COPASI API  4.16.103
Public Member Functions | Private Member Functions | Private Attributes | Friends | List of all members
COptMethodEP2 Class Reference

#include <COptMethodEP2.h>

Inheritance diagram for COptMethodEP2:
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Collaboration diagram for COptMethodEP2:
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Public Member Functions

 COptMethodEP2 (const COptMethodEP2 &src)
 
virtual void copy (int o, int d)
 
virtual void exchange (int o, int d)
 
virtual int fittest (void)
 
double Get_BestFoundSoFar_candidate ()
 
int Get_NumGeneration ()
 
int Get_NumParameter ()
 
int Get_PopulationSize ()
 
virtual bool optimise ()
 
virtual void select (int method)
 
void Set_BestFoundSoFar (int num)
 
void Set_CandidateValue (int i, double num)
 
void Set_individual (int i, int j, double num)
 
void Set_Maximum (double num)
 
void Set_Minimum (double num)
 
void Set_murvar (double num)
 
void Set_NumGeneration (int num)
 
void Set_NumParameter (int num)
 
void Set_PopulationSize (int num)
 
virtual void swap (int o, int d)
 
virtual void TrackDataFile (int i)
 
virtual ~COptMethodEP2 ()
 
- Public Member Functions inherited from COptMethod
 COptMethod (const COptMethod &src, const CCopasiContainer *pParent=NULL)
 
virtual bool initialize ()
 
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

 COptMethodEP2 ()
 

Private Attributes

int BestFoundSoFar
 
double * CandidateValue
 
double * CandidateValueRate
 
int * CrossPoint
 
CVector< CVector< C_FLOAT64 > > individual
 
double Maximum
 
double Minimum
 
int NumCrossPoint
 
int NumGeneration
 
int NumParameter
 
int PopulationSize
 
int * WinScore
 

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
virtual bool cleanup ()
 
 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 43 of file COptMethodEP2.h.

Constructor & Destructor Documentation

COptMethodEP2::COptMethodEP2 ( )
private

Default Constructor

Definition at line 50 of file COptMethodEP2.cpp.

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

50  : COptMethod(CCopasiMethod::EvolutionaryProgram2)
51 {
52  addParameter("EvolutionaryProgram2.Iterations",
53  CCopasiParameter::UINT,
54  (unsigned C_INT32) 10000);
55  addParameter("EvolutionaryProgram2.PopulationSize",
56  CCopasiParameter::UINT,
57  (unsigned C_INT32) 600);
58  addParameter("EvolutionaryProgram2.RandomGenerator.Type",
59  CCopasiParameter::INT,
60  (C_INT32)CRandom::mt19937);
61  addParameter("EvolutionaryProgram2.RandomGenerator.Seed",
62  CCopasiParameter::INT,
63  (C_INT32) 0);
64 }
C_INT32
#define C_INT32
Definition: copasi.h:90
CCopasiParameterGroup::addParameter
bool addParameter(const CCopasiParameter &parameter)
Definition: CCopasiParameterGroup.cpp:239
COptMethodEP2::COptMethodEP2 ( const COptMethodEP2 &  src)

Copy Constructor

Parameters
constCOptMethodEP2 & src

Definition at line 46 of file COptMethodEP2.cpp.

46  :
47  COptMethod(src)
48 {}
COptMethodEP2::~COptMethodEP2 ( )
virtual

Destructor

Definition at line 69 of file COptMethodEP2.cpp.

70 {}

Member Function Documentation

void COptMethodEP2::copy ( int  o,
int  d 
)
virtual

Definition at line 486 of file COptMethodEP2.cpp.

References CandidateValue, individual, and NumParameter.

487 {
488  int i;
489 
490  for (i = 0; i < NumParameter; i++)
491  {
492  individual[d][i] = individual[o][i];
493  }
494 
495  CandidateValue[d] = CandidateValue[o];
496 }
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
COptMethodEP2::individual
CVector< CVector< C_FLOAT64 > > individual
Definition: COptMethodEP2.h:60
void COptMethodEP2::exchange ( int  o,
int  d 
)
virtual

Definition at line 521 of file COptMethodEP2.cpp.

References CandidateValue, individual, and NumParameter.

Referenced by select().

522 {
523  int i;
524  double tmp;
525 
526  for (i = 0; i < NumParameter; i++)
527  {
528  tmp = individual[d][i];
529  individual[d][i] = individual[o][i];
530  individual[o][i] = tmp;
531  }
532 
533  tmp = CandidateValue[d];
534  CandidateValue[d] = CandidateValue[o];
535  CandidateValue[o] = tmp;
536 }
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
COptMethodEP2::individual
CVector< CVector< C_FLOAT64 > > individual
Definition: COptMethodEP2.h:60
int COptMethodEP2::fittest ( void  )
virtual

Definition at line 633 of file COptMethodEP2.cpp.

References CandidateValue, and PopulationSize.

Referenced by optimise().

634 {
635  int i, b;
636  double f;
637  f = CandidateValue[0];
638  b = 0;
639 
640  for (i = 1; i < PopulationSize; i++)
641  {
642  if (CandidateValue[i] < f)
643  {
644  b = i;
645  f = CandidateValue[i];
646  }
647  }
648 
649  return b;
650 }
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
double COptMethodEP2::Get_BestFoundSoFar_candidate ( )
inline

Definition at line 199 of file COptMethodEP2.h.

References BestFoundSoFar, and CandidateValue.

Referenced by optimise().

200 {
201  return CandidateValue[BestFoundSoFar];
202 }
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
int COptMethodEP2::Get_NumGeneration ( )
inline

Definition at line 204 of file COptMethodEP2.h.

References NumGeneration.

205 {
206  return NumGeneration;
207 }
int COptMethodEP2::Get_NumParameter ( )
inline

Definition at line 194 of file COptMethodEP2.h.

References NumParameter.

195 {
196  return NumParameter;
197 }
int COptMethodEP2::Get_PopulationSize ( )
inline

Definition at line 209 of file COptMethodEP2.h.

References PopulationSize.

210 {
211  return PopulationSize;
212 }
C_INT32 COptMethodEP2::optimise ( void  )
virtual

GA Optimizer Function: Returns: nothing

Reimplemented from COptMethod.

Definition at line 76 of file COptMethodEP2.cpp.

References BestFoundSoFar, C_INT32, COptProblem::calculate(), CandidateValue, CandidateValueRate, CRandom::createGenerator(), CrossPoint, FALSE, fittest(), Get_BestFoundSoFar_candidate(), COptProblem::getCalculateVariableUpdateMethods(), CRandom::getRandomCC(), CCopasiParameter::getValue(), COptProblem::getVariableSize(), individual, linear(), max, Maximum, min, Minimum, COptMethod::mpOptProblem, NumGeneration, NumParameter, PopulationSize, CVector< CType >::resize(), select(), TrackDataFile(), TRUE, and WinScore.

77 {
78  NumGeneration = (C_INT32) getValue("EvolutionaryProgram2.Iterations");
79  PopulationSize = (C_INT32) getValue("EvolutionaryProgram2.PopulationSize");
80  NumParameter = mpOptProblem->getVariableSize();
81 
82  /* Create a random number generator */
83  CRandom::Type Type;
84  Type = (CRandom::Type)(C_INT32) getValue("EvolutionaryProgram2.RandomGenerator.Type");
85  C_INT32 Seed;
86  Seed = (C_INT32) getValue("EvolutionaryProgram2.RandomGenerator.Seed");
87  CRandom * pRand = CRandom::createGenerator(Type, Seed);
88 
89  assert(pRand);
90 
91  const double ** Minimum = mpOptProblem->getParameterMin().array();
92  const double ** Maximum = mpOptProblem->getParameterMax().array();
93 
94  std::vector< UpdateMethod * > & Parameter = mpOptProblem->getCalculateVariableUpdateMethods();
95 
96  double current_best_value, la;
97  int i, j, last_update, u10, u30, u50;
98  bool linear;
99 
100  // create array for function value of candidate
101  CandidateValue = new double[2 * PopulationSize];
102 
103  // create array for function value rate of candidate
104  CandidateValueRate = new double[PopulationSize];
105 
106  // create array for tournament competition strategy
107  WinScore = new int[2 * PopulationSize];
108 
109  // create array for crossover points
110  CrossPoint = new int[NumParameter];
111 
112  // create the population array
113  individual.resize(2 * PopulationSize);
114 
115  // create the individuals
116  for (i = 0; i < 2*PopulationSize; i++)
117  individual[i].resize(NumParameter);
118 
119  // Prepare inital population
120  //Generate the initial population at random
121  for (i = 0; i < PopulationSize; i++)
122  {
123  for (j = 0; j < NumParameter; j++)
124  {
125  try
126  {
127  // determine if linear or log scale
128  linear = FALSE; la = 1.0;
129 
130  if ((*Maximum[j] <= 0.0) || (*Minimum[j] < 0.0)) linear = TRUE;
131  else
132  {
133  la = log10(*Maximum[j]) - log10(std::min(*Minimum[j], std::numeric_limits< C_FLOAT64 >::epsilon()));
134 
135  if (la < 1.8) linear = TRUE;
136  }
137 
138  // set it to a random value within the interval
139  if (linear)
140  individual[i][j] = *Minimum[j] + pRand->getRandomCC() * (*Maximum[j] - *Minimum[j]);
141  else
142  individual[i][j] = *Minimum[j] * pow(10.0, la * pRand->getRandomCC());
143  }
144  catch (int)
145  {
146  individual[i][j] = (*Maximum[j] - *Minimum[j]) * 0.5 + *Minimum[j];
147  }
148  }
149 
150  try
151  {
152  // calculate its fitness value
153  for (int kk = 0; kk < NumParameter; kk++)
154  (*Parameter[kk])(individual[i][kk]);
155 
156  CandidateValue[i] = mpOptProblem->calculate();
157  }
158  catch (int)
159  {
160  CandidateValue[i] = std::numeric_limits< C_FLOAT64 >::max();
161  }
162  } // initialization ends
163 
164  //Set fitness map rate
165  // double q=0.8;
166  // double constant1=100;
167  double constant1 = 100;
168  // double constant2=20;
169  double constant2 = 10;
170  /* for (i=0; i<PopulationSize; i++)
171  {
172  CandidateValueRate[i]=1-q*pow((1-q),i);
173  }
174  */
175  // get the index of the fittest
176  BestFoundSoFar = fittest();
177 
178  // initialise the update registers
179  last_update = 0;
180  u10 = u30 = u50 = 0;
181 
182  // store that value
183  current_best_value = Get_BestFoundSoFar_candidate();
184 
185  std::ofstream finalout("debugopt.dat");
186 
187  if (!finalout)
188  {
189  std::cout << "debugopt.dat cannot be opened!" << std::endl;
190  exit(1);
191  }
192 
193  finalout << "----------------------------- the best result at each generation---------------------" << std::endl;
194  finalout << "Generation\t" << "Best candidate value for object function\t" << "Display " << NumParameter << " parameters" << std::endl;
195  finalout << std::endl;
196  finalout.close();
197 
198  srand(time(NULL)); rand();
199 
200  // Iterations of GA
201  for (i = 0; i < NumGeneration; i++)
202  {
203  std::cout << std::endl;
204  std::cout << "EP2 is processing at generation " << i << std::endl;
205 
206  TrackDataFile(i);
207 
208  select(5);
209 
210  //Mutating all parents
211  for (int nn = PopulationSize; nn < 2*PopulationSize; nn++)
212  {
213  double mut;
214 
215  // mutate the parameters
216  for (int j = 0; j < NumParameter; j++)
217  {
218  if (floor(10*rand() / RAND_MAX) > 5)
219  {
220  // if(i<NumGeneration*0.5) mut = individual[nn-PopulationSize][j]*(1 + pRand->getRandomCC());
221  if (i < NumGeneration*0.5) mut = individual[nn - PopulationSize][j] * (1 + sqrt(constant1 * CandidateValueRate[nn] + constant2) * pRand->getRandomCC());
222  else
223  {
224  if (i < NumGeneration*0.6) mut = individual[nn - PopulationSize][j] * (1 + sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.5 * pRand->getRandomCC());
225  else
226  {
227  if (i < NumGeneration*0.7) mut = individual[nn - PopulationSize][j] * (1 + sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.25 * pRand->getRandomCC());
228  else
229  {
230  if (i < NumGeneration*0.8) mut = individual[nn - PopulationSize][j] * (1 + sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.1 * pRand->getRandomCC());
231  else
232  {
233  if (i < NumGeneration*0.9) mut = individual[nn - PopulationSize][j] * (1 + sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.01 * pRand->getRandomCC());
234  else
235  {
236  if (i < NumGeneration*0.95) mut = individual[nn - PopulationSize][j] * (1 + sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.001 * pRand->getRandomCC());
237  else mut = individual[nn - PopulationSize][j] * (1 + sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.0001 * pRand->getRandomCC());
238  }
239  }
240  }
241  }
242  }
243  }
244  else
245  {
246  if (i < NumGeneration*0.5) mut = individual[nn - PopulationSize][j] * (1 - sqrt(constant1 * CandidateValueRate[nn] + constant2) * pRand->getRandomCC());
247  else
248  {
249  if (i < NumGeneration*0.6) mut = individual[nn - PopulationSize][j] * (1 - sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.5 * pRand->getRandomCC());
250  else
251  {
252  if (i < NumGeneration*0.7) mut = individual[nn - PopulationSize][j] * (1 - sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.25 * pRand->getRandomCC());
253  else
254  {
255  if (i < NumGeneration*0.8) mut = individual[nn - PopulationSize][j] * (1 - sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.1 * pRand->getRandomCC());
256  else
257  {
258  if (i < NumGeneration*0.9) mut = individual[nn - PopulationSize][j] * (1 - sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.01 * pRand->getRandomCC());
259  else
260  {
261  if (i < NumGeneration*0.95) mut = individual[nn - PopulationSize][j] * (1 - sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.001 * pRand->getRandomCC());
262  else mut = individual[nn - PopulationSize][j] * (1 - sqrt(constant1 * CandidateValueRate[nn] + constant2) * 0.0001 * pRand->getRandomCC());
263  }
264  }
265  }
266  }
267  }
268  }
269 
270  // check boundary and force it to be within the bounds
271  if (mut <= *Minimum[j]) mut = *Minimum[j] + std::numeric_limits< C_FLOAT64 >::epsilon();
272  else
273  {
274  if (mut < *Minimum[j]) mut = *Minimum[j];
275  }
276 
277  if (mut >= *Maximum[j]) mut = *Maximum[j] - std::numeric_limits< C_FLOAT64 >::epsilon();
278  else
279  {
280  if (mut > *Maximum[j]) mut = *Maximum[j];
281  }
282 
283  // store it
284  individual[nn][j] = mut;
285  }
286 
287  // evaluate the fitness
288  for (int kk = 0; kk < NumParameter; kk++)
289  (*Parameter[kk])(individual[nn][kk]);
290 
291  CandidateValue[nn] = mpOptProblem->calculate();
292  }
293 
294  // select approprate individuals as new population
295  select(2);
296 
297  // get the index of the fittest
298  BestFoundSoFar = fittest();
299 
300  if (Get_BestFoundSoFar_candidate() != current_best_value)
301  {
302  last_update = i;
303  current_best_value = Get_BestFoundSoFar_candidate();
304  }
305 
306  if (u10) u10--;
307 
308  if (u30) u30--;
309 
310  if (u50) u50--;
311 
312  if ((u50 == 0) && (i - last_update > 50))
313  {
314  for (int mm = PopulationSize / 2; mm < PopulationSize; mm++)
315  {
316  for (int jj = 0; jj < NumParameter; jj++)
317  {
318  try
319  {
320  // determine if linear or log scale
321  linear = FALSE; la = 1.0;
322 
323  if ((*Maximum[jj] <= 0.0) || (*Minimum[jj] < 0.0)) linear = TRUE;
324  else
325  {
326  la = log10(*Maximum[jj]) - log10(std::min(*Minimum[jj], std::numeric_limits< C_FLOAT64 >::epsilon()));
327 
328  if (la < 1.8) linear = TRUE;
329  }
330 
331  // set it to a random value within the interval
332  if (linear)
333  individual[mm][jj] = *Minimum[jj] + pRand->getRandomCC() * (*Maximum[jj] - *Minimum[jj]);
334  else
335  individual[mm][jj] = *Minimum[jj] * pow(10.0, la * pRand->getRandomCC());
336  }
337  catch (int)
338  {
339  individual[mm][jj] = (*Maximum[jj] - *Minimum[jj]) * 0.5 + *Minimum[jj];
340  }
341  }
342 
343  try
344  {
345  // calculate its fitness
346  for (int kk = 0; kk < NumParameter; kk++)
347  (*Parameter[kk])(individual[mm][kk]);
348 
349  CandidateValue[mm] = mpOptProblem->calculate();
350  }
351  catch (int)
352  {
353  CandidateValue[mm] = std::numeric_limits< C_FLOAT64 >::max();
354  }
355  }
356 
357  //end external for loop
358  BestFoundSoFar = fittest();
359  u50 = 50; u30 = 30; u10 = 10;
360  }
361  else
362  {
363  if ((u30 == 0) && (i - last_update > 30))
364  {
365  for (int mm = (int)floor(PopulationSize * 0.7); mm < PopulationSize; mm++)
366  {
367  for (int jj = 0; jj < NumParameter; jj++)
368  {
369  try
370  {
371  // determine if linear or log scale
372  linear = FALSE; la = 1.0;
373 
374  if ((*Maximum[jj] <= 0.0) || (*Minimum[jj] < 0.0)) linear = TRUE;
375  else
376  {
377  la = log10(*Maximum[jj]) - log10(std::min(*Minimum[jj], std::numeric_limits< C_FLOAT64 >::epsilon()));
378 
379  if (la < 1.8) linear = TRUE;
380  }
381 
382  // set it to a random value within the interval
383  if (linear)
384  individual[mm][jj] = *Minimum[jj] + pRand->getRandomCC() * (*Maximum[jj] - *Minimum[jj]);
385  else
386  individual[mm][jj] = *Minimum[jj] * pow(10.0, la * pRand->getRandomCC());
387  }
388  catch (int)
389  {
390  individual[mm][jj] = (*Maximum[jj] - *Minimum[jj]) * 0.5 + *Minimum[jj];
391  }
392  }
393 
394  try
395  {
396  // calculate its fitness
397  for (int kk = 0; kk < NumParameter; kk++)
398  (*Parameter[kk])(individual[mm][kk]);
399 
400  CandidateValue[mm] = mpOptProblem->calculate();
401  }
402  catch (int)
403  {
404  CandidateValue[mm] = std::numeric_limits< C_FLOAT64 >::max();
405  }
406  }
407 
408  //end external for loop
409  BestFoundSoFar = fittest();
410  u30 = 30; u10 = 10;
411  }
412  else
413  {
414  if ((u10 == 0) && (i - last_update > 10))
415  {
416  for (int mm = (int) floor(PopulationSize * 0.9); mm < PopulationSize; mm++)
417  {
418  for (int jj = 0; jj < NumParameter; jj++)
419  {
420  try
421  {
422  // determine if linear or log scale
423  linear = FALSE; la = 1.0;
424 
425  if ((*Maximum[jj] <= 0.0) || (*Minimum[jj] < 0.0)) linear = TRUE;
426  else
427  {
428  la = log10(*Maximum[jj]) - log10(std::min(*Minimum[jj], std::numeric_limits< C_FLOAT64 >::epsilon()));
429 
430  if (la < 1.8) linear = TRUE;
431  }
432 
433  // set it to a random value within the interval
434  if (linear)
435  individual[mm][jj] = *Minimum[jj] + pRand->getRandomCC() * (*Maximum[jj] - *Minimum[jj]);
436  else
437  individual[mm][jj] = *Minimum[jj] * pow(10.0, la * pRand->getRandomCC());
438  }
439  catch (int)
440  {
441  individual[mm][jj] = (*Maximum[jj] - *Minimum[jj]) * 0.5 + *Minimum[jj];
442  }
443  }
444 
445  try
446  {
447  // calculate its fitness
448  for (int kk = 0; kk < NumParameter; kk++)
449  (*Parameter[kk])(individual[mm][kk]);
450 
451  CandidateValue[mm] = mpOptProblem->calculate();
452  }
453  catch (int)
454  {
455  CandidateValue[mm] = std::numeric_limits< C_FLOAT64 >::max();
456  }
457  }
458 
459  //end external for loop
460  BestFoundSoFar = fittest();
461  u10 = 10;
462  //u10=50;
463  }
464  }
465  }
466  } // end iteration of generations
467 
468  //store the combination of the BestFoundSoFar parameter values found so far
469  mpOptProblem->setSolutionVariables(individual[BestFoundSoFar]);
470 
471  //set the BestFoundSoFar function value
472  mpOptProblem->setSolutionValue(CandidateValue[BestFoundSoFar]);
473 
474  //free memory space
475  delete CrossPoint;
476  delete WinScore;
477  delete CandidateValue;
478 
479  std::cout << std::endl;
480  std::cout << "GA has successfully done!" << std::endl;
481 
482  return 0;
483 }
COptProblem::getVariableSize
size_t getVariableSize() const
COptMethodEP2::fittest
virtual int fittest(void)
Definition: COptMethodEP2.cpp:633
TRUE
#define TRUE
Definition: CGA.h:25
linear
qreal linear(qreal a, qreal b, qreal t)
Definition: CQEffectDescription.cpp:12
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
COptProblem::getCalculateVariableUpdateMethods
const std::vector< UpdateMethod * > & getCalculateVariableUpdateMethods() const
Definition: COptProblem.cpp:734
CVector::resize
void resize(size_t size, const bool &copy=false)
Definition: CVector.h:301
COptMethod::mpOptProblem
COptProblem * mpOptProblem
Definition: COptMethod.h:56
C_INT32
#define C_INT32
Definition: copasi.h:90
COptMethodEP2::individual
CVector< CVector< C_FLOAT64 > > individual
Definition: COptMethodEP2.h:60
FALSE
#define FALSE
Definition: CGA.h:26
CRandom::createGenerator
static CRandom * createGenerator(CRandom::Type type=CRandom::mt19937, unsigned C_INT32 seed=0)
Definition: CRandom.cpp:49
COptProblem::calculate
virtual bool calculate()
Definition: COptProblem.cpp:538
CRandom::getRandomCC
virtual C_FLOAT64 getRandomCC()
Definition: CRandom.cpp:235
CCopasiParameter::getValue
const Value & getValue() const
Definition: CCopasiParameter.cpp:247
COptMethodEP2::select
virtual void select(int method)
Definition: COptMethodEP2.cpp:539
COptMethodEP2::TrackDataFile
virtual void TrackDataFile(int i)
Definition: COptMethodEP2.cpp:652
COptMethodEP2::Get_BestFoundSoFar_candidate
double Get_BestFoundSoFar_candidate()
Definition: COptMethodEP2.h:199
COptMethodEP2::CandidateValueRate
double * CandidateValueRate
Definition: COptMethodEP2.h:62
min
#define min(a, b)
Definition: f2c.h:175
max
#define max(a, b)
Definition: f2c.h:176
void COptMethodEP2::select ( int  method)
virtual

Definition at line 539 of file COptMethodEP2.cpp.

References CandidateValue, CandidateValueRate, exchange(), PopulationSize, swap(), and WinScore.

Referenced by optimise().

540 {
541  int i, j, TournamentSize, RandomRival;
542  int RandomIndividual;
543  //srand(time(NULL)); rand();
544 
545  switch (SelectionStrategy)
546  {
547  case 1: // parent-offspring competition
548 
549  for (i = PopulationSize; i < 2*PopulationSize; i++)
550  {
551  // if offspring is fitter keep it
552  for (j = 0; j < PopulationSize; j++)
553  {
554  if (CandidateValue[i] < CandidateValue[j]) exchange(i, j);
555  }
556  }
557 
558  break;
559  case 2: // tournament competition
560  // compete with 20% of the population
561  TournamentSize = PopulationSize / 5;
562 
563  // but at least one
564  if (TournamentSize < 1) TournamentSize = 1;
565 
566  // parents and offspring are all in competition
567  for (i = 0; i < 2*PopulationSize; i++)
568  {
569  WinScore[i] = 0;
570 
571  for (j = 0; j < TournamentSize; j++)
572  {
573  // get random rival
574  RandomRival = (int)fabs(floor((PopulationSize * 2 - 1) * rand() / RAND_MAX));
575 
576  if (CandidateValue[i] <= CandidateValue[RandomRival]) WinScore[i]++;
577  }
578  }
579 
580  // selection of top PopulationSize winners
581  for (i = 0; i < PopulationSize; i++)
582  {
583  for (j = i + 1; j < 2*PopulationSize; j++)
584  {if (WinScore[i] < WinScore[j]) swap(i, j);}
585  }
586 
587  break;
588 
589  // ranking strategy without proportionate-fitness
590  case 3:
591 
592  for (i = 0; i < PopulationSize; i++)
593  {
594  for (j = i + 1; j < 2*PopulationSize; j++)
595  {
596  if (CandidateValue[i] > CandidateValue[j]) exchange(i, j);
597  }
598  }
599 
600  break;
601  // Randomly select P individuals from population of 2P
602  case 4:
603 
604  for (i = 0; i < PopulationSize; i++)
605  {
606  RandomIndividual = (int)fabs(floor((PopulationSize * 2 - 1) * rand() / RAND_MAX));
607  exchange(i, RandomIndividual);
608  }
609 
610  break;
611 
612  // ranking strategy for EP2
613  case 5:
614 
615  for (i = 0; i < PopulationSize; i++)
616  {
617  for (j = i + 1; j < PopulationSize; j++)
618  {
619  if (CandidateValue[i] > CandidateValue[j]) exchange(i, j);
620  }
621  }
622 
623  for (i = 0; i < PopulationSize; i++)
624  {
625  CandidateValueRate[i] = (CandidateValue[i] - CandidateValue[0]) / (CandidateValue[PopulationSize - 1] - CandidateValue[0]);
626  }
627 
628  break;
629  }
630 }
COptMethodEP2::exchange
virtual void exchange(int o, int d)
Definition: COptMethodEP2.cpp:521
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
COptMethodEP2::swap
virtual void swap(int o, int d)
Definition: COptMethodEP2.cpp:499
COptMethodEP2::CandidateValueRate
double * CandidateValueRate
Definition: COptMethodEP2.h:62
void COptMethodEP2::Set_BestFoundSoFar ( int  num)
inline

Definition at line 187 of file COptMethodEP2.h.

References BestFoundSoFar.

188 {
189  BestFoundSoFar = num;
190 }
void COptMethodEP2::Set_CandidateValue ( int  i,
double  num 
)
inline

Definition at line 182 of file COptMethodEP2.h.

References CandidateValue.

183 {
184  CandidateValue[i] = num;
185 }
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
void COptMethodEP2::Set_individual ( int  i,
int  j,
double  num 
)
inline

Definition at line 177 of file COptMethodEP2.h.

References individual.

178 {
179  individual[i][j] = num;
180 }
COptMethodEP2::individual
CVector< CVector< C_FLOAT64 > > individual
Definition: COptMethodEP2.h:60
void COptMethodEP2::Set_Maximum ( double  num)
inline

Definition at line 172 of file COptMethodEP2.h.

References Maximum.

173 {
174  Maximum = num;
175 }
void COptMethodEP2::Set_Minimum ( double  num)
inline

Definition at line 168 of file COptMethodEP2.h.

References Minimum.

169 {
170  Minimum = num;
171 }
void COptMethodEP2::Set_murvar ( double  num)
void COptMethodEP2::Set_NumGeneration ( int  num)
inline

Definition at line 156 of file COptMethodEP2.h.

References NumGeneration.

157 {
158  NumGeneration = num;
159 }
void COptMethodEP2::Set_NumParameter ( int  num)
inline

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.

Definition at line 146 of file COptMethodEP2.h.

References NumParameter.

147 {
148  NumParameter = num;
149 }
void COptMethodEP2::Set_PopulationSize ( int  num)
inline

Definition at line 151 of file COptMethodEP2.h.

References PopulationSize.

152 {
153  PopulationSize = num;
154 }
void COptMethodEP2::swap ( int  o,
int  d 
)
virtual

Definition at line 499 of file COptMethodEP2.cpp.

References CandidateValue, individual, NumParameter, and WinScore.

Referenced by select().

500 {
501  int i;
502  double tmp;
503 
504  for (i = 0; i < NumParameter; i++)
505  {
506  tmp = individual[d][i];
507  individual[d][i] = individual[o][i];
508  individual[o][i] = tmp;
509  }
510 
511  tmp = CandidateValue[d];
512  CandidateValue[d] = CandidateValue[o];
513  CandidateValue[o] = tmp;
514 
515  i = WinScore[d];
516  WinScore[d] = WinScore[o];
517  WinScore[o] = i;
518 }
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
COptMethodEP2::individual
CVector< CVector< C_FLOAT64 > > individual
Definition: COptMethodEP2.h:60
void COptMethodEP2::TrackDataFile ( int  i)
virtual

Definition at line 652 of file COptMethodEP2.cpp.

References BestFoundSoFar, CandidateValue, individual, and NumParameter.

Referenced by optimise().

653 {
654  std::ofstream finalout("debugopt.dat", std::ios::app);
655 
656  if (!finalout)
657  {
658  std::cout << "debugopt.dat cannot be opened!" << std::endl;
659  exit(1);
660  }
661 
662  finalout << "#" << i << "\t" << std::setprecision(8) << CandidateValue[BestFoundSoFar] << std::endl;
663 
664  for (int j = 0; j < NumParameter; j++)
665  {
666  finalout << std::setprecision(8) << individual[BestFoundSoFar][j] << "\t";
667  }
668 
669  finalout << std::endl;
670  finalout << std::endl;
671 
672  finalout.close();
673 }
COptMethodEP2::CandidateValue
double * CandidateValue
Definition: COptMethodEP2.h:61
COptMethodEP2::individual
CVector< CVector< C_FLOAT64 > > individual
Definition: COptMethodEP2.h:60

Friends And Related Function Documentation

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

Member Data Documentation

int COptMethodEP2::BestFoundSoFar
private

Definition at line 56 of file COptMethodEP2.h.

Referenced by Get_BestFoundSoFar_candidate(), optimise(), Set_BestFoundSoFar(), and TrackDataFile().

double* COptMethodEP2::CandidateValue
private

Definition at line 61 of file COptMethodEP2.h.

Referenced by copy(), exchange(), fittest(), Get_BestFoundSoFar_candidate(), optimise(), select(), Set_CandidateValue(), swap(), and TrackDataFile().

double* COptMethodEP2::CandidateValueRate
private

Definition at line 62 of file COptMethodEP2.h.

Referenced by optimise(), and select().

int* COptMethodEP2::CrossPoint
private

Definition at line 64 of file COptMethodEP2.h.

Referenced by optimise().

CVector< CVector < C_FLOAT64 > > COptMethodEP2::individual
private

Definition at line 60 of file COptMethodEP2.h.

Referenced by copy(), exchange(), optimise(), Set_individual(), swap(), and TrackDataFile().

double COptMethodEP2::Maximum
private

Definition at line 54 of file COptMethodEP2.h.

Referenced by optimise(), and Set_Maximum().

double COptMethodEP2::Minimum
private

Definition at line 54 of file COptMethodEP2.h.

Referenced by optimise(), and Set_Minimum().

int COptMethodEP2::NumCrossPoint
private

Definition at line 52 of file COptMethodEP2.h.

int COptMethodEP2::NumGeneration
private

Definition at line 50 of file COptMethodEP2.h.

Referenced by Get_NumGeneration(), optimise(), and Set_NumGeneration().

int COptMethodEP2::NumParameter
private

Definition at line 57 of file COptMethodEP2.h.

Referenced by copy(), exchange(), Get_NumParameter(), optimise(), Set_NumParameter(), swap(), and TrackDataFile().

int COptMethodEP2::PopulationSize
private

Definition at line 51 of file COptMethodEP2.h.

Referenced by fittest(), Get_PopulationSize(), optimise(), select(), and Set_PopulationSize().

int* COptMethodEP2::WinScore
private

Definition at line 65 of file COptMethodEP2.h.

Referenced by optimise(), select(), and swap().

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