#include <COptMethodGASR.h>

Inheritance diagram for COptMethodGASR:

Collaboration diagram for COptMethodGASR:

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

virtual bool	optimise ()

virtual	~COptMethodGASR ()

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 ()

	COptMethodGASR (const CCopasiContainer *pParent=NULL)

bool	creation (size_t first, size_t last=std::numeric_limits< size_t >::max())

bool	crossover (const CVector< C_FLOAT64 > &parent1, const CVector< C_FLOAT64 > &parent2, CVector< C_FLOAT64 > &child1, CVector< C_FLOAT64 > &child2)

bool	evaluate (const CVector< C_FLOAT64 > &individual)

size_t	fittest ()

virtual bool	initialize ()

void	initObjects ()

bool	mutate (CVector< C_FLOAT64 > &individual)

C_FLOAT64	phi (size_t indvNum)

bool	replicate ()

bool	select ()

bool	swap (size_t from, size_t to)

Private Attributes
size_t	mBestIndex

C_FLOAT64	mBestValue

CVector< bool >	mCrossOver

CVector< bool >	mCrossOverFalse

C_FLOAT64	mEvaluationValue

unsigned C_INT32	mGeneration

unsigned C_INT32	mGenerations

size_t	mhGenerations

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

C_FLOAT64	mMutationVarians

C_FLOAT64	mPf

CVector< C_FLOAT64 >	mPhi

unsigned C_INT32	mPopulationSize

CPermutation *	mpPermutation

CRandom *	mpRandom

CVector< C_FLOAT64 >	mValue

size_t	mVariableSize

CVector< size_t >	mWins

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 30 of file COptMethodGASR.h.

Constructor & Destructor Documentation

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

Copy Constructor

Parameters

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

Definition at line 57 of file COptMethodGASR.cpp.

References initObjects().

                                                                 :
   COptMethod(src, pParent),
   mGenerations(0),
   mPopulationSize(0),
   mpRandom(NULL),
   mVariableSize(0),
   mIndividual(0),
   mCrossOverFalse(0),
   mCrossOver(0),
   mValue(0),
   mpPermutation(NULL),
   mWins(0),
   mMutationVarians(0.1),
   mEvaluationValue(std::numeric_limits< C_FLOAT64 >::max()),
   mBestValue(std::numeric_limits< C_FLOAT64 >::max()),
   mBestIndex(C_INVALID_INDEX),
   mGeneration(0)
 {initObjects();}

COptMethodGASR::~COptMethodGASR ( )

virtual

Destructor

Definition at line 77 of file COptMethodGASR.cpp.

References cleanup().

78 {cleanup();}

COptMethodGASR::cleanup

virtual bool cleanup()

Definition: COptMethodGASR.cpp:455

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

private

Default Constructor

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 29 of file COptMethodGASR.cpp.

References CCopasiParameterGroup::addParameter(), C_FLOAT64, C_INT32, CCopasiParameter::DOUBLE, initObjects(), CRandom::mt19937, and CCopasiParameter::UINT.

                                                               :
   COptMethod(CCopasiTask::optimization, CCopasiMethod::GeneticAlgorithmSR, pParent),
   mGenerations(0),
   mPopulationSize(0),
   mpRandom(NULL),
   mVariableSize(0),
   mIndividual(0),
   mCrossOverFalse(0),
   mCrossOver(0),
   mValue(0),
   mpPermutation(NULL),
   mWins(0),
   mMutationVarians(0.1),
   mEvaluationValue(std::numeric_limits< C_FLOAT64 >::max()),
   mBestValue(std::numeric_limits< C_FLOAT64 >::max()),
   mBestIndex(C_INVALID_INDEX),
   mGeneration(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);
   addParameter("Pf", CCopasiParameter::DOUBLE, (C_FLOAT64) 0.475);  //*****ADDED for SR
 
   initObjects();
 }

Member Function Documentation

bool COptMethodGASR::cleanup ( )

privatevirtual

Cleanup arrays and pointers.

Returns: bool success

Reimplemented from COptMethod.

Definition at line 455 of file COptMethodGASR.cpp.

References mIndividual, mpPermutation, mpRandom, and pdelete.

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

 {
   size_t i;
 
   pdelete(mpRandom);
   pdelete(mpPermutation);
 
   for (i = 0; i < mIndividual.size(); i++)
     pdelete(mIndividual[i]);
 
   return true;
 }

bool COptMethodGASR::creation	(	size_t	first,
		size_t	last = `std::numeric_limits<size_t>::max()`
	)

private

Initialise the population

Parameters

size_t	first
size_t	last (default: population size)

Returns: bool success

Definition at line 332 of file COptMethodGASR.cpp.

References C_FLOAT64, evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomCC(), COptItem::getUpperBoundValue(), max, mEvaluationValue, min, mIndividual, mPhi, mPopulationSize, mpRandom, mValue, mVariableSize, and phi().

Referenced by optimise().

 {
   size_t Last = std::min< size_t >(last, mPopulationSize);
 
   size_t i;
   size_t j;
 
   C_FLOAT64 mn;
   C_FLOAT64 mx;
   C_FLOAT64 la;
 
   bool Continue = true;
 
   for (i = first; i < Last && Continue; i++)
     {
       for (j = 0; j < mVariableSize; j++)
         {
           // calculate lower and upper bounds
           COptItem & OptItem = *(*mpOptItem)[j];
           mn = *OptItem.getLowerBoundValue();
           mx = *OptItem.getUpperBoundValue();
 
           C_FLOAT64 & mut = (*mIndividual[i])[j];
 
           try
             {
               // determine if linear or log scale
               if ((mn < 0.0) || (mx <= 0.0))
                 mut = mn + mpRandom->getRandomCC() * (mx - mn);
               else
                 {
                   la = log10(mx) - log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min()));
 
                   if (la < 1.8)
                     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;
             }
 
           // We need to set the value here so that further checks take
           // account of the value.
           (*(*mpSetCalculateVariable)[j])(mut);
         }
 
       // calculate its fitness
       Continue = evaluate(*mIndividual[i]);
       mValue[i] = mEvaluationValue;
 
       /* Calculate the phi value of the individual for SR*/
       mPhi[i] = phi(i);
     }
 
   return Continue;
 }

bool COptMethodGASR::crossover	(	const CVector< C_FLOAT64 > &	parent1,
		const CVector< C_FLOAT64 > &	parent2,
		CVector< C_FLOAT64 > &	child1,
		CVector< C_FLOAT64 > &	child2
	)

private

Parameters

const	CVector< C_FLOAT64 > & parent1
const	CVector< C_FLOAT64 > & parent2
CVector<	C_FLOAT64 > & child1
CVector<	C_FLOAT64 > & child2

Definition at line 144 of file COptMethodGASR.cpp.

References C_INT32, CRandom::getRandomU(), mCrossOver, mCrossOverFalse, mpRandom, and mVariableSize.

Referenced by replicate().

 {
   size_t i, crp;
   size_t nCross = 0;
 
   mCrossOver = mCrossOverFalse;
 
   if (mVariableSize > 1)
     nCross = mpRandom->getRandomU((unsigned C_INT32)(mVariableSize / 2));
 
   if (nCross == 0)
     {
       // if less than 0 just copy parent to child
       child1 = parent1;
       child2 = parent2;
 
       return true;
     }
 
   // choose cross over points;
   // We do not mind if a crossover point gets drawn twice
   for (i = 0; i < nCross; i++)
     {
       crp = mpRandom->getRandomU((unsigned C_INT32)(mVariableSize - 1));
       mCrossOver[crp] = true;
     }
 
   const CVector< C_FLOAT64 > * pParent1 = & parent1;
 
   const CVector< C_FLOAT64 > * pParent2 = & parent2;
 
   const CVector< C_FLOAT64 > * pTmp;
 
   for (i = 0; i < mVariableSize; i++)
     {
       if (mCrossOver[i])
         {
           pTmp = pParent1;
           pParent1 = pParent2;
           pParent2 = pTmp;
         }
 
       child1[i] = (*pParent1)[i];
       child2[i] = (*pParent2)[i];
     }
 
   return true;
 }

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

private

Evaluate the fitness of one individual

Parameters

const CVector< C_FLOAT64 > & individual

Returns: bool continue

Definition at line 81 of file COptMethodGASR.cpp.

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

Referenced by creation(), optimise(), and replicate().

 {
   bool Continue = true;
 
   // We do not need to check whether the parametric constraints are fulfilled
   // since this method allows for parameters outside the bounds
 
   // evaluate the fitness
   Continue = mpOptProblem->calculate();
 
   // We do not need to check whether the functional constraints are fulfilled
   // since this method allows for solutions outside the bounds.
 
   mEvaluationValue = mpOptProblem->getCalculateValue();
 
   return Continue;
 }

size_t COptMethodGASR::fittest ( void )

private

Find the best individual at this generation

Returns: size_t fittest

Definition at line 316 of file COptMethodGASR.cpp.

References C_FLOAT64, C_INVALID_INDEX, max, mPhi, mPopulationSize, and mValue.

Referenced by optimise().

 {
   size_t i, BestIndex = C_INVALID_INDEX;
   C_FLOAT64 BestValue = std::numeric_limits< C_FLOAT64 >::max();
 
   for (i = 0; i < mPopulationSize; i++)
     if (mValue[i] < BestValue && !(mPhi[i] != 0))
       {
         BestIndex = i;
         BestValue = mValue[i];
       }
 
   return BestIndex;
 }

bool COptMethodGASR::initialize ( )

privatevirtual

Initialize arrays and pointer.

Returns: bool success

Reimplemented from COptMethod.

Definition at line 399 of file COptMethodGASR.cpp.

References CProcessReport::addItem(), C_FLOAT64, cleanup(), CRandom::createGenerator(), CCopasiParameter::getValue(), COptMethod::initialize(), mCrossOver, mCrossOverFalse, mGeneration, mGenerations, mhGenerations, mIndividual, mMutationVarians, CCopasiMethod::mpCallBack, mPf, mPhi, COptMethod::mpOptItem, mPopulationSize, mpPermutation, mpRandom, mValue, mVariableSize, mWins, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, CVector< CType >::resize(), and CCopasiParameterGroup::setValue().

Referenced by optimise().

 {
   cleanup();
 
   size_t i;
 
   if (!COptMethod::initialize()) return false;
 
   mGeneration = 0;
   mGenerations = * getValue("Number of Generations").pUINT;
 
   if (mpCallBack)
     mhGenerations =
       mpCallBack->addItem("Current Generation",
                           mGeneration,
                           & mGenerations);
 
   mGeneration++;
 
   mPopulationSize = * getValue("Population Size").pUINT;
   mPf = *(C_FLOAT64*) getValue("Pf").pDOUBLE;
 
   if (mPf < 0.0 || 1.0 < mPf)
     {
       mPf = 0.475;
       setValue("Pf", mPf);
     }
 
   mpRandom =
     CRandom::createGenerator(* (CRandom::Type *) getValue("Random Number Generator").pUINT,
                              * getValue("Seed").pUINT);
 
   mVariableSize = mpOptItem->size();
 
   mIndividual.resize(2 * mPopulationSize);
   mPhi.resize(2 * mPopulationSize);
 
   for (i = 0; i < 2 * mPopulationSize; i++)
     mIndividual[i] = new CVector< C_FLOAT64 >(mVariableSize);
 
   mCrossOverFalse.resize(mVariableSize);
   mCrossOverFalse = false;
   mCrossOver.resize(mVariableSize);
 
   mValue.resize(2 * mPopulationSize);
 
   mpPermutation = new CPermutation(mpRandom, mPopulationSize);
 
   mWins.resize(2 * mPopulationSize);
 
   // initialise the variance for mutations
   mMutationVarians = 0.1;
 
   return true;
 }

void COptMethodGASR::initObjects ( )

private

Initialize contained objects.

Definition at line 394 of file COptMethodGASR.cpp.

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

Referenced by COptMethodGASR().

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

bool COptMethodGASR::mutate ( CVector< C_FLOAT64 > & individual )

private

fm one individual

Parameters

CVector< C_FLOAT64 > & individual

Returns: bool success

Definition at line 122 of file COptMethodGASR.cpp.

References C_FLOAT64, CRandom::getRandomNormal(), mMutationVarians, mpRandom, and mVariableSize.

Referenced by replicate().

 {
   size_t j;
 
   // mutate the parameters
   for (j = 0; j < mVariableSize; j++)
     {
       C_FLOAT64 & mut = individual[j];
 
       // calculate the mutatated parameter
       mut *= mpRandom->getRandomNormal(1, mMutationVarians);
 
       // for SR do not force to be within bounds
 
       // We need to set the value here so that further checks take
       // account of the value.
       (*(*mpSetCalculateVariable)[j])(mut);
     }
 
   return true;
 }

bool COptMethodGASR::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. @ return success;

Reimplemented from COptMethod.

Definition at line 468 of file COptMethodGASR.cpp.

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

 {
   bool Continue = true;
 
   if (!initialize())
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhGenerations);
 
       return false;
     }
 
   // Counters to determine whether the optimization process has stalled
   // They count the number of generations without advances.
   size_t Stalled, Stalled10, Stalled30, Stalled50;
   Stalled = Stalled10 = Stalled30 = Stalled50 = 0;
 
   size_t i;
 
   // initialise the population
   // first individual is the initial guess
   for (i = 0; i < mVariableSize; i++)
     (*mIndividual[0])[i] = (*mpOptItem)[i]->getStartValue();
 
   // calculate the fitness
   size_t j;
   std::vector< UpdateMethod *>::const_iterator itMethod = mpSetCalculateVariable->begin();
 
   // set the paramter values
   for (j = 0; j < mVariableSize; j++, ++itMethod)
     (**itMethod)((*mIndividual[0])[j]);
 
   Continue = evaluate(*mIndividual[0]);
   mValue[0] = mEvaluationValue;
 
   /* Calculate the phi value of the individual for SR*/
   mPhi[0] = phi(0);
 
   // the others are random
   Continue = creation(1, mPopulationSize);
 
   // 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 FOR gener GENERATIONS
   for (mGeneration = 2;
        mGeneration <= mGenerations && Continue;
        mGeneration++, Stalled++, Stalled10++, Stalled30++, Stalled50++)
     {
       // perturb the population if we have stalled for a while
       if (Stalled > 50 && Stalled50 > 50)
         {
           Continue = creation((size_t)(mPopulationSize * 0.5),
                               mPopulationSize);
           Stalled10 = Stalled30 = Stalled50 = 0;
         }
       else if (Stalled > 30 && Stalled30 > 30)
         {
           Continue = creation((size_t)(mPopulationSize * 0.7),
                               mPopulationSize);
           Stalled10 = Stalled30 = 0;
         }
       else if (Stalled > 10 && Stalled10 > 10)
         {
           Continue = creation((size_t)(mPopulationSize * 0.9),
                               mPopulationSize);
           Stalled10 = 0;
         }
       // replicate the individuals
       else
         Continue = replicate();
 
       // select the most fit
       Continue = select();
 
       // get the index of the fittest
       mBestIndex = fittest();
 
       if (mBestIndex != C_INVALID_INDEX &&
           mValue[mBestIndex] < mBestValue)
         {
           Stalled = Stalled10 = Stalled30 = Stalled50 = 0;
           mBestValue = mValue[mBestIndex];
 
           Continue = mpOptProblem->setSolution(mBestValue, *mIndividual[mBestIndex]);
 
           // We found a new best value lets report it.
           mpParentTask->output(COutputInterface::DURING);
         }
 
       if (mpCallBack)
         Continue = mpCallBack->progressItem(mhGenerations);
     }
 
   if (mpCallBack)
     mpCallBack->finishItem(mhGenerations);
 
   cleanup();
 
   return true;
 }

C_FLOAT64 COptMethodGASR::phi ( size_t indvNum )

private

For Stochastic Ranking, evaluate the distance ofparameters to boundaries

Returns: C_FLOAT64 phiVal

Definition at line 276 of file COptMethodGASR.cpp.

References C_FLOAT64, mIndividual, COptMethod::mpOptContraints, and COptMethod::mpOptItem.

Referenced by creation(), optimise(), and replicate().

 {
   C_FLOAT64 phiVal = 0.0;
   C_FLOAT64 phiCalc;
 
   std::vector< COptItem * >::const_iterator it = mpOptItem->begin();
   std::vector< COptItem * >::const_iterator end = mpOptItem->end();
   C_FLOAT64 * pValue = mIndividual[indivNum]->array();
 
   for (; it != end; ++it, pValue++)
     {
       switch ((*it)->checkConstraint())
         {
           case - 1:
             phiCalc = *(*it)->getLowerBoundValue() - *pValue;
             phiVal += phiCalc * phiCalc;
             break;
 
           case 1:
             phiCalc = *pValue - *(*it)->getUpperBoundValue();
             phiVal += phiCalc * phiCalc;
             break;
         }
     }
 
   it = mpOptContraints->begin();
   end = mpOptContraints->end();
 
   for (; it != end; ++it)
     {
       phiCalc = (*it)->getConstraintViolation();
 
       if (phiCalc > 0.0)
         phiVal += phiCalc * phiCalc;
     }
 
   return phiVal;
 }

bool COptMethodGASR::replicate ( void )

private

Replicate the individuals with crossover

Returns: bool continue

Definition at line 196 of file COptMethodGASR.cpp.

References crossover(), evaluate(), mEvaluationValue, mIndividual, mPhi, mPopulationSize, mpPermutation, mutate(), mValue, CPermutation::next(), phi(), and CPermutation::shuffle().

Referenced by optimise().

 {
   size_t i;
   bool Continue = true;
 
   // generate a random order for the parents
   mpPermutation->shuffle();
 
   // reproduce in consecutive pairs
   for (i = 0; i < mPopulationSize / 2; i++)
     crossover(*mIndividual[mpPermutation->next()],
               *mIndividual[mpPermutation->next()],
               *mIndividual[mPopulationSize + i * 2],
               *mIndividual[mPopulationSize + i * 2 + 1]);
 
   // check if there is one left over and just copy it
   if (mPopulationSize % 2 > 0)
     *mIndividual[2 * mPopulationSize - 1] = *mIndividual[mPopulationSize - 1];
 
   // mutate the offspring
   for (i = mPopulationSize; i < 2 * mPopulationSize && Continue; i++)
     {
       mutate(*mIndividual[i]);
       Continue = evaluate(*mIndividual[i]);
       mValue[i] = mEvaluationValue;
 
       /* Calculate the phi value of the individual for SR*/
       mPhi[i] = phi(i);
     }
 
   return Continue;
 }

bool COptMethodGASR::select ( )

private

Select surviving population

Returns: bool success

Definition at line 230 of file COptMethodGASR.cpp.

References CRandom::getRandomOO(), mPf, mPhi, mPopulationSize, mpRandom, mValue, and swap().

Referenced by optimise().

 {
   size_t i, j;
   size_t TotalPopulation = 2 * mPopulationSize;
   bool wasSwapped;
   size_t sweepNum = TotalPopulation;  // This is default based on paper
 
   // Selection Method for Stochastic Ranking
   // stochastic ranking "bubble sort"
 
   for (i = 0; i < sweepNum; i++) // Here sweepNum is optimal number of sweeps from paper
     {
       wasSwapped = false;
 
       // :TODO: since we are only interested in mPopulationSize highest ranked
       // individuals the upper limit of the loop can be improved.
       for (j = 0; j < TotalPopulation - 1; j++)  // lambda is number of individuals
         {
           if ((mPhi[j] == 0 && mPhi[j + 1] == 0) ||              // within bounds
               (mpRandom->getRandomOO() < mPf))      // random chance to compare values outside bounds
             {
               // compare obj fcn using mValue alternative code
               if (mValue[j] > mValue[j + 1])
                 {
                   swap(j, j + 1);
                   wasSwapped = true;
                 }
             }
           else //mPhi values are not equal and not within boundary
             {
               if (mPhi[j] > mPhi[j + 1]) // j further outside then j+1
                 {
                   swap(j, j + 1);
                   wasSwapped = true;
                 }
             }
         }
 
       // if no swap then break
       if (wasSwapped == false) break;
     }
 
   return true;
 }

bool COptMethodGASR::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 99 of file COptMethodGASR.cpp.

References C_FLOAT64, mIndividual, mPhi, mValue, and mWins.

Referenced by select().

 {
   CVector< C_FLOAT64 > * pTmp = mIndividual[to];
   mIndividual[to] = mIndividual[from];
   mIndividual[from] = pTmp;
 
   //**** Added for swapping individual Phi values also for Stochastic Ranking
   C_FLOAT64 dTmp = mPhi[to];
   mPhi[to] = mPhi[from];
   mPhi[from] = dTmp;
 
   dTmp = mValue[to];
   mValue[to] = mValue[from];
   mValue[from] = dTmp;
 
   size_t iTmp = mWins[to];
   mWins[to] = mWins[from];
   mWins[from] = iTmp;
 
   return true;
 }

Friends And Related Function Documentation

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

friend

Member Data Documentation

size_t COptMethodGASR::mBestIndex

private

Definition at line 227 of file COptMethodGASR.h.

Referenced by optimise().

C_FLOAT64 COptMethodGASR::mBestValue

private

The best value so far.

Definition at line 226 of file COptMethodGASR.h.

Referenced by optimise().

CVector< bool > COptMethodGASR::mCrossOver

private

Vector of crossover points.

Definition at line 196 of file COptMethodGASR.h.

Referenced by crossover(), and initialize().

CVector< bool > COptMethodGASR::mCrossOverFalse

private

Vector used to initialize the crossover point to false

Definition at line 191 of file COptMethodGASR.h.

Referenced by crossover(), and initialize().

C_FLOAT64 COptMethodGASR::mEvaluationValue

private

The value of the last evaluation.

Definition at line 221 of file COptMethodGASR.h.

Referenced by creation(), evaluate(), optimise(), and replicate().

unsigned C_INT32 COptMethodGASR::mGeneration

private

Definition at line 228 of file COptMethodGASR.h.

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

unsigned C_INT32 COptMethodGASR::mGenerations

private

number of generations

Definition at line 151 of file COptMethodGASR.h.

Referenced by initialize(), and optimise().

size_t COptMethodGASR::mhGenerations

private

Handle to the process report item "Current Generation"

Definition at line 156 of file COptMethodGASR.h.

Referenced by initialize(), and optimise().

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

private

for array of individuals w/ candidate values for the parameters

Definition at line 181 of file COptMethodGASR.h.

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

C_FLOAT64 COptMethodGASR::mMutationVarians

private

variance for mutations

Definition at line 216 of file COptMethodGASR.h.

Referenced by initialize(), and mutate().

C_FLOAT64 COptMethodGASR::mPf

private

Probability value used for SR ****

Definition at line 171 of file COptMethodGASR.h.

Referenced by initialize(), and select().

CVector< C_FLOAT64 > COptMethodGASR::mPhi

private

For Stochastic Ranking. Used for array of Phi values for the individuals

Definition at line 186 of file COptMethodGASR.h.

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

unsigned C_INT32 COptMethodGASR::mPopulationSize

private

size of the population

Definition at line 161 of file COptMethodGASR.h.

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

CPermutation* COptMethodGASR::mpPermutation

private

A permutation of integers used to create the informants;

Definition at line 206 of file COptMethodGASR.h.

Referenced by cleanup(), initialize(), and replicate().

CRandom* COptMethodGASR::mpRandom

private

a pointer to the randomnumber generator.

Definition at line 166 of file COptMethodGASR.h.

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

CVector< C_FLOAT64 > COptMethodGASR::mValue

private

array of values of objective function f/ individuals

Definition at line 201 of file COptMethodGASR.h.

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

size_t COptMethodGASR::mVariableSize

private

number of parameters

Definition at line 176 of file COptMethodGASR.h.

Referenced by creation(), crossover(), initialize(), mutate(), and optimise().

CVector< size_t > COptMethodGASR::mWins

private

number of wins of each individual in the tournament

Definition at line 211 of file COptMethodGASR.h.

Referenced by initialize(), and swap().

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