COPASI API  4.40.278
CTrajectoryMethodDsaLsodar Class Reference

#include <CTrajectoryMethodDsaLsodar.h>

Inheritance diagram for CTrajectoryMethodDsaLsodar:
[legend]

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 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 ()
 

Protected Attributes

C_FLOAT64 mA0
 
CVectorCore< C_FLOAT64mAmu
 
size_t mFirstReactionSpeciesIndex
 
bool mMaxStepsReached
 
size_t mNextReactionIndex
 
C_FLOAT64 mNextReactionTime
 
size_t mNumReactions
 
CPartition mPartition
 
C_FLOAT64mpLowerLimit
 
unsigned C_INT32mpMaxSteps
 
unsigned C_INT32mpPartitioningInterval
 
C_FLOAT64mpPartitioningSteps
 
CRandommpRandomGenerator
 
CVectorCore< CMathObjectmPropensityObjects
 
C_FLOAT64mpUpperLimit
 
CVectorCore< CMathReactionmReactions
 
CTrajectoryMethod::Status mStatus
 
size_t mStepsAfterPartitionSystem
 
CVector< CCore::CUpdateSequencemUpdateSequences
 
- Protected Attributes inherited from CLsodaMethod
Data mData
 
State mLastRootState
 
CVector< C_FLOAT64mLastSuccessState
 
C_INT mLsodaStatus
 
eRootMasking mRootMasking
 
C_FLOAT64 mTime
 
- 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
 

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< 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 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 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 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
constCDataContainer * pParent
constCTaskEnum::Method & methodType (default: DsaLsodar)
constCTaskEnum::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
constCTrajectoryMethodDsaLsodar & src
constCDataContainer * 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 ( )

◆ calculateTotalPropensity()

void CTrajectoryMethodDsaLsodar::calculateTotalPropensity ( )

◆ 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

◆ 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()

◆ 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
constsize_t & index

Executes the specified reaction in the system once.

Parameters
indexA size_t specifying the index of the reaction, which will be fired.
timeThe 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

◆ integrateDeterministicPart()

void CTrajectoryMethodDsaLsodar::integrateDeterministicPart ( const C_FLOAT64 deltaT)

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

Parameters
constC_FLOAT64 & deltaT.

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

Referenced by doSingleStep().

◆ isValidProblem()

◆ start()

◆ stateChange()

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

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

Parameters
constCMath::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
constdouble & deltaT
constbool & 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: