#include <COptProblem.h>

Inheritance diagram for COptProblem:

Collaboration diagram for COptProblem:

Public Member Functions
COptItem &	addOptItem (const CCopasiObjectName &objectCN)

virtual bool	calculate ()

virtual bool	calculateStatistics (const C_FLOAT64 &factor=1.0e-003, const C_FLOAT64 &resolution=1.0e-009)

virtual bool	checkFunctionalConstraints ()

virtual bool	checkParametricConstraints ()

	COptProblem (const CCopasiTask::Type &type=CCopasiTask::optimization, const CCopasiContainer *pParent=NULL)

	COptProblem (const COptProblem &src, const CCopasiContainer *pParent=NULL)

virtual bool	elevateChildren ()

const bool &	getCalculateStatistics () const

const C_FLOAT64 &	getCalculateValue () const

const std::vector < UpdateMethod * > &	getCalculateVariableUpdateMethods () const

const std::vector< COptItem * > &	getConstraintList () const

const C_FLOAT64 &	getExecutionTime () const

const unsigned C_INT32 &	getFunctionEvaluations () const

const std::string	getObjectiveFunction ()

COptItem &	getOptItem (const size_t &index)

const std::vector< COptItem * > &	getOptItemList () const

size_t	getOptItemSize () const

const bool &	getRandomizeStartValues () const

const C_FLOAT64 &	getSolutionValue () const

const CVector< C_FLOAT64 > &	getSolutionVariables () const

CCopasiTask::Type	getSubtaskType () const

const CVector< C_FLOAT64 > &	getVariableGradients () const

size_t	getVariableSize () const

void	incrementEvaluations (unsigned C_INT32 increment)

virtual bool	initialize ()

virtual bool	initializeSubtaskBeforeOutput ()

const bool &	maximize () const

virtual void	print (std::ostream *ostream) const

virtual void	printResult (std::ostream *ostream) const

void	randomizeStartValues ()

void	rememberStartValues ()

bool	removeOptItem (const size_t &index)

void	reset ()

void	resetEvaluations ()

virtual bool	restore (const bool &updateModel)

void	restoreModel (const bool &updateModel)

void	setCalculateStatistics (const bool &calculate)

virtual bool	setCallBack (CProcessReport *pCallBack)

void	setMaximize (const bool &maximize)

virtual bool	setModel (CModel *pModel)

bool	setObjectiveFunction (const std::string &infix)

void	setRandomizeStartValues (const bool &randomize)

virtual bool	setSolution (const C_FLOAT64 &value, const CVector< C_FLOAT64 > &variables)

bool	setSubtaskType (const CCopasiTask::Type &subtaskType)

bool	swapOptItem (const size_t &iFrom, const size_t &iTo)

virtual	~COptProblem ()

Public Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL)

CModel *	getModel () const

const CCopasiTask::Type &	getType () const

virtual	~CCopasiProblem ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

bool	addParameter (const CCopasiParameter &parameter)

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 ()

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 ()

Public Member Functions inherited from CCopasiParameter
	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 ()

Public Member Functions inherited from CCopasiContainer
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 ()

Public Member Functions inherited from CCopasiObject
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 ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

Static Public Attributes
static const unsigned int	ValidSubtasks []

Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Attributes
C_FLOAT64	mCalculateValue

unsigned C_INT32	mConstraintCounter

unsigned C_INT32	mCounter

CCopasiTimer	mCPUTime

unsigned C_INT32	mFailedConstraintCounter

unsigned C_INT32	mFailedCounter

CVector< C_FLOAT64 >	mGradient

bool	mHaveStatistics

size_t	mhCounter

size_t	mhSolutionValue

std::vector< Refresh * >	mInitialRefreshMethods

CVector< C_FLOAT64 >	mOriginalVariables

std::vector< COptItem * > *	mpConstraintItems

CCopasiParameterGroup *	mpGrpConstraints

CCopasiParameterGroup *	mpGrpItems

CExpression *	mpObjectiveExpression

std::vector< COptItem * > *	mpOptItems

bool *	mpParmCalculateStatistics

bool *	mpParmMaximize

std::string *	mpParmObjectiveExpression

bool *	mpParmRandomizeStartValues

std::string *	mpParmSubtaskCN

CCopasiTask *	mpSubtask

std::vector< Refresh * >	mRefreshConstraints

std::vector< Refresh * >	mRefreshMethods

C_FLOAT64	mSolutionValue

CVector< C_FLOAT64 >	mSolutionVariables

bool	mStoreResults

std::vector< UpdateMethod * >	mUpdateMethods

C_FLOAT64	mWorstValue

Protected Attributes inherited from CCopasiProblem
CProcessReport *	mpCallBack

CModel *	mpModel

CReport *	mpReport

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Private Member Functions
void	initializeParameter ()

void	initObjects ()

Friends
std::ostream &	operator<< (std::ostream &os, const COptProblem &o)

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator

typedef CCopasiContainer::objectMap::iterator	name_iterator

typedef std::vector < CCopasiParameter * >	parameterGroup

Public Types inherited from CCopasiParameter
enum	Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID }

Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Protected Types inherited from CCopasiObject
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 }

Protected Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiTask::Type &type, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiContainer
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 ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 49 of file COptProblem.h.

Constructor & Destructor Documentation

COptProblem::COptProblem	(	const CCopasiTask::Type &	type = `CCopasiTask::optimization`,
		const CCopasiContainer *	pParent = `NULL`
	)

Default constructor

Parameters

const	CCopasiTask::Type & type (default: optimization)
const	CCopasiContainer * pParent (default: NULL)

Definition at line 67 of file COptProblem.cpp.

References initializeParameter(), and initObjects().

                                                           :
   CCopasiProblem(type, pParent),
   mWorstValue(0.0),
   mpParmSubtaskCN(NULL),
   mpParmObjectiveExpression(NULL),
   mpParmMaximize(NULL),
   mpParmRandomizeStartValues(NULL),
   mpParmCalculateStatistics(NULL),
   mpGrpItems(NULL),
   mpGrpConstraints(NULL),
   mpOptItems(NULL),
   mpConstraintItems(NULL),
   mpSubtask(NULL),
   mpObjectiveExpression(NULL),
   mUpdateMethods(),
   mInitialRefreshMethods(),
   mRefreshMethods(),
   mRefreshConstraints(),
   mCalculateValue(0),
   mSolutionVariables(),
   mOriginalVariables(),
   mSolutionValue(0),
   mCounter(0),
   mFailedCounter(0),
   mConstraintCounter(0),
   mFailedConstraintCounter(0),
   mCPUTime(CCopasiTimer::PROCESS, this),
   mhSolutionValue(C_INVALID_INDEX),
   mhCounter(C_INVALID_INDEX),
   mStoreResults(false),
   mHaveStatistics(false),
   mGradient(0)
 {
   initializeParameter();
   initObjects();
 }

COptProblem::COptProblem	(	const COptProblem &	src,
		const CCopasiContainer *	pParent = `NULL`
	)

Copy constructor.

Parameters

const	COptProblem & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 106 of file COptProblem.cpp.

References initializeParameter(), and initObjects().

                                                           :
   CCopasiProblem(src, pParent),
   mWorstValue(src.mWorstValue),
   mpParmSubtaskCN(NULL),
   mpParmObjectiveExpression(NULL),
   mpParmMaximize(NULL),
   mpParmRandomizeStartValues(NULL),
   mpParmCalculateStatistics(NULL),
   mpGrpItems(NULL),
   mpGrpConstraints(NULL),
   mpOptItems(NULL),
   mpConstraintItems(NULL),
   mpSubtask(NULL),
   mpObjectiveExpression(NULL),
   mUpdateMethods(),
   mInitialRefreshMethods(),
   mRefreshMethods(),
   mRefreshConstraints(),
   mCalculateValue(src.mCalculateValue),
   mSolutionVariables(src.mSolutionVariables),
   mOriginalVariables(src.mOriginalVariables),
   mSolutionValue(src.mSolutionValue),
   mCounter(0),
   mFailedCounter(0),
   mConstraintCounter(0),
   mFailedConstraintCounter(0),
   mCPUTime(CCopasiTimer::PROCESS, this),
   mhSolutionValue(C_INVALID_INDEX),
   mhCounter(C_INVALID_INDEX),
   mStoreResults(src.mStoreResults),
   mHaveStatistics(src.mHaveStatistics),
   mGradient(src.mGradient)
 {
   initializeParameter();
   initObjects();
 }

COptProblem::~COptProblem ( )

virtual

Destructor

Definition at line 145 of file COptProblem.cpp.

146 {}

Member Function Documentation

COptItem & COptProblem::addOptItem ( const CCopasiObjectName & objectCN )

Add an optimization item to the problem.

Parameters

const CCopasiObjectName & objectCN

Returns: COptItem optItemAdded

Definition at line 708 of file COptProblem.cpp.

References CCopasiParameterGroup::addParameter(), CCopasiObject::getObjectDataModel(), mpGrpItems, and COptItem::setObjectCN().

 {
   CCopasiDataModel* pDataModel = getObjectDataModel();
   assert(pDataModel != NULL);
 
   COptItem * pItem = new COptItem(pDataModel);
   pItem->setObjectCN(objectCN);
 
   mpGrpItems->addParameter(pItem);
 
   return *pItem;
 }

bool COptProblem::calculate ( void )

virtual

Do the calculating based on CalculateVariables and fill CalculateResults with the results.

Returns: bool continue

calculate() decides whether the problem is a steady state problem or a trajectory problem based on whether the pointer to that type of problem is null or not. It then calls the process() method for that type of problem. Currently process takes ofstream& as a parameter but it will change so that process() takes no parameters.

Reimplemented in CFitProblem, and CRealProblem.

Definition at line 538 of file COptProblem.cpp.

References CExpression::calcValue(), CCopasiMessage::getLastMessage(), CCopasiTask::getProblem(), CCopasiTask::getType(), CCopasiTask::initialize(), mCalculateValue, mCounter, mFailedCounter, mhCounter, mInitialRefreshMethods, CCopasiProblem::mpCallBack, mpObjectiveExpression, mpParmMaximize, mpSubtask, mRefreshMethods, mStoreResults, CCopasiTask::NO_OUTPUT, CCopasiTask::ONLY_TIME_SERIES, pdelete, CCopasiTask::process(), CProcessReport::progressItem(), and CCopasiTask::timeCourse.

 {
   mCounter++;
   bool success = false;
   COutputHandler * pOutputHandler = NULL;
 
   if (mpSubtask == NULL)
     return false;
 
   if (mStoreResults &&
       mpSubtask->getType() == CCopasiTask::timeCourse)
     {
       static_cast< CTrajectoryProblem * >(mpSubtask->getProblem())->setTimeSeriesRequested(true);
 
       pOutputHandler = new COutputHandler();
       mpSubtask->initialize(CCopasiTask::ONLY_TIME_SERIES, pOutputHandler, NULL);
     }
 
   try
     {
       // Update all initial values which depend on the optimization items.
       std::vector< Refresh * >::const_iterator it = mInitialRefreshMethods.begin();
       std::vector< Refresh * >::const_iterator end = mInitialRefreshMethods.end();
 
       for (; it != end; ++it)
         (**it)();
 
       success = mpSubtask->process(true);
 
       // Refresh all values needed to calculate the objective function.
       it = mRefreshMethods.begin();
       end = mRefreshMethods.end();
 
       for (; it != end; ++it)
         (**it)();
 
       mCalculateValue = *mpParmMaximize ? -mpObjectiveExpression->calcValue() : mpObjectiveExpression->calcValue();
     }
 
   catch (CCopasiException & /*Exception*/)
     {
       // We do not want to clog the message cue.
       CCopasiMessage::getLastMessage();
 
       success = false;
     }
 
   catch (...)
     {
       success = false;
     }
 
   if (mStoreResults &&
       mpSubtask->getType() == CCopasiTask::timeCourse)
     {
       mStoreResults = false;
       mpSubtask->initialize(CCopasiTask::NO_OUTPUT, NULL, NULL);
       pdelete(pOutputHandler);
     }
 
   if (!success || isnan(mCalculateValue))
     {
       mFailedCounter++;
       mCalculateValue = std::numeric_limits< C_FLOAT64 >::infinity();
     }
 
   if (mpCallBack) return mpCallBack->progressItem(mhCounter);
 
   return true;
 }

bool COptProblem::calculateStatistics	(	const C_FLOAT64 &	factor = `1.0e-003`,
		const C_FLOAT64 &	resolution = `1.0e-009`
	)

virtual

Calculate the statistics for the problem

Parameters

const	C_FLOAT64 & factor (Default: 1.0e-003)
const	C_FLOAT64 & resolution (Default: 1.0e-009)

Reimplemented in CFitProblem.

Definition at line 609 of file COptProblem.cpp.

References C_FLOAT64, calculate(), CCopasiObject::getRefresh(), mCalculateValue, mCPUTime, mGradient, mHaveStatistics, mpParmCalculateStatistics, mpParmMaximize, mSolutionValue, mSolutionVariables, mStoreResults, mUpdateMethods, mWorstValue, CVector< CType >::resize(), and CVectorCore< CType >::size().

Referenced by COptTask::process().

 {
   // Set the current values to the solution values.
   size_t i, imax = mSolutionVariables.size();
 
   mGradient.resize(imax);
   mGradient = std::numeric_limits<C_FLOAT64>::quiet_NaN();
 
   // Recalculate the best solution.
   for (i = 0; i < imax; i++)
     (*mUpdateMethods[i])(mSolutionVariables[i]);
 
   // This is necessary so that the result can be displayed.
   mStoreResults = true;
   calculate();
   mStoreResults = false;
 
   // Make sure the timer is accurate.
   mCPUTime.getRefresh();
 
   if (mSolutionValue == mWorstValue)
     return false;
 
   if (*mpParmCalculateStatistics)
     {
       mHaveStatistics = true;
 
       C_FLOAT64 Current;
       C_FLOAT64 Delta;
 
       // Calculate the gradient
       for (i = 0; i < imax; i++)
         {
           Current = mSolutionVariables[i];
 
           if (fabs(Current) > resolution)
             {
               (*mUpdateMethods[i])(Current * (1.0 + factor));
               Delta = 1.0 / (Current * factor);
             }
           else
             {
               (*mUpdateMethods[i])(resolution);
               Delta = 1.0 / resolution;
             }
 
           calculate();
 
           mGradient[i] = ((*mpParmMaximize ? -mCalculateValue : mCalculateValue) - mSolutionValue) * Delta;
 
           // Restore the value
           (*mUpdateMethods[i])(Current);
         }
 
       calculate();
 
       // Make sure the timer is accurate.
       (*mCPUTime.getRefresh())();
     }
 
   return true;
 }

bool COptProblem::checkFunctionalConstraints ( )

virtual

Check whether all functional constraints are fulfilled.

Returns: bool fulfilled

Reimplemented in CFitProblem.

Definition at line 507 of file COptProblem.cpp.

References mConstraintCounter, mFailedConstraintCounter, mpConstraintItems, and mRefreshConstraints.

 {
   // Make sure the constraint values are up to date.
   std::vector< Refresh *>::const_iterator itRefresh = mRefreshConstraints.begin();
   std::vector< Refresh *>::const_iterator endRefresh = mRefreshConstraints.end();
 
   for (; itRefresh != endRefresh; ++itRefresh)
     (**itRefresh)();
 
   std::vector< COptItem * >::const_iterator it = mpConstraintItems->begin();
   std::vector< COptItem * >::const_iterator end = mpConstraintItems->end();
 
   mConstraintCounter++;
 
   for (; it != end; ++it)
     if ((*it)->checkConstraint())
       {
         mFailedConstraintCounter++;
         return false;
       }
 
   return true;
 }

bool COptProblem::checkParametricConstraints ( )

virtual

Check whether all parameters are within their boundaries.

Returns: bool within

Definition at line 496 of file COptProblem.cpp.

References mpOptItems.

Referenced by COptMethodSteepestDescent::evaluate(), COptMethodHookeJeeves::evaluate(), COptMethodNelderMead::evaluate(), COptMethodLevenbergMarquardt::evaluate(), COptMethodPraxis::evaluate(), COptMethodTruncatedNewton::evaluate(), COptMethodSA::optimise(), and COptMethodCoranaWalk::optimise().

 {
   std::vector< COptItem * >::const_iterator it = mpOptItems->begin();
   std::vector< COptItem * >::const_iterator end = mpOptItems->end();
 
   for (; it != end; ++it)
     if ((*it)->checkConstraint()) return false;
 
   return true;
 }

bool COptProblem::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns: bool success

Reimplemented from CCopasiParameterGroup.

Reimplemented in CFitProblem.

Definition at line 167 of file COptProblem.cpp.

References C_INVALID_INDEX, CCopasiRootContainer::getFunctionList(), CCopasiVectorN< CType >::getIndex(), CEvaluationTree::getInfix(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CFunctionDB::loadedFunctions(), mpConstraintItems, mpGrpConstraints, mpGrpItems, mpOptItems, mpParmObjectiveExpression, mpParmSubtaskCN, CCopasiParameter::Value::pSTRING, CCopasiParameterGroup::removeParameter(), setObjectiveFunction(), setSubtaskType(), CCopasiTask::steadyState, and CCopasiTask::timeCourse.

Referenced by CFitProblem::elevateChildren(), and initializeParameter().

 {
   // We need to handle the old file format which had two different task keys
   if (mpParmSubtaskCN != NULL)
     {
       CCopasiParameter * pParameter;
 
       if ((pParameter = getParameter("Steady-State")) != NULL)
         {
           if (*pParameter->getValue().pSTRING != "")
             {
               setSubtaskType(CCopasiTask::steadyState);
             }
 
           removeParameter("Steady-State");
         }
 
       if ((pParameter = getParameter("Time-Course")) != NULL)
         {
           if (*pParameter->getValue().pSTRING != "")
             {
               setSubtaskType(CCopasiTask::timeCourse);
             }
 
           removeParameter("Time-Course");
         }
 
       // If no subtask is defined we default to steady-state
       if (*mpParmSubtaskCN == "")
         setSubtaskType(CCopasiTask::steadyState);
     }
 
   // Handle old file format in which the objective expression was stored in the function DB
   if (mpParmObjectiveExpression != NULL)
     {
       CCopasiParameter * pParameter = getParameter("ObjectiveFunction");
       CExpression * pObjectiveFunction = NULL;
 
       // We do not use the key to find the objective function because keys are not re-mapped
       // for unknown parameters, instead we rely on the uniqueness of the name and the fact that
       // this is the only expression in the list.
       size_t Index = CCopasiRootContainer::getFunctionList()->loadedFunctions().getIndex("Objective Function");
 
       if (Index != C_INVALID_INDEX)
         {
           pObjectiveFunction =
             dynamic_cast<CExpression *>(CCopasiRootContainer::getFunctionList()->loadedFunctions()[Index]);
         }
 
       if (pObjectiveFunction != NULL &&
           pParameter != NULL)
         {
           *mpParmObjectiveExpression = pObjectiveFunction->getInfix();
 
           removeParameter("ObjectiveFunction");
         }
 
       setObjectiveFunction(*mpParmObjectiveExpression);
     }
 
   mpGrpItems =
     elevate<CCopasiParameterGroup, CCopasiParameterGroup>(mpGrpItems);
 
   if (!mpGrpItems) return false;
 
   std::vector<CCopasiParameter *> * pValue =
     mpGrpItems->CCopasiParameter::getValue().pGROUP;
 
   index_iterator it = pValue->begin();
   index_iterator end = pValue->end();
 
   for (; it != end; ++it)
     if (!elevate<COptItem, CCopasiParameterGroup>(*it)) return false;
 
   mpOptItems =
     static_cast<std::vector<COptItem * > * >(mpGrpItems->CCopasiParameter::getValue().pVOID);
 
   mpGrpConstraints =
     elevate<CCopasiParameterGroup, CCopasiParameterGroup>(mpGrpConstraints);
 
   if (!mpGrpConstraints) return false;
 
   pValue = mpGrpConstraints->CCopasiParameter::getValue().pGROUP;
 
   it = pValue->begin();
   end = pValue->end();
 
   for (; it != end; ++it)
     if (!elevate<COptItem, CCopasiParameterGroup>(*it)) return false;
 
   mpConstraintItems =
     static_cast<std::vector<COptItem * > * >(mpGrpConstraints->CCopasiParameter::getValue().pVOID);
 
   return true;
 }

const bool & COptProblem::getCalculateStatistics ( ) const

Retrieve whether we have to calculate statistics

Returns: const bool & maximize

Definition at line 838 of file COptProblem.cpp.

References mpParmCalculateStatistics.

Referenced by CQFittingResult::enterProtected(), CQFittingWidget::loadTask(), CQOptimizationWidget::loadTask(), CQFittingWidget::saveTask(), and CQOptimizationWidget::saveTask().

839 {return *mpParmCalculateStatistics;}

COptProblem::mpParmCalculateStatistics

bool * mpParmCalculateStatistics

Definition: COptProblem.h:416

const C_FLOAT64 & COptProblem::getCalculateValue ( ) const

Retrieve the result of a calculation

Definition at line 673 of file COptProblem.cpp.

References mCalculateValue.

674 {return mCalculateValue;}

COptProblem::mCalculateValue

C_FLOAT64 mCalculateValue

Definition: COptProblem.h:474

const std::vector< UpdateMethod * > & COptProblem::getCalculateVariableUpdateMethods ( ) const

Retrieve the update methods for the variables for calculation.

Returns: const std::vector< UpdateMethod * > & updateMethods

Definition at line 734 of file COptProblem.cpp.

References mUpdateMethods.

Referenced by COptMethod::initialize(), and COptMethodEP2::optimise().

735 {return mUpdateMethods;}

COptProblem::mUpdateMethods

std::vector< UpdateMethod * > mUpdateMethods

Definition: COptProblem.h:451

const std::vector< COptItem * > & COptProblem::getConstraintList ( ) const

Retrieve the list of constraints.

Returns: const std::vector< COptItem * > & constraintList

Definition at line 731 of file COptProblem.cpp.

References mpConstraintItems.

Referenced by COptMethod::initialize().

732 {return *mpConstraintItems;}

COptProblem::mpConstraintItems

std::vector< COptItem * > * mpConstraintItems

Definition: COptProblem.h:436

const C_FLOAT64 & COptProblem::getExecutionTime ( ) const

Retrieve the objective function.

Returns: const C_FLOAT64 & executionTime

Definition at line 850 of file COptProblem.cpp.

References CCopasiTimer::getElapsedTimeSeconds(), and mCPUTime.

Referenced by CQOptimizationResult::enterProtected(), CQFittingResultTab1::load(), CQOptimizationResult::slotSave(), and CQFittingResult::slotSave().

 {
   return mCPUTime.getElapsedTimeSeconds();
 }

const unsigned C_INT32 & COptProblem::getFunctionEvaluations ( ) const

Retrieve the evaluation counter.

Returns: const unsigned C_INT32 & functionEvaluations

Definition at line 841 of file COptProblem.cpp.

References mCounter.

Referenced by CQOptimizationResult::enterProtected(), CQFittingResult::enterProtected(), CQFittingResultTab1::load(), COptMethodSS::localmin(), CQOptimizationResult::slotSave(), and CQFittingResult::slotSave().

842 {return mCounter;}

COptProblem::mCounter

unsigned C_INT32 mCounter

Definition: COptProblem.h:494

const std::string COptProblem::getObjectiveFunction ( )

Retrieve the objective function.

Returns: const std::string infix.

Definition at line 747 of file COptProblem.cpp.

References mpParmObjectiveExpression.

Referenced by CQOptimizationWidget::loadTask(), and CQOptimizationWidget::saveTask().

 {
   return *mpParmObjectiveExpression;
 }

COptItem & COptProblem::getOptItem ( const size_t & index )

Retrieve the 'index' optimization item.

Parameters

const size_t & index

Returns: COptItem optItem

Definition at line 702 of file COptProblem.cpp.

703 {return *(*mpOptItems)[index];}

const std::vector< COptItem * > & COptProblem::getOptItemList ( ) const

Retrieve the list of optimization parameters.

Returns: const std::vector< COptItem * > & optItemList

Definition at line 728 of file COptProblem.cpp.

References mpOptItems.

Referenced by CQOptimizationResult::enterProtected(), CQFittingResult::enterProtected(), COptMethod::initialize(), and COptMethodSS::localmin().

729 {return *mpOptItems;}

COptProblem::mpOptItems

std::vector< COptItem * > * mpOptItems

Definition: COptProblem.h:431

size_t COptProblem::getOptItemSize ( ) const

Retrieve the number of optimization items.

Returns: const size_t size

Definition at line 705 of file COptProblem.cpp.

References mpGrpItems, and CCopasiParameterGroup::size().

706 {return mpGrpItems->size();}

COptProblem::mpGrpItems

CCopasiParameterGroup * mpGrpItems

Definition: COptProblem.h:421

CCopasiParameterGroup::size

size_t size() const

Definition: CCopasiParameterGroup.cpp:512

const bool & COptProblem::getRandomizeStartValues ( ) const

Retrieve whether we have to calculate statistics

Returns: const bool & randomize

Definition at line 803 of file COptProblem.cpp.

References mpParmRandomizeStartValues.

Referenced by CQFittingWidget::loadTask(), CQOptimizationWidget::loadTask(), CQFittingWidget::saveTask(), and CQOptimizationWidget::saveTask().

804 {return *mpParmRandomizeStartValues;}

COptProblem::mpParmRandomizeStartValues

bool * mpParmRandomizeStartValues

Definition: COptProblem.h:411

const C_FLOAT64 & COptProblem::getSolutionValue ( ) const

Retrieve the result for the solution

Definition at line 699 of file COptProblem.cpp.

References mSolutionValue.

Referenced by CQOptimizationResult::enterProtected(), CQFittingResultTab1::load(), COptMethodSS::localmin(), CQOptimizationResult::slotSave(), and CQFittingResult::slotSave().

700 {return mSolutionValue;}

COptProblem::mSolutionValue

C_FLOAT64 mSolutionValue

Definition: COptProblem.h:489

const CVector< C_FLOAT64 > & COptProblem::getSolutionVariables ( ) const

Retrieve the solution variables

Definition at line 676 of file COptProblem.cpp.

References mSolutionVariables.

Referenced by CQOptimizationResult::enterProtected(), CQFittingResult::enterProtected(), COptMethodSS::localmin(), COptMethodSS::optimise(), COptMethodCoranaWalk::optimise(), COptMethodNelderMead::optimise(), COptMethodSA::optimise(), and CQFittingItemWidget::slotReset().

677 {return mSolutionVariables;}

COptProblem::mSolutionVariables

CVector< C_FLOAT64 > mSolutionVariables

Definition: COptProblem.h:479

CCopasiTask::Type COptProblem::getSubtaskType ( ) const

Retrieve the subtask type

Returns: CCopasiTask::Type subtaskType

Definition at line 781 of file COptProblem.cpp.

References CCopasiObject::getObjectAncestor(), CCopasiObject::getObjectDataModel(), CCopasiTask::getType(), mpParmSubtaskCN, mpSubtask, CCopasiDataModel::ObjectFromName(), and CCopasiTask::unset.

Referenced by CQOptimizationWidget::loadTask(), and CQOptimizationWidget::saveTask().

 {
   std::vector< CCopasiContainer * > ListOfContainer;
   ListOfContainer.push_back(getObjectAncestor("Vector"));
   mpSubtask =
     dynamic_cast< CCopasiTask * >(const_cast< CCopasiObject *>(getObjectDataModel()->ObjectFromName(ListOfContainer, *mpParmSubtaskCN)));
 
   if (mpSubtask == NULL)
     return CCopasiTask::unset;
 
   return mpSubtask->getType();
 }

const CVector< C_FLOAT64 > & COptProblem::getVariableGradients ( ) const

Retrieve the gradients for each solution variable.

Returns: const CVector< C_FLOAT64 > & variableGradients

Definition at line 679 of file COptProblem.cpp.

References mGradient.

Referenced by CQOptimizationResult::enterProtected(), and CQFittingResult::enterProtected().

680 {return mGradient;}

COptProblem::mGradient

CVector< C_FLOAT64 > mGradient

Definition: COptProblem.h:541

size_t COptProblem::getVariableSize ( ) const

Retrieve the size of the variable vectors.

Returns: size_t VariableSize

Referenced by COptMethodEP2::optimise().

void COptProblem::incrementEvaluations ( unsigned C_INT32 increment )

Adds increment to the function evaluation counter

Parameters

unsigned C_INT32 increment

Definition at line 844 of file COptProblem.cpp.

References mCounter.

Referenced by COptMethodSS::localmin().

845 {mCounter += increment;}

COptProblem::mCounter

unsigned C_INT32 mCounter

Definition: COptProblem.h:494

bool COptProblem::initialize ( )

virtual

Do all necessary initialization so that calls to calculate will be successful. This is called once from CCopasiTask::process()

Returns: bool success

Reimplemented from CCopasiProblem.

Reimplemented in CFitProblem.

Definition at line 328 of file COptProblem.cpp.

References CModel::buildInitialRefreshSequence(), CCopasiObject::buildUpdateSequence(), CExpression::compile(), CModel::compileIfNecessary(), CCopasiMessage::ERROR, CCopasiObject::getDirectDependencies(), CEvaluationTree::getInfix(), CCopasiObject::getObjectParent(), CCopasiTask::getReport(), CReport::getStream(), CModel::getUptoDateObjects(), mConstraintCounter, MCOptimization, mCounter, mCPUTime, mFailedConstraintCounter, mFailedCounter, mInitialRefreshMethods, mOriginalVariables, CCopasiProblem::mpCallBack, mpConstraintItems, CCopasiProblem::mpModel, mpObjectiveExpression, mpOptItems, mpParmMaximize, CCopasiProblem::mpReport, mpSubtask, mRefreshConstraints, mRefreshMethods, mSolutionValue, mSolutionVariables, mUpdateMethods, mWorstValue, pTask, CVector< CType >::resize(), and CCopasiTimer::start().

Referenced by CFitProblem::initialize(), COptTask::initialize(), and COptMethodSS::initialize().

 {
   mWorstValue = (*mpParmMaximize ? - std::numeric_limits<C_FLOAT64>::infinity() : std::numeric_limits<C_FLOAT64>::infinity());
 
   if (!mpModel) return false;
 
   mpModel->compileIfNecessary(mpCallBack);
 
   bool success = true;
 
   mpReport = NULL;
   mCounter = 0;
   mFailedCounter = 0;
   mConstraintCounter = 0;
   mFailedConstraintCounter = 0;
 
   mSolutionValue = mWorstValue;
 
   std::vector< CCopasiContainer * > ContainerList;
   ContainerList.push_back(mpModel);
 
   COptTask * pTask = dynamic_cast<COptTask *>(getObjectParent());
 
   if (pTask)
     {
       ContainerList.push_back(pTask);
       mpReport = &pTask->getReport();
 
       if (!mpReport->getStream()) mpReport = NULL;
     }
 
   if (mpSubtask != NULL)
     ContainerList.push_back(mpSubtask);
 
   size_t i;
   size_t Size = mpOptItems->size();
 
   mUpdateMethods.resize(Size);
   mSolutionVariables.resize(Size);
   mOriginalVariables.resize(Size);
 
   mSolutionVariables = std::numeric_limits<C_FLOAT64>::quiet_NaN();
   mOriginalVariables = std::numeric_limits<C_FLOAT64>::quiet_NaN();
 
   std::vector< COptItem * >::iterator it = mpOptItems->begin();
   std::vector< COptItem * >::iterator end = mpOptItems->end();
 
   if (it == end)
     {
       CCopasiMessage(CCopasiMessage::ERROR, MCOptimization + 6);
       return false;
     }
 
   std::set< const CCopasiObject * > changedObjects;
 
   for (i = 0; it != end; ++it, i++)
     {
       success &= (*it)->compile(ContainerList);
 
       mUpdateMethods[i] = (*it)->getUpdateMethod();
       changedObjects.insert((*it)->getObject());
       mOriginalVariables[i] = *(*it)->COptItem::getObjectValue();
     }
 
   changedObjects.erase(NULL);
   mInitialRefreshMethods = mpModel->buildInitialRefreshSequence(changedObjects);
 
   it = mpConstraintItems->begin();
   end = mpConstraintItems->end();
 
   // We need to build a refresh sequence so the constraint values are updated
   std::set< const CCopasiObject * > Objects;
 
   for (i = 0; it != end; ++it, i++)
     {
       success &= (*it)->compile(ContainerList);
 
       Objects.insert((*it)->getDirectDependencies().begin(),
                      (*it)->getDirectDependencies().end());
     }
 
   mRefreshConstraints = CCopasiObject::buildUpdateSequence(Objects, mpModel->getUptoDateObjects());
 
   mCPUTime.start();
 
   if (mpObjectiveExpression == NULL ||
       mpObjectiveExpression->getInfix() == "" ||
       !mpObjectiveExpression->compile(ContainerList))
     {
       mRefreshMethods.clear();
       CCopasiMessage(CCopasiMessage::ERROR, MCOptimization + 5);
       return false;
     }
 
   mRefreshMethods = CCopasiObject::buildUpdateSequence(mpObjectiveExpression->getDirectDependencies(), mpModel->getUptoDateObjects());
 
   return success;
 }

void COptProblem::initializeParameter ( )

private

Allocates all group parameters and assures that they are properly initialized.

Definition at line 148 of file COptProblem.cpp.

References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, CCopasiParameter::CN, elevateChildren(), CCopasiParameter::EXPRESSION, CCopasiParameter::getValue(), mpGrpConstraints, mpGrpItems, mpParmCalculateStatistics, mpParmMaximize, mpParmObjectiveExpression, mpParmRandomizeStartValues, mpParmSubtaskCN, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pCN, and CCopasiParameter::Value::pEXPRESSION.

Referenced by COptProblem().

 {
   mpParmSubtaskCN =
     assertParameter("Subtask", CCopasiParameter::CN, CCopasiObjectName(""))->getValue().pCN;
   mpParmObjectiveExpression =
     assertParameter("ObjectiveExpression", CCopasiParameter::EXPRESSION, std::string(""))->getValue().pEXPRESSION;
   mpParmMaximize =
     assertParameter("Maximize", CCopasiParameter::BOOL, false)-> getValue().pBOOL;
   mpParmRandomizeStartValues =
     assertParameter("Randomize Start Values", CCopasiParameter::BOOL, false)-> getValue().pBOOL;
   mpParmCalculateStatistics =
     assertParameter("Calculate Statistics", CCopasiParameter::BOOL, true)-> getValue().pBOOL;
 
   mpGrpItems = assertGroup("OptimizationItemList");
   mpGrpConstraints = assertGroup("OptimizationConstraintList");
 
   elevateChildren();
 }

bool COptProblem::initializeSubtaskBeforeOutput ( )

virtual

perform at least the initializations of the subtask that must be done before the output is initialized.

Definition at line 303 of file COptProblem.cpp.

References CCopasiObject::getObjectAncestor(), CCopasiObject::getObjectDataModel(), CCopasiTask::initialize(), mpParmSubtaskCN, mpSubtask, CCopasiTask::NO_OUTPUT, and CCopasiDataModel::ObjectFromName().

Referenced by COptTask::initialize(), and COptMethodSS::initialize().

 {
   if (mpParmSubtaskCN != NULL)
     {
       std::vector< CCopasiContainer * > ListOfContainer;
       ListOfContainer.push_back(getObjectAncestor("Vector"));
       mpSubtask =
         dynamic_cast< CCopasiTask * >(getObjectDataModel()->ObjectFromName(ListOfContainer, *mpParmSubtaskCN));
 
       try
         {
           if (mpSubtask != NULL)
             return mpSubtask->initialize(CCopasiTask::NO_OUTPUT, NULL, NULL);
         }
 
       catch (...) {}
 
       return false;
     }
 
   // We have a CFitProblem for which it is OK not to have a subtask.
   mpSubtask = NULL;
   return true;
 }

void COptProblem::initObjects ( )

private

Definition at line 296 of file COptProblem.cpp.

References CCopasiContainer::addObjectReference(), CCopasiContainer::addVectorReference(), mCounter, mSolutionValue, mSolutionVariables, CCopasiObject::ValueDbl, and CCopasiObject::ValueInt.

Referenced by COptProblem().

 {
   addObjectReference("Function Evaluations", mCounter, CCopasiObject::ValueInt);
   addObjectReference("Best Value", mSolutionValue, CCopasiObject::ValueDbl);
   addVectorReference("Best Parameters", mSolutionVariables, CCopasiObject::ValueDbl);
 }

const bool & COptProblem::maximize ( ) const

Check whether we have to maximize

Returns: const bool & maximize

Definition at line 797 of file COptProblem.cpp.

References mpParmMaximize.

Referenced by CQOptimizationWidget::loadTask(), CQOptimizationWidget::saveTask(), and setMaximize().

798 {return *mpParmMaximize;}

COptProblem::mpParmMaximize

bool * mpParmMaximize

Definition: COptProblem.h:406

void COptProblem::print ( std::ostream * ostream ) const

virtual

This is the output method for any object. The default implementation provided with CCopasiObject uses the ostream operator<< of the object to print the object.To override this default behavior one needs to reimplement the virtual print function.

Parameters

std::ostream * ostream

Reimplemented from CCopasiProblem.

Reimplemented in CFitProblem.

Definition at line 855 of file COptProblem.cpp.

856 {*ostream << *this;}

void COptProblem::printResult ( std::ostream * ostream ) const

virtual

This is the output method for any result of a problem. The default implementation provided with CCopasiProblem. Does only print "Not implemented." To override this default behavior one needs to reimplement the virtual printResult function.

Parameters

std::ostream * ostream

Reimplemented from CCopasiProblem.

Reimplemented in CFitProblem.

Definition at line 858 of file COptProblem.cpp.

References C_FLOAT64, CCopasiTimer::getElapsedTime(), CCopasiTimeVariable::getMilliSeconds(), CCopasiTimeVariable::getSeconds(), CCopasiTimeVariable::LL2String(), mCounter, mCPUTime, mpOptItems, mSolutionValue, mSolutionVariables, and CVectorCore< CType >::size().

 {
   std::ostream & os = *ostream;
 
   if (mSolutionVariables.size() == 0)
     {
       return;
     }
 
   os << "    Objective Function Value:\t" << mSolutionValue << std::endl;
 
   CCopasiTimeVariable CPUTime = const_cast<COptProblem *>(this)->mCPUTime.getElapsedTime();
 
   os << "    Function Evaluations:\t" << mCounter << std::endl;
   os << "    CPU Time [s]:\t"
      << CCopasiTimeVariable::LL2String(CPUTime.getSeconds(), 1) << "."
      << CCopasiTimeVariable::LL2String(CPUTime.getMilliSeconds(true), 3) << std::endl;
   os << "    Evaluations/Second [1/s]:\t" << mCounter / (C_FLOAT64)(CPUTime.getMilliSeconds() / 1e3) << std::endl;
   os << std::endl;
 
   std::vector< COptItem * >::const_iterator itItem =
     mpOptItems->begin();
   std::vector< COptItem * >::const_iterator endItem =
     mpOptItems->end();
 
   size_t i;
 
   for (i = 0; itItem != endItem; ++itItem, i++)
     {
       os << "    " << (*itItem)->getObjectDisplayName() << ": "
          << mSolutionVariables[i] << std::endl;
     }
 }

void COptProblem::randomizeStartValues ( )

Randomize the start values if requested

Definition at line 806 of file COptProblem.cpp.

References mpOptItems, and mpParmRandomizeStartValues.

Referenced by CFitTask::process(), and COptTask::process().

 {
   if (*mpParmRandomizeStartValues)
     {
       std::vector< COptItem * >::iterator it = mpOptItems->begin();
       std::vector< COptItem * >::iterator end = mpOptItems->end();
 
       for (; it != end; ++it)
         {
           (*it)->setStartValue((*it)->getRandomValue());
         }
     }
 
   return;
 }

void COptProblem::rememberStartValues ( )

Remember the start values;

Definition at line 822 of file COptProblem.cpp.

References mpOptItems.

Referenced by CFitTask::process(), and COptTask::process().

 {
   std::vector< COptItem * >::iterator it = mpOptItems->begin();
   std::vector< COptItem * >::iterator end = mpOptItems->end();
 
   for (; it != end; ++it)
     {
       (*it)->rememberStartValue();
     }
 
   return;
 }

bool COptProblem::removeOptItem ( const size_t & index )

Remove an optimization items.

Parameters

const size_t & index

Returns: bool success

Definition at line 721 of file COptProblem.cpp.

References mpGrpItems, and CCopasiParameterGroup::removeParameter().

722 {return mpGrpItems->removeParameter(index);}

COptProblem::mpGrpItems

CCopasiParameterGroup * mpGrpItems

Definition: COptProblem.h:421

CCopasiParameterGroup::removeParameter

bool removeParameter(const std::string &name)

Definition: CCopasiParameterGroup.cpp:309

void COptProblem::reset ( )

Reset counters and objective value.

Definition at line 269 of file COptProblem.cpp.

References mCounter, mpParmMaximize, and mSolutionValue.

Referenced by COptMethodSS::localmin(), and setCallBack().

 {
   mSolutionValue = (*mpParmMaximize ? - std::numeric_limits<C_FLOAT64>::infinity() : std::numeric_limits<C_FLOAT64>::infinity());
   mCounter = 0;
 }

void COptProblem::resetEvaluations ( )

Resets the function evaluation counter

Definition at line 847 of file COptProblem.cpp.

References mCounter.

Referenced by COptMethodSS::localmin(), and COptTask::process().

848 {mCounter = 0;}

COptProblem::mCounter

unsigned C_INT32 mCounter

Definition: COptProblem.h:494

bool COptProblem::restore ( const bool & updateModel )

virtual

Do all necessary restore procedures so that the model and task are in the same state as before.

Parameters

const bool & updateModel

Returns: bool success

Reimplemented from CCopasiProblem.

Reimplemented in CFitProblem.

Definition at line 478 of file COptProblem.cpp.

References mConstraintCounter, MCOptimization, mCounter, mFailedConstraintCounter, mFailedCounter, mpSubtask, CCopasiTask::restore(), restoreModel(), and CCopasiMessage::WARNING.

Referenced by CFitProblem::restore().

 {
   bool success = true;
 
   if (mpSubtask != NULL)
     success &= mpSubtask->restore();
 
   restoreModel(updateModel);
 
   if (mFailedCounter * 20 > mCounter) // > 5% failure rate
     CCopasiMessage(CCopasiMessage::WARNING, MCOptimization + 8, mFailedCounter, mCounter);
 
   if (10 * mFailedConstraintCounter > 8 * mConstraintCounter) // > 80 % failure rate
     CCopasiMessage(CCopasiMessage::WARNING, MCOptimization + 9, mFailedConstraintCounter, mConstraintCounter);
 
   return success;
 }

void COptProblem::restoreModel ( const bool & updateModel )

Do all necessary restore procedures for the model is in the same state as before.

Parameters

const bool & updateModel

Definition at line 427 of file COptProblem.cpp.

References CVectorCore< CType >::array(), CModel::buildInitialRefreshSequence(), C_FLOAT64, mOriginalVariables, CCopasiProblem::mpModel, mpOptItems, mSolutionValue, mSolutionVariables, and mWorstValue.

Referenced by CScanTask::processCallback(), and restore().

 {
   std::vector<COptItem * >::iterator it = mpOptItems->begin();
   std::vector<COptItem * >::iterator end = mpOptItems->end();
   const C_FLOAT64 * pTmp;
   std::set< const CCopasiObject * > ChangedObjects;
 
   if (updateModel && mSolutionValue != mWorstValue)
     {
       // Set the model values and start values to the solution values
       pTmp = mSolutionVariables.array();
 
       for (; it != end; ++it, pTmp++)
         {
           if ((*it)->getObject())
             {
               (*(*it)->COptItem::getUpdateMethod())(*pTmp);
               (*it)->setStartValue(*pTmp);
 
               ChangedObjects.insert((*it)->getObject());
             }
         }
     }
   else
     {
       // Reset the model values to the original values
       pTmp = mOriginalVariables.array();
 
       for (; it != end; ++it, pTmp++)
         {
           if ((*it)->getObject())
             {
               if (!isnan(*pTmp))
                 (*(*it)->COptItem::getUpdateMethod())(*pTmp);
 
               ChangedObjects.insert((*it)->getObject());
             }
         }
     }
 
   // We need to update the dependent initial values
   std::vector< Refresh * > UpdateSequence = mpModel->buildInitialRefreshSequence(ChangedObjects);
   std::vector< Refresh * >::iterator itUpdate = UpdateSequence.begin();
   std::vector< Refresh * >::iterator endUpdate = UpdateSequence.end();
 
   for (; itUpdate != endUpdate; ++itUpdate)
     {
       (**itUpdate)();
     }
 }

void COptProblem::setCalculateStatistics ( const bool & calculate )

Set whether we have to calculate statistics

Parameters

const bool & calculate

Definition at line 835 of file COptProblem.cpp.

References calculate(), and mpParmCalculateStatistics.

Referenced by COptMethodSS::initialize(), Arguments::prepareModel(), CQFittingWidget::saveTask(), and CQOptimizationWidget::saveTask().

836 {*mpParmCalculateStatistics = calculate;}

COptProblem::mpParmCalculateStatistics

bool * mpParmCalculateStatistics

Definition: COptProblem.h:416

COptProblem::calculate

virtual bool calculate()

Definition: COptProblem.cpp:538

bool COptProblem::setCallBack ( CProcessReport * pCallBack )

virtual

Set the call back of the problem

Parameters

CProcessReport * pCallBack

Returns: bool success

Reimplemented from CCopasiProblem.

Reimplemented in CFitProblem.

Definition at line 275 of file COptProblem.cpp.

References CProcessReport::addItem(), mCounter, mhCounter, mhSolutionValue, CCopasiProblem::mpCallBack, mSolutionValue, reset(), and CCopasiProblem::setCallBack().

Referenced by COptMethodSS::initialize(), and CFitProblem::setCallBack().

 {
   CCopasiProblem::setCallBack(pCallBack);
 
   if (pCallBack)
     {
       reset();
 
       // We need to reset mSolutionValue to correctly initialize the progress item.
       mhSolutionValue =
         mpCallBack->addItem("Best Value",
                             mSolutionValue);
       // We need to reset mCounter to correctly initialize the progress item.
       mhCounter =
         mpCallBack->addItem("Function Evaluations",
                             mCounter);
     }
 
   return true;
 }

void COptProblem::setMaximize ( const bool & maximize )

Set whether we have to maximize the objective function

Parameters

const bool & maximize

Definition at line 794 of file COptProblem.cpp.

References maximize(), and mpParmMaximize.

Referenced by CQOptimizationWidget::saveTask().

795 {*mpParmMaximize = maximize;}

COptProblem::maximize

const bool & maximize() const

Definition: COptProblem.cpp:797

COptProblem::mpParmMaximize

bool * mpParmMaximize

Definition: COptProblem.h:406

bool COptProblem::setModel ( CModel * pModel )

virtual

Set the model of the problem

Parameters

CModel * pModel

Returns: bool success

Reimplemented from CCopasiProblem.

Reimplemented in CFitProblem.

Definition at line 263 of file COptProblem.cpp.

References CCopasiProblem::mpModel.

Referenced by CFitProblem::setModel().

 {
   mpModel = pModel;
   return true;
 }

bool COptProblem::setObjectiveFunction ( const std::string & infix )

Set optimization function

Parameters

const std::string & infix

Returns: bool success

Definition at line 737 of file COptProblem.cpp.

References mpObjectiveExpression, mpParmObjectiveExpression, and CExpression::setInfix().

Referenced by elevateChildren(), and CQOptimizationWidget::saveTask().

 {
   *mpParmObjectiveExpression = infix;
 
   if (mpObjectiveExpression == NULL)
     mpObjectiveExpression = new CExpression("Expression", this);
 
   return mpObjectiveExpression->setInfix(infix);
 }

void COptProblem::setRandomizeStartValues ( const bool & randomize )

Set whether we have to randomize start values

Parameters

const bool & randomize

Definition at line 800 of file COptProblem.cpp.

References mpParmRandomizeStartValues.

Referenced by COptMethodSS::initialize(), Arguments::prepareModel(), CQFittingWidget::saveTask(), and CQOptimizationWidget::saveTask().

801 {*mpParmRandomizeStartValues = randomize;}

COptProblem::mpParmRandomizeStartValues

bool * mpParmRandomizeStartValues

Definition: COptProblem.h:411

bool COptProblem::setSolution	(	const C_FLOAT64 &	value,
		const CVector< C_FLOAT64 > &	variables
	)

virtual

Set the solution.

Parameters

const	C_FLOAT64 & value
const	CVector< C_FLOAT64 > & variables

Returns: bool continue;

Reimplemented in CFitProblem.

Definition at line 682 of file COptProblem.cpp.

References mhSolutionValue, CCopasiProblem::mpCallBack, mpParmMaximize, mSolutionValue, mSolutionVariables, and CProcessReport::progressItem().

 {
   mSolutionValue = *mpParmMaximize ? -value : value;
   mSolutionVariables = variables;
 
   bool Continue = true;
 
   if (value == -std::numeric_limits< C_FLOAT64 >::infinity())
     Continue = false;
 
   if (mpCallBack)
     Continue &= mpCallBack->progressItem(mhSolutionValue);
 
   return Continue;
 }

bool COptProblem::setSubtaskType ( const CCopasiTask::Type & subtaskType )

Set subtask type

Parameters

const CCopasiTask::Type & subtaskType

Returns: success

Definition at line 752 of file COptProblem.cpp.

References CCopasiObject::getCN(), CCopasiObject::getObjectAncestor(), CCopasiObject::getObjectDataModel(), CCopasiProblem::getType(), mpParmSubtaskCN, mpSubtask, and CCopasiVector< T >::size().

Referenced by elevateChildren(), and CQOptimizationWidget::saveTask().

 {
   mpSubtask = NULL;
   *mpParmSubtaskCN = "";
 
   CCopasiVectorN< CCopasiTask > * pTasks =
     dynamic_cast< CCopasiVectorN< CCopasiTask > *>(getObjectAncestor("Vector"));
 
   CCopasiDataModel* pDataModel = getObjectDataModel();
 
   if (pTasks == NULL && pDataModel)
     pTasks = pDataModel->getTaskList();
 
   if (pTasks)
     {
       size_t i, imax = pTasks->size();
 
       for (i = 0; i < imax; i++)
         if ((*pTasks)[i]->getType() == subtaskType)
           {
             mpSubtask = (*pTasks)[i];
             *mpParmSubtaskCN = mpSubtask->getCN();
             return true;
           }
     }
 
   return false;
 }

bool COptProblem::swapOptItem	(	const size_t &	iFrom,
		const size_t &	iTo
	)

Swap two optimization items.

Parameters

const	size_t & iFrom
const	size_t & iTo

Returns: bool success

Definition at line 724 of file COptProblem.cpp.

References mpGrpItems, and CCopasiParameterGroup::swap().

726 {return mpGrpItems->swap(iFrom, iTo);}

COptProblem::mpGrpItems

CCopasiParameterGroup * mpGrpItems

Definition: COptProblem.h:421

CCopasiParameterGroup::swap

bool swap(const size_t &iFrom, const size_t &iTo)

Definition: CCopasiParameterGroup.cpp:489

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const COptProblem &	o
	)

friend

Output stream operator

Parameters

ostream	& os
const	COptProblem & A

Returns: ostream & os

Definition at line 892 of file COptProblem.cpp.

 {
   os << "Problem Description:" << std::endl;
 
   os << "Subtask: " << std::endl;
 
   if (o.mpSubtask)
     o.mpSubtask->getDescription().print(&os);
   else
     os << "No Subtask specified.";
 
   os << std::endl;
 
   if (o.mpObjectiveExpression)
     {
       os << "Objective Function:" << std::endl;
       os << "    " << o.mpObjectiveExpression->getDisplayString() << std::endl;
       os << std:: endl;
     }
 
   os << "List of Optimization Items:" << std::endl;
 
   std::vector< COptItem * >::const_iterator itItem =
     o.mpOptItems->begin();
   std::vector< COptItem * >::const_iterator endItem =
     o.mpOptItems->end();
 
   for (; itItem != endItem; ++itItem)
     os << "    " << **itItem << std::endl;
 
   itItem = o.mpConstraintItems->begin();
   endItem = o.mpConstraintItems->end();
 
   for (; itItem != endItem; ++itItem)
     os << "    " << **itItem << std::endl;
 
   return os;
 }

Member Data Documentation

C_FLOAT64 COptProblem::mCalculateValue

protected

A vector of results for calculate

Definition at line 474 of file COptProblem.h.

Referenced by CFitProblem::calculate(), calculate(), CFitProblem::calculateStatistics(), calculateStatistics(), and getCalculateValue().

unsigned C_INT32 COptProblem::mConstraintCounter

protected

Counter of constraint checks

Definition at line 504 of file COptProblem.h.

Referenced by CFitProblem::checkFunctionalConstraints(), checkFunctionalConstraints(), initialize(), and restore().

unsigned C_INT32 COptProblem::mCounter

protected

Counter of evaluations

Definition at line 494 of file COptProblem.h.

Referenced by CFitProblem::calculate(), calculate(), CFitProblem::calculateCrossValidation(), getFunctionEvaluations(), incrementEvaluations(), initialize(), initObjects(), CFitProblem::printResult(), printResult(), reset(), resetEvaluations(), restore(), and setCallBack().

CCopasiTimer COptProblem::mCPUTime

protected

A CPU Timer

Definition at line 514 of file COptProblem.h.

Referenced by CFitProblem::calculateStatistics(), calculateStatistics(), getExecutionTime(), initialize(), CFitProblem::printResult(), and printResult().

unsigned C_INT32 COptProblem::mFailedConstraintCounter

protected

Counter of failed constraint checks

Definition at line 509 of file COptProblem.h.

Referenced by CFitProblem::checkFunctionalConstraints(), checkFunctionalConstraints(), initialize(), and restore().

unsigned C_INT32 COptProblem::mFailedCounter

protected

Counter of failed evaluations

Definition at line 499 of file COptProblem.h.

Referenced by CFitProblem::calculate(), calculate(), CFitProblem::calculateCrossValidation(), initialize(), and restore().

CVector< C_FLOAT64 > COptProblem::mGradient

protected

The gradient vector for the parameters

Definition at line 541 of file COptProblem.h.

Referenced by CFitProblem::calculateStatistics(), calculateStatistics(), getVariableGradients(), and CFitProblem::printResult().

bool COptProblem::mHaveStatistics

protected

Indicates whether the statistics have been calculated for the current result

Definition at line 536 of file COptProblem.h.

Referenced by CFitProblem::calculateStatistics(), calculateStatistics(), CFitProblem::initialize(), and CFitProblem::printResult().

size_t COptProblem::mhCounter

protected

Handle of "Function Evaluations" process report item

Definition at line 524 of file COptProblem.h.

Referenced by CFitProblem::calculate(), calculate(), CFitProblem::calculateCrossValidation(), and setCallBack().

size_t COptProblem::mhSolutionValue

protected

Handle of "Best Value" process report item

Definition at line 519 of file COptProblem.h.

Referenced by setCallBack(), and setSolution().

std::vector< Refresh * > COptProblem::mInitialRefreshMethods

protected

A vector of refresh methods which need to be called update all initial values which depend on the optimization items.

Definition at line 457 of file COptProblem.h.

Referenced by calculate(), and initialize().

CVector< C_FLOAT64 > COptProblem::mOriginalVariables

protected

A vector of solution variables

Definition at line 484 of file COptProblem.h.

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), initialize(), and restoreModel().

std::vector<COptItem *>* COptProblem::mpConstraintItems

protected

A pointer to the vector of optimization constraints

Definition at line 436 of file COptProblem.h.

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), CFitProblem::checkFunctionalConstraints(), checkFunctionalConstraints(), CFitProblem::elevateChildren(), elevateChildren(), getConstraintList(), CFitProblem::initialize(), initialize(), and operator<<().

CCopasiParameterGroup* COptProblem::mpGrpConstraints

protected

A pointer to the value of the CCopasiParameter holding the OptimizationConstraints

Definition at line 426 of file COptProblem.h.

Referenced by elevateChildren(), and initializeParameter().

CCopasiParameterGroup* COptProblem::mpGrpItems

protected

A pointer to the value of the CCopasiParameterGroup holding the OptimizationItems

Definition at line 421 of file COptProblem.h.

Referenced by addOptItem(), elevateChildren(), getOptItemSize(), initializeParameter(), removeOptItem(), and swapOptItem().

CExpression* COptProblem::mpObjectiveExpression

protected

The objective function which should be minimized or maximized.

Definition at line 446 of file COptProblem.h.

Referenced by calculate(), initialize(), operator<<(), and setObjectiveFunction().

std::vector<COptItem *>* COptProblem::mpOptItems

protected

A pointer to the vector of optimization items

Definition at line 431 of file COptProblem.h.

Referenced by CFitProblem::calculate(), checkParametricConstraints(), CFitProblem::elevateChildren(), elevateChildren(), getOptItemList(), CFitProblem::initialize(), initialize(), operator<<(), CFitProblem::printResult(), printResult(), randomizeStartValues(), rememberStartValues(), and restoreModel().

bool* COptProblem::mpParmCalculateStatistics

protected

A pointer to the value of the CCopasiParameter holding Calculate Statistics

Definition at line 416 of file COptProblem.h.

Referenced by CFitProblem::calculateStatistics(), calculateStatistics(), getCalculateStatistics(), initializeParameter(), CFitProblem::printResult(), and setCalculateStatistics().

bool* COptProblem::mpParmMaximize

protected

A pointer to the value of the CCopasiParameter holding Maximize

Definition at line 406 of file COptProblem.h.

Referenced by calculate(), calculateStatistics(), initialize(), CFitProblem::initializeParameter(), initializeParameter(), maximize(), reset(), setMaximize(), and setSolution().

std::string* COptProblem::mpParmObjectiveExpression

protected

A pointer to the value of the CCopasiParameter holding the ObjectiveFunctionKey A pointer to the value of the CCopasiParameter holding the infix expression of the objective function

Definition at line 401 of file COptProblem.h.

Referenced by elevateChildren(), getObjectiveFunction(), CFitProblem::initializeParameter(), initializeParameter(), and setObjectiveFunction().

bool* COptProblem::mpParmRandomizeStartValues

protected

A pointer to the value of the CCopasiParameter holding Randomize Start Values

Definition at line 411 of file COptProblem.h.

Referenced by getRandomizeStartValues(), initializeParameter(), randomizeStartValues(), and setRandomizeStartValues().

std::string* COptProblem::mpParmSubtaskCN

protected

A pointer to the value of the CCopasiParameter holding the CN for the subtask

Definition at line 390 of file COptProblem.h.

Referenced by elevateChildren(), getSubtaskType(), CFitProblem::initializeParameter(), initializeParameter(), initializeSubtaskBeforeOutput(), and setSubtaskType().

CCopasiTask* COptProblem::mpSubtask

mutableprotected

Pointer to the subtask to be used in the optimization

Definition at line 441 of file COptProblem.h.

Referenced by calculate(), getSubtaskType(), initialize(), initializeSubtaskBeforeOutput(), operator<<(), restore(), and setSubtaskType().

std::vector< Refresh * > COptProblem::mRefreshConstraints

protected

A vector of refresh methods which need to be called retrieve the values of constraints.

Definition at line 469 of file COptProblem.h.

Referenced by checkFunctionalConstraints(), and initialize().

std::vector< Refresh * > COptProblem::mRefreshMethods

protected

A vector of refresh methods which need to be called retrieve the value of the objective function.

Definition at line 463 of file COptProblem.h.

Referenced by calculate(), and initialize().

C_FLOAT64 COptProblem::mSolutionValue

protected

A vector of solution results

Definition at line 489 of file COptProblem.h.

Referenced by CFitProblem::calculateCrossValidation(), CFitProblem::calculateStatistics(), calculateStatistics(), getSolutionValue(), initialize(), initObjects(), CFitProblem::printResult(), printResult(), reset(), restoreModel(), setCallBack(), and setSolution().

CVector< C_FLOAT64 > COptProblem::mSolutionVariables

protected

A vector of solution variables

Definition at line 479 of file COptProblem.h.

Referenced by CFitProblem::calculateCrossValidation(), CFitProblem::calculateStatistics(), calculateStatistics(), getSolutionVariables(), CFitProblem::initialize(), initialize(), initObjects(), CFitProblem::printResult(), printResult(), restoreModel(), and setSolution().

bool COptProblem::mStoreResults

protected

Indicates whether the results shall be stored. The default is false.

Definition at line 530 of file COptProblem.h.

Referenced by CFitProblem::calculate(), calculate(), CFitProblem::calculateCrossValidation(), CFitProblem::calculateStatistics(), calculateStatistics(), and CFitProblem::initialize().

std::vector< UpdateMethod * > COptProblem::mUpdateMethods

protected

A vector of update method to the values of the optimization items.

Definition at line 451 of file COptProblem.h.

Referenced by CFitProblem::calculateStatistics(), calculateStatistics(), getCalculateVariableUpdateMethods(), and initialize().

C_FLOAT64 COptProblem::mWorstValue

protected

A static value containing Infinity.

Definition at line 385 of file COptProblem.h.

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), CFitProblem::calculateStatistics(), calculateStatistics(), CFitProblem::initialize(), initialize(), and restoreModel().

const unsigned int COptProblem::ValidSubtasks

static

Initial value:

=
{
  CCopasiTask::steadyState,
  CCopasiTask::timeCourse,
  CCopasiTask::scan,
  CCopasiTask::parameterFitting,
  CCopasiTask::mca,
  CCopasiTask::lyap,
  CCopasiTask::tssAnalysis,
  CCopasiTask::sens,
  CCopasiTask::crosssection,
  CCopasiTask::lna,
  CCopasiTask::unset
}

The methods which can be selected for performing this task.

File name: COptProblem.cpp

Programmer: Yongqun He Contact email: yohe@.nosp@m.vt.e.nosp@m.du Purpose: This is the source file of the COptProblem class. It specifies the optimization problem with its own members and functions. It's used by COptAlgorithm class and COptimization class

Definition at line 57 of file COptProblem.h.

Referenced by CQOptimizationWidget::init().

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

Public Member Functions

Static Public Attributes

Protected Attributes

Private Member Functions

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation