#include <CTrajectoryMethodDsaLsodar.h>

Inheritance diagram for CTrajectoryMethodDsaLsodar:

Classes
class	CPartition

Public Member Functions
void	calculatePropensities ()

void	calculateTotalPropensity ()

void	cleanup ()

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

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

virtual C_FLOAT64	doSingleStep (C_FLOAT64 currentTime, C_FLOAT64 endTime)

virtual bool	elevateChildren ()

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

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

void	fireReaction (const size_t &index)

void	integrateDeterministicPart (const C_FLOAT64 &deltaT)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

virtual void	start ()

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

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

	~CTrajectoryMethodDsaLsodar ()

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

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

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)

	~CLsodaMethod ()

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 ()

Protected Attributes
C_FLOAT64	mA0

CVectorCore< C_FLOAT64 >	mAmu

size_t	mFirstReactionSpeciesIndex

bool	mMaxStepsReached

size_t	mNextReactionIndex

C_FLOAT64	mNextReactionTime

size_t	mNumReactions

CPartition	mPartition

C_FLOAT64 *	mpLowerLimit

unsigned C_INT32 *	mpMaxSteps

unsigned C_INT32 *	mpPartitioningInterval

C_FLOAT64 *	mpPartitioningSteps

CRandom *	mpRandomGenerator

CVectorCore< CMathObject >	mPropensityObjects

C_FLOAT64 *	mpUpperLimit

CVectorCore< CMathReaction >	mReactions

CTrajectoryMethod::Status	mStatus

size_t	mStepsAfterPartitionSystem

CVector< CCore::CUpdateSequence >	mUpdateSequences

Protected Attributes inherited from CLsodaMethod
Data	mData

State	mLastRootState

CVector< C_FLOAT64 >	mLastSuccessState

C_INT	mLsodaStatus

eRootMasking	mRootMasking

C_FLOAT64	mTime

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
	CTrajectoryMethodDsaLsodar ()

void	initializeParameter ()

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 CLsodaMethod
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 *)

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 CLsodaMethod
enum	eRootMasking { NONE = 0 , ALL , DISCRETE }

Protected Member Functions inherited from CLsodaMethod
void	destroyRootMask ()

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 Attributes inherited from CTrajectoryMethod
static const bool	ReducedModel

Constructor & Destructor Documentation

◆ CTrajectoryMethodDsaLsodar() [1/3]

CTrajectoryMethodDsaLsodar::CTrajectoryMethodDsaLsodar ( )

private

Default constructor.

◆ CTrajectoryMethodDsaLsodar() [2/3]

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

Specific constructor

Parameters

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

Default constructor.

References CRandom::createGenerator(), initializeParameter(), mpRandomGenerator, and CRandom::mt19937.

◆ CTrajectoryMethodDsaLsodar() [3/3]

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

Copy constructor

Parameters

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

References CRandom::createGenerator(), initializeParameter(), mpRandomGenerator, and CRandom::mt19937.

◆ ~CTrajectoryMethodDsaLsodar()

CTrajectoryMethodDsaLsodar::~CTrajectoryMethodDsaLsodar ( )

Destructor.

References cleanup(), and DESTRUCTOR_TRACE.

Member Function Documentation

◆ calculatePropensities()

void CTrajectoryMethodDsaLsodar::calculatePropensities ( )

Calculate the propensities of all stochastic reactions

References CVectorCore< CType >::array(), CMathObject::calculateValue(), mNumReactions, mPartition, mPropensityObjects, and CTrajectoryMethodDsaLsodar::CPartition::mStochasticReactions.

Referenced by integrateDeterministicPart(), and stateChange().

◆ calculateTotalPropensity()

void CTrajectoryMethodDsaLsodar::calculateTotalPropensity ( )

Calculate the total propensity

References CVectorCore< CType >::array(), C_FLOAT64, mA0, mAmu, mNumReactions, mPartition, and CTrajectoryMethodDsaLsodar::CPartition::mStochasticReactions.

Referenced by fireReaction(), and stateChange().

◆ cleanup()

void CTrajectoryMethodDsaLsodar::cleanup ( )

Cleans up memory, etc.

References mpRandomGenerator, and pdelete.

Referenced by ~CTrajectoryMethodDsaLsodar().

◆ doSingleStep()

C_FLOAT64 CTrajectoryMethodDsaLsodar::doSingleStep	(	C_FLOAT64	currentTime,
		C_FLOAT64	endTime
	)

virtual

Simulates the system over the next interval of time. The current time and the end time of the current step() are given as arguments.

Parameters

currentTime	A C_FLOAT64 specifying the current time
endTime	A C_FLOAT64 specifying the end time of the step()

Returns: A C_FLOAT giving the new time

References CVectorCore< CType >::array(), C_FLOAT64, C_INVALID_INDEX, CMath::ContinuousSimulation, fireReaction(), CRandom::getRandomOO(), integrateDeterministicPart(), mA0, mAmu, CTrajectoryMethod::mContainerState, CTrajectoryMethodDsaLsodar::CPartition::mHasStochastic, min, mNextReactionIndex, mNextReactionTime, mNumReactions, mPartition, mpPartitioningInterval, mpPartitioningSteps, mpRandomGenerator, mStatus, mStepsAfterPartitionSystem, CTrajectoryMethodDsaLsodar::CPartition::mStochasticReactions, CTrajectoryMethod::NORMAL, CTrajectoryMethodDsaLsodar::CPartition::rePartition(), and stateChange().

Referenced by step().

◆ elevateChildren()

bool CTrajectoryMethodDsaLsodar::elevateChildren ( )

virtual

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

Returns: bool success

Reimplemented from CLsodaMethod.

References CLsodaMethod::elevateChildren(), and initializeParameter().

◆ evalF()

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

virtual

This evaluates the derivatives

Reimplemented from CLsodaMethod.

References CVectorCore< CType >::array(), C_FLOAT64, CLsodaMethod::Data::dim, CMathContainer::getRate(), CLsodaMethod::mData, CTrajectoryMethodDsaLsodar::CPartition::mDeterministicReactions, CTrajectoryMethodDsaLsodar::CPartition::mFirstReactionSpeciesIndex, mNumReactions, CTrajectoryMethodDsaLsodar::CPartition::mNumReactionSpecies, mPartition, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, CTrajectoryMethodDsaLsodar::CPartition::mpFirstReactionValue, and CMathContainer::updateSimulatedValues().

◆ evalR()

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

virtual

This evaluates the roots

Reimplemented from CLsodaMethod.

◆ fireReaction()

void CTrajectoryMethodDsaLsodar::fireReaction ( const size_t & index )

Executes the specified reaction in the system once.

Parameters

const size_t & index

Executes the specified reaction in the system once.

Parameters

index	A size_t specifying the index of the reaction, which will be fired.
time	The current time

References CMathContainer::applyUpdateSequence(), C_INVALID_INDEX, calculateTotalPropensity(), CMath::ContinuousSimulation, mNextReactionIndex, mNextReactionTime, CCopasiMethod::mpContainer, mReactions, mUpdateSequences, and CLsodaMethod::stateChange().

Referenced by doSingleStep().

◆ initializeParameter()

void CTrajectoryMethodDsaLsodar::initializeParameter ( )

private

Initialize the method parameter

References CCopasiParameterGroup::assertParameter(), C_FLOAT64, C_INT32, mpLowerLimit, mpMaxSteps, mpPartitioningInterval, mpPartitioningSteps, mpUpperLimit, CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.

Referenced by CTrajectoryMethodDsaLsodar(), and elevateChildren().

◆ integrateDeterministicPart()

void CTrajectoryMethodDsaLsodar::integrateDeterministicPart ( const C_FLOAT64 & deltaT )

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

Parameters

const C_FLOAT64 & deltaT.

References calculatePropensities(), CCopasiMethod::mpContainer, CTrajectoryMethod::mpReducedModel, mStatus, CLsodaMethod::step(), and CMathContainer::updateSimulatedValues().

Referenced by doSingleStep().

◆ isValidProblem()

bool CTrajectoryMethodDsaLsodar::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, CTrajectoryProblem::getDuration(), CMathContainer::getEvents(), CMathContainer::getModel(), CCopasiMethod::getSubType(), CTrajectoryMethod::isValidProblem(), MCTrajectoryMethod, CTaskEnum::MethodName, CCopasiMethod::mpContainer, mpLowerLimit, mpUpperLimit, CVectorCore< CType >::size(), and CModel::suitableForStochasticSimulation().

◆ start()

void CTrajectoryMethodDsaLsodar::start ( )

virtual

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

Reimplemented from CLsodaMethod.

◆ stateChange()

void CTrajectoryMethodDsaLsodar::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 CLsodaMethod.

References C_INVALID_INDEX, calculatePropensities(), calculateTotalPropensity(), mNextReactionIndex, mNextReactionTime, and CLsodaMethod::stateChange().

Referenced by doSingleStep().

◆ step()

CTrajectoryMethod::Status CTrajectoryMethodDsaLsodar::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 CLsodaMethod.

References C_FLOAT64, doSingleStep(), CCopasiMessage::EXCEPTION, MCTrajectoryMethod, min, CTrajectoryMethod::mpContainerStateTime, mpMaxSteps, mStatus, and CTrajectoryMethod::NORMAL.

Member Data Documentation

◆ mA0

C_FLOAT64 CTrajectoryMethodDsaLsodar::mA0

protected

Total propensity (sum over mAmu[i])

Referenced by calculateTotalPropensity(), doSingleStep(), and start().

◆ mAmu

CVectorCore< C_FLOAT64 > CTrajectoryMethodDsaLsodar::mAmu

protected

A vector referencing the math container's propensity values

Referenced by calculateTotalPropensity(), doSingleStep(), and start().

◆ mFirstReactionSpeciesIndex

size_t CTrajectoryMethodDsaLsodar::mFirstReactionSpeciesIndex

protected

Index of the first species determined by reactions in CState

Referenced by CTrajectoryMethodDsaLsodar::CPartition::intialize(), CTrajectoryMethodDsaLsodar::CPartition::rePartition(), and start().

◆ mMaxStepsReached

bool CTrajectoryMethodDsaLsodar::mMaxStepsReached

protected

◆ mNextReactionIndex

size_t CTrajectoryMethodDsaLsodar::mNextReactionIndex

protected

The index of the next reaction which fires

Referenced by doSingleStep(), fireReaction(), and stateChange().

◆ mNextReactionTime

C_FLOAT64 CTrajectoryMethodDsaLsodar::mNextReactionTime

protected

The time the next reaction fires

Referenced by doSingleStep(), fireReaction(), and stateChange().

◆ mNumReactions

size_t CTrajectoryMethodDsaLsodar::mNumReactions

protected

The particle and reaction numbers

Referenced by calculatePropensities(), calculateTotalPropensity(), doSingleStep(), evalF(), and start().

◆ mPartition

CPartition CTrajectoryMethodDsaLsodar::mPartition

protected

The partition of the system

Referenced by calculatePropensities(), calculateTotalPropensity(), doSingleStep(), evalF(), and start().

◆ mpLowerLimit

C_FLOAT64* CTrajectoryMethodDsaLsodar::mpLowerLimit

protected

Pointer to the method parameter "Lower Limit"

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

◆ mpMaxSteps

unsigned C_INT32* CTrajectoryMethodDsaLsodar::mpMaxSteps

protected

Pointer to the method parameter "Max Internal Steps"

Referenced by initializeParameter(), and step().

◆ mpPartitioningInterval

unsigned C_INT32* CTrajectoryMethodDsaLsodar::mpPartitioningInterval

protected

Pointer to the method parameter "Partitioning Interval"

Referenced by doSingleStep(), and initializeParameter().

◆ mpPartitioningSteps

C_FLOAT64* CTrajectoryMethodDsaLsodar::mpPartitioningSteps

protected

Pointer to the method parameter "Partitioning Stepsize"

Referenced by doSingleStep(), and initializeParameter().

◆ mpRandomGenerator

CRandom* CTrajectoryMethodDsaLsodar::mpRandomGenerator

protected

The random number generator.

Referenced by cleanup(), CTrajectoryMethodDsaLsodar(), and doSingleStep().

◆ mPropensityObjects

CVectorCore< CMathObject > CTrajectoryMethodDsaLsodar::mPropensityObjects

protected

A vector referencing the math container's propensity objects

Referenced by calculatePropensities(), and start().

◆ mpUpperLimit

C_FLOAT64* CTrajectoryMethodDsaLsodar::mpUpperLimit

protected

Pointer to the method parameter "Upper Limit"

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

◆ mReactions

CVectorCore< CMathReaction > CTrajectoryMethodDsaLsodar::mReactions

protected

A vector referencing the math container's reactions

Referenced by fireReaction(), and start().

◆ mStatus

CTrajectoryMethod::Status CTrajectoryMethodDsaLsodar::mStatus

protected

The return status of LSODA integration

Referenced by doSingleStep(), integrateDeterministicPart(), and step().

◆ mStepsAfterPartitionSystem

size_t CTrajectoryMethodDsaLsodar::mStepsAfterPartitionSystem

protected

Number of elementary steps after the last partitioning.

Referenced by doSingleStep().

◆ mUpdateSequences

CVector< CCore::CUpdateSequence > CTrajectoryMethodDsaLsodar::mUpdateSequences

protected

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

Referenced by fireReaction(), and start().

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

Classes

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

◆ CTrajectoryMethodDsaLsodar() [1/3]

◆ CTrajectoryMethodDsaLsodar() [2/3]

◆ CTrajectoryMethodDsaLsodar() [3/3]

◆ ~CTrajectoryMethodDsaLsodar()

Member Function Documentation

◆ calculatePropensities()

◆ calculateTotalPropensity()

◆ cleanup()

◆ doSingleStep()

◆ elevateChildren()

◆ evalF()

◆ evalR()

◆ fireReaction()

◆ initializeParameter()

◆ integrateDeterministicPart()

◆ isValidProblem()

◆ start()

◆ stateChange()

◆ step()

Member Data Documentation

◆ mA0

◆ mAmu

◆ mFirstReactionSpeciesIndex

◆ mMaxStepsReached

◆ mNextReactionIndex

◆ mNextReactionTime

◆ mNumReactions

◆ mPartition

◆ mpLowerLimit

◆ mpMaxSteps

◆ mpPartitioningInterval

◆ mpPartitioningSteps

◆ mpRandomGenerator

◆ mPropensityObjects

◆ mpUpperLimit

◆ mReactions

◆ mStatus

◆ mStepsAfterPartitionSystem

◆ mUpdateSequences