|
COPASI API
4.40.278
|
#include <COptMethodNelderMead.h>
Public Member Functions | |
| COptMethodNelderMead (const CDataContainer *pParent, const CTaskEnum::Method &methodType=CTaskEnum::Method::NelderMead, const CTaskEnum::Task &taskType=CTaskEnum::Task::optimization) | |
| COptMethodNelderMead (const COptMethodNelderMead &src, const CDataContainer *pParent) | |
| virtual const CVector< C_FLOAT64 > * | getBestParameters () const |
| virtual C_FLOAT64 | getBestValue () const |
| virtual const CVector< C_FLOAT64 > * | getCurrentParameters () const |
| virtual C_FLOAT64 | getCurrentValue () const |
| virtual unsigned C_INT32 | getMaxLogVerbosity () const |
| virtual bool | optimise () |
| virtual | ~COptMethodNelderMead () |
Public Member Functions inherited from COptMethod | |
| COptMethod (const CDataContainer *pParent, const CTaskEnum::Method &methodType, const CTaskEnum::Task &taskType, const bool ¶llel) | |
| COptMethod (const COptMethod &src, const CDataContainer *pParent) | |
| const COptLog & | getMethodLog () const |
| virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
| void | setProblem (COptProblem *problem) |
| virtual | ~COptMethod () |
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 ¶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 |
| virtual bool | elevateChildren () |
| 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 () |
Private Member Functions | |
| virtual bool | cleanup () |
| COptMethodNelderMead () | |
| const C_FLOAT64 & | evaluate () |
| virtual bool | initialize () |
| void | initObjects () |
Private Attributes | |
| C_FLOAT64 | mBestValue |
| CVector< C_FLOAT64 > | mCentroid |
| bool | mContinue |
| CVector< C_FLOAT64 > | mCurrent |
| C_FLOAT64 | mEvaluationValue |
| size_t | mhIteration |
| unsigned C_INT32 | mIteration |
| unsigned C_INT32 | mIterationLimit |
| C_FLOAT64 | mScale |
| CMatrix< C_FLOAT64 > | mSimplex |
| CVector< C_FLOAT64 > | mStep |
| C_FLOAT64 | mTolerance |
| CVector< C_FLOAT64 > | mValue |
| size_t | mVariableSize |
Additional Inherited Members | |
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 |
Protected Member Functions inherited from COptMethod | |
| 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 COptMethod | |
| static std::pair< C_FLOAT64, bool > | objectiveValue (COptProblem *pProblem, const CVectorCore< C_FLOAT64 > ¶meters) |
| static void | reflect (COptProblem *pProblem, const C_FLOAT64 &bestValue, C_FLOAT64 &objectiveValue) |
Protected Attributes inherited from COptMethod | |
| unsigned C_INT32 | mLogVerbosity |
| CMathContext | mMathContext |
| COptLog | mMethodLog |
| bool | mParallel |
| COptTask * | mpParentTask |
| COptProblemContext | mProblemContext |
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 |
| COptMethodNelderMead::COptMethodNelderMead | ( | const CDataContainer * | pParent, |
| const CTaskEnum::Method & | methodType = CTaskEnum::Method::NelderMead, |
||
| const CTaskEnum::Task & | taskType = CTaskEnum::Task::optimization |
||
| ) |
Specific constructor
| const | CDataContainer * pParent |
| const | CTaskEnum::Method & methodType (default: NelderMead) |
| const | CTaskEnum::Task & taskType (default: optimization) |
References CCopasiParameterGroup::assertParameter(), C_FLOAT64, C_INT32, initObjects(), CCopasiParameter::UDOUBLE, and CCopasiParameter::UINT.
| COptMethodNelderMead::COptMethodNelderMead | ( | const COptMethodNelderMead & | src, |
| const CDataContainer * | pParent | ||
| ) |
Copy Constructor
| const | COptMethodNelderMead & src |
| const | CDataContainer * pParent (default: NULL) |
References initObjects().
|
virtual |
Destructor
References cleanup().
|
private |
Default Constructor
|
privatevirtual |
Cleanup arrays and pointers.
Reimplemented from COptMethod.
Referenced by initialize(), and ~COptMethodNelderMead().
|
private |
Evaluate the objective function
References CContext< Data >::master(), mBestValue, mContinue, mEvaluationValue, and COptMethod::mProblemContext.
Referenced by optimise().
|
virtual |
|
virtual |
|
virtual |
Returns the maximum verbosity at which the method can log.
Reimplemented from COptMethod.
|
privatevirtual |
Initialize arrays and pointer.
Reimplemented from COptMethod.
References CProcessReportLevel::addItem(), cleanup(), COptMethod::initialize(), CContext< Data >::master(), mBestValue, mCentroid, mContinue, mCurrent, mhIteration, mIteration, mIterationLimit, COptMethod::mProblemContext, CCopasiMethod::mProcessReport, mScale, mSimplex, mStep, mTolerance, mValue, mVariableSize, CMatrix< CType >::resize(), and CVector< CType >::resize().
Referenced by optimise().
|
private |
Initialize contained objects.
References CDataContainer::addObjectReference(), mIteration, and CDataObject::ValueInt.
Referenced by COptMethodNelderMead().
|
virtual |
Execute the optimization algorithm calling simulation routine when needed. It is noted that this procedure can give feedback of its progress by the callback function set with SetCallback. @ return success;
Reimplemented from COptMethod.
References C_FLOAT64, COptItem::checkConstraint(), COutputInterface::DURING, COptLog::enterLogEntry(), evaluate(), CProcessReportLevel::finishItem(), COptItem::getLowerBoundValue(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), initialize(), CContext< Data >::master(), max, mBestValue, mCentroid, mContinue, mCurrent, mEvaluationValue, mhIteration, mIteration, mIterationLimit, COptMethod::mLogVerbosity, COptMethod::mMethodLog, COutputInterface::MONITORING, COptMethod::mpParentTask, COptMethod::mProblemContext, CCopasiMethod::mProcessReport, mScale, mSimplex, mStep, mTolerance, mValue, mVariableSize, CCopasiTask::output(), and CProcessReportLevel::progressItem().
|
private |
The best value found so far
Referenced by evaluate(), getBestValue(), getCurrentValue(), initialize(), and optimise().
The centroid of the simplex
Referenced by initialize(), and optimise().
|
private |
Flag indicating whether the computation shall continue
Referenced by evaluate(), initialize(), and optimise().
The current solution guess
Referenced by getBestParameters(), getCurrentParameters(), initialize(), and optimise().
|
private |
The result of a function evaluation
Referenced by evaluate(), and optimise().
|
private |
Handle to the process report item "Current Iteration"
Referenced by initialize(), and optimise().
|
private |
The number of iterations
Referenced by initialize(), initObjects(), and optimise().
|
private |
The maximum number of iterations
Referenced by initialize(), and optimise().
|
private |
The scale
Referenced by initialize(), and optimise().
The simplex
Referenced by initialize(), and optimise().
The step taken
Referenced by initialize(), and optimise().
|
private |
The tolerance
Referenced by initialize(), and optimise().
Array of values of objective function for each corner of the simplex
Referenced by initialize(), and optimise().
|
private |
number of parameters
Referenced by initialize(), and optimise().