The CTSSAMethod class is the base class for all time scale separation analysis methods. More...

#include <CTSSAMethod.h>

Inheritance diagram for CTSSAMethod:

Public Member Functions
virtual void	createAnnotationsM ()

	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 void	initializeOutput ()

virtual void	initializeParameter ()

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

virtual bool	setAnnotationM (size_t s)=0

void	setProblem (CTSSAProblem *problem)

void	setVectors (int slowMode)

virtual void	start ()

virtual void	step (const double &deltaT)

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 void	printResult (std::ostream *ostream) const

virtual bool	setCallBack (CProcessReportLevel callBack)

void	setMathContainer (CMathContainer *pContainer)

virtual	~CCopasiMethod ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

void	addParameter (CCopasiParameter *pParameter)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

virtual bool	applyData (const CData &data, CUndoData::CChangeSet &changes)

CCopasiParameterGroup *	assertGroup (const std::string &name, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

template<class CType >
CType *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue, const CCopasiParameter::UserInterfaceFlag &flag=CCopasiParameter::UserInterfaceFlag::All)

index_iterator	beginIndex () const

const_name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CDataContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &objectType="ParameterGroup")

void	clear ()

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

index_iterator	endIndex () const

const_name_iterator	endName () const

CCopasiParameterGroup &	getElementTemplates ()

const CCopasiParameterGroup &	getElementTemplates () const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

virtual size_t	getIndex (const CDataObject *pObject) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const size_t &index) const

std::string	getKey (const std::string &name) const

virtual const std::string &	getName (const size_t &index) const

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

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter *	getParameter (std::string name)

const CCopasiParameter *	getParameter (std::string name) const

CCopasiParameter::Type	getType (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

template<class CType >
CType &	getValue (const size_t &index)

template<class CType >
const CType &	getValue (const size_t &index) const

template<class CType >
CType &	getValue (const std::string &name)

template<class CType >
const CType &	getValue (const std::string &name) const

bool	haveTemplate () const

virtual CUndoObjectInterface *	insert (const CData &data)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

virtual bool	remove (CDataObject *pObject)

bool	removeParameter (CCopasiParameter *pParameter)

bool	removeParameter (const size_t &index)

bool	removeParameter (const std::string &name)

virtual void	setUserInterfaceFlag (const UserInterfaceFlag &flag)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

size_t	size (const UserInterfaceFlag &require=UserInterfaceFlag::None, const UserInterfaceFlag &exclude=UserInterfaceFlag::None) const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual CData	toData () const

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

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CDataContainer *pParent)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CDataContainer pParent=NO_PARENT, const std::string &objectType="Parameter")

virtual CCommonName	getCN () const override

template<class CType >
const CType &	getDefault () const

virtual const std::string &	getKey () const override

virtual std::string	getObjectDisplayName () const override

const CCopasiParameter::Type &	getType () const

const UserInterfaceFlag &	getUserInterfaceFlag () const

template<class CType >
std::vector< std::pair< CType, CType > > &	getValidValues ()

template<class CType >
const std::vector< std::pair< CType, CType > > &	getValidValues () const

void *	getValidValuesPointer () const

template<class CType >
CType &	getValue ()

template<class CType >
const CType &	getValue () const

virtual void *	getValuePointer () const override

CDataObject *	getValueReference () const

bool	hasValidValues () const

bool	isBasic () const

bool	isDefault () const

bool	isEditable () const

bool	isUnsupported () const

bool	isValidValue (const bool &value) const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const CCommonName &value) const

template<class CType >
bool	isValidValue (const CType &) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setDefault (const CType &defaultValue)

bool	setDefault (const std::vector< CCopasiParameter * > &defaultValue)

virtual bool	setObjectParent (const CDataContainer *pParent) override

template<class CType , class Enum >
bool	setValidValues (const CEnumAnnotation< CType, Enum > &validValues)

template<class CType >
bool	setValidValues (const std::vector< std::pair< CType, CType > > &validValues)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

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

virtual bool	appendDeletedDependentData (CUndoData &undoData) const

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

	CDataContainer (const std::string &name, const CDataContainer *pParent=NO_PARENT, const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)

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

void	getDescendants (CDataObject::DataObjectSet &descendants, const bool &recursive=false) const

virtual objectMap &	getObjects ()

virtual const objectMap &	getObjects () const

virtual const std::string	getUnits () const override

virtual const CDataObject *	getValueObject () const override

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

virtual	~CDataContainer ()

Public Member Functions inherited from CDataObject
void	addIssue (const CIssue &issue)

void	addReference (const CDataContainer *pReference)

virtual void	calculateValue () override

	CDataObject (const CDataObject &src, const CDataContainer *pParent=NULL)

virtual void	destruct () override

virtual const CDataObject *	getDataObject () const override

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

CDataModel *	getObjectDataModel () const

const CObjectInterface *	getObjectFromCN (const CCommonName &cn) const

const std::string &	getObjectName () const

CDataContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const override

virtual const CValidity &	getValidity () const override

bool	hasFlag (const Flag &flag) const

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

bool	prerequisitsContains (const DataObjectSet &objects) const

void	removeIssue (const CIssue &issue)

void	removeReference (const CDataContainer *pReference)

bool	setObjectName (const std::string &name)

void	validityChanged (const CValidity &changedValidity) override

void	validityRemoved (const CValidity &changedValidity)

virtual	~CDataObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

	CObjectInterface (const CObjectInterface &src)

virtual	~CObjectInterface ()

Public Member Functions inherited from CUndoObjectInterface
	CUndoObjectInterface ()

	CUndoObjectInterface (const CUndoObjectInterface &src)

bool	generateUuid ()

const xg::Guid &	getUuid () const

bool	setUuid (const std::string &uuid)

bool	setUuid (const xg::Guid &uuid)

virtual	~CUndoObjectInterface ()

Protected Member Functions
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
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
	CTSSAMethod ()

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 CTSSAMethod class is the base class for all time scale separation analysis methods.

Constructor & Destructor Documentation

◆ CTSSAMethod() [1/3]

CTSSAMethod::CTSSAMethod ( )

private

Default constructor.

◆ CTSSAMethod() [2/3]

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

Specific constructor

Parameters

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

CTSSAMethod class. This class describes the interface to all time scale separation analysis methods. The various method like ILDM or CSP have to be derived from this class. Default constructor.

◆ CTSSAMethod() [3/3]

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

Copy constructor.

Parameters

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

Copy constructor.

Parameters

const CTSSAMethod & src

◆ ~CTSSAMethod()

CTSSAMethod::~CTSSAMethod ( )

virtual

Destructor.

References mpLsodaMethod, and pdelete.

Member Function Documentation

◆ calculateDerivatives()

void CTSSAMethod::calculateDerivatives	(	C_FLOAT64 *	X1,
		C_FLOAT64 *	Y1,
		bool	useReducedModel
	)

protected

References C_FLOAT64, CMathContainer::getValues(), mConcentration2Number, mDim, mNumber2Concentration, CCopasiMethod::mpContainer, mpFirstSpecies, mpFirstSpeciesRate, CMathContainer::setValues(), and CMathContainer::updateSimulatedValues().

Referenced by CILDMMethod::deuflhard(), CILDMModifiedMethod::deuflhard_metab(), CILDMMethod::newton(), CILDMModifiedMethod::newton_for_timestep(), CILDMModifiedMethod::newton_new(), and CILDMModifiedMethod::step().

◆ createAnnotationsM()

void CTSSAMethod::createAnnotationsM ( )

virtual

create the CArraAnnotations for every ILDM-tab in the CQTSSAResultSubWidget input for each CArraAnnotations is a seperate CMatrix

Create the CArraAnnotations for every ILDM-tab in the CQTSSAResultSubWidget. Input for each CArraAnnotations is a separate CMatrix.

Reimplemented in CILDMModifiedMethod, CILDMMethod, and CCSPMethod.

◆ elevateChildren()

bool CTSSAMethod::elevateChildren ( )

protectedvirtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

References initializeParameter().

◆ emptyVectors()

void CTSSAMethod::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.

◆ getCurrentStep()

const int & CTSSAMethod::getCurrentStep ( ) const

Retrieve the current step

References mCurrentStep.

◆ getTable()

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

References mapTableToName.

◆ getTableNames()

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

References tableNames.

◆ getTimeForStep()

C_FLOAT64 CTSSAMethod::getTimeForStep ( int step ) const

Returns: required time-value from timevector

References mCurrentTime, and step().

Referenced by CCSPMethod::printResult(), and CILDMModifiedMethod::printResult().

◆ getVec_TimeScale()

CVector< C_FLOAT64 > CTSSAMethod::getVec_TimeScale ( int step )

Returns: mVec_TimeScale for visualization in ILDM-tab in the CQTSSAResultSubWidget

return mVec_TimeScale for visualization in ILDM-tab in the CQTSSAResultSubWidget

References mVec_TimeScale, and step().

◆ initializeOutput()

void CTSSAMethod::initializeOutput ( )

virtual

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

Reimplemented in CILDMModifiedMethod, CILDMMethod, and CCSPMethod.

Referenced by CTSSATask::initialize(), and CTSSATask::updateMatrices().

◆ initializeParameter()

void CTSSAMethod::initializeParameter ( )

virtual

Initialize the method parameter

Reimplemented in CILDMModifiedMethod, CILDMMethod, and CCSPMethod.

References C_FLOAT64, C_INT32, CMethodFactory::create(), CTaskEnum::deterministic, mpLsodaMethod, CCopasiParameterGroup::setValue(), and CTaskEnum::timeCourse.

Referenced by elevateChildren(), CCSPMethod::initializeParameter(), CILDMMethod::initializeParameter(), and CILDMModifiedMethod::initializeParameter().

◆ integrationMethodStart()

void CTSSAMethod::integrationMethodStart ( )

protected

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

References mpLsodaMethod, and CLsodaMethod::start().

Referenced by CCSPMethod::start(), CILDMMethod::start(), and CILDMModifiedMethod::start().

◆ integrationStep()

void CTSSAMethod::integrationStep ( const double & deltaT )

protected

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

References mpLsodaMethod, and CLsodaMethod::step().

Referenced by CCSPMethod::step(), CILDMMethod::step(), and CILDMModifiedMethod::step().

◆ isValidProblem()

bool CTSSAMethod::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CCopasiMethod.

References CModelEntity::ASSIGNMENT, CDataVector< CType >::begin(), CDataVector< CType >::end(), CCopasiMessage::ERROR, fatalError, CModel::getCompartments(), CModel::getEvents(), CModel::getMetabolites(), CMathContainer::getModel(), CModel::getModelValues(), CModel::getNumAssignmentMetabs(), CModel::getNumODEMetabs(), CCopasiMethod::getSubType(), CCopasiMethod::isValidProblem(), MCTSSAMethod, CCopasiMethod::mpContainer, CModelEntity::ODE, CDataVector< CType >::size(), CCopasiParameterGroup::size(), CTaskEnum::tssCSP, CTaskEnum::tssILDM, and CTaskEnum::tssILDMModified.

◆ map_index()

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

protected

MAP_INDEX used for sorting of SchurDecompostion

References C_FLOAT64, C_INT, and max.

Referenced by schur().

◆ map_index_desc()

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

protected

This is the test only. We try to reorder the Schur matrix from slowest mode (on the bottom) to the fastest (on the top) The function map_index_desc() is used on the end of schur() in order to produce the orthogonal slow space

References C_FLOAT64, C_INT, and min.

Referenced by schur_desc().

◆ mat_anal_fast_space()

void CTSSAMethod::mat_anal_fast_space ( C_INT & slow )

protected

MAT_ANAL_fast_space: mathematical analysis of matrices mTdInverse for post-analysis

References C_FLOAT64, C_INT, mDim, mTdInverse, mVfast_space, and CMatrix< CType >::resize().

Referenced by CILDMModifiedMethod::deuflhard_metab(), CILDMMethod::step(), and CILDMModifiedMethod::step().

◆ mat_anal_fast_space_thomas()

void CTSSAMethod::mat_anal_fast_space_thomas ( C_INT & slow )

protected

MAT_ANAL_fast_space: mathematical analysis of matrices mTdInverse for post-analysis

References C_FLOAT64, C_INT, mDim, mNumber2Concentration, mQ, mVfast_space, mY_initial, and CVector< CType >::resize().

◆ mat_anal_metab()

void CTSSAMethod::mat_anal_metab ( C_INT & slow )

protected

MAT_ANAL_METAB: mathematical analysis of matrices mTd for post-analysis

References C_INT, mDim, mTd, mVslow_metab, and CVector< CType >::resize().

Referenced by CILDMMethod::step(), and CILDMModifiedMethod::step().

◆ mat_anal_mod()

void CTSSAMethod::mat_anal_mod ( C_INT & slow )

protected

This is not very elegant solution. But I don't know the better one.

MAT_ANAL_MOD: mathematical analysis of matrices mTdInverse for post-analysis

References C_INT, mDim, mTdInverse, mVslow, CMatrix< CType >::resize(), and CVector< CType >::resize().

Referenced by CILDMMethod::step(), and CILDMModifiedMethod::step().

◆ mat_anal_mod_space()

void CTSSAMethod::mat_anal_mod_space ( C_INT & slow )

protected

MAT_ANAL_MOD_space: mathematical analysis of matrices mTdInverse for post-analysis

References C_FLOAT64, C_INT, mDim, mTdInverse, mVslow_space, and CMatrix< CType >::resize().

Referenced by CILDMMethod::step(), and CILDMModifiedMethod::step().

◆ orthog()

double CTSSAMethod::orthog	(	C_INT &	number1,
		C_INT &	number2
	)

protected

References C_FLOAT64, C_INT, mDim, and mTdInverse.

Referenced by CILDMMethod::step().

◆ schur()

void CTSSAMethod::schur ( C_INT & info )

protected

SCHUR: Schur Decomposition of Jacobian (reordered). Output: mQ - transformation matrix mR - block upper triangular matrix (with ordered eigenvalues)

References CVectorCore< CType >::array(), C_INT, dgees_(), dtrexc_(), fatalError, CCopasiMethod::getSubType(), map_index(), mDim, mJacobian_initial, mQ, mR, CVector< CType >::resize(), CTaskEnum::tssCSP, CTaskEnum::tssILDM, CTaskEnum::tssILDMModified, update_nid(), and update_pid().

Referenced by CCSPMethod::cspstep(), CILDMMethod::step(), and CILDMModifiedMethod::step().

◆ schur_desc()

void CTSSAMethod::schur_desc ( C_INT & info )

protected

SCHUR_desc: Schur Decomposition of Jacobian (reordered). Output: mQ_desc - transformation matrix mR_desc - block upper triangular matrix (with ordered eigenvalues)

References CVectorCore< CType >::array(), C_INT, dgees_(), dtrexc_(), map_index_desc(), mDim, mJacobian_initial, mQ_desc, mR_desc, CVector< CType >::resize(), update_nid(), and update_pid().

Referenced by CILDMMethod::step().

◆ setAnnotationM()

virtual bool CTSSAMethod::setAnnotationM ( size_t s )

pure virtual

Implemented in CILDMModifiedMethod, CILDMMethod, and CCSPMethod.

◆ setProblem()

void CTSSAMethod::setProblem ( CTSSAProblem * problem )

Set a pointer to the problem. This method is used by CTSSA

Parameters

CTSSAProblem * problem

References mpProblem.

Referenced by CTSSATask::initialize().

◆ setVectors()

void CTSSAMethod::setVectors ( int slowMode )

upgrade all vectors with values from actually calculalion for current step

upgrade all vectors with values from actually calculation for current step

◆ start()

void CTSSAMethod::start ( )

virtual

This instructs the method to prepare for integration

This instructs the method to calculate a a time step of deltaT starting with the initialState given. The new state (after deltaT) is expected in the current state. The return value is the actual time step taken.

Reimplemented in CILDMModifiedMethod, CILDMMethod, and CCSPMethod.

References CVectorCore< CType >::array(), CModel::getCompartments(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getCountIndependentSpecies(), CMathContainer::getCountODEs(), CMathContainer::getModel(), CModel::getNumber2QuantityFactor(), CModel::getQuantity2NumberFactor(), CMathContainer::getRate(), CMathContainer::getState(), CVectorCore< CType >::initialize(), mConcentration2Number, mContainerState, mDim, mNumber2Concentration, CCopasiMethod::mpContainer, mpContainerStateTime, mpFirstSpecies, mpFirstSpeciesRate, mpLsodaMethod, and CCopasiMethod::setMathContainer().

Referenced by CTSSATask::processStart(), CCSPMethod::start(), CILDMMethod::start(), and CILDMModifiedMethod::start().

◆ step()

void CTSSAMethod::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

This instructs the method to calculate a 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 time step taken.

Parameters

const double & deltaT

Reimplemented in CILDMModifiedMethod, CILDMMethod, and CCSPMethod.

Referenced by getTimeForStep(), getVec_TimeScale(), and CTSSATask::processStep().