Migration from SVN

moeo/tutorial/CMakeLists.txt

@@ -0,0 +1,22 @@
+######################################################################################
+### 0) Include MO sources
+######################################################################################
+
+include_directories(${MO_SRC_DIR}/src)
+
+######################################################################################
+### 1) Define flowshop paths
+######################################################################################
+
+set(FLOWSHOP_SRC_DIR ${MOEO_SRC_DIR}/tutorial/examples/flowshop)
+set(FLOWSHOP_BINARY_DIR ${MOEO_BIN_DIR}/tutorial/examples/flowshop)
+
+######################################################################################
+### 2) Include lessons subdirectories
+######################################################################################
+
+add_subdirectory(examples)
+add_subdirectory(Lesson1)
+add_subdirectory(Lesson2)
+add_subdirectory(Lesson3)
+add_subdirectory(Lesson4)

moeo/tutorial/Lesson1/CMakeLists.txt

@@ -0,0 +1,23 @@
+# Lesson 1
+
+######################################################################################
+### 0) Define files
+######################################################################################
+
+set(files Sch1)
+
+######################################################################################
+### 1) Create the lesson 
+######################################################################################
+
+add_lesson(moeo Lesson1 "${files}")
+
+######################################################################################
+### 2) Include dependencies
+######################################################################################
+
+include_directories(${EO_SRC_DIR}/src
+                    ${EO_SRC_DIR}/utils
+					${MOEO_SRC_DIR}/src)
+
+

moeo/tutorial/Lesson1/Sch1.cpp

@@ -0,0 +1,140 @@
+/*
+* <Sch1.cpp>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Abdelhakim Deneche, Arnaud Liefooghe
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+
+#include <stdio.h>
+#include <moeo>
+#include <es/eoRealInitBounded.h>
+#include <es/eoRealOp.h>
+
+using namespace std;
+
+
+// the moeoObjectiveVectorTraits : minimizing 2 objectives
+class Sch1ObjectiveVectorTraits : public moeoObjectiveVectorTraits
+{
+public:
+    static bool minimizing (int i)
+    {
+        return true;
+    }
+    static bool maximizing (int i)
+    {
+        return false;
+    }
+    static unsigned int nObjectives ()
+    {
+        return 2;
+    }
+};
+
+
+// objective vector of real values
+typedef moeoRealObjectiveVector < Sch1ObjectiveVectorTraits > Sch1ObjectiveVector;
+
+
+// multi-objective evolving object for the Sch1 problem
+class Sch1 : public moeoRealVector < Sch1ObjectiveVector >
+{
+public:
+    Sch1() : moeoRealVector < Sch1ObjectiveVector > (1)
+    {}
+};
+
+
+// evaluation of objective functions
+class Sch1Eval : public moeoEvalFunc < Sch1 >
+{
+public:
+    void operator () (Sch1 & _sch1)
+    {
+        if (_sch1.invalidObjectiveVector())
+        {
+            Sch1ObjectiveVector objVec;
+            double x = _sch1[0];
+            objVec[0] = x * x;
+            objVec[1] = (x - 2.0) * (x - 2.0);
+            _sch1.objectiveVector(objVec);
+        }
+    }
+};
+
+
+// main
+int main (int argc, char *argv[])
+{
+    eoParser parser(argc, argv);  // for user-parameter reading
+    eoState state;                // to keep all things allocated
+
+    // parameters
+    unsigned int POP_SIZE = parser.createParam((unsigned int)(100), "popSize", "Population size",'P',"Param").value();
+    unsigned int MAX_GEN = parser.createParam((unsigned int)(100), "maxGen", "Maximum number of generations",'G',"Param").value();
+    double M_EPSILON = parser.createParam(0.01, "mutEpsilon", "epsilon for mutation",'e',"Param").value();
+    double P_CROSS = parser.createParam(0.25, "pCross", "Crossover probability",'C',"Param").value();
+    double P_MUT = parser.createParam(0.35, "pMut", "Mutation probability",'M',"Param").value();
+
+    // objective functions evaluation
+    Sch1Eval eval;
+
+    // crossover and mutation
+    eoQuadCloneOp < Sch1 > xover;
+    eoUniformMutation < Sch1 > mutation (M_EPSILON);
+
+    // generate initial population
+    eoRealVectorBounds bounds (1, 0.0, 2.0);	// [0, 2]
+    eoRealInitBounded < Sch1 > init (bounds);
+    eoPop < Sch1 > pop (POP_SIZE, init);
+
+    // build NSGA-II
+    moeoNSGAII < Sch1 > nsgaII (MAX_GEN, eval, xover, P_CROSS, mutation, P_MUT);
+
+    // help ?
+    make_help(parser);
+
+    // run the algo
+    nsgaII (pop);
+
+    // extract first front of the final population using an moeoArchive (this is the output of nsgaII)
+    moeoUnboundedArchive < Sch1 > arch;
+    arch(pop);
+
+    // printing of the final archive
+    cout << "Final Archive" << endl;
+    arch.sortedPrintOn (cout);
+    cout << endl;
+
+    return EXIT_SUCCESS;
+}

moeo/tutorial/Lesson1/Sch1.param

@@ -0,0 +1,14 @@
+
+######                 General    ######
+# --help=0                                 # -h : Prints this message
+# --stopOnUnknownParam=1                   # Stop if unkown param entered
+
+######    Param                   ######
+--popSize=100                            # -P : Population size
+--maxGen=100                             # -G : Maximum number of generations
+--mutEpsilon=0.01                        # -e : epsilon for mutation
+--pCross=0.25                            # -C : Crossover probability
+--pMut=0.35                              # -M : Mutation probability
+
+######    Persistence             ######
+# --status=./Sch1.status                   # Status file

moeo/tutorial/Lesson2/CMakeLists.txt

@@ -0,0 +1,23 @@
+# Lesson 2
+
+######################################################################################
+### 0) Define files
+######################################################################################
+
+set(files FlowShopEA)
+    
+######################################################################################
+### 1) Create the lesson 
+######################################################################################
+
+add_lesson(moeo Lesson2 "${files}")
+
+######################################################################################
+### 2) Include dependencies
+######################################################################################
+
+include_directories(${EO_SRC_DIR}/src)
+include_directories(${MOEO_SRC_DIR}/src)
+include_directories(${FLOWSHOP_SRC_DIR})
+
+target_link_libraries(FlowShopEA moeo flowshop eo eoutils)

moeo/tutorial/Lesson2/FlowShopEA.cpp

@@ -0,0 +1,139 @@
+/*
+* <FlowShopEA.cpp>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Arnaud Liefooghe
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+
+
+// moeo general include
+#include <moeo>
+// for the creation of an evaluator
+#include <make_eval_FlowShop.h>
+// for the creation of an initializer
+#include <make_genotype_FlowShop.h>
+// for the creation of the variation operators
+#include <make_op_FlowShop.h>
+// how to initialize the population
+#include <do/make_pop.h>
+// checks for help demand, and writes the status file and make_help; in libutils
+void make_help(eoParser & _parser);
+// definition of the representation
+#include <FlowShop.h>
+
+
+using namespace std;
+
+
+int main(int argc, char* argv[])
+{
+    try
+    {
+
+        eoParser parser(argc, argv);  // for user-parameter reading
+        eoState state;                // to keep all things allocated
+
+
+        /*** the representation-dependent things ***/
+
+        // The fitness evaluation
+        eoEvalFuncCounter<FlowShop>& eval = do_make_eval(parser, state);
+        // the genotype (through a genotype initializer)
+        eoInit<FlowShop>& init = do_make_genotype(parser, state);
+        // the variation operators
+        eoGenOp<FlowShop>& op = do_make_op(parser, state);
+
+
+        /*** the representation-independent things ***/
+
+        // initialization of the population
+        eoPop<FlowShop>& pop = do_make_pop(parser, state, init);
+        // definition of the archive
+        moeoUnboundedArchive<FlowShop> arch;
+        // stopping criteria
+        unsigned int maxGen = parser.createParam((unsigned int)(100), "maxGen", "Maximum number of gen.",'G',"Stopping criterion").value();
+        eoGenContinue<FlowShop> term(maxGen);
+        // checkpointing
+        eoCheckPoint<FlowShop> checkpoint(term);
+        moeoArchiveUpdater < FlowShop > updater(arch, pop);
+        checkpoint.add(updater);
+        // fitness assignment
+        moeoDominanceDepthFitnessAssignment <FlowShop> fitnessAssignment;
+        // diversity preservation
+        moeoFrontByFrontCrowdingDiversityAssignment <FlowShop> diversityAssignment;
+        // comparator
+        moeoFitnessThenDiversityComparator <FlowShop> comparator;
+        // selection scheme
+        moeoDetTournamentSelect <FlowShop> select(comparator, 2);
+        // replacement scheme
+        moeoElitistReplacement <FlowShop> replace(fitnessAssignment, diversityAssignment, comparator);
+        // breeder
+        eoGeneralBreeder <FlowShop> breed(select, op);
+        // algorithm
+        moeoEasyEA <FlowShop> algo (checkpoint, eval, breed, replace, fitnessAssignment, diversityAssignment);
+
+
+        /*** Go ! ***/
+
+        // help ?
+        make_help(parser);
+
+        // first evalution (for printing)
+        apply<FlowShop>(eval, pop);
+
+        // printing of the initial population
+        cout << "Initial Population\n";
+        pop.sortedPrintOn(cout);
+        cout << endl;
+
+        // run the algo
+        algo(pop);
+
+        // printing of the final population
+        cout << "Final Population\n";
+        pop.sortedPrintOn(cout);
+        cout << endl;
+
+        // printing of the final archive
+        cout << "Final Archive\n";
+        arch.sortedPrintOn(cout);
+        cout << endl;
+
+
+    }
+    catch (exception& e)
+    {
+        cout << e.what() << endl;
+    }
+    return EXIT_SUCCESS;
+}

moeo/tutorial/Lesson2/FlowShopEA.param

@@ -0,0 +1,21 @@
+
+######                 General    ######
+--help=0                                   # -h : Prints this message
+--stopOnUnknownParam=1                     # Stop if unkown param entered
+# --seed=1203083493                        # -S : Random number seed
+
+######    Evolution Engine        ######
+--popSize=100                              # -P : Population Size
+
+######    Representation          ######
+--BenchmarkFile=../examples/flowshop/benchs/020_10_01.txt # -B : Benchmark file name REQUIRED
+
+######    Stopping criterion      ######
+--maxGen=100                               # -G : Maximum number of generations
+
+######    Variation Operators     ######
+--crossRate=1                              # Relative rate for the only crossover
+--shiftMutRate=0.5                         # Relative rate for shift mutation
+--exchangeMutRate=0.5                      # Relative rate for exchange mutation
+--pCross=0.25                              # -c : Probability of Crossover
+--pMut=0.35                                # -m : Probability of Mutation

moeo/tutorial/Lesson3/CMakeLists.txt

@@ -0,0 +1,23 @@
+# Lesson 3
+
+######################################################################################
+### 0) Define files
+######################################################################################
+
+set(files FlowShopEA2)
+    
+######################################################################################
+### 1) Create the lesson 
+######################################################################################
+
+add_lesson(moeo Lesson3 "${files}")
+
+######################################################################################
+### 2) Include dependencies
+######################################################################################
+
+include_directories(${EO_SRC_DIR}/src)
+include_directories(${MOEO_SRC_DIR}/src)
+include_directories(${FLOWSHOP_SRC_DIR})
+
+target_link_libraries(FlowShopEA2 moeo flowshop eo eoutils)

moeo/tutorial/Lesson3/FlowShopEA2.cpp

@@ -0,0 +1,132 @@
+/*
+* <FlowShopEA.cpp>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Arnaud Liefooghe
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+
+
+// moeo general include
+#include <moeo>
+// for the creation of an evaluator
+#include <make_eval_FlowShop.h>
+// for the creation of an initializer
+#include <make_genotype_FlowShop.h>
+// for the creation of the variation operators
+#include <make_op_FlowShop.h>
+// how to initialize the population
+#include <do/make_pop.h>
+// the stopping criterion
+#include <do/make_continue_moeo.h>
+// outputs (stats, population dumps, ...)
+#include <do/make_checkpoint_moeo.h>
+// evolution engine (selection and replacement)
+#include <do/make_ea_moeo.h>
+// simple call to the algo
+#include <do/make_run.h>
+// checks for help demand, and writes the status file and make_help; in libutils
+void make_help(eoParser & _parser);
+// definition of the representation
+#include <FlowShop.h>
+
+
+using namespace std;
+
+
+int main(int argc, char* argv[])
+{
+  try
+    {
+
+      eoParser parser(argc, argv);  // for user-parameter reading
+      eoState state;                // to keep all things allocated
+
+
+      /*** the representation-dependent things ***/
+
+      // The fitness evaluation
+      eoEvalFuncCounter<FlowShop>& eval = do_make_eval(parser, state);
+      // the genotype (through a genotype initializer)
+      eoInit<FlowShop>& init = do_make_genotype(parser, state);
+      // the variation operators
+      eoGenOp<FlowShop>& op = do_make_op(parser, state);
+
+
+      /*** the representation-independent things ***/
+
+      // initialization of the population
+      eoPop<FlowShop>& pop = do_make_pop(parser, state, init);
+      // definition of the archive
+      moeoUnboundedArchive<FlowShop> arch;
+      // stopping criteria
+      eoContinue<FlowShop>& term = do_make_continue_moeo(parser, state, eval);
+      // output
+      eoCheckPoint<FlowShop>& checkpoint = do_make_checkpoint_moeo(parser, state, eval, term, pop, arch);
+      // algorithm
+      eoAlgo<FlowShop>& algo = do_make_ea_moeo(parser, state, eval, checkpoint, op, arch);
+
+
+      /*** Go ! ***/
+
+      // help ?
+      make_help(parser);
+
+      // first evalution (for printing)
+      apply<FlowShop>(eval, pop);
+
+      // printing of the initial population
+      cout << "Initial Population\n";
+      pop.sortedPrintOn(cout);
+      cout << endl;
+
+      // run the algo
+      algo(pop);
+
+      // printing of the final population
+      cout << "Final Population\n";
+      pop.sortedPrintOn(cout);
+      cout << endl;
+
+      // printing of the final archive
+      cout << "Final Archive\n";
+      arch.sortedPrintOn(cout);
+      cout << endl;
+
+
+    }
+  catch (exception& e)
+    {
+      cout << e.what() << endl;
+    }
+  return EXIT_SUCCESS;
+}

moeo/tutorial/Lesson3/FlowShopEA2.param

@@ -0,0 +1,49 @@
+
+######                 General    ######
+--help=0                                   # -h : Prints this message
+--stopOnUnknownParam=1                     # Stop if unkown param entered
+# --seed=1183379758                        # -S : Random number seed
+
+######    Evolution Engine        ######
+--popSize=100                              # -P : Population Size
+--updateArch=1                             # Update the archive at each gen.
+--fitness=IndicatorBased                 # -F : Fitness assignment scheme: Dummy, DomDepth or IndicatorBased
+--indicator=Epsilon                        # -i : Binary indicator for IndicatorBased: Epsilon, Hypervolume
+--rho=1.1                                  # -r : reference point for the hypervolume indicator
+--kappa=0.05                               # -k : Scaling factor kappa for IndicatorBased
+--diversity=Crowding                       # -D : Diversity assignment scheme: Dummy, Sharing(nicheSize) or Crowding
+--comparator=FitnessThenDiversity          # -C : Comparator scheme: FitnessThenDiversity, DiversityThenFitness or Aggregative
+--selection=DetTour(2)                     # -S : Selection scheme: DetTour(T), StochTour(t) or Random
+--replacement=Elitist                      # -R : Replacement scheme: Elitist, Environmental or Generational
+--nbOffspring=100%                         # -O : Number of offspring (percentage or absolute)
+
+######    Output                  ######
+--resDir=Res                               # Directory to store DISK outputs
+--eraseDir=1                               # erase files in dirName if any
+--printPop=0                               # Print sorted pop. every gen.
+--storeArch=0                              # Store the archive's objective vectors at each gen.
+--contribution=0                           # Store the contribution of the archive at each gen.
+--entropy=0                                # Store the entropy of the archive at each gen.
+
+######    Persistence             ######
+--Load=                                    # -L : A save file to restart from
+--recomputeFitness=0                       # -r : Recompute the fitness after re-loading the pop.?
+--saveFrequency=0                          # Save every F generation (0 = only final state, absent = never)
+--saveTimeInterval=0                       # Save every T seconds (0 or absent = never)
+--status=./FlowShopEA.status               # Status file
+
+######    Representation          ######
+--BenchmarkFile=../examples/flowshop/benchs/020_10_01.txt  # -B : Benchmark file name REQUIRED
+
+######    Stopping criterion      ######
+--maxGen=100                               # -G : Maximum number of generations (0 = none)
+--maxEval=0                                # -E : Maximum number of evaluations (0 = none)
+--maxTime=0                                # -T : Maximum running time in seconds (0 = none)
+#--CtrlC=1                                 # -C : Terminate current generation upon Ctrl C (only available on Unix platforms)
+
+######    Variation Operators     ######
+--crossRate=1                              # Relative rate for the only crossover
+--shiftMutRate=0.5                         # Relative rate for shift mutation
+--exchangeMutRate=0.5                      # Relative rate for exchange mutation
+--pCross=0.25                              # -c : Probability of Crossover
+--pMut=0.35                                # -m : Probability of Mutation

moeo/tutorial/Lesson4/CMakeLists.txt

@@ -0,0 +1,23 @@
+# Lesson 4
+
+######################################################################################
+### 0) Define files
+######################################################################################
+
+set(files FlowShopDMLS)
+    
+######################################################################################
+### 1) Create the lesson 
+######################################################################################
+
+add_lesson(moeo Lesson4 "${files}")
+
+include_directories(${EO_SRC_DIR}/src)
+include_directories(${MOEO_SRC_DIR}/src)
+include_directories(${FLOWSHOP_SRC_DIR})
+
+######################################################################################
+### 2) Include dependencies
+######################################################################################
+
+target_link_libraries(FlowShopDMLS moeo flowshop eo eoutils)

moeo/tutorial/Lesson4/FlowShopDMLS.cpp

@@ -0,0 +1,144 @@
+/*
+* <FlowShopDMLS.cpp>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Arnaud Liefooghe
+* Jérémie Humeau
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+
+
+// moeo general include
+#include <moeo>
+// for the creation of an evaluator
+#include <make_eval_FlowShop.h>
+// for the creation of an initializer
+#include <make_genotype_FlowShop.h>
+// for the creation of the variation operators
+#include <make_op_FlowShop.h>
+// how to initialize the population
+#include <do/make_pop.h>
+// checks for help demand, and writes the status file and make_help; in libutils
+void make_help(eoParser & _parser);
+// definition of the representation
+#include <FlowShop.h>
+
+#include <problems/permutation/moShiftNeighbor.h>
+#include <neighborhood/moOrderNeighborhood.h>
+#include <utils/moeoFullEvalByCopy.h>
+
+using namespace std;
+
+
+int main(int argc, char* argv[])
+{
+    try
+    {
+
+    	//define a neighbor
+        typedef moShiftNeighbor<FlowShop, FlowShopObjectiveVector> Neighbor;
+
+        eoParser parser(argc, argv);  // for user-parameter reading
+        eoState state;                // to keep all things allocated
+
+        unsigned int maxGen = parser.createParam((unsigned int)(100), "maxGen", "Maximum number of gen.",'G',"Stopping criterion").value();
+        unsigned int nhSize = parser.createParam((unsigned int)(20), "nhSize", "neighborhood size",'G',"Evolution Engine").value();
+
+        /*** the representation-dependent things ***/
+
+        // The fitness evaluation
+        eoEvalFuncCounter<FlowShop>& eval = do_make_eval(parser, state);
+        // the genotype (through a genotype initializer)
+        eoInit<FlowShop>& init = do_make_genotype(parser, state);
+
+        /*** the representation-independent things ***/
+
+        // initialization of the population
+        eoPop<FlowShop>& pop = do_make_pop(parser, state, init);
+        // definition of the archive
+        moeoUnboundedArchive<FlowShop> arch;
+        // stopping criteria
+
+        //Continuator
+        eoGenContinue<FlowShop> term(maxGen);
+
+        // checkpointing
+        eoCheckPoint<FlowShop> checkpoint(term);
+        moeoArchiveUpdater < FlowShop > updater(arch, pop);
+        checkpoint.add(updater);
+
+        //neighborhood
+        moOrderNeighborhood<Neighbor> neighborhood((nhSize-1) * (nhSize-1));
+        //neighbor Evaluation function
+        moeoFullEvalByCopy<Neighbor> moEval(eval);
+
+        //Selection in the archive
+        moeoNumberUnvisitedSelect<FlowShop> select(1);
+        //explorer
+        moeoFirstImprovingNeighborhoodExplorer<Neighbor> explor(neighborhood, moEval);
+
+        //DMLS(1.1>)
+        moeoUnifiedDominanceBasedLS<Neighbor> algo(checkpoint, eval, arch, explor, select);
+
+
+        /*** Go ! ***/
+
+        // help ?
+        make_help(parser);
+
+        // first evalution (for printing)
+        apply<FlowShop>(eval, pop);
+        for(unsigned int i=0; i<pop.size(); i++)
+        	pop[i].fitness(0);
+
+
+        // printing of the initial population
+        cout << "Initial Population\n";
+        pop.sortedPrintOn(cout);
+        cout << endl;
+
+        // run the algo
+        algo(pop);
+
+        // printing of the final archive
+        cout << "Final Archive\n";
+        arch.sortedPrintOn(cout);
+        cout << endl;
+
+
+    }
+    catch (exception& e)
+    {
+        cout << e.what() << endl;
+    }
+    return EXIT_SUCCESS;
+}

moeo/tutorial/Lesson4/FlowShopDMLS.param

@@ -0,0 +1,20 @@
+
+######                 General    ######
+# --help=0                                 # -h : Prints this message
+# --stopOnUnknownParam=1                   # Stop if unkown param entered
+# --seed=1275660123                        # -S : Random number seed
+
+######    Evolution Engine        ######
+# --nhSize=20                              # -G : neighborhood size
+# --popSize=20                             # -P : Population Size
+
+######    Persistence             ######
+# --Load=                                  # -L : A save file to restart from
+# --recomputeFitness=0                     # -r : Recompute the fitness after re-loading the pop.?
+# --status=./FlowShopDMLS.status           # Status file
+
+######    Representation          ######
+# --BenchmarkFile=../examples/flowshop/benchs/020_20_01.txt # -B : Benchmark file name
+
+######    Stopping criterion      ######
+# --maxGen=100                             # -G : Maximum number of gen.

moeo/tutorial/examples/CMakeLists.txt

@@ -0,0 +1,6 @@
+######################################################################################
+### 0) Include subdirectories
+######################################################################################
+
+add_subdirectory(flowshop)
+

moeo/tutorial/examples/flowshop/CMakeLists.txt

@@ -0,0 +1,49 @@
+######################################################################################
+### 0) Include lessons subdirectories
+######################################################################################
+
+include_directories(${EO_SRC_DIR}/src)
+include_directories(${MOEO_SRC_DIR}/src)
+include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+
+######################################################################################
+### 2) Define output paths
+######################################################################################
+
+set(FLOWSHOP_LIB_OUTPUT_PATH ${FLOWSHOP_BINARY_DIR}/lib)
+set(LIBRARY_OUTPUT_PATH ${FLOWSHOP_LIB_OUTPUT_PATH})
+
+######################################################################################
+### 3) Set flowshop sources
+######################################################################################
+
+set(FLOWSHOP_SOURCES   
+        FlowShopBenchmarkParser.cpp 
+        FlowShopEval.cpp 
+        FlowShopObjectiveVectorTraits.cpp 
+        FlowShopOpCrossoverQuad.cpp 
+        FlowShop.cpp)
+
+######################################################################################
+### 4) Create flowshop library
+######################################################################################
+
+add_library(flowshop STATIC ${FLOWSHOP_SOURCES})
+add_dependencies(flowshop moeo)
+
+target_link_libraries(flowshop eo)
+
+install(TARGETS flowshop ARCHIVE DESTINATION local/${LIB} COMPONENT libraries)
+
+######################################################################################
+### 5) Installing benchs
+######################################################################################
+
+install(DIRECTORY benchs DESTINATION local/include${INSTALL_SUB_DIR}/moeo/tutorial/flowshop COMPONENT tutorial)
+
+######################################################################################
+### 6) Look for headers
+######################################################################################
+
+file(GLOB HDRS *.h)
+install(FILES ${HDRS} DESTINATION local/include${INSTALL_SUB_DIR}/moeo/tutorial/examples/flowshop COMPONENT headers)

moeo/tutorial/examples/flowshop/FlowShop.cpp

@@ -0,0 +1,43 @@
+/*
+* <FlowShop.cpp>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Arnaud Liefooghe
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+
+#include <FlowShop.h>
+
+std::string FlowShop::className() const
+  {
+    return "FlowShop";
+  }

moeo/tutorial/examples/flowshop/FlowShop.h

@@ -0,0 +1,58 @@
+/*
+* <FlowShop.h>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Arnaud Liefooghe
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+
+#ifndef FLOWSHOP_H_
+#define FLOWSHOP_H_
+
+#include <core/moeoVector.h>
+#include <FlowShopObjectiveVector.h>
+
+/**
+ *  Structure of the genotype for the flow-shop scheduling problem: a vector of unsigned int int.
+ */
+class FlowShop: public moeoVector < FlowShopObjectiveVector , unsigned int >
+  {
+  public:
+
+    /**
+     * class name
+     */
+    std::string className() const;
+
+  };
+
+#endif /*FLOWSHOP_H_*/

moeo/tutorial/examples/flowshop/FlowShopBenchmarkParser.cpp

@@ -0,0 +1,136 @@
+/*
+* <FlowShopBenchmarkParser.cpp>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Arnaud Liefooghe
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+#include <iostream>
+#include <stdexcept>
+#include "FlowShopBenchmarkParser.h"
+
+FlowShopBenchmarkParser::FlowShopBenchmarkParser(const std::string _benchmarkFileName)
+{
+    init(_benchmarkFileName);
+}
+
+
+const unsigned int FlowShopBenchmarkParser::getM()
+{
+    return M;
+}
+
+
+const unsigned int FlowShopBenchmarkParser::getN()
+{
+    return N;
+}
+
+
+const std::vector< std::vector<unsigned int> > FlowShopBenchmarkParser::getP()
+{
+    return p;
+}
+
+
+const std::vector<unsigned int> FlowShopBenchmarkParser::getD()
+{
+    return d;
+}
+
+
+void FlowShopBenchmarkParser::printOn(std::ostream & _os) const
+{
+    _os << "M=" << M << " N=" << N << std::endl;
+    _os << "*** processing times" << std::endl;
+    for (unsigned int i=0; i<M; i++)
+    {
+        for (unsigned int j=0; j<N; j++)
+        {
+            _os << p[i][j] << " ";
+        }
+        _os << std::endl;
+    }
+    _os << "*** due-dates" << std::endl;
+    for (unsigned int j=0; j<N; j++)
+    {
+        _os << d[j] << " ";
+    }
+    _os << std::endl << std::endl;
+}
+
+
+void FlowShopBenchmarkParser::init(const std::string _benchmarkFileName)
+{
+    std::string buffer;
+    std::string::size_type start, end;
+    std::ifstream inputFile(_benchmarkFileName.data(), std::ios::in);
+    // opening of the benchmark file
+    if (! inputFile)
+        throw std::runtime_error("*** ERROR : Unable to open the benchmark file");
+    // number of jobs (N)
+    getline(inputFile, buffer, '\n');
+    N = atoi(buffer.data());
+    // number of machines M
+    getline(inputFile, buffer, '\n');
+    M = atoi(buffer.data());
+    // initial and current seeds (not used)
+    getline(inputFile, buffer, '\n');
+    // processing times and due-dates
+    // p = std::vector< std::vector<unsigned int> > (M,N);
+    p.resize(M);
+    for (unsigned int j=0 ; j<M ; j++)
+    {
+        p[j].resize(N);
+    }
+    d = std::vector<unsigned int> (N);
+    // for each job...
+    for (unsigned int j=0 ; j<N ; j++)
+    {
+        // index of the job (<=> j)
+        getline(inputFile, buffer, '\n');
+        // due-date of the job j
+        getline(inputFile, buffer, '\n');
+        d[j] = atoi(buffer.data());
+        // processing times of the job j on each machine
+        getline(inputFile, buffer, '\n');
+        start = buffer.find_first_not_of(" ");
+        for (unsigned int i=0 ; i<M ; i++)
+        {
+            end = buffer.find_first_of(" ", start);
+            p[i][j] = atoi(buffer.substr(start, end-start).data());
+            start = buffer.find_first_not_of(" ", end);
+        }
+    }
+    // closing of the input file
+    inputFile.close();
+}

moeo/tutorial/examples/flowshop/FlowShopBenchmarkParser.h

@@ -0,0 +1,110 @@
+/*
+* <FlowShopBenchmarkParser.h>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Arnaud Liefooghe
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+
+#ifndef FLOWSHOPBENCHMARKPARSER_H_
+#define FLOWSHOPBENCHMARKPARSER_H_
+
+#include <stdlib.h>
+#include <fstream>
+#include <string>
+#include <vector>
+
+/**
+ * Class to handle parameters of a flow-shop instance from a benchmark file
+ */
+class FlowShopBenchmarkParser
+  {
+  public:
+
+    /**
+     * Ctor
+     * @param _benchmarkFileName the name of the benchmark file
+     */
+    FlowShopBenchmarkParser(const std::string _benchmarkFileName);
+
+
+    /**
+     * the number of machines
+     */
+    const unsigned int getM();
+
+
+    /**
+     * the number of jobs
+     */
+    const unsigned int getN();
+
+
+    /**
+     * the processing times
+     */
+    const std::vector < std::vector < unsigned int > > getP();
+
+
+    /**
+     * the due-dates
+     */
+    const std::vector < unsigned int > getD();
+
+
+    /**
+     * printing...
+     */
+    void printOn(std::ostream & _os) const;
+
+
+  private:
+
+    /** number of machines */
+    unsigned int M;
+    /** number of jobs */
+    unsigned int N;
+    /** p[i][j] = processing time of job j on machine i */
+    std::vector < std::vector < unsigned int > > p;
+    /** d[j] = due-date of the job j */
+    std::vector < unsigned int > d;
+
+
+    /**
+     * Initialisation of the parameters with the data contained in the benchmark file
+     * @param _benchmarkFileName the name of the benchmark file
+     */
+    void init(const std::string _benchmarkFileName);
+
+  };
+
+#endif /*FLOWSHOPBENCHMARKPARSER_H_*/

moeo/tutorial/examples/flowshop/FlowShopEval.cpp

@@ -0,0 +1,95 @@
+/*
+* <FlowShopEval.cpp>
+* Copyright (C) DOLPHIN Project-Team, INRIA Futurs, 2006-2007
+* (C) OPAC Team, LIFL, 2002-2007
+*
+* Arnaud Liefooghe
+*
+* This software is governed by the CeCILL license under French law and
+* abiding by the rules of distribution of free software.  You can  use,
+* modify and/ or redistribute the software under the terms of the CeCILL
+* license as circulated by CEA, CNRS and INRIA at the following URL
+* "http://www.cecill.info".
+*
+* As a counterpart to the access to the source code and  rights to copy,
+* modify and redistribute granted by the license, users are provided only
+* with a limited warranty  and the software's author,  the holder of the
+* economic rights,  and the successive licensors  have only  limited liability.
+*
+* In this respect, the user's attention is drawn to the risks associated
+* with loading,  using,  modifying and/or developing or reproducing the
+* software by the user in light of its specific status of free software,
+* that may mean  that it is complicated to manipulate,  and  that  also
+* therefore means  that it is reserved for developers  and  experienced
+* professionals having in-depth computer knowledge. Users are therefore
+* encouraged to load and test the software's suitability as regards their
+* requirements in conditions enabling the security of their systems and/or
+* data to be ensured and,  more generally, to use and operate it in the
+* same conditions as regards security.
+* The fact that you are presently reading this means that you have had
+* knowledge of the CeCILL license and that you accept its terms.
+*
+* ParadisEO WebSite : http://paradiseo.gforge.inria.fr
+* Contact: paradiseo-help@lists.gforge.inria.fr
+*
+*/
+//-----------------------------------------------------------------------------
+
+#include <FlowShopEval.h>
+
+
+FlowShopEval::FlowShopEval(unsigned int _M, unsigned int _N, const std::vector< std::vector<unsigned int> > & _p, const std::vector<unsigned int> & _d) :
+        M(_M), N (_N), p(_p), d(_d)
+{}
+
+
+void FlowShopEval::operator()(FlowShop & _flowshop)
+{
+    FlowShopObjectiveVector objVector;
+    objVector[0] = makespan(_flowshop);
+    objVector[1] = tardiness(_flowshop);
+    _flowshop.objectiveVector(objVector);
+}
+
+
+
+double FlowShopEval::makespan(const FlowShop & _flowshop)
+{
+    // completion times computation for each job on each machine
+    // C[i][j] = completion of the jth job of the scheduling on the ith machine
+    std::vector< std::vector<unsigned int> > C = completionTime(_flowshop);
+    return C[M-1][_flowshop[N-1]];
+}
+
+
+double FlowShopEval::tardiness(const FlowShop & _flowshop)
+{
+    // completion times computation for each job on each machine
+    // C[i][j] = completion of the jth job of the scheduling on the ith machine
+    std::vector< std::vector<unsigned int> > C = completionTime(_flowshop);
+    // tardiness computation
+    unsigned int long sum = 0;
+    for (unsigned int j=0 ; j<N ; j++)
+        sum += (unsigned int) std::max (0, (int) (C[M-1][_flowshop[j]] - d[_flowshop[j]]));
+    return sum;
+}
+
+
+std::vector< std::vector<unsigned int> > FlowShopEval::completionTime(const FlowShop & _flowshop)
+{
+    std::vector< std::vector<unsigned int> > C;
+    C.resize(M);
+    for (unsigned int i=0;i<M;i++)
+    {
+        C[i].resize(N);
+    }
+    C[0][_flowshop[0]] = p[0][_flowshop[0]];
+    for (unsigned int j=1; j<N; j++)
+        C[0][_flowshop[j]] = C[0][_flowshop[j-1]] + p[0][_flowshop[j]];
+    for (unsigned int i=1; i<M; i++)
+        C[i][_flowshop[0]] = C[i-1][_flowshop[0]] + p[i][_flowshop[0]];
+    for (unsigned int i=1; i<M; i++)
+        for (unsigned int j=1; j<N; j++)
+            C[i][_flowshop[j]] = std::max(C[i][_flowshop[j-1]], C[i-1][_flowshop[j]]) + p[i][_flowshop[j]];
+    return C;
+}