#include <CTimeSensLsodaMethod.h>

Inheritance diagram for CTimeSensLsodaMethod:

Classes
struct	Data

struct	State

Public Member Functions
virtual void	copySensitivitiesToResultMatrix ()

	CTimeSensLsodaMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::deterministic, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)

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

virtual bool	elevateChildren ()

virtual void	evalF (const C_FLOAT64 t, const C_FLOAT64 y, C_FLOAT64 *ydot)

virtual void	evalJ (const C_FLOAT64 t, const C_FLOAT64 y, const C_INT ml, const C_INT mu, C_FLOAT64 pd, const C_INT nRowPD)

virtual void	evalR (const C_FLOAT64 t, const C_FLOAT64 y, const C_INT nr, C_FLOAT64 r)

virtual void	start ()

virtual void	stateChange (const CMath::StateChange &change)

virtual Status	step (const double &deltaT, const bool &final=false)

	~CTimeSensLsodaMethod ()

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

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

const CVectorCore< C_INT > &	getRoots () const

void	initializeDerivativesCalculations (bool reduced)

virtual void	initResult ()

const bool &	integrateReducedModel () const

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

void	setProblem (CTimeSensProblem *problem)

	~CTimeSensMethod ()

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 ()

Static Public Member Functions
static void	EvalF (const C_INT n, const C_FLOAT64 t, const C_FLOAT64 y, C_FLOAT64 ydot)

static void	EvalJ (const C_INT n, const C_FLOAT64 t, const C_FLOAT64 y, const C_INT ml, const C_INT mu, C_FLOAT64 pd, const C_INT *nRowPD)

static void	EvalR (const C_INT n, const C_FLOAT64 t, const C_FLOAT64 y, const C_INT nr, C_FLOAT64 *r)

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 *)

Protected Types
enum	eRootMasking { NONE = 0 , ALL , DISCRETE }

Protected Member Functions
void	destroyRootMask ()

Protected Member Functions inherited from CTimeSensMethod
void	calculate_dAssignments_dPar (CMatrix< C_FLOAT64 > &s)

void	calculate_dAssignments_dState (CMatrix< C_FLOAT64 > &s, bool reduced)

void	calculate_dInitialState_dPar (CMatrix< C_FLOAT64 > &s)

void	calculate_dRate_dPar (CMatrix< C_FLOAT64 > &s, bool reduced)

void	output (const bool &useMoieties)

virtual void	signalMathContainerChanged ()

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

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

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
Data	mData

State	mLastRootState

CVector< C_FLOAT64 >	mLastSuccessState

C_INT	mLsodaStatus

eRootMasking	mRootMasking

C_FLOAT64	mTime

Protected Attributes inherited from CTimeSensMethod
CMatrix< C_FLOAT64 >	mAssignmentJacobian

CVector< C_FLOAT64 * >	mAssTargetValuePointers

CVectorCore< C_FLOAT64 >	mContainerState

CMatrix< C_FLOAT64 >	mdAssignment_dPar

CMatrix< C_FLOAT64 >	mdRate_dPar

CMatrix< C_FLOAT64 >	mJacobian

size_t	mNumAssTargets
	Number of assignment targets for which sensitivities are calculated. More...

unsigned C_INT32	mNumParameters

CVector< C_FLOAT64 * >	mParameterInitialValuePointers
	the pointers to the values of the objects as provided by the problem (generally initial values) More...

CVector< bool >	mParameterIsInitialConcentration

CVector< C_FLOAT64 * >	mParameterTransientValuePointers
	the pointers as used during the simulation, initial values of fixed quantities are replaced by their transient counterparts. More...

C_FLOAT64 *	mpContainerStateTime

CTimeSensProblem *	mpProblem

const bool *	mpReducedModel

CTimeSensTask *	mpTask

CVectorCore< C_INT >	mRootsFound

CCore::CUpdateSequence	mSeq1

CCore::CUpdateSequence	mSeq2

CCore::CUpdateSequence	mSeq3

size_t	mSystemSize

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
void	createRootMask ()

	CTimeSensLsodaMethod ()

bool	hasStateChanged (const CVectorCore< C_FLOAT64 > &startState) const

void	initializeParameter ()

void	maskRoots (CVectorCore< C_FLOAT64 > &rootValues)

CTimeSensMethod::Status	peekAhead ()

void	resetState (State &state)

void	saveState (State &state, const CTimeSensMethod::Status &status) const

void	setRootMaskType (const eRootMasking &maskType)

Private Attributes
CVector< C_FLOAT64 >	mAtol

CVectorCore< bool >	mDiscreteRoots

CVector< C_FLOAT64 >	mDWork

std::ostringstream	mErrorMsg

CVector< C_INT >	mIWork

C_INT	mJType

CLSODA	mLSODA

CLSODAR	mLSODAR

C_INT	mNumRoots

C_FLOAT64 *	mpAbsoluteTolerance

bool	mPeekAheadMode

unsigned C_INT32 *	mpMaxInternalSteps

C_FLOAT64 *	mpMaxInternalStepSize

C_FLOAT64 *	mpRelativeTolerance

const C_FLOAT64 *	mpYdot

unsigned C_INT32	mRootCounter

CVector< bool >	mRootMask

State	mSavedState

C_FLOAT64	mTargetTime

C_INT	mTask

CVector< C_FLOAT64 >	mVariables

Additional Inherited Members
Public Types inherited from CTimeSensMethod
enum	Status { FAILURE = -1 , NORMAL = 0 , ROOT = 1 }

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 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

Static Protected Member Functions inherited from CTimeSensMethod
static void	printObjectSet (const std::string &s, const CObjectInterface::ObjectSet &os)
	some methods for doing debug output More...

static void	printUpdateSeq (const std::string &s, const CCore::CUpdateSequence &us)

Static Protected Attributes inherited from CTimeSensMethod
static const bool	ReducedModel

Member Enumeration Documentation

◆ eRootMasking

enum CTimeSensLsodaMethod::eRootMasking

protected

Enumerator
NONE
ALL
DISCRETE

Constructor & Destructor Documentation

◆ CTimeSensLsodaMethod() [1/3]

CTimeSensLsodaMethod::CTimeSensLsodaMethod ( )

private

Constructor.

◆ CTimeSensLsodaMethod() [2/3]

CTimeSensLsodaMethod::CTimeSensLsodaMethod	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType = `CTaskEnum::Method::deterministic`,
		const CTaskEnum::Task &	taskType = `CTaskEnum::Task::timeCourse`
	)

Specific constructor

Parameters

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

References CTimeSensLsodaMethod::Data::dim, initializeParameter(), mData, and CTimeSensLsodaMethod::Data::pMethod.

◆ CTimeSensLsodaMethod() [3/3]

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

Copy constructor.

Parameters

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

References CTimeSensLsodaMethod::Data::dim, initializeParameter(), mData, and CTimeSensLsodaMethod::Data::pMethod.

◆ ~CTimeSensLsodaMethod()

CTimeSensLsodaMethod::~CTimeSensLsodaMethod ( )

Destructor.

References CVectorCore< CType >::array(), and CTimeSensMethod::mRootsFound.

Member Function Documentation

◆ copySensitivitiesToResultMatrix()

void CTimeSensLsodaMethod::copySensitivitiesToResultMatrix ( )

virtual

copies the sensitivity values from the state vector to the (annotated) result matrix

Implements CTimeSensMethod.

References C_FLOAT64, CTimeSensMethod::calculate_dAssignments_dPar(), CTimeSensMethod::calculate_dAssignments_dState(), CTimeSensProblem::getNumTargets(), CTimeSensProblem::getScaledStateResult(), CTimeSensProblem::getScaledTargetsResult(), CTimeSensProblem::getStateResult(), CTimeSensProblem::getTargetsResult(), CTimeSensMethod::mAssignmentJacobian, CTimeSensMethod::mAssTargetValuePointers, CTimeSensMethod::mdAssignment_dPar, CTimeSensMethod::mNumParameters, CTimeSensMethod::mParameterTransientValuePointers, CTimeSensMethod::mpContainerStateTime, CTimeSensMethod::mpProblem, CTimeSensMethod::mpReducedModel, CTimeSensMethod::mSystemSize, and mVariables.

Referenced by start().

◆ createRootMask()

void CTimeSensLsodaMethod::createRootMask ( )

private

Create a mask which hides all roots being constant and zero.

References ALL, CVectorCore< CType >::begin(), C_FLOAT64, C_INT, CMathContainer::calculateRootDerivatives(), CVectorCore< CType >::end(), CMathContainer::getRootIsDiscrete(), CMathContainer::getRoots(), min, CCopasiMethod::mpContainer, CTimeSensMethod::mpReducedModel, mRootMask, mRootMasking, CTimeSensMethod::mRootsFound, CVector< CType >::resize(), CVectorCore< CType >::size(), and CMathContainer::updateRootValues().

Referenced by setRootMaskType().

◆ destroyRootMask()

void CTimeSensLsodaMethod::destroyRootMask ( )

protected

Destroy the mask which hides all roots being constant and zero.

References mRootMask, mRootMasking, and NONE.

Referenced by start().

◆ elevateChildren()

bool CTimeSensLsodaMethod::elevateChildren ( )

virtual

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

Returns: bool success

Reimplemented from CCopasiParameterGroup.

References initializeParameter().

◆ evalF()

void CTimeSensLsodaMethod::evalF	(	const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		C_FLOAT64 *	ydot
	)

virtual

References CMatrix< CType >::array(), CVectorCore< CType >::array(), C_FLOAT64, CTimeSensMethod::calculate_dRate_dPar(), CMathContainer::calculateJacobian(), CTimeSensMethod::mdRate_dPar, CTimeSensMethod::mJacobian, CTimeSensMethod::mNumParameters, CCopasiMethod::mpContainer, CTimeSensMethod::mpContainerStateTime, CTimeSensMethod::mpReducedModel, mpYdot, CTimeSensMethod::mSystemSize, mVariables, and CMathContainer::updateSimulatedValues().

Referenced by EvalF().

◆ EvalF()

void CTimeSensLsodaMethod::EvalF	(	const C_INT *	n,
		const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		C_FLOAT64 *	ydot
	)

static

This evaluates the derivatives

References evalF(), and CTimeSensLsodaMethod::Data::pMethod.

Referenced by step().

◆ evalJ()

void CTimeSensLsodaMethod::evalJ	(	const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		const C_INT *	ml,
		const C_INT *	mu,
		C_FLOAT64 *	pd,
		const C_INT *	nRowPD
	)

virtual

Referenced by EvalJ().

◆ EvalJ()

void CTimeSensLsodaMethod::EvalJ	(	const C_INT *	n,
		const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		const C_INT *	ml,
		const C_INT *	mu,
		C_FLOAT64 *	pd,
		const C_INT *	nRowPD
	)

static

This evaluates the Jacobian

References evalJ(), and CTimeSensLsodaMethod::Data::pMethod.

Referenced by step().

◆ evalR()

void CTimeSensLsodaMethod::evalR	(	const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		const C_INT *	nr,
		C_FLOAT64 *	r
	)

virtual

References CMathContainer::getRoots(), CMathContainer::getState(), maskRoots(), CCopasiMethod::mpContainer, CTimeSensMethod::mpContainerStateTime, CTimeSensMethod::mpReducedModel, mRootMasking, NONE, and CMathContainer::updateRootValues().

Referenced by EvalR().

◆ EvalR()

void CTimeSensLsodaMethod::EvalR	(	const C_INT *	n,
		const C_FLOAT64 *	t,
		const C_FLOAT64 *	y,
		const C_INT *	nr,
		C_FLOAT64 *	r
	)

static

This evaluates the roots

References evalR(), and CTimeSensLsodaMethod::Data::pMethod.

Referenced by step().

◆ hasStateChanged()

bool CTimeSensLsodaMethod::hasStateChanged ( const CVectorCore< C_FLOAT64 > & startState ) const

private

References CVectorCore< CType >::array(), C_FLOAT64, CMathContainer::getCountFixedEventTargets(), mAtol, CTimeSensMethod::mContainerState, CCopasiMethod::mpContainer, mpRelativeTolerance, and CVectorCore< CType >::size().

Referenced by peekAhead(), and step().

◆ initializeParameter()

void CTimeSensLsodaMethod::initializeParameter ( )

private

Initialize the method parameter

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, mpAbsoluteTolerance, mpMaxInternalSteps, mpMaxInternalStepSize, CTimeSensMethod::mpReducedModel, mpRelativeTolerance, CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.

Referenced by CTimeSensLsodaMethod(), and elevateChildren().

◆ maskRoots()

void CTimeSensLsodaMethod::maskRoots ( CVectorCore< C_FLOAT64 > & rootValues )

private

Mask roots which are constant and zero.

Parameters

CVectorCore< C_FLOAT64 > & rootValues

References CVectorCore< CType >::array(), C_FLOAT64, mRootMask, and CVectorCore< CType >::size().

Referenced by evalR().

◆ peekAhead()

CTimeSensMethod::Status CTimeSensLsodaMethod::peekAhead ( )

private

Peek ahead to detect simultaneous roots.

References ALL, CVectorCore< CType >::array(), C_FLOAT64, C_INT, CTimeSensLsodaMethod::State::ContainerState, CTimeSensMethod::FAILURE, CMathContainer::getRoots(), hasStateChanged(), max, mLastRootState, mLsodaStatus, CCopasiMethod::mpContainer, mPeekAheadMode, mpRelativeTolerance, mRootCounter, mRootMask, CTimeSensMethod::mRootsFound, mSavedState, mTargetTime, mTime, CTimeSensMethod::NORMAL, resetState(), CTimeSensMethod::ROOT, saveState(), setRootMaskType(), CVectorCore< CType >::size(), CTimeSensLsodaMethod::State::Status, and step().

Referenced by step().

◆ resetState()

void CTimeSensLsodaMethod::resetState ( CTimeSensLsodaMethod::State & state )

private

◆ saveState()

void CTimeSensLsodaMethod::saveState	(	CTimeSensLsodaMethod::State &	state,
		const CTimeSensMethod::Status &	status
	)		const

private

◆ setRootMaskType()

void CTimeSensLsodaMethod::setRootMaskType ( const eRootMasking & maskType )

private

Set the root mask type and update the root mask accordingly

References ALL, CVectorCore< CType >::array(), CVectorCore< CType >::begin(), C_FLOAT64, createRootMask(), DISCRETE, CVectorCore< CType >::end(), CMathContainer::getRootIsDiscrete(), CMathContainer::getRoots(), mDiscreteRoots, min, mNumRoots, CCopasiMethod::mpContainer, CTimeSensMethod::mpReducedModel, mRootMask, mRootMasking, NONE, CVector< CType >::resize(), and CMathContainer::updateRootValues().

Referenced by peekAhead(), stateChange(), and step().

◆ start()

void CTimeSensLsodaMethod::start ( )

virtual

This instructs the method to prepare for integration

Reimplemented from CTimeSensMethod.

References CVectorCore< CType >::array(), C_FLOAT64, C_INT, CTimeSensMethod::calculate_dInitialState_dPar(), CTimeSensLsodaMethod::State::ContainerState, copySensitivitiesToResultMatrix(), destroyRootMask(), CTimeSensLsodaMethod::Data::dim, CTimeSensMethod::FAILURE, CTrajectoryProblem::getAutomaticStepSize(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getRate(), CMathContainer::getRootIsDiscrete(), CMathContainer::getRoots(), CVectorCore< CType >::initialize(), CMathContainer::initializeAtolVector(), mAtol, CTimeSensMethod::mContainerState, mData, mDiscreteRoots, CTimeSensMethod::mdRate_dPar, mDWork, mErrorMsg, mIWork, CTimeSensMethod::mJacobian, mJType, mLastRootState, mLSODA, mLSODAR, mLsodaStatus, CTimeSensMethod::mNumParameters, mNumRoots, mpAbsoluteTolerance, CCopasiMethod::mpContainer, CTimeSensMethod::mpContainerStateTime, mPeekAheadMode, mpMaxInternalSteps, mpMaxInternalStepSize, CTimeSensMethod::mpProblem, CTimeSensMethod::mpReducedModel, mpYdot, mRootCounter, CTimeSensMethod::mRootsFound, mSavedState, CTimeSensMethod::mSystemSize, mTargetTime, mTask, mTime, mVariables, CMatrix< CType >::resize(), CVector< CType >::resize(), CTimeSensLsodaMethod::State::RootsFound, saveState(), CInternalSolver::setOstream(), CVectorCore< CType >::size(), and CTimeSensMethod::start().

◆ stateChange()

void CTimeSensLsodaMethod::stateChange ( const CMath::StateChange & change )

virtual

Inform the trajectory method that the state has changed outside its control

Parameters

const CMath::StateChange & change

Reimplemented from CTimeSensMethod.

References CVectorCore< CType >::array(), C_FLOAT64, CTimeSensLsodaMethod::State::ContainerState, CMath::ContinuousSimulation, CMath::EventSimulation, CTimeSensMethod::FAILURE, CMath::FixedEventTarget, CMathContainer::getCountFixedEventTargets(), CTimeSensMethod::mContainerState, mLastRootState, mLsodaStatus, mNumRoots, CCopasiMethod::mpContainer, CTimeSensMethod::mpContainerStateTime, mPeekAheadMode, CTimeSensMethod::mpReducedModel, mSavedState, CTimeSensMethod::mSystemSize, mTime, mVariables, NONE, setRootMaskType(), CMath::State, CTimeSensLsodaMethod::State::Status, and CMathContainer::updateSimulatedValues().

Referenced by step().

◆ step()

CTimeSensMethod::Status CTimeSensLsodaMethod::step	(	const double &	deltaT,
		const bool &	final = `false`
	)

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
const	bool & final (default: false)

Returns: Status status

Reimplemented from CTimeSensMethod.

References ALL, CVectorCore< CType >::array(), C_FLOAT64, C_INT, CTimeSensLsodaMethod::State::ContainerState, CTimeSensLsodaMethod::Data::dim, DISCRETE, EvalF(), EvalJ(), EvalR(), CCopasiMessage::EXCEPTION, CTimeSensMethod::FAILURE, CMathContainer::getCountFixedEventTargets(), CMathContainer::getState(), hasStateChanged(), CMathContainer::isStateValid(), mAtol, CTimeSensMethod::mContainerState, MCTrajectoryMethod, mData, mDWork, mErrorMsg, mIWork, mJType, mLastRootState, mLastSuccessState, mLSODA, mLSODAR, mLsodaStatus, mNumRoots, CCopasiMethod::mpContainer, CTimeSensMethod::mpContainerStateTime, mPeekAheadMode, mpMaxInternalSteps, CTimeSensMethod::mpReducedModel, mpRelativeTolerance, mRootCounter, mRootMask, mRootMasking, CTimeSensMethod::mRootsFound, mSavedState, CTimeSensMethod::mSystemSize, mTargetTime, mTask, mTime, mVariables, NONE, CTimeSensMethod::NORMAL, peekAhead(), resetState(), CTimeSensMethod::ROOT, CTimeSensLsodaMethod::State::RootsFound, saveState(), setRootMaskType(), CVectorCore< CType >::size(), CMath::State, stateChange(), CTimeSensLsodaMethod::State::Status, and CMathContainer::updateSimulatedValues().

Referenced by peekAhead().

Member Data Documentation

◆ mAtol

CVector< C_FLOAT64 > CTimeSensLsodaMethod::mAtol

private

A vector of absolute tolerances.

Referenced by hasStateChanged(), start(), and step().

◆ mData

Data CTimeSensLsodaMethod::mData

protected

mData.dim is the dimension of the ODE system. mData.pMethod contains CTimeSensLsodaMethod * this to be used in the static method EvalF

Referenced by CTimeSensLsodaMethod(), start(), and step().

◆ mDiscreteRoots

CVectorCore< bool > CTimeSensLsodaMethod::mDiscreteRoots

private

A which indicates whether roots change only discretely.

Referenced by setRootMaskType(), and start().

◆ mDWork

CVector< C_FLOAT64 > CTimeSensLsodaMethod::mDWork

private

LSODA C_FLOAT64 work area

Referenced by resetState(), saveState(), start(), and step().

◆ mErrorMsg

std::ostringstream CTimeSensLsodaMethod::mErrorMsg

private

A pointer to the absolute tolerances excluding fixed event targets. Stream to capture LSODA error messages

Referenced by start(), and step().

◆ mIWork

CVector< C_INT > CTimeSensLsodaMethod::mIWork

private

LSODA C_INT work area

Referenced by resetState(), saveState(), start(), and step().

◆ mJType

C_INT CTimeSensLsodaMethod::mJType

private

The way LSODA calculates the jacobian

Referenced by start(), and step().

◆ mLastRootState

State CTimeSensLsodaMethod::mLastRootState

protected

The last state having a root

Referenced by peekAhead(), start(), stateChange(), and step().

◆ mLastSuccessState

CVector< C_FLOAT64 > CTimeSensLsodaMethod::mLastSuccessState

protected

The state after the last successful integration step

Referenced by step().

◆ mLSODA

CLSODA CTimeSensLsodaMethod::mLSODA

private

The LSODA integrator

Referenced by start(), and step().

◆ mLSODAR

CLSODAR CTimeSensLsodaMethod::mLSODAR

private

The LSODA integrator

Referenced by resetState(), saveState(), start(), and step().

◆ mLsodaStatus

C_INT CTimeSensLsodaMethod::mLsodaStatus

protected

LSODA state.

Referenced by peekAhead(), resetState(), start(), stateChange(), and step().

◆ mNumRoots

C_INT CTimeSensLsodaMethod::mNumRoots

private

Number of roots

Referenced by setRootMaskType(), start(), stateChange(), and step().

◆ mpAbsoluteTolerance

C_FLOAT64* CTimeSensLsodaMethod::mpAbsoluteTolerance

private

A pointer to the value of "Absolute Tolerance"

Referenced by initializeParameter(), and start().

◆ mPeekAheadMode

bool CTimeSensLsodaMethod::mPeekAheadMode

private

A Boolean indicating whether we are in peekAhead mode

Referenced by peekAhead(), start(), stateChange(), and step().

◆ mpMaxInternalSteps

unsigned C_INT32* CTimeSensLsodaMethod::mpMaxInternalSteps

private

A pointer to the value of "Max Internal Steps"

Referenced by initializeParameter(), start(), and step().

◆ mpMaxInternalStepSize

C_FLOAT64* CTimeSensLsodaMethod::mpMaxInternalStepSize

private

A pointer to the value of "Max Internal Step Size"

Referenced by initializeParameter(), and start().

◆ mpRelativeTolerance

C_FLOAT64* CTimeSensLsodaMethod::mpRelativeTolerance

private

A pointer to the value of "Relative Tolerance"

Referenced by hasStateChanged(), initializeParameter(), peekAhead(), and step().

◆ mpYdot

const C_FLOAT64* CTimeSensLsodaMethod::mpYdot

private

Pointer to the array with right hand side values of the math container.

Referenced by evalF(), and start().

◆ mRootCounter

unsigned C_INT32 CTimeSensLsodaMethod::mRootCounter

private

Root counter to determine whether the internal step limit is exceeded.

Referenced by peekAhead(), start(), and step().

◆ mRootMask

CVector< bool > CTimeSensLsodaMethod::mRootMask

private

A mask which hides all roots being constant and zero.

Referenced by createRootMask(), destroyRootMask(), maskRoots(), peekAhead(), resetState(), saveState(), setRootMaskType(), and step().

◆ mRootMasking

eRootMasking CTimeSensLsodaMethod::mRootMasking

protected

A Boolean flag indicating whether we should try masking roots

Referenced by createRootMask(), destroyRootMask(), evalR(), resetState(), saveState(), setRootMaskType(), and step().

◆ mSavedState

State CTimeSensLsodaMethod::mSavedState

private

Referenced by peekAhead(), start(), stateChange(), and step().

◆ mTargetTime

C_FLOAT64 CTimeSensLsodaMethod::mTargetTime

private

Store the targeted end time to determine whether the internal step limit is exceeded.

Referenced by peekAhead(), start(), and step().

◆ mTask

C_INT CTimeSensLsodaMethod::mTask

private

The task instructions to the integrator

Referenced by start(), and step().

◆ mTime

C_FLOAT64 CTimeSensLsodaMethod::mTime

protected

Current time.

Referenced by peekAhead(), resetState(), saveState(), start(), stateChange(), and step().

◆ mVariables

CVector< C_FLOAT64 > CTimeSensLsodaMethod::mVariables

private

Pointer to the array with left hand side values of the math container. the vector that contains the extended system

Referenced by copySensitivitiesToResultMatrix(), evalF(), start(), stateChange(), and step().

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

Classes

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Member Enumeration Documentation

◆ eRootMasking

Constructor & Destructor Documentation

◆ CTimeSensLsodaMethod() [1/3]

◆ CTimeSensLsodaMethod() [2/3]

◆ CTimeSensLsodaMethod() [3/3]

◆ ~CTimeSensLsodaMethod()

Member Function Documentation

◆ copySensitivitiesToResultMatrix()

◆ createRootMask()

◆ destroyRootMask()

◆ elevateChildren()

◆ evalF()

◆ EvalF()

◆ evalJ()

◆ EvalJ()

◆ evalR()

◆ EvalR()

◆ hasStateChanged()

◆ initializeParameter()

◆ maskRoots()

◆ peekAhead()

◆ resetState()

◆ saveState()

◆ setRootMaskType()

◆ start()

◆ stateChange()

◆ step()

Member Data Documentation

◆ mAtol

◆ mData

◆ mDiscreteRoots

◆ mDWork

◆ mErrorMsg

◆ mIWork

◆ mJType

◆ mLastRootState

◆ mLastSuccessState

◆ mLSODA

◆ mLSODAR

◆ mLsodaStatus

◆ mNumRoots

◆ mpAbsoluteTolerance

◆ mPeekAheadMode

◆ mpMaxInternalSteps

◆ mpMaxInternalStepSize

◆ mpRelativeTolerance

◆ mpYdot

◆ mRootCounter

◆ mRootMask

◆ mRootMasking

◆ mSavedState

◆ mTargetTime

◆ mTask

◆ mTime

◆ mVariables