& Reactions = pModel->getReactions();
   const CReaction * pReaction;
 
   imax = Reactions.size();
 
   os << "Reaction" << "\t";
 
   os << "Flux";
   Units = pModel->getQuantityRateUnitsDisplayString();
 
   if (Units != "")
     os << " (" << Units << ")";
 
   os << "\t";
 
   os << "Particle Flux";
   Units = pModel->getFrequencyUnitsDisplayString();;
 
   if (Units != "")
     os << " (" << Units << ")";
 
   os << std::endl;
 
   for (i = 0; i < imax; ++i)
     {
       pReaction = Reactions[i];
       os << pReaction->getObjectName() << "\t";
       os << pReaction->getFlux() << "\t";
       os << pReaction->getParticleFlux() << std::endl;
     }
 
   os << std::endl;
 
   if (static_cast<CSteadyStateProblem *>(A.mpProblem)->isJacobianRequested())
     {
       os << *A.mpJacobianAnn << std::endl;
 
       if (static_cast<CSteadyStateProblem *>(A.mpProblem)->isStabilityAnalysisRequested())
         {
           os << "Eigenvalues\treal\timaginary" << std::endl;
           imax = A.mEigenValues.getR().size();
 
           for (i = 0; i < imax; i++)
             os << "\t" << A.mEigenValues.getR()[i] << "\t" << A.mEigenValues.getI()[i] << std::endl;
 
           os << std::endl;
         }
 
       os << *A.mpJacobianXAnn << std::endl;
 
       if (static_cast<CSteadyStateProblem *>(A.mpProblem)->isStabilityAnalysisRequested())
         {
           os << "Eigenvalues\treal\timaginary" << std::endl;
           imax = A.mEigenValuesX.getR().size();
 
           for (i = 0; i < imax; i++)
             os << "\t" << A.mEigenValuesX.getR()[i] << "\t" << A.mEigenValuesX.getI()[i] << std::endl;
 
           os << std::endl;
         }
     }
 
   if (static_cast<CSteadyStateProblem *>(A.mpProblem)->isStabilityAnalysisRequested())
     {
       os << "Stability Analysis of the Reduced System" << std::endl;
       os << A.mEigenValuesX << std::endl;
     }
 
   return os;
 }

Member Data Documentation

bool CSteadyStateTask::mCalculateReducedSystem

private

Whether the model is actually reducible and calculating stability of the reduced steady states makes sense

Definition at line 75 of file CSteadyStateTask.h.

Referenced by initialize().

CEigen CSteadyStateTask::mEigenValues

private

The Eigenvalues of the Jacobian of the system

Definition at line 80 of file CSteadyStateTask.h.

Referenced by getEigenValues(), operator<<(), and process().

CMatrix<C_FLOAT64> CSteadyStateTask::mEigenvaluesMatrix

private

The Eigenvalues matrix of the Jacobian of the system

Definition at line 90 of file CSteadyStateTask.h.

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

CEigen CSteadyStateTask::mEigenValuesX

private

The Eigenvalues of the Jacobian of the reduced system

Definition at line 85 of file CSteadyStateTask.h.

Referenced by getEigenValuesReduced(), operator<<(), and process().

CMatrix<C_FLOAT64> CSteadyStateTask::mEigenvaluesXMatrix

private

The Eigenvalues matrix of the Jacobian of the reduced system

Definition at line 95 of file CSteadyStateTask.h.

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

CMatrix< C_FLOAT64 > CSteadyStateTask::mJacobian

private

The jacobian of the steady state.

Definition at line 61 of file CSteadyStateTask.h.

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

CMatrix< C_FLOAT64 > CSteadyStateTask::mJacobianX

private

The jacobian of the steady state.

Definition at line 66 of file CSteadyStateTask.h.

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

CArrayAnnotation* CSteadyStateTask::mpEigenvaluesJacobianAnn

private

Definition at line 97 of file CSteadyStateTask.h.

Referenced by initObjects().

CArrayAnnotation* CSteadyStateTask::mpEigenvaluesJacobianXAnn

private

Definition at line 98 of file CSteadyStateTask.h.

Referenced by initObjects().

CArrayAnnotation* CSteadyStateTask::mpJacobianAnn

private

Definition at line 68 of file CSteadyStateTask.h.

Referenced by getJacobianAnnotated(), initialize(), initObjects(), operator<<(), and updateMatrices().

CArrayAnnotation* CSteadyStateTask::mpJacobianXAnn

private

Definition at line 69 of file CSteadyStateTask.h.

Referenced by getJacobianXAnnotated(), initialize(), initObjects(), operator<<(), and updateMatrices().

CState* CSteadyStateTask::mpSteadyState

private

A pointer to the found steady state.

Definition at line 56 of file CSteadyStateTask.h.

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

CSteadyStateMethod::ReturnCode CSteadyStateTask::mResult

private

The result of the steady state analysis.

Definition at line 103 of file CSteadyStateTask.h.

Referenced by getResult(), and process().

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

Private Attributes
bool	mCalculateReducedSystem

CEigen	mEigenValues

CMatrix< C_FLOAT64 >	mEigenvaluesMatrix

CEigen	mEigenValuesX

CMatrix< C_FLOAT64 >	mEigenvaluesXMatrix

CMatrix< C_FLOAT64 >	mJacobian

CMatrix< C_FLOAT64 >	mJacobianX

CArrayAnnotation *	mpEigenvaluesJacobianAnn

CArrayAnnotation *	mpEigenvaluesJacobianXAnn

CArrayAnnotation *	mpJacobianAnn

CArrayAnnotation *	mpJacobianXAnn

CState *	mpSteadyState

CSteadyStateMethod::ReturnCode	mResult

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation