CHybridNextReactionLSODAMethod Class Reference

#include <CHybridNextReactionLSODAMethod.h>

Inheritance diagram for CHybridNextReactionLSODAMethod:

Classes
class	LSODA

Public Member Functions
	CHybridNextReactionLSODAMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::hybridLSODA, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
	CHybridNextReactionLSODAMethod (const CHybridNextReactionLSODAMethod &src, const CDataContainer *pParent)
void	evalF (C_FLOAT64 *ydot)
virtual void	integrateDeterministicPart (C_FLOAT64 ds)
virtual void	start ()
virtual void	stateChange (const CMath::StateChange &change)
Public Member Functions inherited from CHybridMethod
	CHybridMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::hybrid, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
	CHybridMethod (const CHybridMethod &src, const CDataContainer *pParent)
virtual bool	elevateChildren ()
virtual bool	isValidProblem (const CCopasiProblem *pProblem)
virtual Status	step (const double &deltaT, const bool &final=false)
	~CHybridMethod ()
Public Member Functions inherited from CTrajectoryMethod
	CTrajectoryMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
	CTrajectoryMethod (const CTrajectoryMethod &src, const CDataContainer *pParent)
const CVectorCore< C_INT > &	getRoots () const
const bool &	integrateReducedModel () const
void	setProblem (CTrajectoryProblem *problem)
	~CTrajectoryMethod ()
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 ()

Private Member Functions
	CHybridNextReactionLSODAMethod ()
void	initializeParameter ()

Private Attributes
LSODA	mLSODA

Additional Inherited Members
Public Types inherited from CTrajectoryMethod
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 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
Protected Types inherited from CHybridMethod
enum	metabStatus { LOW = 0 , HIGH }
Protected Member Functions inherited from CHybridMethod
void	calculateDerivative (CVectorCore< C_FLOAT64 > &deriv)
void	cleanup ()
C_FLOAT64	doSingleStep (C_FLOAT64 currentTime, C_FLOAT64 endTime)
C_FLOAT64	generateReactionTime (size_t rIndex)
void	getStochTimeAndIndex (C_FLOAT64 &ds, size_t &rIndex)
void	insertDeterministicReaction (size_t rIndex)
void	partitionSystem ()
void	removeDeterministicReaction (size_t rIndex)
void	setupDependencyGraph ()
void	setupMetab2React ()
void	setupPartition ()
void	setupPriorityQueue ()
void	updatePriorityQueue (size_t rIndex, C_FLOAT64 time)
void	updateTauMu (size_t rIndex, C_FLOAT64 time)
Protected Member Functions inherited from CTrajectoryMethod
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)
Static Protected Member Functions inherited from CHybridMethod
static C_INT32	checkModel (CModel *model)
Protected Attributes inherited from CHybridMethod
std::vector< C_FLOAT64 >	mAmu
std::vector< C_FLOAT64 >	mAmuOld
CVectorCore< C_FLOAT64 >	mCurrentState
CDependencyGraph	mDG
size_t	mFirstMetabIndex
CHybridStochFlag *	mFirstReactionFlag
C_FLOAT64	mLowerStochLimit
size_t	mMaxBalance
size_t	mMaxIntBeforeStep
unsigned C_INT32	mMaxSteps
bool	mMaxStepsReached
std::vector< std::set< size_t > >	mMetab2React
CVector< metabStatus >	mMetabFlags
size_t	mNumVariableMetabs
unsigned C_INT32	mPartitioningInterval
const C_FLOAT64 *	mpFirstMetabValue
CIndexedPriorityQueue	mPQ
CRandom *	mpRandomGenerator
unsigned C_INT32	mRandomSeed
size_t	mRateOffset
std::vector< CHybridStochFlag >	mReactionFlags
CVectorCore< CMathReaction >	mReactions
CVectorCore< C_FLOAT64 >	mSpeciesRates
size_t	mStepsAfterPartitionSystem
CVector< CCore::CUpdateSequence >	mUpdateSequences
C_FLOAT64	mUpperStochLimit
bool	mUseRandomSeed
Protected Attributes inherited from CTrajectoryMethod
CVectorCore< C_FLOAT64 >	mContainerState
C_FLOAT64 *	mpContainerStateTime
CTrajectoryProblem *	mpProblem
const bool *	mpReducedModel
CTrajectoryTask *	mpTask
CVectorCore< C_INT >	mRootsFound
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
Static Protected Attributes inherited from CTrajectoryMethod
static const bool	ReducedModel

Detailed Description

CHybridNextReactionLSODAMethod

First approach to an hybrid algorithm. Gibson's Next Reaction method is combined with the LSODA numerical integrator.

File name: CHybridNextReactionLSODAMethod.h Author: Email:

Last change: 08, May 2006

(C) European Media Lab 2003.

Constructor & Destructor Documentation

CHybridNextReactionLSODAMethod() [1/3]

CHybridNextReactionLSODAMethod::CHybridNextReactionLSODAMethod ( )

private

Constructor.

CHybridNextReactionLSODAMethod() [2/3]

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

Specific constructor

Parameters

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

CHybridNextReactionLSODAMethod

First approach to an hybrid algorithm. Gibson's Next Reaction method is combined with the LSODA numerical integrator.

File name: CHybridNextReactionLSODAMethod.h Author: Email:

Last change: 08, May 2006

(C) European Media Lab 2003.

References initializeParameter().

CHybridNextReactionLSODAMethod() [3/3]

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

Copy constructor.

Parameters

const	CHybridNextReactionRKMethod & src
const	CDataContainer * pParent

References initializeParameter().

Member Function Documentation

evalF()

void CHybridNextReactionLSODAMethod::evalF

(

C_FLOAT64 *

ydot

)

References CHybridMethod::calculateDerivative(), CHybridMethod::mFirstMetabIndex, and CHybridMethod::mNumVariableMetabs.

Referenced by CHybridNextReactionLSODAMethod::LSODA::evalF().

initializeParameter()

void CHybridNextReactionLSODAMethod::initializeParameter ( )

private

Intialize the method parameter

References CCopasiParameterGroup::addParameter(), CCopasiParameterGroup::beginIndex(), C_FLOAT64, CCopasiParameterGroup::endIndex(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), mLSODA, CCopasiParameterGroup::removeParameter(), and CCopasiParameterGroup::setValue().

Referenced by CHybridNextReactionLSODAMethod().

integrateDeterministicPart()

void CHybridNextReactionLSODAMethod::integrateDeterministicPart ( C_FLOAT64  ds )

virtual

Integrates the deterministic reactions of the system over the specified time interval.

Parameters

ds	A C_FLOAT64 specifying the stepsize.

Implements CHybridMethod.

References mLSODA, and CLsodaMethod::step().

start()

void CHybridNextReactionLSODAMethod::start ( )

virtual

This instructs the method to prepare for integration

Reimplemented from CHybridMethod.

References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), CCopasiParameterGroup::getParameter(), mLSODA, CCopasiMethod::mpContainer, CCopasiMethod::setMathContainer(), CHybridMethod::start(), and CLsodaMethod::start().

stateChange()

void CHybridNextReactionLSODAMethod::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 CTrajectoryMethod.

References mLSODA, and CLsodaMethod::stateChange().

Member Data Documentation

mLSODA

LSODA CHybridNextReactionLSODAMethod::mLSODA

private

Referenced by initializeParameter(), integrateDeterministicPart(), start(), and stateChange().

---

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

• CHybridNextReactionLSODAMethod.h
• CHybridNextReactionLSODAMethod.cpp