#include <COptMethodEP.h>

Inheritance diagram for COptMethodEP:

Collaboration diagram for COptMethodEP:

Public Member Functions
	COptMethodEP (const COptMethodEP &src, const CCopasiContainer *pParent=NULL)

virtual bool	optimise ()

virtual	~COptMethodEP ()

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

bool	isBounded (void)

virtual bool	isValidProblem (const CCopasiProblem *pProblem)

void	setProblem (COptProblem *problem)

virtual	~COptMethod ()

Public Member Functions inherited from CCopasiMethod
	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 ()

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 ()

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 ()

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 ()

Private Member Functions
virtual bool	cleanup ()

	COptMethodEP (const CCopasiContainer *pParent=NULL)

bool	creation ()

bool	evaluate (const CVector< C_FLOAT64 > &individual)

size_t	fittest ()

virtual bool	initialize ()

void	initObjects ()

bool	mutate (size_t i)

bool	replicate ()

bool	select ()

bool	swap (size_t from, size_t to)

Private Attributes
size_t	mBestIndex

C_FLOAT64	mBestValue

unsigned C_INT32	mCurrentIteration

C_FLOAT64	mEvaluationValue

unsigned C_INT32	mGeneration

unsigned C_INT32	mGenerations

size_t	mhGenerations

std::vector< CVector < C_FLOAT64 > * >	mIndividual

CVector< size_t >	mLosses

CVector< size_t >	mPivot

unsigned C_INT32	mPopulationSize

CRandom *	mpRandom

CVector< C_FLOAT64 >	mValue

size_t	mVariableSize

std::vector< CVector < C_FLOAT64 > * >	mVariance

double	tau1

double	tau2

Friends
COptMethod *	COptMethod::createMethod (CCopasiMethod::SubType subType)

Additional Inherited Members
Public Types inherited from CCopasiMethod
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 }

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 COptMethod
static COptMethod *	createMethod (CCopasiMethod::SubType subType=CCopasiMethod::RandomSearch)

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)

Static Public Attributes inherited from CCopasiMethod
static const std::string	SubTypeName []

static const char *	XMLSubType []

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 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 COptMethod
	COptMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiMethod
	CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, 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)

Protected Attributes inherited from COptMethod
const bool	mBounds

const std::vector< COptItem * > *	mpOptContraints

const std::vector< COptItem * > *	mpOptItem

COptProblem *	mpOptProblem

COptTask *	mpParentTask

const std::vector < UpdateMethod * > *	mpSetCalculateVariable

Protected Attributes inherited from CCopasiMethod
CProcessReport *	mpCallBack

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

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

Detailed Description

Definition at line 27 of file COptMethodEP.h.

Constructor & Destructor Documentation

COptMethodEP::COptMethodEP ( const CCopasiContainer * pParent = NULL )

private

Default Constructor

Definition at line 28 of file COptMethodEP.cpp.

References CCopasiParameterGroup::addParameter(), C_INT32, initObjects(), CRandom::mt19937, and CCopasiParameter::UINT.

                                                           :
   COptMethod(CCopasiTask::optimization, CCopasiMethod::EvolutionaryProgram, pParent),
   mGenerations(0),
   mGeneration(0),
   mPopulationSize(0),
   mpRandom(NULL),
   mBestIndex(C_INVALID_INDEX),
   mLosses(0),
   mBestValue(std::numeric_limits< C_FLOAT64 >::max()),
   mEvaluationValue(std::numeric_limits< C_FLOAT64 >::max()),
   mValue(0),
   mVariableSize(0),
   mIndividual(0),
   mVariance(0)
 {
   addParameter("Number of Generations", CCopasiParameter::UINT, (unsigned C_INT32) 200);
   addParameter("Population Size", CCopasiParameter::UINT, (unsigned C_INT32) 20);
   addParameter("Random Number Generator", CCopasiParameter::UINT, (unsigned C_INT32) CRandom::mt19937);
   addParameter("Seed", CCopasiParameter::UINT, (unsigned C_INT32) 0);
 
   initObjects();
 }

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

Copy Constructor

Parameters

const COptMethodEP & src

Definition at line 51 of file COptMethodEP.cpp.

References initObjects().

                                                             : COptMethod(src, pParent),
   mGenerations(0),
   mGeneration(0),
   mPopulationSize(0),
   mpRandom(NULL),
   mBestIndex(C_INVALID_INDEX),
   mLosses(0),
   mBestValue(std::numeric_limits< C_FLOAT64 >::max()),
   mEvaluationValue(std::numeric_limits< C_FLOAT64 >::max()),
   mValue(0),
   mVariableSize(0),
   mIndividual(0),
   mVariance(0)
 {initObjects();}

COptMethodEP::~COptMethodEP ( )

virtual

Destructor

Definition at line 67 of file COptMethodEP.cpp.

References cleanup().

 {
   cleanup();
 }

Member Function Documentation

bool COptMethodEP::cleanup ( )

privatevirtual

Cleanup arrays and pointers.

Returns: bool success

Reimplemented from COptMethod.

Definition at line 145 of file COptMethodEP.cpp.

References mIndividual, mpRandom, mVariance, and pdelete.

Referenced by initialize(), optimise(), and ~COptMethodEP().

 {
   size_t i;
   // pdelete all used variables
   pdelete(mpRandom);
 
   for (i = 0; i < mIndividual.size(); i++)
     {
       pdelete(mIndividual[i]);
       pdelete(mVariance[i]);
     }
 
   return true;
 }

bool COptMethodEP::creation ( )

private

Initialise the population

Parameters

size_t	first
size_t	last (default: population size)

Returns: bool continue

Definition at line 233 of file COptMethodEP.cpp.

References C_FLOAT64, COptItem::checkConstraint(), COptItem::checkLowerBound(), COptItem::checkUpperBound(), evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomCC(), CRandom::getRandomNormal(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), max, mEvaluationValue, min, mIndividual, mPopulationSize, mpRandom, mValue, mVariableSize, and mVariance.

Referenced by optimise().

 {
   size_t i;
   size_t j;
 
   C_FLOAT64 mn;
   C_FLOAT64 mx;
   C_FLOAT64 la;
 
   bool Continue = true;
 
   // set the first individual to the initial guess
 
   for (i = 0; i < mVariableSize; i++)
     {
       C_FLOAT64 & mut = (*mIndividual[0])[i];
       COptItem & OptItem = *(*mpOptItem)[i];
 
       mut = OptItem.getStartValue();
 
       // force it to be within the bounds
       switch (OptItem.checkConstraint(mut))
         {
           case - 1:
             mut = *OptItem.getLowerBoundValue();
 
             if (!OptItem.checkLowerBound(mut)) // Inequality
               {
                 if (mut == 0.0)
                   mut = std::numeric_limits< C_FLOAT64 >::min();
                 else
                   mut += mut * std::numeric_limits< C_FLOAT64 >::epsilon();
               }
 
             break;
 
           case 1:
             mut = *OptItem.getUpperBoundValue();
 
             if (!OptItem.checkUpperBound(mut)) // Inequality
               {
                 if (mut == 0.0)
                   mut = - std::numeric_limits< C_FLOAT64 >::min();
                 else
                   mut -= mut * std::numeric_limits< C_FLOAT64 >::epsilon();
               }
 
             break;
         }
 
       // We need to set the value here so that further checks take
       // account of the value.
       (*(*mpSetCalculateVariable)[i])(mut);
 
       // Set the variance for this parameter.
       (*mVariance[0])[i] = fabs(mut) * 0.5;
     }
 
   Continue = evaluate(*mIndividual[0]);
   mValue[0] = mEvaluationValue;
   //candx[0] = evaluate(0);
 
   // and copy it to the rest
   // for(i=1; i<half; i++)
   //  candx[i] = candx[0];
   // set the other half to random values within the boundaries
   // for(i=half; i<mVariableSizeze; i++)
 
   for (i = 1; i < mPopulationSize; i++)
     {
       for (j = 0; j < mVariableSize; j++)
         {
           C_FLOAT64 & mut = (*mIndividual[i])[j];
           COptItem & OptItem = *(*mpOptItem)[j];
 
           // calculate lower and upper bounds
           mn = *OptItem.getLowerBoundValue();
           mx = *OptItem.getUpperBoundValue();
 
           try
             {
               // First determine the location of the interval
               // Secondly determine whether to distribute the parameter linearly or not
               // depending on the location and act uppon it.
               if (0.0 <= mn) // the interval [mn, mx) is in [0, inf)
                 {
                   la = log10(mx) - log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min()));
 
                   if (la < 1.8 || !(mn > 0.0)) // linear
                     mut = mn + mpRandom->getRandomCC() * (mx - mn);
                   else
                     mut = pow(10.0, log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min())) + la * mpRandom->getRandomCC());
                 }
               else if (mx > 0) // 0 is in the interval (mn, mx)
                 {
                   la = log10(mx) + log10(-mn);
 
                   if (la < 3.6) // linear
                     mut = mn + mpRandom->getRandomCC() * (mx - mn);
                   else
                     {
                       C_FLOAT64 mean = (mx + mn) * 0.5;
                       C_FLOAT64 sigma = mean * 0.01;
 
                       do
                         {
                           mut = mpRandom->getRandomNormal(mean, sigma);
                         }
                       while ((mut < mn) || (mut > mx));
                     }
                 }
               else // the interval (mn, mx] is in (-inf, 0]
                 {
                   // Switch lower and upper bound and change sign, i.e.,
                   // we can treat it similarly as location 1:
                   mx = - *OptItem.getLowerBoundValue();
                   mn = - *OptItem.getUpperBoundValue();
 
                   la = log10(mx) - log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min()));
 
                   if (la < 1.8 || !(mn > 0.0)) // linear
                     mut = - (mn + mpRandom->getRandomCC() * (mx - mn));
                   else
                     mut = - pow(10.0, log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min())) + la * mpRandom->getRandomCC());
                 }
             }
 
           catch (...)
             {
               mut = (mx + mn) * 0.5;
             }
 
           // force it to be within the bounds
           switch (OptItem.checkConstraint(mut))
             {
               case - 1:
                 mut = *OptItem.getLowerBoundValue();
 
                 if (!OptItem.checkLowerBound(mut)) // Inequality
                   {
                     if (mut == 0.0)
                       mut = std::numeric_limits< C_FLOAT64 >::min();
                     else
                       mut += mut * std::numeric_limits< C_FLOAT64 >::epsilon();
                   }
 
                 break;
 
               case 1:
                 mut = *OptItem.getUpperBoundValue();
 
                 if (!OptItem.checkUpperBound(mut)) // Inequality
                   {
                     if (mut == 0.0)
                       mut = - std::numeric_limits< C_FLOAT64 >::min();
                     else
                       mut -= mut * std::numeric_limits< C_FLOAT64 >::epsilon();
                   }
 
                 break;
             }
 
           // We need to set the value here so that further checks take
           // account of the value.
           (*(*mpSetCalculateVariable)[j])(mut);
 
           // Set the variance for this parameter.
           (*mVariance[i])[j] = fabs(mut) * 0.5;
         }
 
       // calculate its fitness
       Continue = evaluate(*mIndividual[i]);
       mValue[i] = mEvaluationValue;
     }
 
   return Continue;
 }

bool COptMethodEP::evaluate ( const CVector< C_FLOAT64 > & individual )

private

Evaluate the objective function for the current parameters

Returns: const C_FLOAT64 & objectiveValue

Definition at line 209 of file COptMethodEP.cpp.

References COptProblem::calculate(), COptProblem::checkFunctionalConstraints(), COptProblem::getCalculateValue(), mEvaluationValue, and COptMethod::mpOptProblem.

Referenced by creation(), and mutate().

 {
   bool Continue = true;
 
   // We do not need to check whether the parametric constraints are fulfilled
   // since the parameters are created within the bounds.
 
   // evaluate the fitness
   Continue = mpOptProblem->calculate();
 
   // check whether the functional constraints are fulfilled
   if (!mpOptProblem->checkFunctionalConstraints())
     mEvaluationValue = std::numeric_limits<C_FLOAT64>::infinity();
   else
     mEvaluationValue = mpOptProblem->getCalculateValue();
 
   return Continue;
 }

size_t COptMethodEP::fittest ( void )

private

Find the best individual at this generation

Returns: size_t fittest

Definition at line 471 of file COptMethodEP.cpp.

References C_FLOAT64, mLosses, mPopulationSize, and mValue.

Referenced by optimise().

 {
   size_t i, BestIndex = 0;
   C_FLOAT64 BestValue = mValue[0];
 
   for (i = 1; i < mPopulationSize && !mLosses[i]; i++)
     if (mValue[i] < BestValue)
       {
         BestIndex = i;
         BestValue = mValue[i];
       }
 
   return BestIndex;
 }

bool COptMethodEP::initialize ( )

privatevirtual

Initialize arrays and pointer.

Returns: bool success

Reimplemented from COptMethod.

Definition at line 160 of file COptMethodEP.cpp.

References CProcessReport::addItem(), cleanup(), CRandom::createGenerator(), CCopasiParameter::getValue(), COptMethod::initialize(), mGeneration, mGenerations, mhGenerations, mIndividual, mLosses, CCopasiMethod::mpCallBack, COptMethod::mpOptItem, mPopulationSize, mpRandom, mValue, mVariableSize, mVariance, CCopasiParameter::Value::pUINT, CVector< CType >::resize(), tau1, and tau2.

Referenced by optimise().

 {
   cleanup();
 
   size_t i;
 
   if (!COptMethod::initialize()) return false;
 
   mGenerations = * getValue("Number of Generations").pUINT;
   mGeneration = 0;
 
   if (mpCallBack)
     mhGenerations =
       mpCallBack->addItem("Current Generation",
                           mGeneration,
                           & mGenerations);
 
   mGeneration++;
 
   mPopulationSize = * getValue("Population Size").pUINT;
   mpRandom =
     CRandom::createGenerator(* (CRandom::Type *) getValue("Random Number Generator").pUINT,
                              * getValue("Seed").pUINT);
 
   mVariableSize = mpOptItem->size();
 
   mIndividual.resize(2 * mPopulationSize);
   mVariance.resize(2 * mPopulationSize);
 
   for (i = 0; i < 2 * mPopulationSize; i++)
     {
       mIndividual[i] = new CVector< C_FLOAT64 >(mVariableSize);
       mVariance[i] = new CVector< C_FLOAT64 >(mVariableSize);
     }
 
   mValue.resize(2 * mPopulationSize);
   mValue = std::numeric_limits< C_FLOAT64 >::infinity();
 
   mLosses.resize(2 * mPopulationSize);
   mLosses = 0;
 
   // Initialize the parameters to update the variances
   tau1 = 1.0 / sqrt(2 * double(mVariableSize));
   tau2 = 1.0 / sqrt(2 * sqrt(double(mVariableSize)));
 
   return true;
 }

void COptMethodEP::initObjects ( )

private

Initialize contained objects.

Definition at line 228 of file COptMethodEP.cpp.

References CCopasiContainer::addObjectReference(), mGeneration, and CCopasiObject::ValueInt.

Referenced by COptMethodEP().

 {
   addObjectReference("Current Generation", mGeneration, CCopasiObject::ValueInt);
 }

bool COptMethodEP::mutate ( size_t i )

private

Mutate one individual

Parameters

CVector< C_FLOAT64 > & individual

Returns: bool success

Definition at line 511 of file COptMethodEP.cpp.

References C_FLOAT64, COptItem::checkConstraint(), evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomNormal01(), COptItem::getUpperBoundValue(), max, mEvaluationValue, mIndividual, mpRandom, mValue, mVariableSize, mVariance, tau1, and tau2.

Referenced by replicate().

 {
   size_t j;
   C_FLOAT64 v1;
 
   CVector<C_FLOAT64> & Individual = *mIndividual[i];
   CVector<C_FLOAT64> & Variance = *mVariance[i];
 
   v1 = mpRandom->getRandomNormal01();
 
   // update the variances
   for (j = 0; j < mVariableSize; j++)
     {
       C_FLOAT64 & mut = Individual[j];
       COptItem & OptItem = *(*mpOptItem)[j];
 
       try
         {
           // update the parameter for the variances
           Variance[j] =
             std::max(Variance[j] * exp(tau1 * v1 + tau2 * mpRandom->getRandomNormal01()), 1e-8);
 
           // calculate the mutated parameter
           mut += Variance[j] * mpRandom->getRandomNormal01();
         }
 
       catch (...)
         {
           mut = (*OptItem.getUpperBoundValue() + *OptItem.getLowerBoundValue()) * 0.5;
         }
 
       // force it to be within the bounds
       switch (OptItem.checkConstraint(mut))
         {
           case - 1:
             mut = *OptItem.getLowerBoundValue();
             break;
 
           case 1:
             mut = *OptItem.getUpperBoundValue();
             break;
         }
 
       // We need to set the value here so that further checks take
       // account of the value.
       (*(*mpSetCalculateVariable)[j])(mut);
     }
 
   // calculate its fitness
   bool Continue = evaluate(Individual);
   mValue[i] = mEvaluationValue;
 
   return Continue;
 }

bool COptMethodEP::optimise ( void )

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.

Reimplemented from COptMethod.

Definition at line 72 of file COptMethodEP.cpp.

References C_INVALID_INDEX, cleanup(), creation(), COutputInterface::DURING, CProcessReport::finishItem(), fittest(), initialize(), mBestIndex, mBestValue, mGeneration, mGenerations, mhGenerations, mIndividual, CCopasiMethod::mpCallBack, COptMethod::mpOptProblem, COptMethod::mpParentTask, mValue, CCopasiTask::output(), CProcessReport::progressItem(), replicate(), select(), and COptProblem::setSolution().

 {
   if (!initialize())
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhGenerations);
 
       return false;
     }
 
   bool Continue = true;
 
   // Initialize the population
   Continue = creation();
 
   // get the index of the fittest
   mBestIndex = fittest();
 
   if (mBestIndex != C_INVALID_INDEX)
     {
       // and store that value
       mBestValue = mValue[mBestIndex];
       Continue = mpOptProblem->setSolution(mBestValue, *mIndividual[mBestIndex]);
 
       // We found a new best value lets report it.
       mpParentTask->output(COutputInterface::DURING);
     }
 
   if (!Continue)
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhGenerations);
 
       cleanup();
       return true;
     }
 
   // iterate over Generations
   for (mGeneration = 2; mGeneration <= mGenerations && Continue; mGeneration++)
     {
       // replicate the individuals
       Continue = replicate();
 
       // select the most fit
       Continue = select();
 
       // get the index of the fittest
       mBestIndex = fittest();
 
       if (mBestIndex != C_INVALID_INDEX &&
           mValue[mBestIndex] < mBestValue)
         {
           mBestValue = mValue[mBestIndex];
 
           Continue = mpOptProblem->setSolution(mBestValue, *mIndividual[mBestIndex]);
 
           // We found a new best value lets report it.
           //if (mpReport) mpReport->printBody();
           mpParentTask->output(COutputInterface::DURING);
         }
 
       if (mpCallBack)
         Continue = mpCallBack->progressItem(mhGenerations);
     }
 
   if (mpCallBack)
     mpCallBack->finishItem(mhGenerations);
 
   cleanup();
 
   return true;
 }

bool COptMethodEP::replicate ( void )

private

Replicate the individuals with crossover

Returns: bool continue

Definition at line 486 of file COptMethodEP.cpp.

References mIndividual, mPopulationSize, mutate(), mValue, mVariableSize, and mVariance.

Referenced by optimise().

 {
   size_t i;
   size_t j;
   bool Continue = true;
 
   // iterate over parents
   for (i = 0; i < mPopulationSize && Continue; i++)
     {
       // replicate them
       for (j = 0; j < mVariableSize; j++)
         {
           (*mIndividual[mPopulationSize + i])[j] = (*mIndividual[i])[j];
           (*mVariance[mPopulationSize + i])[j] = (*mVariance[i])[j];
         }
 
       mValue[mPopulationSize + i] = mValue[i];
 
       // possibly mutate the offspring
       Continue = mutate(mPopulationSize + i);
     }
 
   return Continue;
 }

bool COptMethodEP::select ( )

private

Select surviving population

Returns: bool success

Definition at line 411 of file COptMethodEP.cpp.

References applyPartialPivot(), CVectorCore< CType >::array(), C_INT32, CRandom::getRandomU(), mLosses, mPivot, mPopulationSize, mpRandom, mValue, partialSortWithPivot(), and swap().

Referenced by optimise().

 {
   size_t i, j, nopp, opp;
   size_t TotalPopulation = 2 * mPopulationSize;
 
   // tournament competition
   mLosses = 0; // Set all losses to 0.
 
   // compete with ~ 20% of the TotalPopulation
   nopp = std::max<size_t>(1, mPopulationSize / 5);
 
   // parents and offspring are all in competition
   for (i = 0; i < TotalPopulation; i++)
     for (j = 0; j < nopp; j++)
       {
         // get random opponent
         do
           {
             opp = mpRandom->getRandomU((unsigned C_INT32)(TotalPopulation - 1));
           }
         while (i == opp);
 
         if (mValue[i] < mValue[opp])
           mLosses[opp]++;
         else
           mLosses[i]++;
       }
 
   partialSortWithPivot(mLosses.array(),
                        mLosses.array() + mPopulationSize,
                        mLosses.array() + TotalPopulation,
                        mPivot);
 
   FSwapClass<COptMethodEP, size_t, bool> Swap(this, &COptMethodEP::swap);
   applyPartialPivot(mPivot, mPopulationSize, Swap);
 
   return true;
 }

bool COptMethodEP::swap	(	size_t	from,
		size_t	to
	)

private

Swap individuals from and to

Parameters

size_t	from
size_t	to

Returns: bool success

Definition at line 450 of file COptMethodEP.cpp.

References C_FLOAT64, mIndividual, mLosses, mValue, and mVariance.

Referenced by select().

 {
   CVector< C_FLOAT64 > * pTmp = mIndividual[to];
   mIndividual[to] = mIndividual[from];
   mIndividual[from] = pTmp;
 
   pTmp = mVariance[to];
   mVariance[to] = mVariance[from];
   mVariance[from] = pTmp;
 
   C_FLOAT64 dTmp = mValue[to];
   mValue[to] = mValue[from];
   mValue[from] = dTmp;
 
   size_t iTmp = mLosses[to];
   mLosses[to] = mLosses[from];
   mLosses[from] = iTmp;
 
   return true;
 }

Friends And Related Function Documentation

COptMethod* COptMethod::createMethod ( CCopasiMethod::SubType subType )

friend

Member Data Documentation

size_t COptMethodEP::mBestIndex

private

Definition at line 151 of file COptMethodEP.h.

Referenced by optimise().

C_FLOAT64 COptMethodEP::mBestValue

private

The best value found so far.

Definition at line 165 of file COptMethodEP.h.

Referenced by optimise().

unsigned C_INT32 COptMethodEP::mCurrentIteration

private

The current iteration

Definition at line 195 of file COptMethodEP.h.

C_FLOAT64 COptMethodEP::mEvaluationValue

private

The value of the last evaluation.

Definition at line 170 of file COptMethodEP.h.

Referenced by creation(), evaluate(), and mutate().

unsigned C_INT32 COptMethodEP::mGeneration

private

size of the population

Definition at line 134 of file COptMethodEP.h.

Referenced by initialize(), initObjects(), and optimise().

unsigned C_INT32 COptMethodEP::mGenerations

private

number of generations

Definition at line 129 of file COptMethodEP.h.

Referenced by initialize(), and optimise().

size_t COptMethodEP::mhGenerations

private

Handle to the process report item "Current Generation"

Definition at line 139 of file COptMethodEP.h.

Referenced by initialize(), and optimise().

std::vector< CVector < C_FLOAT64 > * > COptMethodEP::mIndividual

private

for array of individuals w/ candidate values for the parameters

Definition at line 185 of file COptMethodEP.h.

Referenced by cleanup(), creation(), initialize(), mutate(), optimise(), replicate(), and swap().

CVector< size_t > COptMethodEP::mLosses

private

number of wins of each individual in the tournament

Definition at line 160 of file COptMethodEP.h.

Referenced by fittest(), initialize(), select(), and swap().

CVector<size_t> COptMethodEP::mPivot

private

Pivot vector used for sorting

Definition at line 200 of file COptMethodEP.h.

Referenced by select().

unsigned C_INT32 COptMethodEP::mPopulationSize

private

size of the population

Definition at line 144 of file COptMethodEP.h.

Referenced by creation(), fittest(), initialize(), replicate(), and select().

CRandom* COptMethodEP::mpRandom

private

a pointer to the randomnumber generator.

Definition at line 149 of file COptMethodEP.h.

Referenced by cleanup(), creation(), initialize(), mutate(), and select().

CVector<C_FLOAT64> COptMethodEP::mValue

private

array of values of objective function f/ individuals

Definition at line 175 of file COptMethodEP.h.

Referenced by creation(), fittest(), initialize(), mutate(), optimise(), replicate(), select(), and swap().

size_t COptMethodEP::mVariableSize

private

number of parameters

Definition at line 180 of file COptMethodEP.h.

Referenced by creation(), initialize(), mutate(), and replicate().

std::vector< CVector < C_FLOAT64 > * > COptMethodEP::mVariance

private

for array of variances w/ variance values for the parameters

Definition at line 190 of file COptMethodEP.h.

Referenced by cleanup(), creation(), initialize(), mutate(), replicate(), and swap().

double COptMethodEP::tau1

private

Definition at line 153 of file COptMethodEP.h.

Referenced by initialize(), and mutate().

double COptMethodEP::tau2

private

Definition at line 155 of file COptMethodEP.h.

Referenced by initialize(), and mutate().

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

Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation