COPASI API  4.40.278
CHybridNextReactionLSODAMethod Class Reference

#include <CHybridNextReactionLSODAMethod.h>

Inheritance diagram for CHybridNextReactionLSODAMethod:
[legend]

Classes

class  LSODA
 

Public Member Functions

 CHybridNextReactionLSODAMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::hybridLSODA, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
 
 CHybridNextReactionLSODAMethod (const CHybridNextReactionLSODAMethod &src, const CDataContainer *pParent)
 
void evalF (C_FLOAT64 *ydot)
 
virtual void integrateDeterministicPart (C_FLOAT64 ds)
 
virtual void start ()
 
virtual void stateChange (const CMath::StateChange &change)
 
- Public Member Functions inherited from CHybridMethod
 CHybridMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::hybrid, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
 
 CHybridMethod (const CHybridMethod &src, const CDataContainer *pParent)
 
virtual bool elevateChildren ()
 
virtual bool isValidProblem (const CCopasiProblem *pProblem)
 
virtual Status step (const double &deltaT, const bool &final=false)
 
 ~CHybridMethod ()
 
- Public Member Functions inherited from CTrajectoryMethod
 CTrajectoryMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse)
 
 CTrajectoryMethod (const CTrajectoryMethod &src, const CDataContainer *pParent)
 
const CVectorCore< C_INT > & getRoots () const
 
const bool & integrateReducedModel () const
 
void setProblem (CTrajectoryProblem *problem)
 
 ~CTrajectoryMethod ()
 
- Public Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src, const CDataContainer *pParent)
 
virtual void clearCallBack ()
 
const CProcessReportLevelgetCallBack () const
 
CMathContainergetMathContainer () const
 
const CTaskEnum::MethodgetSubType () const
 
const CTaskEnum::TaskgetType () const
 
virtual void load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH)
 
CCopasiMethodoperator= (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)
 
CCopasiParameterGroupassertGroup (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
 
CCopasiParameterGroupgetElementTemplates ()
 
const CCopasiParameterGroupgetElementTemplates () const
 
CCopasiParameterGroupgetGroup (const size_t &index)
 
const CCopasiParameterGroupgetGroup (const size_t &index) const
 
CCopasiParameterGroupgetGroup (const std::string &name)
 
const CCopasiParameterGroupgetGroup (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 CObjectInterfacegetObject (const CCommonName &cn) const
 
CCopasiParametergetParameter (const size_t &index)
 
const CCopasiParametergetParameter (const size_t &index) const
 
CCopasiParametergetParameter (std::string name)
 
const CCopasiParametergetParameter (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 CUndoObjectInterfaceinsert (const CData &data)
 
CCopasiParameterGroupoperator= (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::TypegetType () const
 
const UserInterfaceFlaggetUserInterfaceFlag () 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
 
CDataObjectgetValueReference () 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
 
CCopasiParameteroperator= (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 objectMapgetObjects ()
 
virtual const objectMapgetObjects () const
 
virtual const std::string getUnits () const override
 
virtual const CDataObjectgetValueObject () 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 CDataObjectgetDataObject () const override
 
CDataContainergetObjectAncestor (const std::string &type) const
 
CDataModelgetObjectDataModel () const
 
const CObjectInterfacegetObjectFromCN (const CCommonName &cn) const
 
const std::string & getObjectName () const
 
CDataContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const CObjectInterface::ObjectSetgetPrerequisites () const override
 
virtual const CValiditygetValidity () const override
 
bool hasFlag (const Flag &flag) const
 
virtual bool isPrerequisiteForContext (const CObjectInterface *pObject, const CCore::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const override
 
bool prerequisitsContains (const DataObjectSet &objects) const
 
void removeIssue (const CIssue &issue)
 
void removeReference (const CDataContainer *pReference)
 
bool setObjectName (const std::string &name)
 
void validityChanged (const CValidity &changedValidity) override
 
void validityRemoved (const CValidity &changedValidity)
 
virtual ~CDataObject ()
 
- Public Member Functions inherited from CObjectInterface
 CObjectInterface ()
 
 CObjectInterface (const CObjectInterface &src)
 
virtual ~CObjectInterface ()
 
- Public Member Functions inherited from CUndoObjectInterface
 CUndoObjectInterface ()
 
 CUndoObjectInterface (const CUndoObjectInterface &src)
 
bool generateUuid ()
 
const xg::Guid & getUuid () const
 
bool setUuid (const std::string &uuid)
 
bool setUuid (const xg::Guid &uuid)
 
virtual ~CUndoObjectInterface ()
 

Private Member Functions

 CHybridNextReactionLSODAMethod ()
 
void initializeParameter ()
 

Private Attributes

LSODA mLSODA
 

Additional Inherited Members

- Public Types inherited from CTrajectoryMethod
enum  Status { FAILURE = -1 , NORMAL = 0 , ROOT = 1 }
 
- Public Types inherited from CCopasiParameterGroup
typedef CDataObjectMap::const_type_iterator< CCopasiParameterconst_name_iterator
 
typedef std::vector< CCopasiParameter * > elements
 
typedef elements::iterator index_iterator
 
typedef CDataObjectMap::type_iterator< CCopasiParametername_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< eUserInterfaceFlagUserInterfaceFlag
 
- 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 CCopasiParameterfromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataContainer
static CDataContainerfromData (const CData &data, CUndoObjectInterface *pParent)
 
- Static Public Member Functions inherited from CDataObject
static CDataObjectfromData (const CData &data, CUndoObjectInterface *pParent)
 
static void sanitizeObjectName (std::string &name)
 
- Static Public Member Functions inherited from CObjectInterface
static const CDataObjectDataObject (const CObjectInterface *pInterface)
 
static CObjectInterfaceGetObjectFromCN (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, TypeTypeName
 
static const CEnumAnnotation< std::string, TypeXMLType
 
- Static Public Attributes inherited from CDataContainer
static const CObjectInterface::ContainerList EmptyList
 
- Protected Types inherited from CHybridMethod
enum  metabStatus { LOW = 0 , HIGH }
 
- Protected Member Functions inherited from CHybridMethod
void calculateDerivative (CVectorCore< C_FLOAT64 > &deriv)
 
void cleanup ()
 
C_FLOAT64 doSingleStep (C_FLOAT64 currentTime, C_FLOAT64 endTime)
 
C_FLOAT64 generateReactionTime (size_t rIndex)
 
void getStochTimeAndIndex (C_FLOAT64 &ds, size_t &rIndex)
 
void insertDeterministicReaction (size_t rIndex)
 
void partitionSystem ()
 
void removeDeterministicReaction (size_t rIndex)
 
void setupDependencyGraph ()
 
void setupMetab2React ()
 
void setupPartition ()
 
void setupPriorityQueue ()
 
void updatePriorityQueue (size_t rIndex, C_FLOAT64 time)
 
void updateTauMu (size_t rIndex, C_FLOAT64 time)
 
- Protected Member Functions inherited from CTrajectoryMethod
void output (const bool &useMoieties)
 
virtual void signalMathContainerChanged ()
 
- Protected Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src)
 
 CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType)
 
- Protected Member Functions inherited from CCopasiParameterGroup
 CCopasiParameterGroup ()
 
- Protected Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src)
 
- Protected Member Functions inherited from CDataContainer
template<class CType >
CDataMatrixReference< CType > * addMatrixReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
template<class CType >
CDataObjectReference< CType > * addObjectReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
template<class CType >
CDataVectorReference< CType > * addVectorReference (const std::string &name, CType &reference, const CFlags< Flag > &flag=CFlags< Flag >::None)
 
 CDataContainer (const CDataContainer &src)
 
void initObjects ()
 
- Protected Member Functions inherited from CDataObject
 CDataObject ()
 
 CDataObject (const std::string &name, const CDataContainer *pParent=static_cast< CDataContainer * >((void *) 0), const std::string &type="CN", const CFlags< Flag > &flag=CFlags< Flag >::None)
 
- Static Protected Member Functions inherited from CHybridMethod
static C_INT32 checkModel (CModel *model)
 
- Protected Attributes inherited from CHybridMethod
std::vector< C_FLOAT64mAmu
 
std::vector< C_FLOAT64mAmuOld
 
CVectorCore< C_FLOAT64mCurrentState
 
CDependencyGraph mDG
 
size_t mFirstMetabIndex
 
CHybridStochFlagmFirstReactionFlag
 
C_FLOAT64 mLowerStochLimit
 
size_t mMaxBalance
 
size_t mMaxIntBeforeStep
 
unsigned C_INT32 mMaxSteps
 
bool mMaxStepsReached
 
std::vector< std::set< size_t > > mMetab2React
 
CVector< metabStatusmMetabFlags
 
size_t mNumVariableMetabs
 
unsigned C_INT32 mPartitioningInterval
 
const C_FLOAT64mpFirstMetabValue
 
CIndexedPriorityQueue mPQ
 
CRandommpRandomGenerator
 
unsigned C_INT32 mRandomSeed
 
size_t mRateOffset
 
std::vector< CHybridStochFlagmReactionFlags
 
CVectorCore< CMathReactionmReactions
 
CVectorCore< C_FLOAT64mSpeciesRates
 
size_t mStepsAfterPartitionSystem
 
CVector< CCore::CUpdateSequencemUpdateSequences
 
C_FLOAT64 mUpperStochLimit
 
bool mUseRandomSeed
 
- Protected Attributes inherited from CTrajectoryMethod
CVectorCore< C_FLOAT64mContainerState
 
C_FLOAT64mpContainerStateTime
 
CTrajectoryProblemmpProblem
 
const bool * mpReducedModel
 
CTrajectoryTaskmpTask
 
CVectorCore< C_INTmRootsFound
 
- Protected Attributes inherited from CCopasiMethod
CMathContainermpContainer
 
CProcessReportLevel mProcessReport
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
void * mpDefault
 
void * mpValidValues
 
void * mpValue
 
CDataObjectmpValueReference
 
UserInterfaceFlag mUserInterfaceFlag
 
- Protected Attributes inherited from CDataContainer
objectMap mObjects
 
- Protected Attributes inherited from CDataObject
ObjectSet mPrerequisits
 
std::set< CDataContainer * > mReferences
 
- Protected Attributes inherited from CObjectInterface
CValidity mValidity
 
- Static Protected Attributes inherited from CTrajectoryMethod
static const bool ReducedModel
 

Detailed Description

CHybridNextReactionLSODAMethod

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

File name: CHybridNextReactionLSODAMethod.h Author: Email:

Last change: 08, May 2006

(C) European Media Lab 2003.

Constructor & Destructor Documentation

◆ CHybridNextReactionLSODAMethod() [1/3]

CHybridNextReactionLSODAMethod::CHybridNextReactionLSODAMethod ( )
private

Constructor.

◆ CHybridNextReactionLSODAMethod() [2/3]

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

Specific constructor

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

CHybridNextReactionLSODAMethod

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

File name: CHybridNextReactionLSODAMethod.h Author: Email:

Last change: 08, May 2006

(C) European Media Lab 2003.

References initializeParameter().

◆ CHybridNextReactionLSODAMethod() [3/3]

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

Copy constructor.

Parameters
constCHybridNextReactionRKMethod & src
constCDataContainer * pParent

References initializeParameter().

Member Function Documentation

◆ evalF()

◆ initializeParameter()

◆ integrateDeterministicPart()

void CHybridNextReactionLSODAMethod::integrateDeterministicPart ( C_FLOAT64  ds)
virtual

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

Parameters
dsA C_FLOAT64 specifying the stepsize.

Implements CHybridMethod.

References mLSODA, and CLsodaMethod::step().

◆ start()

void CHybridNextReactionLSODAMethod::start ( )
virtual

◆ stateChange()

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

Inform the trajectory method that the state has changed outside its control

Parameters
constCMath::StateChange & change

Reimplemented from CTrajectoryMethod.

References mLSODA, and CLsodaMethod::stateChange().

Member Data Documentation

◆ mLSODA

LSODA CHybridNextReactionLSODAMethod::mLSODA
private

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