#include <COptMethodSRES.h>

Inheritance diagram for COptMethodSRES:

Collaboration diagram for COptMethodSRES:

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

virtual bool	optimise ()

virtual	~COptMethodSRES ()

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 ()

	COptMethodSRES (const CCopasiContainer *pParent=NULL)

bool	creation (size_t first)

bool	evaluate (const CVector< C_FLOAT64 > &individual)

size_t	fittest ()

virtual bool	initialize ()

void	initObjects ()

bool	mutate ()

C_FLOAT64	phi (size_t indvNum)

bool	replicate ()

void	select ()

bool	swap (size_t from, size_t to)

Private Attributes
C_FLOAT64	mBestValue

C_FLOAT64	mEvaluationValue

unsigned C_INT32	mGeneration

unsigned C_INT32	mGenerations

size_t	mhGenerations

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

CVector< C_FLOAT64 >	mMaxVariance

C_FLOAT64	mPf

CVector< C_FLOAT64 >	mPhi

unsigned C_INT32	mPopulationSize

CRandom *	mpRandom

double	mTau

double	mTauPrime

CVector< C_FLOAT64 >	mValue

size_t	mVariableSize

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

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

COptMethodSRES class

Definition at line 27 of file COptMethodSRES.h.

Constructor & Destructor Documentation

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

Copy Constructor

Parameters

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

Definition at line 57 of file COptMethodSRES.cpp.

References initObjects().

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

COptMethodSRES::~COptMethodSRES ( )

virtual

Destructor

Definition at line 71 of file COptMethodSRES.cpp.

References cleanup().

72 {cleanup();}

COptMethodSRES::cleanup

virtual bool cleanup()

Definition: COptMethodSRES.cpp:586

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

private

Default Constructor

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 35 of file COptMethodSRES.cpp.

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

                                                               :
   COptMethod(CCopasiTask::optimization, CCopasiMethod::SRES, pParent),
   mGenerations(0),
   mPopulationSize(0),
   mpRandom(NULL),
   mVariableSize(0),
   mIndividual(0),
   mEvaluationValue(std::numeric_limits< C_FLOAT64 >::max()),
   mValue(0),
   mBestValue(std::numeric_limits< C_FLOAT64 >::max()),
   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 COptMethodSRES::cleanup ( )

privatevirtual

Cleanup arrays and pointers.

Returns: bool success

Reimplemented from COptMethod.

Definition at line 586 of file COptMethodSRES.cpp.

References mIndividual, mpRandom, mVariance, and pdelete.

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

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

bool COptMethodSRES::creation ( size_t first )

private

Initialise the population

Parameters

size_t first

Returns: bool continue

Definition at line 293 of file COptMethodSRES.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, COptItem::checkConstraint(), COptItem::checkLowerBound(), COptItem::checkUpperBound(), evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomCC(), CRandom::getRandomNormal(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), max, mEvaluationValue, min, mIndividual, mMaxVariance, mPhi, mPopulationSize, mpRandom, mValue, mVariableSize, mVariance, and phi().

Referenced by optimise().

 {
   size_t i;
   size_t j;
 
   C_FLOAT64 mn;
   C_FLOAT64 mx;
   C_FLOAT64 la;
 
   bool Continue = true;
 
   std::vector< CVector < C_FLOAT64 > * >::iterator it =
     mIndividual.begin() + first;
   std::vector< CVector < C_FLOAT64 > * >::iterator end =
     mIndividual.begin() + mPopulationSize;
   std::vector< CVector < C_FLOAT64 > * >::iterator itVariance =
     mVariance.begin() + first;
 
   C_FLOAT64 * pVariable, * pVariableEnd, * pVariance, * pMaxVariance;
   C_FLOAT64 * pPhi = mPhi.array() + first;
   C_FLOAT64 * pValue = mValue.array() + first;
 
   // set the first individual to the initial guess
   if (it == mIndividual.begin())
     {
       pVariable = (*it)->array();
       pVariableEnd = pVariable + mVariableSize;
       pVariance = (*itVariance)->array();
       pMaxVariance = mMaxVariance.array();
 
       for (j = 0; pVariable != pVariableEnd; ++pVariable, ++pVariance, ++pMaxVariance, ++j)
         {
           C_FLOAT64 & mut = *pVariable;
           COptItem & OptItem = *(*mpOptItem)[j];
 
           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)[j])(mut);
 
           // Set the variance for this parameter.
           *pVariance = std::min(*OptItem.getUpperBoundValue() - mut, mut - *OptItem.getLowerBoundValue()) / sqrt(double(mVariableSize));
         }
 
       Continue = evaluate(**it);
       *pValue++ = mEvaluationValue;
       *pPhi++ = phi(0);
 
       ++it;
       ++itVariance;
       ++first;
     }
 
   for (i = first; it < end ; ++it, ++itVariance, ++i)
     {
       pVariable = (*it)->array();
       pVariableEnd = pVariable + mVariableSize;
       pVariance = (*itVariance)->array();
       pMaxVariance = mMaxVariance.array();
 
       for (j = 0; pVariable != pVariableEnd; ++pVariable, ++pVariance, ++pMaxVariance, ++j)
         {
           C_FLOAT64 & mut = *pVariable;
           COptItem & OptItem = *(*mpOptItem)[j];
 
           // calculate lower and upper bounds
           mn = *OptItem.getLowerBoundValue();
           mx = *OptItem.getUpperBoundValue();
 
           try
             {
               // First determine the location of the intervall
               // 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.
           *pVariance = std::min(*OptItem.getUpperBoundValue() - mut, mut - *OptItem.getLowerBoundValue()) / sqrt(double(mVariableSize));
         }
 
       // calculate its fitness
       Continue = evaluate(**it);
       *pValue++ = mEvaluationValue;
       *pPhi++ = phi(i);
     }
 
   return Continue;
 }

bool COptMethodSRES::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 75 of file COptMethodSRES.cpp.

References COptProblem::calculate(), 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 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 COptMethodSRES::fittest ( void )

private

Find the best individual at this generation

Returns: size_t fittest

Definition at line 277 of file COptMethodSRES.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 COptMethodSRES::initialize ( )

privatevirtual

Initialize arrays and pointer.

Returns: bool success

Reimplemented from COptMethod.

Definition at line 498 of file COptMethodSRES.cpp.

References CProcessReport::addItem(), C_FLOAT64, childrate, cleanup(), CRandom::createGenerator(), COptItem::getLowerBoundValue(), COptItem::getUpperBoundValue(), CCopasiParameter::getValue(), COptMethod::initialize(), mBestValue, mGeneration, mGenerations, mhGenerations, mIndividual, mMaxVariance, CCopasiMethod::mpCallBack, mPf, mPhi, COptMethod::mpOptItem, mPopulationSize, mpRandom, mTau, mTauPrime, mValue, mVariableSize, mVariance, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, CVector< CType >::resize(), and CCopasiParameterGroup::setValue().

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;
 
   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(childrate * mPopulationSize);
 
   for (i = 0; i < childrate * mPopulationSize; i++)
     mIndividual[i] = new CVector< C_FLOAT64 >(mVariableSize);
 
   mVariance.resize(childrate * mPopulationSize);
 
   for (i = 0; i < childrate * mPopulationSize; i++)
     mVariance[i] = new CVector< C_FLOAT64 >(mVariableSize);
 
   mMaxVariance.resize(mVariableSize);
 
   for (i = 0; i < mVariableSize; i++)
     {
       COptItem & OptItem = *(*mpOptItem)[i];
 
       try
         {
           mMaxVariance[i] =
             (*OptItem.getUpperBoundValue() - *OptItem.getLowerBoundValue()) / sqrt(double(mVariableSize));
         }
       catch (...)
         {
           mMaxVariance[i] = 1.0e3;
         }
     }
 
   mValue.resize(childrate * mPopulationSize);
   mValue = std::numeric_limits<C_FLOAT64>::infinity();
   mBestValue = std::numeric_limits<C_FLOAT64>::infinity();
 
   mPhi.resize(childrate * mPopulationSize);
 
   try
     {
       /*
       C_FLOAT64 alpha = 0.2;
       C_FLOAT64 chi = 1 / (2 * sqrt(double(mVariableSize))) + 1 / (2 * double(mVariableSize));
       C_FLOAT64 varphi = sqrt(2/chi * log(1/alpha) *exp(chi/2 -(1-alpha)));
       */
 
       C_FLOAT64 varphi = 1;
       mTau = varphi / sqrt(2 * sqrt(double(mVariableSize)));
       mTauPrime = varphi / sqrt(2 * double(mVariableSize));
     }
   catch (...)
     {
       mTau = mTauPrime = 1;
     }
 
   return true;
 }

void COptMethodSRES::initObjects ( )

private

Initialize contained objects.

Definition at line 493 of file COptMethodSRES.cpp.

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

Referenced by COptMethodSRES().

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

bool COptMethodSRES::mutate ( )

private

Mutate the new generation

Definition at line 161 of file COptMethodSRES.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, C_INVALID_INDEX, COptItem::checkConstraint(), evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomNormal01(), COptItem::getUpperBoundValue(), mEvaluationValue, min, mIndividual, mMaxVariance, mPhi, mPopulationSize, mpRandom, mTau, mTauPrime, mValue, mVariableSize, mVariance, and phi().

Referenced by replicate().

 {
   std::vector< CVector < C_FLOAT64 > * >::iterator it = mIndividual.begin() + mPopulationSize;
   std::vector< CVector < C_FLOAT64 > * >::iterator end = mIndividual.end();
   std::vector< CVector < C_FLOAT64 > * >::iterator itVariance = mVariance.begin() + mPopulationSize;
 
   C_FLOAT64 * pVariable, * pVariableEnd, * pVariance, * pMaxVariance;
   C_FLOAT64 * pPhi = mPhi.array() + mPopulationSize;
   C_FLOAT64 * pValue = mValue.array() + mPopulationSize;
 
   bool Continue = true;
   size_t i, j;
   C_FLOAT64 v1;
 
   // Mutate each new individual
   for (i = mPopulationSize; it != end && Continue; ++it, ++itVariance, ++i)
     {
       pVariable = (*it)->array();
       pVariableEnd = pVariable + mVariableSize;
       pVariance = (*itVariance)->array();
       pMaxVariance = mMaxVariance.array();
 
       v1 = mpRandom->getRandomNormal01();
 
       for (j = 0; pVariable != pVariableEnd; ++pVariable, ++pVariance, ++pMaxVariance, ++j)
         {
           C_FLOAT64 & mut = *pVariable;
           C_FLOAT64 Store = mut;
 
           COptItem & OptItem = *(*mpOptItem)[j];
 
           size_t l = C_INVALID_INDEX;
 
           try
             {
               // update the parameter for the variances
               *pVariance =
                 std::min(*pVariance * exp(mTauPrime * v1 + mTau * mpRandom->getRandomNormal01()), *pMaxVariance);
 
               for (l = 0; l < 10; l++)
                 {
                   // calculate the mutated parameter
                   mut = Store + *pVariance * mpRandom->getRandomNormal01();
 
                   if (OptItem.checkConstraint(mut) == 0)
                     break;
                 }
             }
 
           catch (...)
             {
               mut = (*OptItem.getUpperBoundValue() + *OptItem.getLowerBoundValue()) * 0.5;
             }
 
           if (l == 10)
             mut = Store;
 
           // We need to set the value here so that further checks take
           // account of the value.
           (*(*mpSetCalculateVariable)[j])(mut);
         }
 
       // calculate its fitness
       Continue = evaluate(**it);
       *pValue++ = mEvaluationValue;
       *pPhi++ = phi(i);
     }
 
   return Continue;
 }

bool COptMethodSRES::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 641 of file COptMethodSRES.cpp.

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

 {
   bool Continue = true;
   size_t BestIndex = C_INVALID_INDEX;
 
 #ifdef RANDOMIZE
   // Counters to determine whether the optimization process has stalled
   // They count the number of generations without advances.
   size_t Stalled10, Stalled20, Stalled40, Stalled80;
   Stalled10 = Stalled20 = Stalled40 = Stalled80 = 0;
 #endif // RANDOMIZE
 
   if (!initialize())
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhGenerations);
 
       return false;
     }
 
   // initialise the population
   Continue = creation(0);
 
   // get the index of the fittest
   BestIndex = fittest();
 
   if (BestIndex != C_INVALID_INDEX)
     {
       // and store that value
       mBestValue = mValue[BestIndex];
       Continue = mpOptProblem->setSolution(mBestValue, *mIndividual[BestIndex]);
 
       // 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
 #ifdef RANDOMIZE
 
   for (mGeneration = 2;
        mGeneration <= mGenerations && Continue;
        mGeneration++, Stalled10++, Stalled20++, Stalled40++, Stalled80++)
     {
       // perturb the population if we have stalled for a while
       if (Stalled80 > 80)
         {
           Continue = creation((size_t)(mPopulationSize * 0.2));
           Stalled10 = Stalled20 = Stalled40 = Stalled80 = 0;
         }
       else if (Stalled40 > 40)
         {
           Continue = creation((size_t)(mPopulationSize * 0.6));
           Stalled10 = Stalled20 = Stalled40 = 0;
         }
       else if (Stalled20 > 20)
         {
           Continue = creation((size_t)(mPopulationSize * 0.8));
           Stalled10 = Stalled20 = 0;
         }
       else if (Stalled10 > 10)
         {
           Continue = creation((size_t)(mPopulationSize * 0.9));
           Stalled10 = 0;
         }
 
 #else
 
   for (mGeneration = 2;
        mGeneration <= mGenerations && Continue;
        mGeneration++)
     {
 #endif // RANDOMIZE
       Continue = replicate();
 
       // select the most fit
       select();
 
       // get the index of the fittest
       BestIndex = fittest();
 
       if (BestIndex != C_INVALID_INDEX &&
           mValue[BestIndex] < mBestValue)
         {
 #ifdef RANDOMIZE
           Stalled10 = Stalled20 = Stalled40 = Stalled80 = 0;
 #endif // RANDOMIZE
           mBestValue = mValue[BestIndex];
 
           Continue = mpOptProblem->setSolution(mBestValue, *mIndividual[BestIndex]);
 
           // We found a new best value lets report it.
           mpParentTask->output(COutputInterface::DURING);
         }
 
       if (mpCallBack)
         Continue = mpCallBack->progressItem(mhGenerations);
     }
 
   if (mpCallBack)
     mpCallBack->finishItem(mhGenerations);
 
   return true;
 }

C_FLOAT64 COptMethodSRES::phi ( size_t indvNum )

private

For Stochastic Ranking, evaluate the distance ofparameters to boundaries

Returns: C_FLOAT64 phiVal

Definition at line 602 of file COptMethodSRES.cpp.

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

Referenced by creation(), and mutate().

 {
   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 COptMethodSRES::replicate ( void )

private

Replicate the individuals with crossover

Returns: bool continue

Definition at line 114 of file COptMethodSRES.cpp.

References C_FLOAT64, childrate, CRandom::getRandomU(), mIndividual, mPopulationSize, mpRandom, mutate(), mVariableSize, and mVariance.

Referenced by optimise().

 {
   bool Continue = true;
 
   size_t Parent;
   size_t i, j;
 
   std::vector< CVector < C_FLOAT64 > * >::iterator itSrc = mIndividual.begin();
   std::vector< CVector < C_FLOAT64 > * >::iterator endSrc = itSrc + mPopulationSize;
   std::vector< CVector < C_FLOAT64 > * >::iterator itTarget = endSrc;
 
   std::vector< CVector < C_FLOAT64 > * >::iterator itSrcVariance = mVariance.begin();
   std::vector< CVector < C_FLOAT64 > * >::iterator itTargetVariance = itSrcVariance + mPopulationSize;
 
   C_FLOAT64 * pVariance, * pVarianceEnd, * pParentVariance;
 
   // iterate over parents
   for (i = 0; itSrc != endSrc && Continue; ++itSrc, ++itSrcVariance, ++i)
     {
       // iterate over the child rate - 1 since the first child is the
       // parent.
       for (j = 1; j < childrate; ++j, ++itTarget, ++itTargetVariance)
         {
           // first just copy the individuals
           **itTarget = **itSrc;
           **itTargetVariance = **itSrcVariance;
 
           // do recombination on the sigma
           // since sigmas already have one parent's component
           // need only average with the sigmas of the other parent
           Parent = (i + mpRandom->getRandomU(mPopulationSize - 1)) % mPopulationSize;
 
           pVariance = (*itTargetVariance)->array();
           pVarianceEnd = pVariance + mVariableSize;
           pParentVariance = mVariance[Parent]->array();
 
           for (; pVariance != pVarianceEnd; ++pVariance, ++pParentVariance)
             *pVariance = (*pVariance + *pParentVariance) * .5;
         }
     }
 
   Continue &= mutate();
 
   return Continue;
 }

void COptMethodSRES::select ( )

private

Select surviving population

Returns: success

Definition at line 233 of file COptMethodSRES.cpp.

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

Referenced by optimise().

 {
   size_t i, j;
   size_t TotalPopulation = mIndividual.size();
   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
             {
               if (mPhi[j] > mPhi[j + 1]) // j further outside then j+1
                 {
                   swap(j, j + 1);
                   wasSwapped = true;
                 }
             }
         }
 
       // if nothing was swapped, then they're ordered!
       if (wasSwapped == false) break;
     }
 }

bool COptMethodSRES::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 93 of file COptMethodSRES.cpp.

References C_FLOAT64, mIndividual, mPhi, 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;
 
   dTmp = mPhi[to];
   mPhi[to] = mPhi[from];
   mPhi[from] = dTmp;
 
   return true;
 }