COPASI API
4.40.278
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#include <CStochasticRungeKuttaRI5.h>
Public Member Functions | |
CStochasticRungeKuttaRI5 (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::stochasticRunkeKuttaRI5, const CTaskEnum::Task &taskType=CTaskEnum::Task::timeCourse) | |
CStochasticRungeKuttaRI5 (const CStochasticRungeKuttaRI5 &src, const CDataContainer *pParent) | |
virtual bool | elevateChildren () |
void | evalRoot (const double &time, CVectorCore< C_FLOAT64 > &rootValues) |
virtual void | start () |
virtual void | stateChange (const CMath::StateChange &change) |
virtual Status | step (const double &deltaT, const bool &final=false) |
~CStochasticRungeKuttaRI5 () | |
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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 |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
void | setProblem (CTrajectoryProblem *problem) |
~CTrajectoryMethod () | |
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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 () |
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bool | addGroup (const std::string &name) |
void | addParameter (CCopasiParameter *pParameter) |
bool | addParameter (const CCopasiParameter ¶meter) |
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 () |
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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 () |
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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 () |
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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 () |
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CObjectInterface () | |
CObjectInterface (const CObjectInterface &src) | |
virtual | ~CObjectInterface () |
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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 | |
void | buildStage1 () |
void | buildStage2 () |
void | buildStage3 () |
C_FLOAT64 | calculateSmallestPhysicalValue () const |
void | calculateStateVariables (const double &time) |
void | createRootMask () |
CStochasticRungeKuttaRI5 () | |
void | destroyRootMask () |
void | evalNoise (C_FLOAT64 *pNoise, const size_t &noiseDimension) |
void | evalRate (C_FLOAT64 *rates) |
void | generateRandomNumbers () |
void | initializeParameter () |
CTrajectoryMethod::Status | internalStep () |
C_FLOAT64 | randomIHat () |
C_FLOAT64 | randomITilde () |
Additional Inherited Members | |
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enum | Status { FAILURE = -1 , NORMAL = 0 , ROOT = 1 } |
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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 |
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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 |
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typedef CDataObjectMap | objectMap |
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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 } |
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typedef std::vector< const CDataContainer * > | ContainerList |
typedef std::set< const CObjectInterface * > | ObjectSet |
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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) |
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static CDataContainer * | fromData (const CData &data, CUndoObjectInterface *pParent) |
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static CDataObject * | fromData (const CData &data, CUndoObjectInterface *pParent) |
static void | sanitizeObjectName (std::string &name) |
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static const CDataObject * | DataObject (const CObjectInterface *pInterface) |
static CObjectInterface * | GetObjectFromCN (const ContainerList &listOfContainer, const CCommonName &objName) |
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template<class CType > | |
static CType * | fromData (const CData &, CUndoObjectInterface *) |
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static const CEnumAnnotation< std::string, Type > | TypeName |
static const CEnumAnnotation< std::string, Type > | XMLType |
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static const CObjectInterface::ContainerList | EmptyList |
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void | output (const bool &useMoieties) |
virtual void | signalMathContainerChanged () |
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CCopasiMethod (const CCopasiMethod &src) | |
CCopasiMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType) | |
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CCopasiParameterGroup () | |
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CCopasiParameter (const CCopasiParameter &src) | |
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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 () |
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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) | |
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CVectorCore< C_FLOAT64 > | mContainerState |
C_FLOAT64 * | mpContainerStateTime |
CTrajectoryProblem * | mpProblem |
const bool * | mpReducedModel |
CTrajectoryTask * | mpTask |
CVectorCore< C_INT > | mRootsFound |
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CMathContainer * | mpContainer |
CProcessReportLevel | mProcessReport |
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std::string | mKey |
void * | mpDefault |
void * | mpValidValues |
void * | mpValue |
CDataObject * | mpValueReference |
UserInterfaceFlag | mUserInterfaceFlag |
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objectMap | mObjects |
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ObjectSet | mPrerequisits |
std::set< CDataContainer * > | mReferences |
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CValidity | mValidity |
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static const bool | ReducedModel |
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Constructor.
CStochasticRungeKuttaRI5::CStochasticRungeKuttaRI5 | ( | const CDataContainer * | pParent, |
const CTaskEnum::Method & | methodType = CTaskEnum::Method::stochasticRunkeKuttaRI5 , |
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const CTaskEnum::Task & | taskType = CTaskEnum::Task::timeCourse |
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Specific constructor
const | CDataContainer * pParent |
const | CTaskEnum::Method & methodType (default: deterministic) |
const | CTaskEnum::Task & taskType (default: timeCourse) |
References evalRoot(), initializeParameter(), and mpRootValueCalculator.
CStochasticRungeKuttaRI5::CStochasticRungeKuttaRI5 | ( | const CStochasticRungeKuttaRI5 & | src, |
const CDataContainer * | pParent | ||
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Copy constructor.
const CStochasticRungeKuttaRI5 & | src |
const | CDataContainer * pParent (default: NULL) |
References CVectorCore< CType >::initialize(), initializeParameter(), mContainerNoise, mContainerRates, mContainerRoots, mContainerVariables, and mRoots.
CStochasticRungeKuttaRI5::~CStochasticRungeKuttaRI5 | ( | ) |
Destructor.
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References CMatrix< CType >::array(), CVectorCore< CType >::begin(), c01, c11, c21, C_FLOAT64, evalNoise(), evalRate(), mA, mB, mBB, mContainerVariables, mH10, mNumNoise, mNumVariables, CTrajectoryMethod::mpContainerStateTime, mRandomIHat, mRandomIMatrix, mStepSize, mSumAll1, mSumPartial1, and mTime.
Referenced by calculateStateVariables().
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References A021, A121, A221, CMatrix< CType >::array(), B021, B121, B221, CVectorCore< CType >::begin(), c02, c12, c22, C_FLOAT64, CVectorCore< CType >::end(), evalNoise(), evalRate(), mA, mB, mBB, mContainerVariables, mH10, mH20, mH2k, mHH2k, mNumNoise, mNumVariables, CTrajectoryMethod::mpContainerStateTime, mRandomIHat, mRandomIMatrix, mSqrtStepSize, mStepSize, mSumAll1, mSumAll2, mSumPartial1, mSumPartial2, and mTime.
Referenced by calculateStateVariables().
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References A031, A032, A131, A132, A231, A232, B031, B032, B131, B132, B231, B232, CVectorCore< CType >::begin(), c03, c13, c23, C_FLOAT64, CVectorCore< CType >::end(), evalNoise(), evalRate(), mA, mB, mBB, mContainerVariables, mH10, mH30, mH3k, mHH3k, mNumNoise, mNumVariables, CTrajectoryMethod::mpContainerStateTime, mSqrtStepSize, mStepSize, mSumAll1, mSumAll2, mSumPartial1, mSumPartial2, and mTime.
Referenced by calculateStateVariables().
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References CVectorCore< CType >::begin(), C_FLOAT64, CVectorCore< CType >::end(), mAtol, mContainerVariables, mpForcePhysicalCorrectness, and mPhysicalValues.
Referenced by evalRoot(), and internalStep().
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References alpha1, alpha2, alpha3, CMatrix< CType >::array(), CVectorCore< CType >::array(), CVectorCore< CType >::begin(), beta11, beta12, beta13, beta21, beta22, beta23, beta31, beta32, beta33, beta41, beta42, beta43, buildStage1(), buildStage2(), buildStage3(), C_FLOAT64, CVectorCore< CType >::end(), mA, mB, mBB, mContainerVariables, mH10, mLastCalculatedTime, mLastCalculatedVariables, mNumNoise, mNumVariables, CTrajectoryMethod::mpContainerStateTime, mpInternalStepSize, mRandomIHat, mRandomIMatrix, mSqrtStepSize, mStepSize, and mTime.
Referenced by evalRoot(), and internalStep().
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References CRootFinder::ALL, CVectorCore< CType >::array(), CVectorCore< CType >::begin(), C_FLOAT64, C_INT, CMathContainer::calculateRootDerivatives(), CRootFinder::CONTINUOUS, CRootFinder::DISCRETE, CVectorCore< CType >::end(), CMathContainer::getRootIsDiscrete(), mContainerRoots, min, mNumRoots, CCopasiMethod::mpContainer, mRootMask, mRootMasking, CVector< CType >::resize(), and CMathContainer::updateSimulatedValues().
Referenced by internalStep().
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References CVectorCore< CType >::begin(), C_FLOAT64, C_INT, CRootFinder::DISCRETE, CVectorCore< CType >::end(), CRootFinder::getRootError(), mContainerRoots, min, CCopasiMethod::mpContainer, mRootFinder, mRootMask, mRootMasking, CRootFinder::NONE, and CMathContainer::updateSimulatedValues().
Referenced by stateChange().
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This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
References initializeParameter().
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This evaluates the noise
References CMathContainer::applyUpdateSequence(), CVectorCore< CType >::begin(), C_FLOAT64, mContainerNoise, mNoiseUpdateSequences, mNumVariables, CCopasiMethod::mpContainer, and CMathContainer::resetNoise().
Referenced by buildStage1(), buildStage2(), and buildStage3().
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This evaluates the derivatives
References CVectorCore< CType >::begin(), C_FLOAT64, mContainerRates, mNumVariables, CCopasiMethod::mpContainer, and CMathContainer::updateSimulatedValues().
Referenced by buildStage1(), buildStage2(), and buildStage3().
void CStochasticRungeKuttaRI5::evalRoot | ( | const double & | time, |
CVectorCore< C_FLOAT64 > & | rootValues | ||
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This evaluates the roots
References CVectorCore< CType >::begin(), C_FLOAT64, calculateSmallestPhysicalValue(), calculateStateVariables(), mContainerRoots, mNumRoots, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, CVectorCore< CType >::size(), and CMathContainer::updateRootValues().
Referenced by CStochasticRungeKuttaRI5().
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References CMatrix< CType >::array(), CVectorCore< CType >::begin(), C_FLOAT64, mInternalSteps, mLastCalculatedTime, mNumNoise, mRandomIHat, mRandomIMatrix, mRandomITilde, randomIHat(), and randomITilde().
Referenced by internalStep().
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Initialize the method parameter
References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, mpAbsoluteTolerance, mpForcePhysicalCorrectness, mpInternalStepSize, mpMaxInternalSteps, mpRootRelativeTolerance, CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.
Referenced by CStochasticRungeKuttaRI5(), and elevateChildren().
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References CRootFinder::ALL, CVectorCore< CType >::begin(), C_FLOAT64, C_INT, calculateSmallestPhysicalValue(), calculateStateVariables(), CRootFinder::checkRoots(), createRootMask(), CRootFinder::DISCRETE, CVectorCore< CType >::end(), CCopasiMessage::EXCEPTION, CTrajectoryMethod::FAILURE, fatalError, generateRandomNumbers(), CRootFinder::getRootTime(), CRootFinder::InvalidInterval, CMathContainer::isStateValid(), max, mContainerVariables, MCTrajectoryMethod, mH10, min, mInternalSteps, mNumRoots, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mpForcePhysicalCorrectness, mpInternalStepSize, mpMaxInternalSteps, mpPhysicalCorrectnessRootFound, mpRootRelativeTolerance, mRootFinder, mRootMasking, CTrajectoryMethod::mRootsFound, mTargetTime, mTime, CTrajectoryMethod::NORMAL, CRootFinder::NotAdvanced, CRootFinder::NotFound, CMath::NoToggle, CRootFinder::restart(), CTrajectoryMethod::ROOT, and CRootFinder::RootFound.
Referenced by step().
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References CRandom::getRandomU(), and mpRandom.
Referenced by generateRandomNumbers().
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References CRandom::getRandomU(), and mpRandom.
Referenced by generateRandomNumbers().
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This instructs the method to prepare for integration
Reimplemented from CTrajectoryMethod.
References CVectorCore< CType >::begin(), CMathUpdateSequence::begin(), C_FLOAT64, C_INT, CMath::Compartment, CCore::Default, CRootFinder::DISCRETE, CMathUpdateSequence::empty(), CVectorCore< CType >::end(), CMathUpdateSequence::end(), CMathContainer::getCountFixedEventTargets(), CMathContainer::getCountNoise(), CMathObject::getEntityType(), CMathContainer::getMathObject(), CMathContainer::getNoise(), CMathContainer::getNoiseInputObjects(), CMathContainer::getRandomGenerator(), CMathContainer::getRate(), CMathContainer::getRootIsDiscrete(), CMathContainer::getRoots(), CRootFinder::getRootValues(), CMathContainer::getStateObjects(), CRootFinder::getToggledRoots(), CMathContainer::getTransientDependencies(), CMathDependencyGraph::getUpdateSequence(), CVectorCore< CType >::initialize(), CRootFinder::initialize(), CMathContainer::initializeAtolVector(), CMathUpdateSequence::insert(), mA, mAtol, mB, mBB, mContainerNoise, mContainerRates, mContainerRoots, CTrajectoryMethod::mContainerState, mContainerVariables, mH10, mH20, mH2k, mH30, mH3k, mHH2k, mHH3k, mLastCalculatedTime, mNoiseInputValues, mNoiseUpdateSequences, mNumNoise, mNumRoots, mNumVariables, mpAbsoluteTolerance, CCopasiMethod::mpContainer, CTrajectoryMethod::mpContainerStateTime, mPhysicalValues, mpInternalStepSize, mpPhysicalCorrectnessRootFound, mpRandom, mpRootRelativeTolerance, mpRootValueCalculator, mRandomIHat, mRandomIMatrix, mRandomITilde, mRootFinder, mRootMask, mRoots, CTrajectoryMethod::mRootsFound, mSqrtStepSize, mStepSize, mSumAll1, mSumAll2, mSumPartial1, mSumPartial2, mTargetTime, mTime, CRootFinder::NONE, CMatrix< CType >::resize(), CVector< CType >::resize(), CVectorCore< CType >::size(), CMath::Species, and CTrajectoryMethod::start().
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Inform the trajectory method that the state has changed outside its control
const | CMath::StateChange & change |
Reimplemented from CTrajectoryMethod.
References CMath::ContinuousSimulation, destroyRootMask(), CFlags< Enum >::isSet(), mContainerVariables, mH10, mLastCalculatedTime, mRootFinder, CRootFinder::restart(), and CMath::State.
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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.
const | double & deltaT |
const | bool & final (default: false) |
Reimplemented from CTrajectoryMethod.
References CTrajectoryMethod::FAILURE, CTrajectoryProblem::getAutomaticStepSize(), internalStep(), mInternalSteps, mpInternalStepSize, mpMaxInternalSteps, CTrajectoryMethod::mpProblem, mRootCounter, mTargetDelta, mTargetTime, mTime, and CTrajectoryMethod::NORMAL.
Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), and start().
Referenced by calculateSmallestPhysicalValue(), and start().
Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), and start().
Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), and start().
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Referenced by CStochasticRungeKuttaRI5(), evalNoise(), and start().
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Referenced by CStochasticRungeKuttaRI5(), evalRate(), and start().
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Referenced by createRootMask(), CStochasticRungeKuttaRI5(), destroyRootMask(), evalRoot(), and start().
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Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), internalStep(), start(), and stateChange().
Referenced by buildStage2(), and start().
Referenced by buildStage2(), and start().
Referenced by buildStage3(), and start().
Referenced by buildStage3(), and start().
Referenced by buildStage2(), and start().
Referenced by buildStage3(), and start().
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Referenced by generateRandomNumbers(), internalStep(), and step().
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Referenced by calculateStateVariables(), generateRandomNumbers(), start(), and stateChange().
Referenced by calculateStateVariables().
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Referenced by evalNoise(), and start().
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Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), generateRandomNumbers(), and start().
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Referenced by createRootMask(), evalRoot(), internalStep(), and start().
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Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), evalNoise(), evalRate(), and start().
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A pointer to to the value "Absolute Tolerance"
Referenced by initializeParameter(), and start().
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A pointer to the value "Force Physical Correctness"
Referenced by calculateSmallestPhysicalValue(), initializeParameter(), and internalStep().
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Referenced by calculateSmallestPhysicalValue(), and start().
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A pointer to the value of "Internal Steps Size"
Referenced by calculateStateVariables(), initializeParameter(), internalStep(), start(), and step().
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A pointer to the value of "Max Internal Steps"
Referenced by initializeParameter(), internalStep(), and step().
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A pointer to the value which indicate the physical correctness root was found.
Referenced by internalStep(), and start().
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A pointer to the random number generator
Referenced by randomIHat(), randomITilde(), and start().
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A pointer to the value of "Tolerance for Root Finder"
Referenced by initializeParameter(), internalStep(), and start().
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Referenced by CStochasticRungeKuttaRI5(), and start().
Referenced by buildStage1(), buildStage2(), calculateStateVariables(), generateRandomNumbers(), and start().
Referenced by buildStage1(), buildStage2(), calculateStateVariables(), generateRandomNumbers(), and start().
Referenced by generateRandomNumbers(), and start().
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Referenced by step().
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Referenced by destroyRootMask(), internalStep(), start(), and stateChange().
Referenced by createRootMask(), destroyRootMask(), and start().
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Referenced by createRootMask(), destroyRootMask(), and internalStep().
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Referenced by CStochasticRungeKuttaRI5(), and start().
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Referenced by buildStage2(), buildStage3(), calculateStateVariables(), and start().
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Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), and start().
Referenced by buildStage1(), buildStage2(), buildStage3(), and start().
Referenced by buildStage2(), buildStage3(), and start().
Referenced by buildStage1(), buildStage2(), buildStage3(), and start().
Referenced by buildStage2(), buildStage3(), and start().
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Referenced by internalStep(), start(), and step().
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Referenced by buildStage1(), buildStage2(), buildStage3(), calculateStateVariables(), internalStep(), start(), and step().