#include <COptMethodPS.h>

Inheritance diagram for COptMethodPS:

Collaboration diagram for COptMethodPS:

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

virtual bool	optimise ()

virtual	~COptMethodPS ()

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
void	buildInformants ()

virtual bool	cleanup ()

	COptMethodPS (const CCopasiContainer *pParent=NULL)

bool	create (const size_t &index)

const C_FLOAT64 &	evaluate ()

virtual bool	initialize ()

void	initObjects ()

bool	move (const size_t &index)

bool	reachedStdDeviation ()

Private Attributes
size_t	mBestIndex

CMatrix< C_FLOAT64 >	mBestPositions

CVector< C_FLOAT64 >	mBestValues

bool	mContinue

C_FLOAT64	mEvaluationValue

size_t	mhIteration

CVector< CVector< C_FLOAT64 > >	mIndividuals

std::vector< std::set< size_t > >	mInformants

unsigned C_INT32	mIteration

unsigned C_INT32	mIterationLimit

size_t	mNumInformed

size_t	mNumInformedMin

CPermutation *	mpPermutation

CRandom *	mpRandom

unsigned C_INT32	mSwarmSize

CVector< C_FLOAT64 >	mValues

size_t	mVariableSize

C_FLOAT64	mVariance

CMatrix< C_FLOAT64 >	mVelocities

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 29 of file COptMethodPS.h.

Constructor & Destructor Documentation

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

Copy Constructor

Parameters

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

Definition at line 61 of file COptMethodPS.cpp.

References initObjects().

                                                             :
   COptMethod(src, pParent),
   mIterationLimit(0),
   mSwarmSize(0),
   mVariance(0.0),
   mpRandom(NULL),
   mIteration(0),
   mhIteration(C_INVALID_INDEX),
   mVariableSize(0),
   mIndividuals(),
   mValues(),
   mVelocities(),
   mBestValues(),
   mBestPositions(),
   mpPermutation(NULL),
   mInformants(),
   mNumInformedMin(0),
   mNumInformed(0),
   mBestIndex(0),
   mEvaluationValue(0),
   mContinue(true)
 {initObjects();}

COptMethodPS::~COptMethodPS ( )

virtual

Destructor

Definition at line 85 of file COptMethodPS.cpp.

References cleanup().

86 {cleanup();}

COptMethodPS::cleanup

virtual bool cleanup()

Definition: COptMethodPS.cpp:381

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

private

Default Constructor

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 30 of file COptMethodPS.cpp.

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

                                                           :
   COptMethod(CCopasiTask::optimization, CCopasiMethod::ParticleSwarm, pParent),
   mIterationLimit(0),
   mSwarmSize(0),
   mVariance(0.0),
   mpRandom(NULL),
   mIteration(0),
   mhIteration(C_INVALID_INDEX),
   mVariableSize(0),
   mIndividuals(),
   mValues(),
   mVelocities(),
   mBestValues(),
   mBestPositions(),
   mpPermutation(NULL),
   mInformants(),
   mNumInformedMin(0),
   mNumInformed(0),
   mBestIndex(0),
   mEvaluationValue(0),
   mContinue(true)
 {
   addParameter("Iteration Limit", CCopasiParameter::UINT, (unsigned C_INT32) 2000);
   addParameter("Swarm Size", CCopasiParameter::UINT, (unsigned C_INT32) 50);
   addParameter("Std. Deviation", CCopasiParameter::UDOUBLE, (C_FLOAT64) 1.0e-6);
   addParameter("Random Number Generator", CCopasiParameter::UINT, (unsigned C_INT32) CRandom::mt19937);
   addParameter("Seed", CCopasiParameter::UINT, (unsigned C_INT32) 0);
 
   initObjects();
 }

Member Function Documentation

void COptMethodPS::buildInformants ( )

private

create the informant for each individual

Definition at line 389 of file COptMethodPS.cpp.

References mInformants, mNumInformed, mpPermutation, mSwarmSize, CPermutation::next(), CPermutation::pick(), and CPermutation::shuffle().

Referenced by optimise().

 {
   if (mNumInformed < mSwarmSize)
     mNumInformed++;
   else
     return;
 
   mInformants.clear();
   mInformants.resize(mSwarmSize);
   mpPermutation->shuffle();
 
   size_t i, j;
   size_t Informant;
 
   for (i = 0; i < mSwarmSize; i++)
     {
       mInformants[i].insert(i);
 
       Informant = mpPermutation->pick();
 
       for (j = 1; j < mNumInformed; j++, Informant = mpPermutation->next())
         {
           if (Informant == i)
             {
               Informant = mpPermutation->next();
             }
 
           mInformants[Informant].insert(i);
         }
     }
 
   return;
 }

bool COptMethodPS::cleanup ( )

privatevirtual

Cleanup arrays and pointers.

Returns: bool success

Reimplemented from COptMethod.

Definition at line 381 of file COptMethodPS.cpp.

References mpPermutation, mpRandom, and pdelete.

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

 {
   pdelete(mpRandom);
   pdelete(mpPermutation);
 
   return true;
 }

bool COptMethodPS::create ( const size_t & index )

private

Create the indexed individual in the swarm

Parameters

const size_t & index

Returns: bool continue

Definition at line 194 of file COptMethodPS.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, COptItem::checkConstraint(), COutputInterface::DURING, evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomCC(), CRandom::getRandomNormal(), COptItem::getUpperBoundValue(), max, mBestIndex, mBestPositions, mBestValues, mContinue, min, mIndividuals, COptMethod::mpOptItem, COptMethod::mpOptProblem, COptMethod::mpParentTask, mpRandom, COptMethod::mpSetCalculateVariable, mValues, mVariableSize, mVelocities, CCopasiTask::output(), and COptProblem::setSolution().

Referenced by optimise().

 {
   C_FLOAT64 * pIndividual = mIndividuals[index].array();
   C_FLOAT64 * pEnd = pIndividual + mVariableSize;
   C_FLOAT64 * pVelocity = mVelocities[index];
   C_FLOAT64 * pBestPosition = mBestPositions[index];
   std::vector< COptItem * >::const_iterator itOptItem = mpOptItem->begin();
   std::vector< UpdateMethod * >::const_iterator itSetCalculateVariable = mpSetCalculateVariable->begin();
 
   C_FLOAT64 mn, mx, la;
 
   for (; pIndividual != pEnd;
        ++pIndividual, ++pVelocity, ++pBestPosition, ++itOptItem, ++itSetCalculateVariable)
     {
       COptItem & OptItem = **itOptItem;
 
       // 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
                 {
                   *pIndividual = mn + mpRandom->getRandomCC() * (mx - mn);
                   *pVelocity = mn + mpRandom->getRandomCC() * (mx - mn) - *pIndividual;
                 }
               else
                 {
                   *pIndividual = pow(10.0, log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min())) + la * mpRandom->getRandomCC());
                   *pVelocity =
                     pow(10.0, log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min())) + la * mpRandom->getRandomCC()) - *pIndividual;
                 }
             }
           else if (mx > 0) // 0 is in the interval (mn, mx)
             {
               la = log10(mx) + log10(-mn);
 
               if (la < 3.6) // linear
                 {
                   *pIndividual = mn + mpRandom->getRandomCC() * (mx - mn);
                   *pVelocity = mn + mpRandom->getRandomCC() * (mx - mn) - *pIndividual;
                 }
               else
                 {
                   C_FLOAT64 mean = (mx + mn) * 0.5;
                   C_FLOAT64 sigma = std::min(std::numeric_limits< C_FLOAT64 >::max(), mx - mn) / 3.0;
 
                   do
                     {
                       *pIndividual = mpRandom->getRandomNormal(mean, sigma);
                     }
                   while ((*pIndividual < mn) || (*pIndividual > mx));
 
                   *pVelocity = mpRandom->getRandomNormal(mean, sigma) - *pIndividual;
                 }
             }
           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
                 {
                   *pIndividual = - (mn + mpRandom->getRandomCC() * (mx - mn));
                   *pVelocity = - (mn + mpRandom->getRandomCC() * (mx - mn)) - *pIndividual;
                 }
               else
                 {
                   *pIndividual = - pow(10.0, log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min())) + la * mpRandom->getRandomCC());
                   *pVelocity =
                     - pow(10.0, log10(std::max(mn, std::numeric_limits< C_FLOAT64 >::min())) + la * mpRandom->getRandomCC()) - *pIndividual;
                 }
             }
         }
 
       catch (...)
         {
           *pIndividual = (mx + mn) * 0.5;
           *pVelocity = 0.0;
         }
 
       // force it to be within the bounds
       switch (OptItem.checkConstraint(*pIndividual))
         {
           case - 1:
             *pIndividual = *OptItem.getLowerBoundValue();
             break;
 
           case 1:
             *pIndividual = *OptItem.getUpperBoundValue();
             break;
         }
 
       *pBestPosition = *pIndividual;
 
       // We need to set the value here so that further checks take
       // account of the value.
       (**itSetCalculateVariable)(*pIndividual);
     }
 
   // calculate its fitness
   mBestValues[index] = mValues[index] = evaluate();
 
   if (mBestValues[index] < mBestValues[mBestIndex])
     {
       // and store that value
       mBestIndex = index;
       mContinue &= mpOptProblem->setSolution(mBestValues[index], mIndividuals[index]);
 
       // We found a new best value lets report it.
       mpParentTask->output(COutputInterface::DURING);
     }
 
   return mContinue;
 }

const C_FLOAT64 & COptMethodPS::evaluate ( )

private

Evaluate the fitness of one individual

Returns: const C_FLOAT64 value

Definition at line 89 of file COptMethodPS.cpp.

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

Referenced by create(), move(), and optimise().

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

bool COptMethodPS::initialize ( )

privatevirtual

Initialize arrays and pointer.

Returns: bool success

Reimplemented from COptMethod.

Definition at line 327 of file COptMethodPS.cpp.

References CProcessReport::addItem(), cleanup(), CRandom::createGenerator(), CCopasiParameter::getValue(), COptMethod::initialize(), mBestPositions, mBestValues, mContinue, mhIteration, mIndividuals, mIteration, mIterationLimit, mNumInformed, mNumInformedMin, CCopasiMethod::mpCallBack, COptMethod::mpOptItem, mpPermutation, mpRandom, mSwarmSize, mValues, mVariableSize, mVariance, mVelocities, CCopasiParameter::Value::pUDOUBLE, CCopasiParameter::Value::pUINT, CMatrix< CType >::resize(), CVector< CType >::resize(), and CCopasiParameterGroup::setValue().

Referenced by optimise().

 {
   cleanup();
 
   if (!COptMethod::initialize()) return false;
 
   mIterationLimit = * getValue("Iteration Limit").pUINT;
   mIteration = 0;
 
   if (mpCallBack)
     mhIteration =
       mpCallBack->addItem("Iteration Limit",
                           mIteration,
                           & mIterationLimit);
 
   mSwarmSize = * getValue("Swarm Size").pUINT;
 
   if (mSwarmSize < 5)
     {
       mSwarmSize = 5;
       setValue("Swarm Size", mSwarmSize);
     }
 
   mVariance = *getValue("Std. Deviation").pUDOUBLE;
   mVariance *= mVariance;
 
   mpRandom =
     CRandom::createGenerator(* (CRandom::Type *) getValue("Random Number Generator").pUINT,
                              * getValue("Seed").pUINT);
 
   mVariableSize = mpOptItem->size();
 
   mIndividuals.resize(mSwarmSize);
 
   size_t i;
 
   for (i = 0; i < mSwarmSize; i++)
     mIndividuals[i].resize(mVariableSize);
 
   mValues.resize(mSwarmSize);
   mVelocities.resize(mSwarmSize, mVariableSize);
   mBestValues.resize(mSwarmSize);
   mBestPositions.resize(mSwarmSize, mVariableSize);
 
   mNumInformedMin = std::max<size_t>(mSwarmSize / 10, 5) - 1;
   mNumInformed = mNumInformedMin;
 
   mpPermutation = new CPermutation(mpRandom, mSwarmSize);
 
   mContinue = true;
 
   return mContinue;
 }

void COptMethodPS::initObjects ( )

private

Initialize contained objects.

Definition at line 322 of file COptMethodPS.cpp.

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

Referenced by COptMethodPS().

 {
   addObjectReference("Current Iteration", mIteration, CCopasiObject::ValueInt);
 }

bool COptMethodPS::move ( const size_t & index )

private

Move the indexed individual in the swarm

Parameters

const size_t & index

Returns: bool continue

Definition at line 107 of file COptMethodPS.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, COptItem::checkConstraint(), COutputInterface::DURING, evaluate(), COptItem::getLowerBoundValue(), CRandom::getRandomCC(), COptItem::getUpperBoundValue(), mBestIndex, mBestPositions, mBestValues, mContinue, mEvaluationValue, mIndividuals, mInformants, mNumInformed, mNumInformedMin, COptMethod::mpOptItem, COptMethod::mpOptProblem, COptMethod::mpParentTask, mpRandom, COptMethod::mpSetCalculateVariable, mValues, mVariableSize, mVelocities, CCopasiTask::output(), and COptProblem::setSolution().

Referenced by optimise().

 {
   const C_FLOAT64 w = 1 / (2 * log(2.0));
   const C_FLOAT64 c = 0.5 + log(2.0);
 
   bool Improved = false;
 
   C_FLOAT64 * pIndividual = mIndividuals[index].array();
   C_FLOAT64 * pEnd = pIndividual + mVariableSize;
   C_FLOAT64 * pVelocity = mVelocities[index];
   C_FLOAT64 * pBestPosition = mBestPositions[index];
   std::vector< COptItem * >::const_iterator itOptItem = mpOptItem->begin();
   std::vector< UpdateMethod * >::const_iterator itSetCalculateVariable = mpSetCalculateVariable->begin();
 
   C_FLOAT64 * pBestInformantPosition = mBestPositions[index];
   C_FLOAT64 BestInformantValue = mBestValues[index];
 
   std::set< size_t >::const_iterator itInformant = mInformants[index].begin();
   std::set< size_t >::const_iterator endInformant = mInformants[index].end();
 
   size_t i = mNumInformed + mNumInformedMin;
 
   for (; i && itInformant != endInformant; --i, ++itInformant)
     if (mBestValues[*itInformant] < BestInformantValue)
       {
         BestInformantValue = mBestValues[*itInformant];
         pBestInformantPosition = mBestPositions[*itInformant];
       }
 
   for (; pIndividual != pEnd;
        ++pIndividual, ++pVelocity, ++pBestPosition, ++itOptItem, ++itSetCalculateVariable, ++pBestInformantPosition)
     {
       *pVelocity *= w;
       *pVelocity += c * mpRandom->getRandomCC() * (*pBestPosition - *pIndividual);
       *pVelocity += c * mpRandom->getRandomCC() * (*pBestInformantPosition - *pIndividual);
 
       *pIndividual += *pVelocity;
 
       COptItem & OptItem = **itOptItem;
 
       // force it to be within the bounds
       switch (OptItem.checkConstraint(*pIndividual))
         {
           case - 1:
             *pIndividual = *OptItem.getLowerBoundValue();
             *pVelocity = 0.0;
             break;
 
           case 1:
             *pIndividual = *OptItem.getUpperBoundValue();
             *pVelocity = 0.0;
             break;
         }
 
       // We need to set the value here so that further checks take
       // account of the value.
       (**itSetCalculateVariable)(*pIndividual);
     }
 
   // calculate its fitness
   mValues[index] = evaluate();
 
   // Check if we improved individually
   if (mEvaluationValue < mBestValues[index])
     {
       Improved = true;
 
       // Save the individually best value;
       mBestValues[index] = mEvaluationValue;
       memcpy(mBestPositions[index], mIndividuals[index].array(), sizeof(C_FLOAT64) * mVariableSize);
 
       // Check if we improved globally
       if (mEvaluationValue < mBestValues[mBestIndex])
         {
           // and store that value
           mBestIndex = index;
           mContinue &= mpOptProblem->setSolution(mBestValues[index], mIndividuals[index]);
 
           // We found a new best value lets report it.
           mpParentTask->output(COutputInterface::DURING);
         }
     }
 
   return Improved;
 }

bool COptMethodPS::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 495 of file COptMethodPS.cpp.

References CVectorCore< CType >::array(), buildInformants(), C_FLOAT64, COptItem::checkConstraint(), cleanup(), create(), COutputInterface::DURING, evaluate(), CProcessReport::finishItem(), COptItem::getLowerBoundValue(), COptItem::getStartValue(), COptItem::getUpperBoundValue(), initialize(), mBestIndex, mBestPositions, mBestValues, mContinue, mhIteration, mIndividuals, mIteration, mIterationLimit, move(), CCopasiMethod::mpCallBack, COptMethod::mpOptItem, COptMethod::mpOptProblem, COptMethod::mpParentTask, COptMethod::mpSetCalculateVariable, mSwarmSize, mValues, mVariableSize, mVelocities, CCopasiTask::output(), CProcessReport::progressItem(), reachedStdDeviation(), and COptProblem::setSolution().

 {
   size_t i;
 
   if (!initialize())
     {
       if (mpCallBack)
         mpCallBack->finishItem(mhIteration);
 
       return false;
     }
 
   C_FLOAT64 * pIndividual = mIndividuals[0].array();
   C_FLOAT64 * pEnd = pIndividual + mVariableSize;
   C_FLOAT64 * pVelocity = mVelocities[0];
   C_FLOAT64 * pBestPosition = mBestPositions[0];
   std::vector< COptItem * >::const_iterator itOptItem = mpOptItem->begin();
   std::vector< UpdateMethod * >::const_iterator itSetCalculateVariable = mpSetCalculateVariable->begin();
 
   // initialise the population
   // first individual is the initial guess
   for (; pIndividual != pEnd;
        ++pIndividual, ++pVelocity, ++pBestPosition, ++itOptItem, ++itSetCalculateVariable)
     {
       COptItem & OptItem = **itOptItem;
 
       *pIndividual = OptItem.getStartValue();
 
       // force it to be within the bounds
       switch (OptItem.checkConstraint(*pIndividual))
         {
           case - 1:
             *pIndividual = *OptItem.getLowerBoundValue();
             break;
 
           case 1:
             *pIndividual = *OptItem.getUpperBoundValue();
             break;
         }
 
       *pBestPosition = *pIndividual;
       *pVelocity = 0.0;
 
       // We need to set the value here so that further checks take
       // account of the value.
       (**itSetCalculateVariable)(*pIndividual);
     }
 
   // calculate its fitness
   mBestValues[0] = mValues[0] = evaluate();
 
   // and store that value
   mBestIndex = 0;
   mContinue &= mpOptProblem->setSolution(mBestValues[0], mIndividuals[0]);
 
   // We found a new best value lets report it.
   mpParentTask->output(COutputInterface::DURING);
 
   // the others are random
   for (i = 1; i < mSwarmSize && mContinue; i++)
     create(i);
 
   // create the informant list
   buildInformants();
 
   bool Improved;
 
   for (; mIteration < mIterationLimit && mContinue; mIteration++)
     {
       Improved = false;
 
       for (i = 0; i < mSwarmSize && mContinue; i++)
         Improved |= move(i);
 
       if (!Improved)
         buildInformants();
       else if (reachedStdDeviation())
         break;
 
       if (mpCallBack)
         mContinue &= mpCallBack->progressItem(mhIteration);
     }
 
   if (mpCallBack)
     mpCallBack->finishItem(mhIteration);
 
   cleanup();
 
   return true;
 }

bool COptMethodPS::reachedStdDeviation ( )

private

Definition at line 423 of file COptMethodPS.cpp.

References CVectorCore< CType >::array(), C_FLOAT64, mIndividuals, mNumInformed, mNumInformedMin, mSwarmSize, mValues, mVariableSize, and mVariance.

Referenced by optimise().

 {
   if (mNumInformed > mNumInformedMin + 1)
     mNumInformed--;
 
   // Check whether the swarm has settled
   C_FLOAT64 * pValue = mValues.array();
   C_FLOAT64 * pEnd = pValue + mSwarmSize;
 
   C_FLOAT64 Delta;
 
   C_FLOAT64 Mean = 0.0;
   C_FLOAT64 Variance = 0.0;
   size_t N = 0;
 
   for (; pValue != pEnd; ++pValue)
     {
       // We need to deal with infinity values since they indicate failure
       if (*pValue == std::numeric_limits<C_FLOAT64>::infinity())
         return false;
 
       Delta = *pValue - Mean;
       Mean += Delta / ++N;
       // This uses the new mean, i.e., not Delta * Delta
       Variance += Delta * (*pValue - Mean);
     }
 
   Variance /= (N - 1);
 
   if (Variance > mVariance)
     return false;
 
   // The variance of the function value is smaller than required. We now
   // Check the variance of the flock positions.
   CVector< C_FLOAT64 > FirstMoments(mVariableSize);
   CVector< C_FLOAT64 > SecondMoments(mVariableSize);
   FirstMoments = 0.0;
   SecondMoments = 0.0;
 
   CVector< C_FLOAT64 > * pIndividual = mIndividuals.array();
   CVector< C_FLOAT64 > * pIndividualEnd = pIndividual + mSwarmSize;
 
   C_FLOAT64 * pFirstMoment;
   C_FLOAT64 * pSecondMoment;
   pEnd = FirstMoments.array() + mVariableSize;
 
   for (; pIndividual != pIndividualEnd; ++pIndividual)
     {
       pFirstMoment = FirstMoments.array();
       pSecondMoment = SecondMoments.array();
       pValue = pIndividual->array();
 
       for (; pFirstMoment != pEnd; ++pFirstMoment, ++pSecondMoment, ++pValue)
         {
           *pFirstMoment += *pValue;
           *pSecondMoment += *pValue * *pValue;
         }
     }
 
   pFirstMoment = FirstMoments.array();
   pSecondMoment = SecondMoments.array();
 
   for (; pFirstMoment != pEnd; ++pFirstMoment, ++pSecondMoment)
     {
       Variance = (*pSecondMoment - *pFirstMoment * *pFirstMoment / mSwarmSize) / (mSwarmSize - 1);
 
       if (Variance > mVariance) return false;
     }
 
   return true;
 }