COPASI API  4.40.278
Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | Static Private Member Functions | List of all members
CStochMethod Class Referenceabstract

#include <CStochMethod.h>

Inheritance diagram for CStochMethod:
[legend]

Public Member Functions

 CStochMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::stochastic, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
 
 CStochMethod (const CStochMethod &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)
 
 ~CStochMethod ()
 
- 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

virtual C_FLOAT64 doSingleStep (C_FLOAT64 time, C_FLOAT64 endtime)=0
 
size_t generateReactionIndex ()
 
C_FLOAT64 generateReactionTime ()
 
C_FLOAT64 generateReactionTime (size_t reaction_index)
 
virtual void initMethod ()=0
 
void setupDependencyGraph ()
 
- 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
 
CDependencyGraph mDG
 
size_t mFirstReactionSpeciesIndex
 
size_t mMaxSteps
 
bool mMaxStepsReached
 
size_t mNextReactionIndex
 
C_FLOAT64 mNextReactionTime
 
size_t mNumReactions
 
size_t mNumReactionSpecies
 
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

 CStochMethod ()
 
void initializeParameter ()
 

Static Private Member Functions

static C_INT32 checkModel (CModel *pmodel)
 

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

◆ CStochMethod() [1/3]

CStochMethod::CStochMethod ( )
private

Default constructor.

◆ CStochMethod() [2/3]

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

Specific constructor

Parameters
constCDataContainer * pParent
constCTaskEnum::Method & methodType (default: stochastic)
constCTaskEnum::Task & taskType (default: timeCourse)

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

◆ CStochMethod() [3/3]

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

Copy constructor.

Parameters
constCStochMethod & src,
constCDataContainer * pParent (Default: NULL)

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

◆ ~CStochMethod()

CStochMethod::~CStochMethod ( )

Destructor.

Member Function Documentation

◆ checkModel()

C_INT32 CStochMethod::checkModel ( CModel *  pmodel)
staticprivate

This checks if a model is suitable for stochastic simulation. It returns a suggestion which method to use

Parameters
modelThe model to check
Returns
1: direct method, 2: next reaction method, -1: no stochastic simulation possible

◆ doSingleStep()

virtual C_FLOAT64 CStochMethod::doSingleStep ( C_FLOAT64  time,
C_FLOAT64  endtime 
)
protectedpure virtual

Do one iteration of the simulation

Returns
Current simulation time or -1 if error.

Implemented in CStochNextReactionMethod.

Referenced by step().

◆ elevateChildren()

bool CStochMethod::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().

◆ generateReactionIndex()

size_t CStochMethod::generateReactionIndex ( )
protected

Generate the index of a putative reaction.

Returns
The reaction index

References CVectorCore< CType >::array(), C_FLOAT64, CRandom::getRandomOO(), mA0, mAmu, mNextReactionIndex, mNumReactions, and mpRandomGenerator.

◆ generateReactionTime() [1/2]

C_FLOAT64 CStochMethod::generateReactionTime ( )
protected

Generate the putative time taken before any reaction takes place

Returns
The time before the reaction

References C_FLOAT64, CRandom::getRandomOO(), mA0, and mpRandomGenerator.

Referenced by CStochNextReactionMethod::setupPriorityQueue(), and CStochNextReactionMethod::updatePriorityQueue().

◆ generateReactionTime() [2/2]

C_FLOAT64 CStochMethod::generateReactionTime ( size_t  reaction_index)
protected

Generate the putative time taken before a special reaction takes place

Returns
The time before the reaction

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

◆ initializeParameter()

void CStochMethod::initializeParameter ( )
private

Intialize the method parameter

References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_INT32, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiParameter::INT, CCopasiParameterGroup::removeParameter(), CCopasiParameterGroup::setValue(), and CCopasiParameter::UINT.

Referenced by CStochMethod(), and elevateChildren().

◆ initMethod()

virtual void CStochMethod::initMethod ( )
protectedpure virtual

Initialization.

Implemented in CStochNextReactionMethod.

Referenced by start().

◆ isValidProblem()

bool CStochMethod::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(), CCopasiMethod::getSubType(), CTrajectoryMethod::isValidProblem(), MCTrajectoryMethod, CTaskEnum::MethodName, CCopasiMethod::mpContainer, CVectorCore< CType >::size(), and CModel::suitableForStochasticSimulation().

◆ setupDependencyGraph()

void CStochMethod::setupDependencyGraph ( )
protected

Set up the dependency graph and the balances

References CDependencyGraph::addDependent(), CVectorCore< CType >::array(), CMathUpdateSequence::begin(), CDependencyGraph::clear(), CMathUpdateSequence::end(), mDG, mNumReactions, mPropensityObjects, mUpdateSequences, CDependencyGraph::resize(), and CVectorCore< CType >::size().

Referenced by start().

◆ start()

void CStochMethod::start ( )
virtual

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

Reimplemented from CTrajectoryMethod.

References CVectorCore< CType >::array(), C_FLOAT64, C_INT32, C_INVALID_INDEX, CMathObject::calculateValue(), CMathUpdateSequence::clear(), CCore::Default, CMathReaction::getChangedObjects(), CMathContainer::getCountDependentSpecies(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getCountIndependentSpecies(), CMathContainer::getCountODEs(), CMathContainer::getMathObject(), CMathContainer::getPropensities(), CMathContainer::getRandomGenerator(), CMathContainer::getReactions(), CMathContainer::getTransientDependencies(), CMathDependencyGraph::getUpdateSequence(), CVectorCore< CType >::initialize(), CRandom::initialize(), initMethod(), mA0, mAmu, CTrajectoryMethod::mContainerState, mFirstReactionSpeciesIndex, mMaxSteps, mMaxStepsReached, mNextReactionIndex, mNextReactionTime, mNumReactions, mNumReactionSpecies, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mpRandomGenerator, mPropensityObjects, mReactions, mUpdateSequences, setupDependencyGraph(), CVectorCore< CType >::size(), CTrajectoryMethod::start(), and CMathContainer::updateSimulatedValues().

◆ step()

CTrajectoryMethod::Status CStochMethod::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
constdouble & deltaT
constbool & final (default: false)
Returns
Status status

Reimplemented from CTrajectoryMethod.

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

Member Data Documentation

◆ mA0

C_FLOAT64 CStochMethod::mA0
protected

The sum of the propensities

Referenced by generateReactionIndex(), generateReactionTime(), and start().

◆ mAmu

CVectorCore< C_FLOAT64 > CStochMethod::mAmu
protected

A reference to the math container's propensity values

Referenced by generateReactionIndex(), generateReactionTime(), CStochNextReactionMethod::initMethod(), start(), and CStochNextReactionMethod::updatePriorityQueue().

◆ mDG

CDependencyGraph CStochMethod::mDG
protected

The dependency graph for the next reaction method.

Referenced by setupDependencyGraph(), and CStochNextReactionMethod::updatePriorityQueue().

◆ mFirstReactionSpeciesIndex

size_t CStochMethod::mFirstReactionSpeciesIndex
protected

The Ordered reaction

Referenced by start().

◆ mMaxSteps

size_t CStochMethod::mMaxSteps
protected

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

Referenced by start(), and step().

◆ mMaxStepsReached

bool CStochMethod::mMaxStepsReached
protected

Flag indicating whether the max step are reached.

Referenced by start().

◆ mNextReactionIndex

size_t CStochMethod::mNextReactionIndex
protected

The index of the next reaction which fires

Referenced by generateReactionIndex(), and start().

◆ mNextReactionTime

C_FLOAT64 CStochMethod::mNextReactionTime
protected

The time the next reaction fires

Referenced by start().

◆ mNumReactions

size_t CStochMethod::mNumReactions
protected

Referenced by generateReactionIndex(), setupDependencyGraph(), CStochNextReactionMethod::setupPriorityQueue(), and start().

◆ mNumReactionSpecies

size_t CStochMethod::mNumReactionSpecies
protected

Number of variable metabolites.

Referenced by start().

◆ mpRandomGenerator

CRandom* CStochMethod::mpRandomGenerator
protected

The random number generator

Referenced by CStochMethod(), generateReactionIndex(), generateReactionTime(), and start().

◆ mPropensityObjects

CVectorCore< CMathObject > CStochMethod::mPropensityObjects
protected

A reference to the math container's propensity objects

Referenced by setupDependencyGraph(), and start().

◆ mReactions

CVectorCore< CMathReaction > CStochMethod::mReactions
protected

A reference to the math container's reactions

Referenced by CStochNextReactionMethod::doSingleStep(), and start().

◆ mUpdateSequences

CVector< CCore::CUpdateSequence > CStochMethod::mUpdateSequences
protected

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

Referenced by CStochNextReactionMethod::doSingleStep(), setupDependencyGraph(), and start().

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