The CCSPMethod class implements the CSP method. More...

#include <CCSPMethod.h>

Inheritance diagram for CCSPMethod:

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

	CCSPMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::tssCSP, const CTaskEnum::Task &taskType=CTaskEnum::Task::tssAnalysis)

virtual void	createAnnotationsM ()

void	CSPOutput (C_INT &N, C_INT &M, C_INT &R)

void	emptyVectors ()

const CDataArray *	getFastParticipationIndexAnn () const

const CDataArray *	getFastReactionPointerAnn () const

const CDataArray *	getFastReactionPointerNormedAnn () const

const CDataArray *	getImportanceIndexAnn () const

const CDataArray *	getImportanceIndexNormedRowAnn () const

const CDataArray *	getParticipationIndexAnn () const

const CDataArray *	getParticipationIndexNormedColumnAnn () const

const CDataArray *	getParticipationIndexNormedRowAnn () const

const CDataArray *	getRadicalPointerAnn () const

const CDataArray *	getSlowParticipationIndexAnn () const

virtual void	initializeOutput ()

void	initializeParameter ()

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

virtual bool	setAnnotationM (size_t step)

void	setVectors (int fast)

void	setVectorsToNaN ()

virtual void	start ()

virtual void	step (const double &deltaT)

virtual	~CCSPMethod ()

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

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

void	emptyVectors ()

const int &	getCurrentStep () const

const CDataArray *	getTable (const std::string &name)

const std::vector< std::string > &	getTableNames () const

C_FLOAT64	getTimeForStep (int step) const

CVector< C_FLOAT64 >	getVec_TimeScale (int step)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

void	setProblem (CTSSAProblem *problem)

void	setVectors (int slowMode)

virtual	~CTSSAMethod ()

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 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
void	basisRefinement (C_INT N, C_INT M, const CMatrix< C_FLOAT64 > &ALA, const CMatrix< C_FLOAT64 > &TAU, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &A0, CMatrix< C_FLOAT64 > &B0)

void	calculateJacobian (C_INT &n, CVector< C_FLOAT64 > &y, CMatrix< C_FLOAT64 > &J)

void	CSPImportanceIndex (C_INT &N, C_FLOAT64 &tauM1, CMatrix< C_FLOAT64 > &Q)

void	CSPParticipationIndex (C_INT &N, C_INT &M, C_FLOAT64 &tauM1, CMatrix< C_FLOAT64 > &B0)

void	CSPradicalPointer (C_INT &N, C_INT &M, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B)

void	cspstep (const double &deltaT, C_INT &n, C_INT &m, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B)

void	emptyOutputData (C_INT N, C_INT M, C_INT R)

void	findCandidatesNumber (C_INT &n, C_INT &k, CVector< C_FLOAT64 > &tsc, C_INT &info)

void	findTimeScaleSeparation (C_INT &n, C_INT &k, CVector< C_FLOAT64 > &tsc, C_INT &info)

C_INT	isBlockDiagonal (C_INT N, C_INT M, const CMatrix< C_FLOAT64 > &ALA, const C_FLOAT64 &SMALL)

void	modesAmplitude (C_INT N, const CVector< C_FLOAT64 > &g, const CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &F)

bool	modesAreExhausted (C_INT N, C_INT M, C_FLOAT64 &tauM, C_FLOAT64 &tauM1, CVector< C_FLOAT64 > &g, const CMatrix< C_FLOAT64 > &A, const CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &F)

void	smadd (const CMatrix< C_FLOAT64 > &A, const CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &C, C_INT n1, C_INT n2)

void	sminverse (C_INT n, const CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B)

void	smmult (const CMatrix< C_FLOAT64 > &A, const CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &C, C_INT n1, C_INT n2, C_INT n3)

void	smnorm (C_INT n, CMatrix< C_FLOAT64 > &A, CMatrix< C_FLOAT64 > &B, C_INT n1)

void	smsubst (const CMatrix< C_FLOAT64 > &A, const CMatrix< C_FLOAT64 > &B, CMatrix< C_FLOAT64 > &C, C_INT n1, C_INT n2)

void	yCorrection (C_INT &N, C_INT &M, CVector< C_FLOAT64 > &y, CMatrix< C_FLOAT64 > &TAUM, CMatrix< C_FLOAT64 > &F, CMatrix< C_FLOAT64 > &A)

Protected Member Functions inherited from CTSSAMethod
void	calculateDerivatives (C_FLOAT64 X1, C_FLOAT64 Y1, bool useReducedModel)

bool	elevateChildren ()

void	integrationMethodStart ()

void	integrationStep (const double &deltaT)

void	map_index (C_FLOAT64 eval_r, C_INT index, const C_INT &dim)

void	map_index_desc (C_FLOAT64 eval_r, C_INT index, const C_INT &dim)

void	mat_anal_fast_space (C_INT &slow)

void	mat_anal_fast_space_thomas (C_INT &slow)

void	mat_anal_metab (C_INT &slow)

void	mat_anal_mod (C_INT &slow)

void	mat_anal_mod_space (C_INT &slow)

double	orthog (C_INT &number1, C_INT &number2)

void	schur (C_INT &info)

void	schur_desc (C_INT &info)

void	sylvester (C_INT slow, C_INT &info)

void	update_nid (C_INT index, C_INT nid, const C_INT &dim)

void	update_pid (C_INT index, C_INT pid, const C_INT &dim)

virtual void	updateCurrentTime ()

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
C_FLOAT64	mAerror

CVector< C_FLOAT64 >	mAmplitude

CMatrix< C_FLOAT64 >	mB

C_INT	mCSPbasis

C_FLOAT64	mEps

CVector< C_FLOAT64 >	mFastParticipationIndex

CMatrix< C_FLOAT64 >	mFastParticipationIndexTab

CMatrix< C_FLOAT64 >	mFastReactionPointer

CMatrix< C_FLOAT64 >	mFastReactionPointerNormed

CMatrix< C_FLOAT64 >	mFastReactionPointerNormedTab

CMatrix< C_FLOAT64 >	mFastReactionPointerTab

CVectorCore< const C_FLOAT64 >	mG

CMatrix< C_FLOAT64 >	mI

CMatrix< C_FLOAT64 >	mImportanceIndex

CMatrix< C_FLOAT64 >	mImportanceIndexNormedRow

CMatrix< C_FLOAT64 >	mImportanceIndexNormedRowTab

CMatrix< C_FLOAT64 >	mImportanceIndexTab

C_INT	mIter

CMatrix< C_FLOAT64 >	mParticipationIndex

CMatrix< C_FLOAT64 >	mParticipationIndexNormedColumn

CMatrix< C_FLOAT64 >	mParticipationIndexNormedColumnTab

CMatrix< C_FLOAT64 >	mParticipationIndexNormedRow

CMatrix< C_FLOAT64 >	mParticipationIndexNormedRowTab

CMatrix< C_FLOAT64 >	mParticipationIndexTab

CMatrix< C_FLOAT64 >	mRadicalPointer

CMatrix< C_FLOAT64 >	mRadicalPointerTab

bool	mReducedModel

C_FLOAT64	mRerror

C_INT	mSetVectors

CVector< C_FLOAT64 >	mSlowParticipationIndex

CMatrix< C_FLOAT64 >	mSlowParticipationIndexTab

C_FLOAT64	mTsc

C_INT	mTStep

std::vector< CMatrix< C_FLOAT64 > >	mVec_mFastParticipationIndex

std::vector< CMatrix< C_FLOAT64 > >	mVec_mFastReactionPointer

std::vector< CMatrix< C_FLOAT64 > >	mVec_mFastReactionPointerNormed

std::vector< CMatrix< C_FLOAT64 > >	mVec_mImportanceIndex

std::vector< CMatrix< C_FLOAT64 > >	mVec_mImportanceIndexNormedRow

std::vector< CMatrix< C_FLOAT64 > >	mVec_mParticipationIndex

std::vector< CMatrix< C_FLOAT64 > >	mVec_mParticipationIndexNormedColumn

std::vector< CMatrix< C_FLOAT64 > >	mVec_mParticipationIndexNormedRow

std::vector< CMatrix< C_FLOAT64 > >	mVec_mRadicalPointer

std::vector< CMatrix< C_FLOAT64 > >	mVec_mSlowParticipationIndex

CVectorCore< C_FLOAT64 >	mY

CVector< C_FLOAT64 >	mYerror

CDataArray *	pFastParticipationIndexAnn

CDataArray *	pFastReactionPointerAnn

CDataArray *	pFastReactionPointerNormedAnn

CDataArray *	pImportanceIndexAnn

CDataArray *	pImportanceIndexNormedRowAnn

CDataArray *	pParticipationIndexAnn

CDataArray *	pParticipationIndexNormedColumnAnn

CDataArray *	pParticipationIndexNormedRowAnn

CDataArray *	pRadicalPointerAnn

CDataArray *	pSlowParticipationIndexAnn

Protected Attributes inherited from CTSSAMethod
std::map< std::string, CDataArray * >	mapTableToName

CVector< C_FLOAT64 >	mCfast

C_FLOAT64	mConcentration2Number

CVectorCore< C_FLOAT64 >	mContainerState

int	mCurrentStep

std::vector< C_FLOAT64 >	mCurrentTime

C_INT	mDim

C_FLOAT64	mDtol

C_FLOAT64	mEPS

CMatrix< C_FLOAT64 >	mJacobian

CMatrix< C_FLOAT64 >	mJacobian_initial

C_FLOAT64	mNumber2Concentration

C_FLOAT64 *	mpContainerStateTime

C_FLOAT64 *	mpFirstSpecies

const C_FLOAT64 *	mpFirstSpeciesRate

CLsodaMethod *	mpLsodaMethod

CTSSAProblem *	mpProblem

CMatrix< C_FLOAT64 >	mQ

CMatrix< C_FLOAT64 >	mQ_desc

CMatrix< C_FLOAT64 >	mQz

CMatrix< C_FLOAT64 >	mR

CMatrix< C_FLOAT64 >	mR_desc

C_INT32	mSlow

CMatrix< C_FLOAT64 >	mTd

CMatrix< C_FLOAT64 >	mTd_save

CMatrix< C_FLOAT64 >	mTdInverse

CMatrix< C_FLOAT64 >	mTdInverse_save

std::vector< C_INT >	mVec_SlowModes

std::vector< CVector< C_FLOAT64 > >	mVec_TimeScale

CVector< C_FLOAT64 >	mVfast_space

CMatrix< C_FLOAT64 >	mVslow

CMatrix< C_FLOAT64 >	mVslow_metab

CVector< C_FLOAT64 >	mVslow_space

CVector< C_FLOAT64 >	mY_cons

CVector< C_FLOAT64 >	mY_initial

std::vector< std::string >	tableNames

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
	CCSPMethod ()

Additional Inherited Members
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

The CCSPMethod class implements the CSP method.

more information under: http://copasi.org/Support/User_Manual/Methods/Time_Scale_Separation_Methods/CSP/

Constructor & Destructor Documentation

◆ CCSPMethod() [1/3]

CCSPMethod::CCSPMethod ( )

private

Default constructor.

◆ CCSPMethod() [2/3]

CCSPMethod::CCSPMethod	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType = `CTaskEnum::Method::tssCSP`,
		const CTaskEnum::Task &	taskType = `CTaskEnum::Task::tssAnalysis`
	)

Specific constructor

Parameters

const	CDataContainer * pParent
const	CTaskEnum::Method & methodType (defaulf: tssCSP)
const	CTaskEnum::Task & taskType (default: tssAnalysis)

References createAnnotationsM(), and initializeParameter().

◆ CCSPMethod() [3/3]

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

Copy constructor.

Parameters

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

References createAnnotationsM(), and initializeParameter().

◆ ~CCSPMethod()

CCSPMethod::~CCSPMethod ( )

virtual

Destructor.

Member Function Documentation

◆ basisRefinement()

void CCSPMethod::basisRefinement	(	C_INT	N,
		C_INT	M,
		const CMatrix< C_FLOAT64 > &	ALA,
		const CMatrix< C_FLOAT64 > &	TAU,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	A0,
		CMatrix< C_FLOAT64 > &	B0
	)

protected

Refinement Procedre : Lamm, Combustion Science and Technoligy, 1993.

References C_INT, and TAU.

Referenced by cspstep().

◆ calculateJacobian()

void CCSPMethod::calculateJacobian	(	C_INT &	n,
		CVector< C_FLOAT64 > &	y,
		CMatrix< C_FLOAT64 > &	J
	)

protected

evaluate Jacobian for the current y

◆ createAnnotationsM()

void CCSPMethod::createAnnotationsM ( )

virtual

create the CArraAnnotations for every table in the CQTSSAResultSubWidget input for each CArraAnnotations is a seperate CMatrix

Create the CArraAnnotations for tables in the CQTSSAResultSubWidget. Input for each CArraAnnotations is a separate CMatrix.

Reimplemented from CTSSAMethod.

References CTSSAMethod::mapTableToName, mFastParticipationIndexTab, mFastReactionPointerNormedTab, mFastReactionPointerTab, mImportanceIndexNormedRowTab, mImportanceIndexTab, mParticipationIndexNormedColumnTab, mParticipationIndexNormedRowTab, mParticipationIndexTab, mRadicalPointerTab, mSlowParticipationIndexTab, pFastParticipationIndexAnn, pFastReactionPointerAnn, pFastReactionPointerNormedAnn, pImportanceIndexAnn, pImportanceIndexNormedRowAnn, pParticipationIndexAnn, pParticipationIndexNormedColumnAnn, pParticipationIndexNormedRowAnn, pRadicalPointerAnn, pSlowParticipationIndexAnn, CDataArray::setDescription(), CDataArray::setDimensionDescription(), CDataArray::setMode(), CDataArray::Strings, CTSSAMethod::tableNames, and CDataArray::Vector.

Referenced by CCSPMethod().

◆ CSPImportanceIndex()

void CCSPMethod::CSPImportanceIndex	(	C_INT &	N,
		C_FLOAT64 &	tauM1,
		CMatrix< C_FLOAT64 > &	Q
	)

protected

compute CSP Importance Index

compute CSP Importance Index : a measure of relative importance of the contribution of r-th elementary reaction to the current reaction rate of the i-th species

References C_FLOAT64, C_INT, CMathContainer::getParticleFluxes(), CMathContainer::getReactions(), CMathContainer::getStoichiometry(), mImportanceIndex, mImportanceIndexNormedRow, CCopasiMethod::mpContainer, mReducedModel, mYerror, CMatrix< CType >::resize(), CVector< CType >::resize(), CVectorCore< CType >::size(), and smmult().

Referenced by cspstep().

◆ CSPOutput()

void CCSPMethod::CSPOutput	(	C_INT &	N,
		C_INT &	M,
		C_INT &	R
	)

CSP output

References CStateTemplate::beginIndependent(), C_INT, CMathContainer::getModel(), CDataObject::getObjectName(), CModel::getReactions(), CModel::getStateTemplate(), mAmplitude, mFastReactionPointer, mImportanceIndex, mParticipationIndex, CCopasiMethod::mpContainer, and mRadicalPointer.

Referenced by cspstep().

◆ CSPParticipationIndex()

void CCSPMethod::CSPParticipationIndex	(	C_INT &	N,
		C_INT &	M,
		C_FLOAT64 &	tauM1,
		CMatrix< C_FLOAT64 > &	B0
	)

protected

compute CSP Participation Index

compute CSP Participation Index: a measure of participation of the r-th elementary reaction to the balancing act of the i-th mode It is assumed that forward and reverse reactions are counted as distinct

References C_FLOAT64, C_INT, CMathContainer::getParticleFluxes(), CMathContainer::getReactions(), CMathContainer::getStoichiometry(), mFastParticipationIndex, mParticipationIndex, mParticipationIndexNormedColumn, mParticipationIndexNormedRow, CCopasiMethod::mpContainer, mReducedModel, mSlowParticipationIndex, mYerror, CMatrix< CType >::resize(), CVector< CType >::resize(), and CVectorCore< CType >::size().

Referenced by cspstep().

◆ CSPradicalPointer()

void CCSPMethod::CSPradicalPointer	(	C_INT &	N,
		C_INT &	M,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B
	)

protected

compute CSP radical pointer and fast reaction pointers

some comments on the Qm matrix: Qm(i,i) , i = 0,1,...,N, is a measure of projection of i-th unit vector in the m-th mode, whenever Qm(i,i) is not a small number, species m is said to be a CSP radical

Pmr is a measure of projection of r-th stoichiometric vector in the m-th mode, whenever Pmr is not a small number, the r-th reaction is said to be a fast reaction

References C_FLOAT64, C_INT, CMathContainer::getReactions(), CMathContainer::getStoichiometry(), mFastReactionPointer, mFastReactionPointerNormed, CCopasiMethod::mpContainer, mRadicalPointer, mReducedModel, CMatrix< CType >::resize(), and CVectorCore< CType >::size().

Referenced by cspstep().

◆ cspstep()

void CCSPMethod::cspstep	(	const double &	deltaT,
		C_INT &	n,
		C_INT &	m,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B
	)

protected

Start procedure of the CSP algorithm. S.H. Lam and D.A. Gaussis, International Journal of Chemical Kinetics, 26, pp. 461-486, 1994

compute CSP Participation Index: a measure of participation of the r-th elementary reaction to the balancing act of the i-th mode It is assumed that forward and reverse reactions are counted as distinct

compute CSP Importance Index : a measure of relative importance of the contribution of r-th elementary reaction to the current reaction rate of the i-th species

References CVectorCore< CType >::array(), basisRefinement(), C_FLOAT64, C_INT, CSPImportanceIndex(), CSPOutput(), CSPParticipationIndex(), CSPradicalPointer(), emptyOutputData(), findCandidatesNumber(), CMetab::getCompartment(), CMathObject::getDataObject(), CModelEntity::getInitialValue(), CMathContainer::getMathObject(), CDataObject::getObjectParent(), CMathContainer::getReactions(), isBlockDiagonal(), mAerror, mAmplitude, MCTSSAMethod, mG, mI, mIter, CTSSAMethod::mJacobian, CTSSAMethod::mJacobian_initial, modesAmplitude(), modesAreExhausted(), CCopasiMethod::mpContainer, CTSSAMethod::mpContainerStateTime, CTSSAMethod::mQ, CTSSAMethod::mR, mRerror, mY, mYerror, CMatrix< CType >::resize(), CVector< CType >::resize(), CTSSAMethod::schur(), CVectorCore< CType >::size(), sminverse(), smmult(), smnorm(), smsubst(), and CCopasiMessage::WARNING.

Referenced by step().

◆ emptyOutputData()

void CCSPMethod::emptyOutputData	(	C_INT	N,
		C_INT	M,
		C_INT	R
	)

protected

CSP output : empty

References C_INT, mAmplitude, mFastParticipationIndex, mFastReactionPointer, mFastReactionPointerNormed, mImportanceIndex, mImportanceIndexNormedRow, mParticipationIndex, mParticipationIndexNormedColumn, mParticipationIndexNormedRow, mRadicalPointer, and mSlowParticipationIndex.

Referenced by cspstep().

◆ emptyVectors()

void CCSPMethod::emptyVectors ( )

empty every vector to be able to fill them with new values for a new calculation also nullify the step counter

Empty every vector to be able to fill them with new values for a new calculation. Also nullify the step counter.

References CTSSAMethod::mCurrentStep, CTSSAMethod::mCurrentTime, mVec_mFastParticipationIndex, mVec_mFastReactionPointer, mVec_mFastReactionPointerNormed, mVec_mImportanceIndex, mVec_mImportanceIndexNormedRow, mVec_mParticipationIndex, mVec_mParticipationIndexNormedColumn, mVec_mParticipationIndexNormedRow, mVec_mRadicalPointer, mVec_mSlowParticipationIndex, CTSSAMethod::mVec_SlowModes, and CTSSAMethod::mVec_TimeScale.

Referenced by start().

◆ findCandidatesNumber()

void CCSPMethod::findCandidatesNumber	(	C_INT &	n,
		C_INT &	k,
		CVector< C_FLOAT64 > &	tsc,
		C_INT &	info
	)

protected

find the number of candidates to fast according to the time-scale separation ratio

References C_FLOAT64, C_INT, and mEps.

Referenced by cspstep().

◆ findTimeScaleSeparation()

void CCSPMethod::findTimeScaleSeparation	(	C_INT &	n,
		C_INT &	k,
		CVector< C_FLOAT64 > &	tsc,
		C_INT &	info
	)

protected

find the new number of fast according to the time-scale separation ratio

◆ getFastParticipationIndexAnn()

const CDataArray * CCSPMethod::getFastParticipationIndexAnn ( ) const

References pFastParticipationIndexAnn.

◆ getFastReactionPointerAnn()

const CDataArray * CCSPMethod::getFastReactionPointerAnn ( ) const

References pFastReactionPointerAnn.

◆ getFastReactionPointerNormedAnn()

const CDataArray * CCSPMethod::getFastReactionPointerNormedAnn ( ) const

References pFastReactionPointerNormedAnn.

◆ getImportanceIndexAnn()

const CDataArray * CCSPMethod::getImportanceIndexAnn ( ) const

References pImportanceIndexAnn.

◆ getImportanceIndexNormedRowAnn()

const CDataArray * CCSPMethod::getImportanceIndexNormedRowAnn ( ) const

References pImportanceIndexNormedRowAnn.

◆ getParticipationIndexAnn()

const CDataArray * CCSPMethod::getParticipationIndexAnn ( ) const

References pParticipationIndexAnn.

◆ getParticipationIndexNormedColumnAnn()

const CDataArray * CCSPMethod::getParticipationIndexNormedColumnAnn ( ) const

References pParticipationIndexNormedColumnAnn.

◆ getParticipationIndexNormedRowAnn()

const CDataArray * CCSPMethod::getParticipationIndexNormedRowAnn ( ) const

References pParticipationIndexNormedRowAnn.

◆ getRadicalPointerAnn()

const CDataArray * CCSPMethod::getRadicalPointerAnn ( ) const

return CArrayAnnotation for visualization in the CQTSSAResultSubWidget

References pRadicalPointerAnn.

◆ getSlowParticipationIndexAnn()

const CDataArray * CCSPMethod::getSlowParticipationIndexAnn ( ) const

References pSlowParticipationIndexAnn.

◆ initializeOutput()

void CCSPMethod::initializeOutput ( )

virtual

initialize output for the result elements, this method initializes the output elements so that an output handler can be used afterwards

Predefine the CArrayAnnotation for plots

Reimplemented from CTSSAMethod.

References CDataVector< CType >::add(), CStateTemplate::beginIndependent(), CMathContainer::getModel(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), CModel::getReactions(), CModel::getStateTemplate(), mFastParticipationIndexTab, mImportanceIndexTab, CCopasiMethod::mpContainer, mReducedModel, mSlowParticipationIndexTab, pFastParticipationIndexAnn, pImportanceIndexAnn, pSlowParticipationIndexAnn, CDataArray::resize(), CMatrix< CType >::resize(), CDataArray::setAnnotationString(), CDataArray::setCopasiVector(), and CDataVector< CType >::size().

◆ initializeParameter()

void CCSPMethod::initializeParameter ( )

virtual

Intialize the method parameter

Reimplemented from CTSSAMethod.

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CTSSAMethod::initializeParameter(), CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.

Referenced by CCSPMethod().

◆ isBlockDiagonal()

C_INT CCSPMethod::isBlockDiagonal	(	C_INT	N,
		C_INT	M,
		const CMatrix< C_FLOAT64 > &	ALA,
		const C_FLOAT64 &	SMALL
	)

protected

compute the norm C of the off-diagonal blocks

References C_FLOAT64, C_INT, and max.

Referenced by cspstep().

◆ modesAmplitude()

void CCSPMethod::modesAmplitude	(	C_INT	N,
		const CVector< C_FLOAT64 > &	g,
		const CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	F
	)

protected

compute amplitudes of fast and slow modes

References C_INT.

Referenced by cspstep(), and modesAreExhausted().

◆ modesAreExhausted()

bool CCSPMethod::modesAreExhausted	(	C_INT	N,
		C_INT	M,
		C_FLOAT64 &	tauM,
		C_FLOAT64 &	tauM1,
		CVector< C_FLOAT64 > &	g,
		const CMatrix< C_FLOAT64 > &	A,
		const CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	F
	)

protected

check : whether each of the analysed M modes is exhausted

References C_FLOAT64, C_INT, modesAmplitude(), and mYerror.

Referenced by cspstep().

◆ printResult()

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

virtual

print of the standart report sequence for ILDM Method

Parameters

std::ostream * ostream

Reimplemented from CCopasiMethod.

References CStateTemplate::beginIndependent(), C_INT, C_INT32, CMathContainer::getModel(), CDataObject::getObjectName(), CModel::getReactions(), CModel::getStateTemplate(), CTSSAMethod::getTimeForStep(), CModel::getTimeUnitName(), CTSSAMethod::mDim, CCopasiMethod::mpContainer, mVec_mImportanceIndex, mVec_mParticipationIndex, mVec_mRadicalPointer, CTSSAMethod::mVec_SlowModes, CTSSAMethod::mVec_TimeScale, and CDataVector< CType >::size().

◆ setAnnotationM()

bool CCSPMethod::setAnnotationM ( size_t step )

virtual

set the every CArrayAnnotation for the requested step set the desription of CArayAnnotation for both dimensions

Set the every CArrayAnnotation for the requested step. Set also the description of CArayAnnotation for both dimensions:

dimension description could consists of some std::strings some strings contain the Time Scale values for requested step
dimension description could consists of arrays of CommonNames

Implements CTSSAMethod.

References CDataVector< CType >::add(), CStateTemplate::beginIndependent(), C_INT32, CMathContainer::getModel(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), CModel::getReactions(), CModel::getStateTemplate(), CTSSAMethod::mDim, mFastParticipationIndexTab, mFastReactionPointerNormedTab, mFastReactionPointerTab, mImportanceIndexNormedRowTab, mImportanceIndexTab, mParticipationIndexNormedColumnTab, mParticipationIndexNormedRowTab, mParticipationIndexTab, CCopasiMethod::mpContainer, mRadicalPointerTab, mReducedModel, mSlowParticipationIndexTab, mVec_mFastParticipationIndex, mVec_mFastReactionPointer, mVec_mFastReactionPointerNormed, mVec_mImportanceIndex, mVec_mImportanceIndexNormedRow, mVec_mParticipationIndex, mVec_mParticipationIndexNormedColumn, mVec_mParticipationIndexNormedRow, mVec_mRadicalPointer, mVec_mSlowParticipationIndex, CTSSAMethod::mVec_SlowModes, CTSSAMethod::mVec_TimeScale, pFastParticipationIndexAnn, pFastReactionPointerAnn, pFastReactionPointerNormedAnn, pImportanceIndexAnn, pImportanceIndexNormedRowAnn, pParticipationIndexAnn, pParticipationIndexNormedColumnAnn, pParticipationIndexNormedRowAnn, pRadicalPointerAnn, pSlowParticipationIndexAnn, CDataArray::resize(), CMatrix< CType >::resize(), CDataArray::setAnnotationString(), CDataArray::setCopasiVector(), CDataVector< CType >::size(), and step().

Referenced by step().

◆ setVectors()

void CCSPMethod::setVectors ( int fast )

upgrade all vectors with values from actually calculalion for current step

upgrade all vectors with values from actually calculation for current step

References C_INT, CMathContainer::getReactions(), CTSSAMethod::mCurrentStep, CTSSAMethod::mDim, mFastParticipationIndex, mFastReactionPointer, mFastReactionPointerNormed, mImportanceIndex, mImportanceIndexNormedRow, mParticipationIndex, mParticipationIndexNormedColumn, mParticipationIndexNormedRow, CCopasiMethod::mpContainer, CTSSAMethod::mR, mRadicalPointer, mSlowParticipationIndex, mVec_mFastParticipationIndex, mVec_mFastReactionPointer, mVec_mFastReactionPointerNormed, mVec_mImportanceIndex, mVec_mImportanceIndexNormedRow, mVec_mParticipationIndex, mVec_mParticipationIndexNormedColumn, mVec_mParticipationIndexNormedRow, mVec_mRadicalPointer, mVec_mSlowParticipationIndex, CTSSAMethod::mVec_SlowModes, CTSSAMethod::mVec_TimeScale, and CVectorCore< CType >::size().

Referenced by step().

◆ setVectorsToNaN()

void CCSPMethod::setVectorsToNaN ( )

set vectors to NaN when the reduction was not possible

References C_INT, CMathContainer::getReactions(), CTSSAMethod::mCurrentStep, CTSSAMethod::mDim, CCopasiMethod::mpContainer, CTSSAMethod::mR, mVec_mFastParticipationIndex, mVec_mFastReactionPointer, mVec_mFastReactionPointerNormed, mVec_mImportanceIndex, mVec_mImportanceIndexNormedRow, mVec_mParticipationIndex, mVec_mParticipationIndexNormedColumn, mVec_mParticipationIndexNormedRow, mVec_mRadicalPointer, mVec_mSlowParticipationIndex, CTSSAMethod::mVec_SlowModes, CTSSAMethod::mVec_TimeScale, and CVectorCore< CType >::size().

Referenced by step().

◆ smadd()

void CCSPMethod::smadd	(	const CMatrix< C_FLOAT64 > &	A,
		const CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	C,
		C_INT	n1,
		C_INT	n2
	)

protected

Addition of submatrix

References C_INT.

◆ sminverse()

void CCSPMethod::sminverse	(	C_INT	n,
		const CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B
	)

protected

Inverse submatrix

References CMatrix< CType >::array(), C_INT, and dgesv_().

Referenced by cspstep().

◆ smmult()

void CCSPMethod::smmult	(	const CMatrix< C_FLOAT64 > &	A,
		const CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	C,
		C_INT	n1,
		C_INT	n2,
		C_INT	n3
	)

protected

CSP related staff Multiplication of submatrix

References C_INT.

Referenced by CSPImportanceIndex(), cspstep(), and yCorrection().

◆ smnorm()

void CCSPMethod::smnorm	(	C_INT	n,
		CMatrix< C_FLOAT64 > &	A,
		CMatrix< C_FLOAT64 > &	B,
		C_INT	n1
	)

protected

Normalize submatrix

References C_FLOAT64, and C_INT.

Referenced by cspstep().

◆ smsubst()

void CCSPMethod::smsubst	(	const CMatrix< C_FLOAT64 > &	A,
		const CMatrix< C_FLOAT64 > &	B,
		CMatrix< C_FLOAT64 > &	C,
		C_INT	n1,
		C_INT	n2
	)

protected

Substruction of submatrix

References C_INT.

Referenced by cspstep().

◆ start()

void CCSPMethod::start ( )

virtual

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

Reimplemented from CTSSAMethod.

References C_INT, emptyVectors(), CMathContainer::getCountDependentSpecies(), CMathContainer::getModel(), CModel::getNumber2QuantityFactor(), CMathContainer::getReactions(), CVectorCore< CType >::initialize(), CTSSAMethod::integrationMethodStart(), mAerror, mAmplitude, mB, mCSPbasis, CTSSAMethod::mDim, mEps, mFastParticipationIndex, mFastParticipationIndexTab, mFastReactionPointer, mFastReactionPointerNormed, mG, mI, mImportanceIndex, mImportanceIndexNormedRow, mImportanceIndexTab, mIter, mParticipationIndex, mParticipationIndexNormedColumn, mParticipationIndexNormedRow, CCopasiMethod::mpContainer, CTSSAMethod::mpFirstSpecies, CTSSAMethod::mpFirstSpeciesRate, CTSSAMethod::mpLsodaMethod, mRadicalPointer, mReducedModel, mRerror, mSetVectors, mSlowParticipationIndex, mSlowParticipationIndexTab, mTStep, mVec_mFastParticipationIndex, mVec_mImportanceIndex, mVec_mSlowParticipationIndex, mY, mYerror, pFastParticipationIndexAnn, pImportanceIndexAnn, pSlowParticipationIndexAnn, CDataArray::resize(), CDataVector< CType >::resize(), CMatrix< CType >::resize(), CVector< CType >::resize(), CDataArray::setCopasiVector(), CCopasiParameterGroup::setValue(), CVectorCore< CType >::size(), CTSSAMethod::start(), and CMathContainer::updateSimulatedValues().

◆ step()

void CCSPMethod::step ( const double & deltaT )

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

Reimplemented from CTSSAMethod.

References C_INT, CMathContainer::calculateJacobian(), cspstep(), CTSSAMethod::integrationStep(), mB, CTSSAMethod::mCurrentStep, CTSSAMethod::mDim, CTSSAMethod::mJacobian, CCopasiMethod::mpContainer, mReducedModel, mTStep, CMatrix< CType >::resize(), setAnnotationM(), setVectors(), setVectorsToNaN(), CTSSAMethod::updateCurrentTime(), and CMathContainer::updateSimulatedValues().