#include <CTrajAdaptiveSA.h>

Inheritance diagram for CTrajAdaptiveSA:

Public Member Functions
	CTrajAdaptiveSA (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::adaptiveSA, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)

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

virtual bool	elevateChildren ()

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

virtual void	start ()

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

	~CTrajAdaptiveSA ()

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)

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

	~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 ()

Protected Member Functions
C_FLOAT64	doSingleSSAStep (const C_FLOAT64 &curTime, const C_FLOAT64 &endTime)

C_FLOAT64	doSingleTauLeapStep (const C_FLOAT64 &curTime, const C_FLOAT64 &endTime)

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)

Protected Attributes
C_FLOAT64	mA0

CVectorCore< C_FLOAT64 >	mAmu

unsigned C_INT32	mMaxSteps

bool	mMaxStepsReached

CVector< C_FLOAT64 >	mMethodState

size_t	mNextReactionIndex

C_FLOAT64	mNextReactionTime

size_t	mNumReactions

size_t	mNumReactionSpecies

CVector< const C_FLOAT64 * >	mPartitionedAmu

CVector< CMathReaction * >	mPartitionedDependencies

CRandom *	mpRandomGenerator

CVectorCore< CMathObject >	mPropensityObjects

CVectorCore< CMathReaction >	mReactions

CVector< CCore::CUpdateSequence >	mUpdateSequences

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

Private Member Functions
	CTrajAdaptiveSA ()

void	initializeParameter ()

Private Attributes
CVector< C_FLOAT64 >	mAvgDX

C_FLOAT64	mEpsilon

size_t	mFirstReactionSpeciesIndex

CVector< size_t >	mMaxReactionFiring

CVector< C_FLOAT64 * >	mPartitionedReactionFiring

C_FLOAT64 *	mpMethodSpecies

CVector< C_FLOAT64 >	mReactionFiring

CVector< C_FLOAT64 >	mSigDX

C_FLOAT64	mSSAStepCounter

std::vector< Refresh * >	mTauCalculations

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

Static Protected Attributes inherited from CTrajectoryMethod
static const bool	ReducedModel

Constructor & Destructor Documentation

◆ CTrajAdaptiveSA() [1/3]

CTrajAdaptiveSA::CTrajAdaptiveSA ( )

private

Default constructor.

◆ CTrajAdaptiveSA() [2/3]

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

Specific constructor

Parameters

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

References initializeParameter().

◆ CTrajAdaptiveSA() [3/3]

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

Copy constructor.

Parameters

const	CTrajAdaptiveSA & src,
const	CDataContainer * pParent (Default: NULL)

References initializeParameter().

◆ ~CTrajAdaptiveSA()

CTrajAdaptiveSA::~CTrajAdaptiveSA ( )

Destructor.

Member Function Documentation

◆ doSingleSSAStep()

C_FLOAT64 CTrajAdaptiveSA::doSingleSSAStep	(	const C_FLOAT64 &	curTime,
		const C_FLOAT64 &	endTime
	)

protected

Fire the next reaction if it fire before the endTime

Parameters

const	C_FLOAT64 & curTime
const	C_FLOAT64 & endTime

Returns: C_FLOAT64 timeAfterStep

References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::array(), C_FLOAT64, C_INVALID_INDEX, CCopasiMessage::EXCEPTION, CRandom::getRandomOO(), mA0, mAmu, MCTrajectoryMethod, mNextReactionIndex, mNextReactionTime, mNumReactions, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mpRandomGenerator, mReactions, and mUpdateSequences.

Referenced by step().

◆ doSingleTauLeapStep()

C_FLOAT64 CTrajAdaptiveSA::doSingleTauLeapStep	(	const C_FLOAT64 &	curTime,
		const C_FLOAT64 &	endTime
	)

protected

Fire the next reaction if it fire before the endTime

Parameters

const	C_FLOAT64 & curTime
const	C_FLOAT64 & endTime

Returns: C_FLOAT64 timeAfterStep

References CVectorCore< CType >::array(), C_FLOAT64, C_INVALID_INDEX, CMathObject::calculateValue(), CCopasiMessage::EXCEPTION, CMathReaction::getNumberBalance(), CRandom::getRandomOO(), CRandom::getRandomPoisson(), CMathContainer::getState(), mA0, mAmu, mAvgDX, max, CTrajectoryMethod::mContainerState, MCTrajectoryMethod, mEpsilon, mFirstReactionSpeciesIndex, mMaxReactionFiring, mMethodState, mNumReactions, mNumReactionSpecies, mPartitionedAmu, mPartitionedDependencies, mPartitionedReactionFiring, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mpRandomGenerator, mPropensityObjects, mReactionFiring, mReactions, mSigDX, mSSAStepCounter, CMathContainer::setState(), CVectorCore< CType >::size(), SSA_MULTIPLE, SSA_UPPER_NUM, CMathContainer::updateSimulatedValues(), and UPPER_LIMIT.

Referenced by step().

◆ elevateChildren()

bool CTrajAdaptiveSA::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().

◆ initializeParameter()

void CTrajAdaptiveSA::initializeParameter ( )

private

Initialize the method parameter

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, EPS, CCopasiParameter::INT, and CCopasiParameter::UINT.

Referenced by CTrajAdaptiveSA(), and elevateChildren().

◆ isValidProblem()

bool CTrajAdaptiveSA::isValidProblem ( const CCopasiProblem * pProblem )

virtual

Check if the method is suitable for this problem

Returns: bool suitability of the method

Reimplemented from CTrajectoryMethod.

References CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CMathContainer::getCountODEs(), CTrajectoryProblem::getDuration(), CMathContainer::getEvents(), CMathContainer::getModel(), CMathContainer::getReactions(), CCopasiMethod::getSubType(), CTrajectoryMethod::isValidProblem(), MCTrajectoryMethod, CTaskEnum::MethodName, CCopasiMethod::mpContainer, CVectorCore< CType >::size(), and CModel::suitableForStochasticSimulation().

◆ start()

void CTrajAdaptiveSA::start ( )

virtual

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

Reimplemented from CTrajectoryMethod.

◆ step()

CTrajectoryMethod::Status CTrajAdaptiveSA::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 CTrajectoryMethod.

References C_FLOAT64, doSingleSSAStep(), doSingleTauLeapStep(), CCopasiMessage::EXCEPTION, CTrajectoryProblem::getAutomaticStepSize(), MCTrajectoryMethod, mMaxSteps, CTrajectoryMethod::mpContainerStateTime, CTrajectoryMethod::mpProblem, mSSAStepCounter, and CTrajectoryMethod::NORMAL.

Member Data Documentation

◆ mA0

C_FLOAT64 CTrajAdaptiveSA::mA0

protected

Total propensity (sum over mAmu[i])

Referenced by doSingleSSAStep(), doSingleTauLeapStep(), and start().

◆ mAmu

CVectorCore< C_FLOAT64 > CTrajAdaptiveSA::mAmu

protected

A reference to the math container's propensity values

Referenced by doSingleSSAStep(), doSingleTauLeapStep(), and start().

◆ mAvgDX

CVector< C_FLOAT64 > CTrajAdaptiveSA::mAvgDX

private

The mean and variance of species

Referenced by doSingleTauLeapStep(), and start().

◆ mEpsilon

C_FLOAT64 CTrajAdaptiveSA::mEpsilon

private

The tolerance ratio x(t+t')< eps*x(t)

Referenced by doSingleTauLeapStep(), and start().

◆ mFirstReactionSpeciesIndex

size_t CTrajAdaptiveSA::mFirstReactionSpeciesIndex

private

The Ordered reaction

Referenced by doSingleTauLeapStep(), and start().

◆ mMaxReactionFiring

CVector< size_t > CTrajAdaptiveSA::mMaxReactionFiring

private

The upper fires of the j-th reactions

Referenced by doSingleTauLeapStep(), and start().

◆ mMaxSteps

unsigned C_INT32 CTrajAdaptiveSA::mMaxSteps

protected

max number of single stochastic steps to do in one step()

Referenced by start(), and step().

◆ mMaxStepsReached

bool CTrajAdaptiveSA::mMaxStepsReached

protected

A boolean flag indicating whether the maximum steps have been reached. This is used to avoid multiple messages.

Referenced by start().

◆ mMethodState

CVector<C_FLOAT64 > CTrajAdaptiveSA::mMethodState

protected

The method internal state which contains particle rounded particle numbers.

Referenced by doSingleTauLeapStep().

◆ mNextReactionIndex

size_t CTrajAdaptiveSA::mNextReactionIndex

protected

The index of the next reaction which fires

Referenced by doSingleSSAStep(), and start().

◆ mNextReactionTime

C_FLOAT64 CTrajAdaptiveSA::mNextReactionTime

protected

The time the next reaction fires

Referenced by doSingleSSAStep(), and start().

◆ mNumReactions

size_t CTrajAdaptiveSA::mNumReactions

protected

The particle and reaction numbers

Referenced by doSingleSSAStep(), doSingleTauLeapStep(), and start().

◆ mNumReactionSpecies

size_t CTrajAdaptiveSA::mNumReactionSpecies

protected

Number of variable metabolites.

Referenced by doSingleTauLeapStep(), and start().

◆ mPartitionedAmu

CVector< const C_FLOAT64 * > CTrajAdaptiveSA::mPartitionedAmu

protected

The ordered propensity function

Referenced by doSingleTauLeapStep(), and start().

◆ mPartitionedDependencies

CVector< CMathReaction * > CTrajAdaptiveSA::mPartitionedDependencies

protected

The Ordered reaction

Referenced by doSingleTauLeapStep(), and start().

◆ mPartitionedReactionFiring

CVector< C_FLOAT64 * > CTrajAdaptiveSA::mPartitionedReactionFiring

private

Referenced by doSingleTauLeapStep(), and start().

◆ mpMethodSpecies

C_FLOAT64* CTrajAdaptiveSA::mpMethodSpecies

private

The species pointer for average, variance, and population (ordered)

◆ mpRandomGenerator

CRandom* CTrajAdaptiveSA::mpRandomGenerator

protected

The random number generator

Referenced by doSingleSSAStep(), doSingleTauLeapStep(), and start().

◆ mPropensityObjects

CVectorCore< CMathObject > CTrajAdaptiveSA::mPropensityObjects

protected

A reference to the math container's propensity objects

Referenced by doSingleTauLeapStep(), and start().

◆ mReactionFiring

CVector< C_FLOAT64 > CTrajAdaptiveSA::mReactionFiring

private

The number of fires

Referenced by doSingleTauLeapStep(), and start().

◆ mReactions

CVectorCore< CMathReaction > CTrajAdaptiveSA::mReactions

protected

A reference to the math container's reactions

Referenced by doSingleSSAStep(), doSingleTauLeapStep(), and start().

◆ mSigDX

CVector< C_FLOAT64 > CTrajAdaptiveSA::mSigDX

private

Referenced by doSingleTauLeapStep(), and start().

◆ mSSAStepCounter

C_FLOAT64 CTrajAdaptiveSA::mSSAStepCounter

private

The counter to count the time of doing single SSA

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

◆ mTauCalculations

std::vector< Refresh * > CTrajAdaptiveSA::mTauCalculations

private

Vector of refresh methods which need to be executed to update all values required for simulation

◆ mUpdateSequences

CVector< CCore::CUpdateSequence > CTrajAdaptiveSA::mUpdateSequences

protected

A vector containing the update sequence required to update all propensity values.

Referenced by doSingleSSAStep(), and start().

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CTrajAdaptiveSA() [1/3]

◆ CTrajAdaptiveSA() [2/3]

◆ CTrajAdaptiveSA() [3/3]

◆ ~CTrajAdaptiveSA()

Member Function Documentation

◆ doSingleSSAStep()

◆ doSingleTauLeapStep()

◆ elevateChildren()

◆ initializeParameter()

◆ isValidProblem()

◆ start()

◆ step()

Member Data Documentation

◆ mA0

◆ mAmu

◆ mAvgDX

◆ mEpsilon

◆ mFirstReactionSpeciesIndex

◆ mMaxReactionFiring

◆ mMaxSteps

◆ mMaxStepsReached

◆ mMethodState

◆ mNextReactionIndex

◆ mNextReactionTime

◆ mNumReactions

◆ mNumReactionSpecies

◆ mPartitionedAmu

◆ mPartitionedDependencies

◆ mPartitionedReactionFiring

◆ mpMethodSpecies

◆ mpRandomGenerator

◆ mPropensityObjects

◆ mReactionFiring

◆ mReactions

◆ mSigDX

◆ mSSAStepCounter

◆ mTauCalculations

◆ mUpdateSequences