COPASI API
4.16.103
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#include <COptMethodSteepestDescent.h>
Public Member Functions | |
COptMethodSteepestDescent (const COptMethodSteepestDescent &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | optimise () |
virtual | ~COptMethodSteepestDescent () |
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COptMethod (const COptMethod &src, const CCopasiContainer *pParent=NULL) | |
bool | isBounded (void) |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
void | setProblem (COptProblem *problem) |
virtual | ~COptMethod () |
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CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL) | |
const CCopasiMethod::SubType & | getSubType () const |
const CCopasiTask::Type & | getType () const |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual | ~CCopasiMethod () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type) |
template<class CType > | |
bool | addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value) |
void | addParameter (CCopasiParameter *pParameter) |
CCopasiParameterGroup * | assertGroup (const std::string &name) |
template<class CType > | |
CCopasiParameter * | assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue) |
index_iterator | beginIndex () const |
name_iterator | beginName () const |
CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup") | |
void | clear () |
virtual bool | elevateChildren () |
index_iterator | endIndex () const |
name_iterator | endName () const |
CCopasiParameterGroup * | getGroup (const std::string &name) |
const CCopasiParameterGroup * | getGroup (const std::string &name) const |
CCopasiParameterGroup * | getGroup (const size_t &index) |
const CCopasiParameterGroup * | getGroup (const size_t &index) const |
size_t | getIndex (const std::string &name) const |
std::string | getKey (const std::string &name) const |
std::string | getKey (const size_t &index) const |
virtual const std::string & | getName (const size_t &index) const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &cn) const |
CCopasiParameter * | getParameter (const std::string &name) |
const CCopasiParameter * | getParameter (const std::string &name) const |
CCopasiParameter * | getParameter (const size_t &index) |
const CCopasiParameter * | getParameter (const size_t &index) const |
CCopasiParameter::Type | getType (const std::string &name) const |
CCopasiParameter::Type | getType (const size_t &index) const |
std::string | getUniqueParameterName (const CCopasiParameter *pParameter) const |
const CCopasiParameter::Value & | getValue (const std::string &name) const |
const CCopasiParameter::Value & | getValue (const size_t &index) const |
CCopasiParameter::Value & | getValue (const std::string &name) |
CCopasiParameter::Value & | getValue (const size_t &index) |
CCopasiParameterGroup & | operator= (const CCopasiParameterGroup &rhs) |
bool | removeParameter (const std::string &name) |
bool | removeParameter (const size_t &index) |
template<class CType > | |
bool | setValue (const std::string &name, const CType &value) |
template<class CType > | |
bool | setValue (const size_t &index, const CType &value) |
size_t | size () const |
bool | swap (const size_t &iFrom, const size_t &iTo) |
bool | swap (index_iterator &from, index_iterator &to) |
virtual | ~CCopasiParameterGroup () |
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CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL) | |
CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter") | |
virtual CCopasiObjectName | getCN () const |
virtual const std::string & | getKey () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) const |
const CCopasiParameter::Type & | getType () const |
const Value & | getValue () const |
Value & | getValue () |
virtual void * | getValuePointer () const |
CCopasiObject * | getValueReference () const |
bool | isValidValue (const C_FLOAT64 &value) const |
bool | isValidValue (const C_INT32 &value) const |
bool | isValidValue (const unsigned C_INT32 &value) const |
bool | isValidValue (const bool &value) const |
bool | isValidValue (const std::string &value) const |
bool | isValidValue (const CCopasiObjectName &value) const |
bool | isValidValue (const std::vector< CCopasiParameter * > &value) const |
CCopasiParameter & | operator= (const CCopasiParameter &rhs) |
template<class CType > | |
bool | setValue (const CType &value) |
bool | setValue (const std::vector< CCopasiParameter * > &value) |
virtual | ~CCopasiParameter () |
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virtual bool | add (CCopasiObject *pObject, const bool &adopt=true) |
CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container) | |
CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL) | |
virtual std::string | getChildObjectUnits (const CCopasiObject *pObject) const |
virtual const objectMap & | getObjects () const |
virtual std::string | getUnits () const |
virtual const CCopasiObject * | getValueObject () const |
virtual bool | remove (CCopasiObject *pObject) |
virtual | ~CCopasiContainer () |
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void | addDirectDependency (const CCopasiObject *pObject) |
CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL) | |
void | clearDirectDependencies () |
void | clearRefresh () |
bool | dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const |
void | getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const |
virtual const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () const |
const std::string & | getObjectName () const |
CCopasiContainer * | getObjectParent () const |
const std::string & | getObjectType () const |
virtual const CObjectInterface::ObjectSet & | getPrerequisites () const |
virtual Refresh * | getRefresh () const |
UpdateMethod * | getUpdateMethod () const |
bool | hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const |
bool | hasUpdateMethod () const |
bool | isArray () const |
bool | isContainer () const |
bool | isDataModel () const |
bool | isMatrix () const |
bool | isNameVector () const |
bool | isNonUniqueName () const |
virtual bool | isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const |
bool | isReference () const |
bool | isRoot () const |
bool | isSeparator () const |
bool | isStaticString () const |
bool | isValueBool () const |
bool | isValueDbl () const |
bool | isValueInt () const |
bool | isValueInt64 () const |
bool | isValueString () const |
bool | isVector () const |
virtual bool | mustBeDeleted (const DataObjectSet &deletedObjects) const |
void | removeDirectDependency (const CCopasiObject *pObject) |
void | setDirectDependencies (const DataObjectSet &directDependencies) |
bool | setObjectName (const std::string &name) |
virtual bool | setObjectParent (const CCopasiContainer *pParent) |
void | setObjectValue (const C_FLOAT64 &value) |
void | setObjectValue (const C_INT32 &value) |
void | setObjectValue (const bool &value) |
template<class CType > | |
void | setRefresh (CType *pType, void(CType::*method)(void)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const bool &)) |
virtual | ~CCopasiObject () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Private Member Functions | |
virtual bool | cleanup () |
COptMethodSteepestDescent (const CCopasiContainer *pParent=NULL) | |
C_FLOAT64 | descentLine (const C_FLOAT64 &x) |
const C_FLOAT64 & | evaluate () |
void | gradient () |
virtual bool | initialize () |
void | initObjects () |
Private Attributes | |
C_FLOAT64 | mBestValue |
bool | mContinue |
unsigned C_INT32 | mCurrentIteration |
CVector< C_FLOAT64 > | mGradient |
CVector< C_FLOAT64 > | mIndividual |
unsigned C_INT32 | mIterations |
FDescent * | mpDescent |
C_FLOAT64 | mTolerance |
C_FLOAT64 | mValue |
size_t | mVariableSize |
Friends | |
COptMethod * | COptMethod::createMethod (CCopasiMethod::SubType subType) |
Additional Inherited Members | |
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enum | SubType { unset = 0, RandomSearch, RandomSearchMaster, SimulatedAnnealing, CoranaWalk, DifferentialEvolution, ScatterSearch, GeneticAlgorithm, EvolutionaryProgram, SteepestDescent, HybridGASA, GeneticAlgorithmSR, HookeJeeves, LevenbergMarquardt, NelderMead, SRES, Statistics, ParticleSwarm, Praxis, TruncatedNewton, Newton, deterministic, LSODAR, directMethod, stochastic, tauLeap, adaptiveSA, hybrid, hybridLSODA, hybridODE45, DsaLsodar, tssILDM, tssILDMModified, tssCSP, mcaMethodReder, scanMethod, lyapWolf, sensMethod, EFMAlgorithm, EFMBitPatternTreeAlgorithm, EFMBitPatternAlgorithm, Householder, crossSectionMethod, linearNoiseApproximation } |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
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static COptMethod * | createMethod (CCopasiMethod::SubType subType=CCopasiMethod::RandomSearch) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::string | SubTypeName [] |
static const char * | XMLSubType [] |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
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enum | Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 } |
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COptMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiParameterGroup () | |
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template<class CType > | |
CCopasiObject * | addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
void | initObjects () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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const bool | mBounds |
const std::vector< COptItem * > * | mpOptContraints |
const std::vector< COptItem * > * | mpOptItem |
COptProblem * | mpOptProblem |
COptTask * | mpParentTask |
const std::vector < UpdateMethod * > * | mpSetCalculateVariable |
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CProcessReport * | mpCallBack |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 32 of file COptMethodSteepestDescent.h.
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Default Constructor
Definition at line 26 of file COptMethodSteepestDescent.cpp.
References CCopasiParameterGroup::addParameter(), C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, and CCopasiParameter::UINT.
COptMethodSteepestDescent::COptMethodSteepestDescent | ( | const COptMethodSteepestDescent & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy Constructor
const | COptMethodSteepestDescent & src |
Definition at line 43 of file COptMethodSteepestDescent.cpp.
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Destructor
Definition at line 57 of file COptMethodSteepestDescent.cpp.
References cleanup(), mpDescent, and pdelete.
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Cleanup arrays and pointers.
Reimplemented from COptMethod.
Definition at line 198 of file COptMethodSteepestDescent.cpp.
Referenced by initialize(), and ~COptMethodSteepestDescent().
Descent int the direction of the gradient with step x and evaluate the objective function
const | C_FLOAT64 & x |
Definition at line 250 of file COptMethodSteepestDescent.cpp.
References evaluate(), mGradient, mIndividual, COptMethod::mpSetCalculateVariable, and mVariableSize.
Referenced by optimise().
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Evaluate the objective function for the current parameters
Definition at line 259 of file COptMethodSteepestDescent.cpp.
References COptProblem::calculate(), COptProblem::checkFunctionalConstraints(), COptProblem::checkParametricConstraints(), COptProblem::getCalculateValue(), mBestValue, mContinue, COptMethod::mpOptProblem, and mValue.
Referenced by descentLine(), gradient(), and optimise().
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Calculate the gradient of the objective at the current parameters
Definition at line 223 of file COptMethodSteepestDescent.cpp.
References C_FLOAT64, evaluate(), mContinue, mGradient, COptMethod::mpOptItem, and mVariableSize.
Referenced by optimise().
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Initialize arrays and pointer.
Reimplemented from COptMethod.
Definition at line 204 of file COptMethodSteepestDescent.cpp.
References cleanup(), CCopasiParameter::getValue(), COptMethod::initialize(), mBestValue, mContinue, mGradient, mIndividual, mIterations, COptMethod::mpOptItem, mTolerance, mVariableSize, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, and CVector< CType >::resize().
Referenced by optimise().
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Initialize contained objects.
Definition at line 277 of file COptMethodSteepestDescent.cpp.
References CCopasiContainer::addObjectReference(), mCurrentIteration, and CCopasiObject::ValueInt.
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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.
Reimplemented from COptMethod.
Definition at line 64 of file COptMethodSteepestDescent.cpp.
References C_FLOAT64, COptItem::checkConstraint(), descentLine(), COutputInterface::DURING, evaluate(), FminBrent(), COptItem::getLowerBoundValue(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), gradient(), initialize(), max, mBestValue, mContinue, mCurrentIteration, mGradient, mIndividual, mIterations, mpDescent, COptMethod::mpOptItem, COptMethod::mpOptProblem, COptMethod::mpParentTask, mTolerance, mVariableSize, CCopasiTask::output(), and COptProblem::setSolution().
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The best value found so far.
Definition at line 123 of file COptMethodSteepestDescent.h.
Referenced by evaluate(), initialize(), and optimise().
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Indicates whether there the executions shall continue
Definition at line 118 of file COptMethodSteepestDescent.h.
Referenced by evaluate(), gradient(), initialize(), and optimise().
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The current iteration
Definition at line 153 of file COptMethodSteepestDescent.h.
Referenced by initObjects(), and optimise().
The gradient vector for the objective function
Definition at line 143 of file COptMethodSteepestDescent.h.
Referenced by descentLine(), gradient(), initialize(), and optimise().
A vector of parameters of the current individual
Definition at line 138 of file COptMethodSteepestDescent.h.
Referenced by descentLine(), initialize(), and optimise().
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The maximum number of iterations.
Definition at line 108 of file COptMethodSteepestDescent.h.
Referenced by initialize(), and optimise().
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Functor pointing to the descent method.
Definition at line 148 of file COptMethodSteepestDescent.h.
Referenced by optimise(), and ~COptMethodSteepestDescent().
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The tolerance
Definition at line 113 of file COptMethodSteepestDescent.h.
Referenced by initialize(), and optimise().
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array of values of objective function f/ individuals
Definition at line 128 of file COptMethodSteepestDescent.h.
Referenced by evaluate().
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number of parameters
Definition at line 133 of file COptMethodSteepestDescent.h.
Referenced by descentLine(), gradient(), initialize(), and optimise().