#include <CHybridMethod.h>

Inheritance diagram for CHybridMethod:

Public Member Functions
	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 void	start ()

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)

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 Types
enum	metabStatus { LOW = 0 , HIGH }

Protected Member Functions
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)

virtual void	integrateDeterministicPart (C_FLOAT64 ds)=0

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
static C_INT32	checkModel (CModel *model)

Protected Attributes
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

Private Member Functions
	CHybridMethod ()

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 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

Member Enumeration Documentation

◆ metabStatus

enum CHybridMethod::metabStatus

protected

Status of the metabolites. Particle number can be high or low.

Enumerator
LOW
HIGH

Constructor & Destructor Documentation

◆ CHybridMethod() [1/3]

CHybridMethod::CHybridMethod ( )

private

Constructor.

◆ CHybridMethod() [2/3]

CHybridMethod::CHybridMethod	(	const CDataContainer *	pParent,
		const CTaskEnum::Method &	methodType = `CTaskEnum::Method::hybrid`,
		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)

CHybridMethod

This class implements an hybrid algorithm for the simulation of a biochemical system over time.

File name: CHybridMethod.cpp Author: Juergen Pahle Email: juerg.nosp@m.en.p.nosp@m.ahle@.nosp@m.eml-.nosp@m.r.vil.nosp@m.la-b.nosp@m.osch..nosp@m.de

Last change: 14, December 2004

(C) European Media Lab 2003. Default constructor.

References initializeParameter().

◆ CHybridMethod() [3/3]

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

Copy constructor.

Parameters

const CHybridMethod &	src
const	CDataContainer * pParent

References initializeParameter().

◆ ~CHybridMethod()

CHybridMethod::~CHybridMethod ( )

Destructor.

References cleanup(), and DESTRUCTOR_TRACE.

Member Function Documentation

◆ calculateDerivative()

void CHybridMethod::calculateDerivative ( CVectorCore< C_FLOAT64 > & deriv )

protected

Calculates the derivative of the system and writes it into the vector deriv. Length of deriv must be mNumVariableMetabs. CAUTION: Only deterministic reactions are taken into account. That is, this is only the derivative of the deterministic part of the system.

Parameters

CVectorCore< C_FLOAT64 > & deriv

Calculates the derivative of the system and writes it into the vector deriv. Length of deriv must be mNumVariableMetabs. CAUTION: Only deterministic reactions are taken into account. That is, this is only the derivative of the deterministic part of the system.

Parameters

deriv A vector reference of length mNumVariableMetabs, into which the derivative is written

References CVectorCore< CType >::array(), C_FLOAT64, C_INT32, CMathReaction::getNumberBalance(), CMathReaction::getParticleFluxObject(), CMathObject::getValuePointer(), mFirstReactionFlag, CHybridStochFlag::mIndex, CCopasiMethod::mpContainer, CHybridStochFlag::mpNext, mRateOffset, mReactions, mSpeciesRates, CVectorCore< CType >::size(), and CMathContainer::updateSimulatedValues().

Referenced by CHybridNextReactionLSODAMethod::evalF(), and CHybridNextReactionRKMethod::rungeKutta().

◆ checkModel()

C_INT32 CHybridMethod::checkModel ( CModel * model )

staticprotected

Test the model if it is proper to perform stochastic simulations on. Several properties are tested (e.g. integer stoichometry, all reactions take place in one compartment only, irreversibility...).

Parameters

model The model to be checked

Returns: 1, if hybrid simulation is possible; <0, if an error occured.

Test the model if it is proper to perform stochastic simulations on. Several properties are tested (e.g. integer stoichometry, all reactions take place in one compartment only, irreversibility...).

Returns: 0, if everything is ok; <0, if an error occured.

References C_FLOAT64, C_INT32, CModel::getReactions(), CModel::getStoi(), INT_EPSILON, CMatrix< CType >::numRows(), and CDataVector< CType >::size().

◆ cleanup()

void CHybridMethod::cleanup ( )

protected

Cleans up memory, etc.

Referenced by ~CHybridMethod().

◆ doSingleStep()

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

protected

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

Simulates the system over the next interval of time. The new time after this step is returned.

Parameters

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

Returns: A C_FLOAT giving the new time

References C_FLOAT64, C_INVALID_INDEX, getStochTimeAndIndex(), integrateDeterministicPart(), mFirstReactionFlag, mPartitioningInterval, CTrajectoryMethod::mpContainerStateTime, mPQ, mReactions, mStepsAfterPartitionSystem, partitionSystem(), CIndexedPriorityQueue::size(), CMath::State, CTrajectoryMethod::stateChange(), and updatePriorityQueue().

Referenced by step().

◆ elevateChildren()

bool CHybridMethod::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().

◆ generateReactionTime()

C_FLOAT64 CHybridMethod::generateReactionTime ( size_t rIndex )

protected

Generates a putative reaction time for the given reaction.

Parameters

rIndex A size_t specifying the index of the reaction

Returns: A C_FLOAT64 holding the calculated reaction time

References C_FLOAT64, CRandom::getRandomOO(), mAmu, and mpRandomGenerator.

Referenced by partitionSystem(), setupPriorityQueue(), updatePriorityQueue(), and updateTauMu().

◆ getStochTimeAndIndex()

void CHybridMethod::getStochTimeAndIndex	(	C_FLOAT64 &	ds,
		size_t &	rIndex
	)

protected

Find the reaction index and the reaction time of the stochastic (!) reaction with the lowest reaction time.

Parameters

ds	A reference to a C_FLOAT64. The putative reaction time for the first stochastic reaction is written into this variable.
rIndex	A reference to a size_t. The index of the first stochastic reaction is written into this variable.

References mPQ, CIndexedPriorityQueue::topIndex(), and CIndexedPriorityQueue::topKey().

Referenced by doSingleStep().

◆ initializeParameter()

void CHybridMethod::initializeParameter ( )

private

Intialize the method parameter

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiParameter::INT, LOWER_STOCH_LIMIT, MAX_STEPS, PARTITIONING_INTERVAL, RANDOM_SEED, CCopasiParameterGroup::removeParameter(), CCopasiParameterGroup::setValue(), CCopasiParameter::UINT, UPPER_STOCH_LIMIT, and USE_RANDOM_SEED.

Referenced by CHybridMethod(), and elevateChildren().

◆ insertDeterministicReaction()

void CHybridMethod::insertDeterministicReaction ( size_t rIndex )

protected

Inserts a new deterministic reaction into the linked list in the vector mReactionFlags.

Parameters

rIndex A size_t giving the index of the reaction to be inserted into the list of deterministic reactions.

Inserts a new deterministic reaction into the linked list in the array mReactionFlags.

Parameters

rIndex A size_t giving the index of the reaction to be inserted into the list of deterministic reactions.

References mAmu, mAmuOld, mFirstReactionFlag, CHybridStochFlag::mpPrev, and mReactionFlags.

Referenced by partitionSystem().

◆ integrateDeterministicPart()

virtual void CHybridMethod::integrateDeterministicPart ( C_FLOAT64 ds )

protectedpure virtual

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

Parameters

ds	A C_FLOAT64 specifying the stepsize.

Implemented in CHybridNextReactionRKMethod, and CHybridNextReactionLSODAMethod.

Referenced by doSingleStep().

◆ isValidProblem()

bool CHybridMethod::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, CMathContainer::getCountODEs(), CTrajectoryProblem::getDuration(), CMathContainer::getEvents(), CMathContainer::getModel(), CMathContainer::getReactions(), CCopasiMethod::getSubType(), CTrajectoryMethod::isValidProblem(), MCTrajectoryMethod, CTaskEnum::MethodName, mLowerStochLimit, CCopasiMethod::mpContainer, mUpperStochLimit, CVectorCore< CType >::size(), and CModel::suitableForStochasticSimulation().

◆ partitionSystem()

void CHybridMethod::partitionSystem ( )

protected

Updates the partitioning of the system depending on the particle numbers present.

References C_FLOAT64, CDataObject::calculateValue(), generateReactionTime(), HIGH, insertDeterministicReaction(), CIndexedPriorityQueue::insertStochReaction(), LOW, mAmu, mAmuOld, mCurrentState, mLowerStochLimit, mMetab2React, mMetabFlags, mNumVariableMetabs, CTrajectoryMethod::mpContainerStateTime, mPQ, mReactionFlags, mReactions, mUpperStochLimit, removeDeterministicReaction(), CIndexedPriorityQueue::removeStochReaction(), CMath::State, and CTrajectoryMethod::stateChange().

Referenced by doSingleStep().

◆ removeDeterministicReaction()

void CHybridMethod::removeDeterministicReaction ( size_t rIndex )

protected

Removes a deterministic reaction from the linked list in the vector mReactionFlags.

Parameters

rIndex A size_t giving the index of the reaction to be removed from the list of deterministic reactions.

Removes a deterministic reaction from the linked list in the array mReactionFlags.

Parameters

rIndex A size_t giving the index of the reaction to be removed from the list of deterministic reactions.

References mFirstReactionFlag, CHybridStochFlag::mpPrev, and mReactionFlags.

Referenced by partitionSystem().

◆ setupDependencyGraph()

void CHybridMethod::setupDependencyGraph ( )

protected

Sets up the dependency graph

Sets up the dependency graph.

References CDependencyGraph::addDependent(), CDependencyGraph::clear(), CCore::Default, CMathDependencyGraph::dependsOn(), CMathReaction::getObjectBalance(), CMathContainer::getTransientDependencies(), CMathDependencyGraph::getUpdateSequence(), mDG, CCopasiMethod::mpContainer, mReactions, mUpdateSequences, CDependencyGraph::resize(), and CVectorCore< CType >::size().

Referenced by start().

◆ setupMetab2React()

void CHybridMethod::setupMetab2React ( )

protected

Creates for each metabolite a set of reaction indices. If the metabolite participates in a reaction as substrate, product or modifier this reaction is added to the corresponding set.

References CVectorCore< CType >::array(), mMetab2React, mpFirstMetabValue, mReactions, and CVectorCore< CType >::size().

Referenced by start().

◆ setupPartition()

void CHybridMethod::setupPartition ( )

protected

Creates an initial partitioning of the system. Deterministic and stochastic reactions are determined. The array mStochReactions is initialized.

Creates an initial partitioning of the system. Deterministic and stochastic reactions are determined. The vector mReactionFlags and the vector mMetabFlags are initialized.

References C_FLOAT64, HIGH, LOW, mCurrentState, mFirstReactionFlag, mLowerStochLimit, mMetab2React, mMetabFlags, mNumVariableMetabs, CHybridStochFlag::mpNext, mReactionFlags, mReactions, mUpperStochLimit, CVector< CType >::resize(), and CVectorCore< CType >::size().

Referenced by start().

◆ setupPriorityQueue()

void CHybridMethod::setupPriorityQueue ( )

protected

Sets up the priority queue.

Parameters

startTime The time at which the simulation starts.

References C_FLOAT64, CDataObject::calculateValue(), CIndexedPriorityQueue::clear(), generateReactionTime(), CIndexedPriorityQueue::initializeIndexPointer(), CIndexedPriorityQueue::insertStochReaction(), mAmu, CTrajectoryMethod::mpContainerStateTime, mPQ, mReactionFlags, mReactions, and CVectorCore< CType >::size().

Referenced by start().

◆ start()

void CHybridMethod::start ( )

virtual

This instructs the method to prepare for integration

Reimplemented from CTrajectoryMethod.

Reimplemented in CHybridNextReactionRKMethod, and CHybridNextReactionLSODAMethod.

Referenced by CHybridNextReactionLSODAMethod::start(), and CHybridNextReactionRKMethod::start().

◆ step()

CTrajectoryMethod::Status CHybridMethod::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, doSingleStep(), mMaxSteps, mMaxStepsReached, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, CTrajectoryMethod::NORMAL, CMathContainer::updateSimulatedValues(), and CCopasiMessage::WARNING.

◆ updatePriorityQueue()

void CHybridMethod::updatePriorityQueue	(	size_t	rIndex,
		C_FLOAT64	time
	)

protected

Updates the priority queue.

Parameters

rIndex	A size_t giving the index of the fired reaction
time	A C_FLOAT64 holding the time taken by this reaction

Updates the priority queue.

Parameters

rIndex	A size_t giving the index of the fired reaction (-1, if no stochastic reaction has fired)
time	A C_FLOAT64 holding the current time

References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::array(), C_FLOAT64, C_INVALID_INDEX, CDataObject::calculateValue(), generateReactionTime(), CMathReaction::getPropensityObject(), mAmu, mAmuOld, CCopasiMethod::mpContainer, mPQ, mReactionFlags, mReactions, mUpdateSequences, CVectorCore< CType >::size(), CIndexedPriorityQueue::updateNode(), CMathContainer::updateSimulatedValues(), and updateTauMu().

Referenced by doSingleStep().

◆ updateTauMu()

void CHybridMethod::updateTauMu	(	size_t	rIndex,
		C_FLOAT64	time
	)

protected

Updates the putative reaction time of a stochastic reaction in the priority queue. The corresponding amu and amu_old must be set prior to the call of this method.

Parameters

rIndex	A size_t specifying the index of the reaction
time	A C_FLOAT64 specifying the current time

Updates the putative reaction time of a stochastic reaction in the priority queue. The corresponding amu and amu_old must be set prior to the call of this method.

Parameters

rIndex A size_t specifying the index of the reaction

References C_FLOAT64, generateReactionTime(), CIndexedPriorityQueue::getKey(), mAmu, mAmuOld, mPQ, and CIndexedPriorityQueue::updateNode().

Referenced by updatePriorityQueue().

Member Data Documentation

◆ mAmu

std::vector<C_FLOAT64> CHybridMethod::mAmu

protected

The propensities of the stochastic reactions.

Referenced by generateReactionTime(), insertDeterministicReaction(), partitionSystem(), setupPriorityQueue(), start(), updatePriorityQueue(), and updateTauMu().

◆ mAmuOld

std::vector<C_FLOAT64> CHybridMethod::mAmuOld

protected

Referenced by insertDeterministicReaction(), partitionSystem(), start(), updatePriorityQueue(), and updateTauMu().

◆ mCurrentState

CVectorCore< C_FLOAT64 > CHybridMethod::mCurrentState

protected

Vectors to hold the system state and intermediate results

Referenced by partitionSystem(), CHybridNextReactionRKMethod::rungeKutta(), setupPartition(), and start().

◆ mDG

CDependencyGraph CHybridMethod::mDG

protected

The graph of reactions and their dependent reactions. When a reaction is executed, the propensities for each of its dependents must be updated.

Referenced by setupDependencyGraph().

◆ mFirstMetabIndex

size_t CHybridMethod::mFirstMetabIndex

protected

index of the first metab in CState

Referenced by CHybridNextReactionLSODAMethod::evalF(), and start().

◆ mFirstReactionFlag

CHybridStochFlag* CHybridMethod::mFirstReactionFlag

protected

Referenced by calculateDerivative(), doSingleStep(), insertDeterministicReaction(), removeDeterministicReaction(), and setupPartition().

◆ mLowerStochLimit

C_FLOAT64 CHybridMethod::mLowerStochLimit

protected

Limit for particle numbers. If a particle number is < StochLimit the corresponding reactions must be simulated stochastically.

Referenced by isValidProblem(), partitionSystem(), setupPartition(), and start().

◆ mMaxBalance

size_t CHybridMethod::mMaxBalance

protected

maximal increase of a particle number in one step.

◆ mMaxIntBeforeStep

size_t CHybridMethod::mMaxIntBeforeStep

protected

This is set to maxint - mMaxSteps*mMaxBalance

◆ mMaxSteps

unsigned C_INT32 CHybridMethod::mMaxSteps

protected

Max number of doSingleStep() per step()

Referenced by start(), and step().

◆ mMaxStepsReached

bool CHybridMethod::mMaxStepsReached

protected

Referenced by start(), and step().

◆ mMetab2React

std::vector<std::set <size_t> > CHybridMethod::mMetab2React

protected

Vector of relations between metabolites to reactions.

Referenced by partitionSystem(), setupMetab2React(), setupPartition(), and start().

◆ mMetabFlags

CVector< metabStatus > CHybridMethod::mMetabFlags

protected

Vector holding information on the status of metabolites. They can have low or high particle numbers.

Referenced by partitionSystem(), and setupPartition().

◆ mNumVariableMetabs

size_t CHybridMethod::mNumVariableMetabs

protected

Dimension of the system. Total number of metabolites.

Referenced by CHybridNextReactionLSODAMethod::evalF(), partitionSystem(), CHybridNextReactionRKMethod::rungeKutta(), setupPartition(), start(), and CHybridNextReactionRKMethod::start().

◆ mPartitioningInterval

unsigned C_INT32 CHybridMethod::mPartitioningInterval

protected

The system gets repartitioned after this number of elementary steps.

Referenced by doSingleStep(), and start().

◆ mpFirstMetabValue

const C_FLOAT64* CHybridMethod::mpFirstMetabValue

protected

Referenced by setupMetab2React(), and start().

◆ mPQ

CIndexedPriorityQueue CHybridMethod::mPQ

protected

The set of putative stochastic (!) reactions and associated times at which each reaction occurs. This is represented as a priority queue, sorted by the reaction time. This heap changes dynamically as stochastic reactions become deterministic (delete this reaction from the queue) or vice versa (insert a new reaction into the queue).

Referenced by doSingleStep(), getStochTimeAndIndex(), partitionSystem(), setupPriorityQueue(), updatePriorityQueue(), and updateTauMu().

◆ mpRandomGenerator

CRandom* CHybridMethod::mpRandomGenerator

protected

The random number generator.

Referenced by generateReactionTime(), and start().

◆ mRandomSeed

unsigned C_INT32 CHybridMethod::mRandomSeed

protected

The random seed to use.

Referenced by start().

◆ mRateOffset

size_t CHybridMethod::mRateOffset

protected

Referenced by calculateDerivative(), and start().

◆ mReactionFlags

std::vector<CHybridStochFlag> CHybridMethod::mReactionFlags

protected

Vector to hold information about how many metabolites of a reaction have low particle numbers. If no metabolite of one reaction has low particle numbers this reaction will be simulated det.

Referenced by insertDeterministicReaction(), partitionSystem(), removeDeterministicReaction(), setupPartition(), setupPriorityQueue(), and updatePriorityQueue().

◆ mReactions

CVectorCore< CMathReaction > CHybridMethod::mReactions

protected

A pointer to the reactions of the model.

Referenced by calculateDerivative(), doSingleStep(), partitionSystem(), setupDependencyGraph(), setupMetab2React(), setupPartition(), setupPriorityQueue(), start(), and updatePriorityQueue().

◆ mSpeciesRates

CVectorCore< C_FLOAT64 > CHybridMethod::mSpeciesRates

protected

Referenced by calculateDerivative(), and start().

◆ mStepsAfterPartitionSystem

size_t CHybridMethod::mStepsAfterPartitionSystem

protected

Number of elementary steps after the last partitioning.

Referenced by doSingleStep(), and start().

◆ mUpdateSequences

CVector< CCore::CUpdateSequence > CHybridMethod::mUpdateSequences

protected

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

Referenced by setupDependencyGraph(), start(), and updatePriorityQueue().

◆ mUpperStochLimit

C_FLOAT64 CHybridMethod::mUpperStochLimit

protected

Referenced by isValidProblem(), partitionSystem(), setupPartition(), and start().

◆ mUseRandomSeed

bool CHybridMethod::mUseRandomSeed

protected

Specifies if the mRandomSeed should be used. otherwise a randomly chosen seed is used.

Referenced by start().

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

Public Member Functions

Protected Types

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Member Enumeration Documentation

◆ metabStatus

Constructor & Destructor Documentation

◆ CHybridMethod() [1/3]

◆ CHybridMethod() [2/3]

◆ CHybridMethod() [3/3]

◆ ~CHybridMethod()

Member Function Documentation

◆ calculateDerivative()

◆ checkModel()

◆ cleanup()

◆ doSingleStep()

◆ elevateChildren()

◆ generateReactionTime()

◆ getStochTimeAndIndex()

◆ initializeParameter()

◆ insertDeterministicReaction()

◆ integrateDeterministicPart()

◆ isValidProblem()

◆ partitionSystem()

◆ removeDeterministicReaction()

◆ setupDependencyGraph()

◆ setupMetab2React()

◆ setupPartition()

◆ setupPriorityQueue()

◆ start()

◆ step()

◆ updatePriorityQueue()

◆ updateTauMu()

Member Data Documentation

◆ mAmu

◆ mAmuOld

◆ mCurrentState

◆ mDG

◆ mFirstMetabIndex

◆ mFirstReactionFlag

◆ mLowerStochLimit

◆ mMaxBalance

◆ mMaxIntBeforeStep

◆ mMaxSteps

◆ mMaxStepsReached

◆ mMetab2React

◆ mMetabFlags

◆ mNumVariableMetabs

◆ mPartitioningInterval

◆ mpFirstMetabValue

◆ mPQ

◆ mpRandomGenerator

◆ mRandomSeed

◆ mRateOffset

◆ mReactionFlags

◆ mReactions

◆ mSpeciesRates

◆ mStepsAfterPartitionSystem

◆ mUpdateSequences

◆ mUpperStochLimit

◆ mUseRandomSeed