* Add problems/DTLZ from http://paradiseo.gforge.inria.fr/index.php?n=Problems.DTLZ

problems/DTLZ/CMakeLists.txt

@@ -0,0 +1,106 @@
+######################################################################################
+### 0) Set your application properties
+######################################################################################
+# check cmake version compatibility
+CMAKE_MINIMUM_REQUIRED(VERSION 2.6)
+
+# Define your project name
+PROJECT(DTLZ)
+
+SET(PACKAGE_NAME "DTLZ" CACHE STRING "Package name" FORCE)
+SET(PACKAGE_VERSION "1.0" CACHE STRING "Package version" FORCE)
+
+# regular expression checking
+INCLUDE_REGULAR_EXPRESSION("^.*$" "^$")
+
+# set a language for the entire project.
+ENABLE_LANGUAGE(CXX)
+ENABLE_LANGUAGE(C)
+
+######################################################################################
+
+######################################################################################
+### 1) Include the install configuration file where are defined the main variables
+######################################################################################
+
+INCLUDE(${DTLZ_SOURCE_DIR}/install.cmake)
+
+######################################################################################
+
+######################################################################################
+### 2) Include the sources
+######################################################################################
+######################################
+### Include required modules & utilities
+#####################################################################################
+INCLUDE(CMakeBackwardCompatibilityCXX)
+
+INCLUDE(FindDoxygen)
+
+INCLUDE(CheckLibraryExists)
+               
+INCLUDE(Dart OPTIONAL) 
+                           
+# Set a special flag if the environment is windows (should do the same in a config.g file)
+IF (WIN32)
+	ADD_DEFINITIONS(-D_WINDOWS=1)
+ENDIF (WIN32)
+
+######################################################################################
+
+#####################################################################################
+### Manage the build type
+#####################################################################################
+
+# the user should choose the build type on windows environments,excepted under cygwin (default=none)
+SET(CMAKE_DEFAULT_BUILD_TYPE "Release" CACHE STRING "Variable that stores the default CMake build type" FORCE)
+
+FIND_PROGRAM(MEMORYCHECK_COMMAND
+    NAMES purify valgrind
+    PATHS
+    "/usr/local/bin /usr/bin [HKEY_LOCAL_MACHINE\\SOFTWARE\\Rational Software\\Purify\\Setup;InstallFolder]"
+    DOC "Path to the memory checking command, used for memory error detection.") 
+       
+IF(NOT CMAKE_BUILD_TYPE)
+     SET( CMAKE_BUILD_TYPE 
+          ${CMAKE_DEFAULT_BUILD_TYPE} CACHE STRING 
+          "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." 
+           FORCE)
+ENDIF(NOT CMAKE_BUILD_TYPE)  
+  
+IF(WIN32 AND NOT CYGWIN)
+  IF(CMAKE_CXX_COMPILER MATCHES cl)
+   IF(NOT WITH_SHARED_LIBS)
+     IF(CMAKE_GENERATOR STREQUAL "Visual Studio 8 2005" OR CMAKE_GENERATOR STREQUAL "Visual Studio 9 2008")
+       SET(CMAKE_CXX_FLAGS "/nologo /Gy")
+       SET(CMAKE_CXX_FLAGS_DEBUG "/W3 /MTd /Z7 /Od")
+       SET(CMAKE_CXX_FLAGS_RELEASE "/w /MT /O2 /wd4530")
+       SET(CMAKE_CXX_FLAGS_MINSIZEREL "/MT /O2")
+       SET(CMAKE_CXX_FLAGS_RELWITHDEBINFO "/MTd /Z7 /Od")
+       SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /SUBSYSTEM:CONSOLE")  
+      ENDIF(CMAKE_GENERATOR STREQUAL "Visual Studio 8 2005" OR CMAKE_GENERATOR STREQUAL "Visual Studio 9 2008")
+   ENDIF(NOT WITH_SHARED_LIBS)
+  ENDIF(CMAKE_CXX_COMPILER MATCHES cl)  
+ELSE(WIN32 AND NOT CYGWIN)
+    IF(CMAKE_COMPILER_IS_GNUCXX)
+       SET(CMAKE_CXX_FLAGS_DEBUG  "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g -fprofile-arcs -ftest-coverage -Wall -Wextra -Wno-unused-parameter")                       
+       SET(CMAKE_CXX_FLAGS_RELEASE  "${CMAKE_CXX_FLAGS_RELEASE} -O2")
+       SET(CMAKE_CXX_FLAGS_MINSIZEREL "${CMAKE_CXX_FLAGS_MINSIZEREL} -O6")       
+    ENDIF(CMAKE_COMPILER_IS_GNUCXX)  
+ENDIF(WIN32 AND NOT CYGWIN)
+
+IF(CMAKE_BUILD_TYPE MATCHES Debug)
+    ADD_DEFINITIONS(-DCMAKE_VERBOSE_MAKEFILE=ON)
+ENDIF(CMAKE_BUILD_TYPE MATCHES Debug)
+
+######################################################################################
+### 3) Link the librairies for your executable
+######################################################################################
+
+ADD_SUBDIRECTORY(doc)
+ADD_SUBDIRECTORY(src)
+ADD_SUBDIRECTORY(test)
+ADD_SUBDIRECTORY(application)
+
+######################################################################################
+

problems/DTLZ/README.txt

@@ -0,0 +1,45 @@
+This package contains the source code for DTLZ problems.
+
+# Step 1 - Configuration
+------------------------
+Edit the "install.cmake" file by entering the FULL PATH of the "ParadisEO".
+On Windows write your path with double antislash (ex: C:\\Users\\...)
+
+
+# Step 2 - Build process
+------------------------
+ParadisEO is assumed to be compiled. To download ParadisEO, please visit http://paradiseo.gforge.inria.fr/.
+Go to the DLTZ/build/ directory and lunch cmake:
+(Unix)       > cmake ..
+(Windows)    > cmake .. -G"Visual Studio 9 2008"
+
+Note for windows users: if you don't use VisualStudio 9, enter the name of your generator instead of "VisualStudio 9 2008".
+
+
+# Step 3 - Compilation
+----------------------
+In the DTLZ/build/ directory:
+(Unix)       > make
+(Windows)    Open the VisualStudio solution and compile it (Windows).
+You can refer to this tutorial if you don't know how to compile a solution: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial
+
+
+# Step 4 - Execution
+---------------------
+A toy example is given to test the components. You can run these tests as following.
+To define problem-related components for your own problem, please refer to the tutorials available on the website : http://paradiseo.gforge.inria.fr/.
+In the DTLZ/build/ directory:
+(Unix)       > ctest
+Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial
+
+In the directory "application", there are three ".cpp" which instantiate IBEA, NSGAII and SPEA2 on ZDT problems. To change of algorithms, you can compare these three files and see the few changes to do.
+
+(Unix) After compilation you can run the script "DTLZ/run.sh" and see results in "IBEA.out", "NSGAII.out" and "SPEA2.out". Parameters can be modified in the script.
+
+(Windows) Add argument "IBEA.param", "SPEA2.param" or "NSGAII.param" and execute the corresponding algorithms.
+Windows users, please refer to this tutorial: http://paradiseo.gforge.inria.fr/index.php?n=Paradiseo.VisualCTutorial
+
+# Documentation
+---------------
+The API-documentation is available in doc/html/index.html 
+

problems/DTLZ/application/CMakeLists.txt

@@ -0,0 +1,76 @@
+######################################################################################
+### 1) Include the sources
+######################################################################################
+
+INCLUDE_DIRECTORIES(${PARADISEO_EO_SRC_DIR}/src
+                    ${PARADISEO_MO_SRC_DIR}/src
+                    ${PARADISEO_MOEO_SRC_DIR}/src
+                    ${DTLZ_SOURCE_DIR}/src)
+
+######################################################################################
+
+
+######################################################################################
+### 2) Specify where CMake can find the libraries
+######################################################################################
+
+LINK_DIRECTORIES(${PARADISEO_EO_BIN_DIR}/lib)
+LINK_DIRECTORIES(${PARADISEO_MOEO_BIN_DIR}/lib)
+LINK_DIRECTORIES(${DTLZ_BINARY_DIR}/lib)
+######################################################################################
+
+
+######################################################################################
+### 3) Define your target: just an executable here
+######################################################################################
+
+ADD_EXECUTABLE(DTLZ_SPEA2 DTLZ_SPEA2.cpp)
+ADD_EXECUTABLE(DTLZ_NSGAII DTLZ_NSGAII.cpp)
+ADD_EXECUTABLE(DTLZ_IBEA DTLZ_IBEA.cpp)
+ADD_DEPENDENCIES(DTLZ_SPEA2 lDTLZ)
+ADD_DEPENDENCIES(DTLZ_NSGAII lDTLZ)
+ADD_DEPENDENCIES(DTLZ_IBEA lDTLZ)
+
+######################################################################################
+
+
+######################################################################################
+### 4) Link the librairies for your executable
+######################################################################################
+
+# Only if you need to link libraries
+TARGET_LINK_LIBRARIES(DTLZ_SPEA2 moeo eo eoutils lDTLZ)
+TARGET_LINK_LIBRARIES(DTLZ_NSGAII moeo eo eoutils lDTLZ)
+TARGET_LINK_LIBRARIES(DTLZ_IBEA moeo eo eoutils lDTLZ)
+
+######################################################################################
+
+
+######################################################################################
+### 5) Copy the instances and the "param" file in the build path for an easy use.
+### 
+### --> run the "make install" target to copy the parameter file / instances
+###	in the directory where you build the application
+######################################################################################
+
+ADD_CUSTOM_TARGET(install DEPENDS ${DTLZ_SOURCE_DIR}/application/IBEA.param
+				  ${DTLZ_SOURCE_DIR}/application/NSGAII.param
+				  ${DTLZ_SOURCE_DIR}/application/SPEA2.param
+				  ${DTLZ_SOURCE_DIR}/application)
+ADD_CUSTOM_COMMAND(
+    TARGET install
+    POST_BUILD
+    COMMAND ${CMAKE_COMMAND}
+    ARGS -E copy_if_different
+      ${DTLZ_SOURCE_DIR}/application/IBEA.param
+      ${DTLZ_BINARY_DIR}/application
+    COMMAND ${CMAKE_COMMAND}
+    ARGS -E copy_if_different
+      ${DTLZ_SOURCE_DIR}/application/NSGAII.param
+      ${DTLZ_BINARY_DIR}/application
+    COMMAND ${CMAKE_COMMAND}
+    ARGS -E copy_if_different
+      ${DTLZ_SOURCE_DIR}/application/SPEA2.param
+      ${DTLZ_BINARY_DIR}/application)
+
+######################################################################################

problems/DTLZ/application/DTLZ_IBEA.cpp

@@ -0,0 +1,172 @@
+// moeo general include
+
+#include <iostream>
+#include <fstream>
+#include <moeo>
+#include <es/eoRealInitBounded.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 <DTLZ.h>
+#include <DTLZ1Eval.h>
+#include <DTLZ2Eval.h>
+#include <DTLZ3Eval.h>
+#include <DTLZ4Eval.h>
+#include <DTLZ5Eval.h>
+#include <DTLZ6Eval.h>
+#include <DTLZ7Eval.h>
+#include <SBXCrossover.h>
+#include <PolynomialMutation.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
+
+        unsigned int MAX_GEN = parser.createParam((unsigned int)(10000), "maxGen", "Maximum number of generations",'G',"Param").value();
+        double P_CROSS = parser.createParam(1.0, "pCross", "Crossover probability",'C',"Param").value();
+        double EXT_P_MUT = parser.createParam(1.0, "extPMut", "External Mutation probability",'E',"Param").value();
+        double INT_P_MUT = parser.createParam(0.083, "intPMut", "Internal Mutation probability",'I',"Param").value();
+        unsigned int VEC_SIZE = parser.createParam((unsigned int)(12), "vecSize", "Genotype Size",'V',"Param").value();
+        unsigned int NB_OBJ= parser.createParam((unsigned int)(3), "nbObj", "Number of Objective",'N',"Param").value();
+        std::string OUTPUT_FILE = parser.createParam(std::string("dtlz_ibea"), "outputFile", "Path of the output file",'o',"Output").value();
+        unsigned int EVAL = parser.createParam((unsigned int)(1), "eval", "Number of the DTLZ evaluation fonction",'F',"Param").value();
+        unsigned int DTLZ4_PARAM = parser.createParam((unsigned int)(100), "dtlz4_param", "Parameter of the DTLZ4 evaluation fonction",'P',"Param").value();
+        unsigned int NB_EVAL = parser.createParam((unsigned int)(0), "nbEval", "Number of evaluation before Stop",'P',"Param").value();
+        unsigned int TIME = parser.createParam((unsigned int)(0), "time", "Time(seconds) before Stop",'T',"Param").value();
+
+
+
+        /*** the representation-dependent things ***/
+        std::vector <bool> bObjectives(NB_OBJ);
+        for (unsigned int i=0; i<NB_OBJ ; i++)
+            bObjectives[i]=true;
+        moeoObjectiveVectorTraits::setup(NB_OBJ,bObjectives);
+
+        // The fitness evaluation
+        eoEvalFunc <DTLZ> * eval;
+
+        if (EVAL == 1)
+            eval= new DTLZ1Eval;
+        else if (EVAL == 2)
+            eval= new DTLZ2Eval;
+        else if (EVAL == 3)
+            eval= new DTLZ3Eval;
+        else if (EVAL == 4)
+            eval= new DTLZ4Eval(DTLZ4_PARAM);
+        else if (EVAL == 5)
+            eval= new DTLZ5Eval;
+        else if (EVAL == 6)
+            eval= new DTLZ6Eval;
+        else if (EVAL == 7)
+            eval= new DTLZ7Eval;
+
+        // the genotype (through a genotype initializer)
+        eoRealVectorBounds bounds(VEC_SIZE, 0.0, 1.0);
+
+        eoRealInitBounded <DTLZ> init (bounds);
+        // the variation operators
+        SBXCrossover < DTLZ > xover(bounds, 15);
+
+        PolynomialMutation < DTLZ > mutation (bounds, INT_P_MUT, 20);
+
+        /*** the representation-independent things ***/
+
+        // initialization of the population
+
+        // definition of the archive
+        // stopping criteria
+
+        eoGenContinue<DTLZ> term(MAX_GEN);
+
+        eoEvalFuncCounter<DTLZ> evalFunc(*eval);
+
+        /*eoTimeContinue<DTLZ> timeContinuator(TIME);
+        eoCheckPoint<DTLZ> checkpoint(timeContinuator);*/
+
+        eoCheckPoint<DTLZ>* checkpoint;
+
+        if (TIME > 0)
+            checkpoint = new eoCheckPoint<DTLZ>(*(new eoTimeContinue<DTLZ>(TIME)));
+        else if (NB_EVAL > 0)
+            checkpoint = new eoCheckPoint<DTLZ>(*(new eoEvalContinue<DTLZ>(evalFunc, NB_EVAL)));
+        else {
+            cout << "ERROR!!! : TIME or NB_EVAL must be > 0 : used option --time or --nbEval\n";
+            return EXIT_FAILURE;
+        }
+
+        checkpoint->add(term);
+
+        /*moeoArchiveObjectiveVectorSavingUpdater < DTLZ > updater(arch, OUTPUT_FILE);
+        checkpoint->add(updater);*/
+
+        // algorithm
+
+        eoSGAGenOp < DTLZ > op(xover, P_CROSS, mutation, EXT_P_MUT);
+
+        /*  moeoArchiveUpdater < DTLZ > up(arch, pop);
+                checkpoint.add(up);*/
+
+        //moeoNSGAII<DTLZ> algo(*checkpoint, *eval ,op);
+
+        moeoAdditiveEpsilonBinaryMetric < DTLZObjectiveVector > metric;
+        moeoIBEA<DTLZ> algo(*checkpoint, evalFunc ,op, metric);
+
+
+        /*** Go ! ***/
+
+        // help ?
+
+
+        eoPop<DTLZ>& pop = do_make_pop(parser, state, init);
+
+        make_help(parser);
+
+        // run the algo
+        do_run(algo, pop);
+
+        moeoUnboundedArchive<DTLZ> finalArchive;
+        finalArchive(pop);
+
+        // printing of the final population
+        //cout << "Final Archive \n";
+        //finalArchive.sortedPrintOn(outfile);
+
+        ofstream outfile(OUTPUT_FILE.c_str(), ios::app);
+        if ((unsigned int)outfile.tellp() != 0)
+            outfile << endl;
+
+        for (unsigned int i=0 ; i < finalArchive.size(); i++) {
+            for (unsigned int j=0 ; j<NB_OBJ; j++) {
+                outfile << finalArchive[i].objectiveVector()[j];
+                if (j != NB_OBJ -1)
+                    outfile << " ";
+            }
+            outfile << endl;
+        }
+
+        outfile.close();
+
+    }
+    catch (exception& e)
+    {
+        cout << e.what() << endl;
+    }
+    return EXIT_SUCCESS;
+}

problems/DTLZ/application/DTLZ_NSGAII.cpp

@@ -0,0 +1,169 @@
+// moeo general include
+
+#include <iostream>
+#include <fstream>
+#include <moeo>
+#include <es/eoRealInitBounded.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 <DTLZ.h>
+#include <DTLZ1Eval.h>
+#include <DTLZ2Eval.h>
+#include <DTLZ3Eval.h>
+#include <DTLZ4Eval.h>
+#include <DTLZ5Eval.h>
+#include <DTLZ6Eval.h>
+#include <DTLZ7Eval.h>
+#include <SBXCrossover.h>
+#include <PolynomialMutation.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
+
+        unsigned int MAX_GEN = parser.createParam((unsigned int)(10000), "maxGen", "Maximum number of generations",'G',"Param").value();
+        double P_CROSS = parser.createParam(1.0, "pCross", "Crossover probability",'C',"Param").value();
+        double EXT_P_MUT = parser.createParam(1.0, "extPMut", "External Mutation probability",'E',"Param").value();
+        double INT_P_MUT = parser.createParam(0.083, "intPMut", "Internal Mutation probability",'I',"Param").value();
+        unsigned int VEC_SIZE = parser.createParam((unsigned int)(12), "vecSize", "Genotype Size",'V',"Param").value();
+        unsigned int NB_OBJ= parser.createParam((unsigned int)(3), "nbObj", "Number of Objective",'N',"Param").value();
+        std::string OUTPUT_FILE = parser.createParam(std::string("dtlz_nsgaII"), "outputFile", "Path of the output file",'o',"Output").value();
+        unsigned int EVAL = parser.createParam((unsigned int)(1), "eval", "Number of the DTLZ evaluation fonction",'F',"Param").value();
+        unsigned int DTLZ4_PARAM = parser.createParam((unsigned int)(100), "dtlz4_param", "Parameter of the DTLZ4 evaluation fonction",'P',"Param").value();
+        unsigned int NB_EVAL = parser.createParam((unsigned int)(0), "nbEval", "Number of evaluation before Stop",'P',"Param").value();
+        unsigned int TIME = parser.createParam((unsigned int)(0), "time", "Time(seconds) before Stop",'T',"Param").value();
+
+        /*** the representation-dependent things ***/
+        std::vector <bool> bObjectives(NB_OBJ);
+        for (unsigned int i=0; i<NB_OBJ ; i++)
+            bObjectives[i]=true;
+        moeoObjectiveVectorTraits::setup(NB_OBJ,bObjectives);
+
+        // The fitness evaluation
+        eoEvalFunc <DTLZ> * eval;
+
+        if (EVAL == 1)
+            eval= new DTLZ1Eval;
+        else if (EVAL == 2)
+            eval= new DTLZ2Eval;
+        else if (EVAL == 3)
+            eval= new DTLZ3Eval;
+        else if (EVAL == 4)
+            eval= new DTLZ4Eval(DTLZ4_PARAM);
+        else if (EVAL == 5)
+            eval= new DTLZ5Eval;
+        else if (EVAL == 6)
+            eval= new DTLZ6Eval;
+        else if (EVAL == 7)
+            eval= new DTLZ7Eval;
+
+        // the genotype (through a genotype initializer)
+        eoRealVectorBounds bounds(VEC_SIZE, 0.0, 1.0);
+
+        eoRealInitBounded <DTLZ> init (bounds);
+        // the variation operators
+        SBXCrossover < DTLZ > xover(bounds, 15);
+
+        PolynomialMutation < DTLZ > mutation (bounds, INT_P_MUT, 20);
+
+        /*** the representation-independent things ***/
+
+        // initialization of the population
+
+        // definition of the archive
+        // stopping criteria
+
+        eoGenContinue<DTLZ> term(MAX_GEN);
+
+        eoEvalFuncCounter<DTLZ> evalFunc(*eval);
+
+        /*eoTimeContinue<DTLZ> timeContinuator(TIME);
+        eoCheckPoint<DTLZ> checkpoint(timeContinuator);*/
+
+        eoCheckPoint<DTLZ>* checkpoint;
+
+        if (TIME > 0)
+            checkpoint = new eoCheckPoint<DTLZ>(*(new eoTimeContinue<DTLZ>(TIME)));
+        else if (NB_EVAL > 0)
+            checkpoint = new eoCheckPoint<DTLZ>(*(new eoEvalContinue<DTLZ>(evalFunc, NB_EVAL)));
+        else {
+            cout << "ERROR!!! : TIME or NB_EVAL must be > 0 : used option --time or --nbEval\n";
+            return EXIT_FAILURE;
+        }
+
+        checkpoint->add(term);
+
+        /*moeoArchiveObjectiveVectorSavingUpdater < DTLZ > updater(arch, OUTPUT_FILE);
+        checkpoint->add(updater);*/
+
+        // algorithm
+
+        eoSGAGenOp < DTLZ > op(xover, P_CROSS, mutation, EXT_P_MUT);
+
+        /*  moeoArchiveUpdater < DTLZ > up(arch, pop);
+                checkpoint.add(up);*/
+
+        moeoNSGAII<DTLZ> algo(*checkpoint, evalFunc ,op);
+
+        /*moeoAdditiveEpsilonBinaryMetric < DTLZObjectiveVector > metric;
+        moeoIBEA<DTLZ> algo(checkpoint, eval ,op, metric);*/
+
+
+        /*** Go ! ***/
+
+        // help ?
+
+
+        eoPop<DTLZ>& pop = do_make_pop(parser, state, init);
+
+        make_help(parser);
+        // run the algo
+        do_run(algo, pop);
+
+        moeoUnboundedArchive<DTLZ> finalArchive;
+        finalArchive(pop);
+
+        // printing of the final population
+        //cout << "Final Archive \n";
+        //finalArchive.sortedPrintOn(outfile);
+
+        ofstream outfile(OUTPUT_FILE.c_str(), ios::app);
+        if ((unsigned int)outfile.tellp() != 0)
+            outfile << endl;
+
+        for (unsigned int i=0 ; i < finalArchive.size(); i++) {
+            for (unsigned int j=0 ; j<NB_OBJ; j++) {
+                outfile << finalArchive[i].objectiveVector()[j];
+                if (j != NB_OBJ -1)
+                    outfile << " ";
+            }
+            outfile << endl;
+        }
+
+        outfile.close();
+
+    }
+    catch (exception& e)
+    {
+        cout << e.what() << endl;
+    }
+    return EXIT_SUCCESS;
+}

problems/DTLZ/application/DTLZ_SPEA2.cpp

@@ -0,0 +1,190 @@
+// moeo general include
+
+#include <iostream>
+#include <fstream>
+#include <moeo>
+#include <es/eoRealInitBounded.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>
+
+#include <algo/moeoSPEA2.h>
+#include <archive/moeoSPEA2Archive.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 <DTLZ.h>
+#include <DTLZ1Eval.h>
+#include <DTLZ2Eval.h>
+#include <DTLZ3Eval.h>
+#include <DTLZ4Eval.h>
+#include <DTLZ5Eval.h>
+#include <DTLZ6Eval.h>
+#include <DTLZ7Eval.h>
+#include <SBXCrossover.h>
+#include <PolynomialMutation.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
+
+        unsigned int ARC_SIZE = parser.createParam((unsigned int)(100), "arcSize", "Archive size",'A',"Param").value();
+        unsigned int MAX_GEN = parser.createParam((unsigned int)(10000), "maxGen", "Maximum number of generations",'G',"Param").value();
+        double P_CROSS = parser.createParam(1.0, "pCross", "Crossover probability",'C',"Param").value();
+        double EXT_P_MUT = parser.createParam(1.0, "extPMut", "External Mutation probability",'E',"Param").value();
+        double INT_P_MUT = parser.createParam(0.083, "intPMut", "Internal Mutation probability",'I',"Param").value();
+        unsigned int VEC_SIZE = parser.createParam((unsigned int)(12), "vecSize", "Genotype Size",'V',"Param").value();
+        unsigned int NB_OBJ= parser.createParam((unsigned int)(3), "nbObj", "Number of Objective",'N',"Param").value();
+        unsigned int K = parser.createParam((unsigned int)(10), "k", "k-th nearest neighbor",'K',"Param").value();
+        std::string OUTPUT_FILE = parser.createParam(std::string("dtlz_spea2"), "outputFile", "Path of the output file",'o',"Output").value();
+        unsigned int EVAL = parser.createParam((unsigned int)(1), "eval", "Number of the DTLZ evaluation fonction",'F',"Param").value();
+        unsigned int DTLZ4_PARAM = parser.createParam((unsigned int)(100), "dtlz4_param", "Parameter of the DTLZ4 evaluation fonction",'P',"Param").value();
+        unsigned int NB_EVAL = parser.createParam((unsigned int)(0), "nbEval", "Number of evaluation before Stop",'P',"Param").value();
+        unsigned int TIME = parser.createParam((unsigned int)(0), "time", "Time(seconds) before Stop",'T',"Param").value();
+
+        /*cout << "ARC_SIZE : " << ARC_SIZE << endl;
+        cout << "P_CROSS : " << P_CROSS << endl;
+        cout << "EXT_P_MUT : " << EXT_P_MUT << endl;
+        cout << "INT_P_MUT : " << INT_P_MUT << endl;
+        cout << "VEC_SIZE : " << VEC_SIZE << endl;
+        cout << "NB_OBJ : " << NB_OBJ << endl;
+        cout << "K : " << K << endl;
+        cout << "DTLZ EVAL :" << EVAL << endl;
+        cout << "DTLZ4_PARAM : " << DTLZ4_PARAM << endl;
+        cout << "NB_EVAL : " << NB_EVAL << endl;
+        cout << "TIME : " << TIME << endl;  */
+
+
+        /*** the representation-dependent things ***/
+        std::vector <bool> bObjectives(NB_OBJ);
+        for (unsigned int i=0; i<NB_OBJ ; i++)
+            bObjectives[i]=true;
+        moeoObjectiveVectorTraits::setup(NB_OBJ,bObjectives);
+
+        // The fitness evaluation
+        eoEvalFunc <DTLZ> * eval;
+
+        if (EVAL == 1)
+            eval= new DTLZ1Eval;
+        else if (EVAL == 2)
+            eval= new DTLZ2Eval;
+        else if (EVAL == 3)
+            eval= new DTLZ3Eval;
+        else if (EVAL == 4)
+            eval= new DTLZ4Eval(DTLZ4_PARAM);
+        else if (EVAL == 5)
+            eval= new DTLZ5Eval;
+        else if (EVAL == 6)
+            eval= new DTLZ6Eval;
+        else if (EVAL == 7)
+            eval= new DTLZ7Eval;
+
+        // the genotype (through a genotype initializer)
+        eoRealVectorBounds bounds(VEC_SIZE, 0.0, 1.0);
+
+        eoRealInitBounded <DTLZ> init (bounds);
+        // the variation operators
+        SBXCrossover < DTLZ > xover(bounds, 20);
+
+        PolynomialMutation < DTLZ > mutation (bounds, INT_P_MUT, 20);
+
+        /*** the representation-independent things ***/
+
+        // initialization of the population
+
+        // definition of the archive
+        moeoSPEA2Archive<DTLZ> arch(ARC_SIZE);
+        //moeoUnboundedArchive<DTLZ> arch;
+        // stopping criteria
+
+        eoGenContinue<DTLZ> term(MAX_GEN);
+
+        eoEvalFuncCounter<DTLZ> evalFunc(*eval);
+
+        /*eoTimeContinue<DTLZ> timeContinuator(TIME);
+        eoCheckPoint<DTLZ> checkpoint(timeContinuator);*/
+
+        eoCheckPoint<DTLZ>* checkpoint;
+
+        if (TIME > 0)
+            checkpoint = new eoCheckPoint<DTLZ>(*(new eoTimeContinue<DTLZ>(TIME)));
+        else if (NB_EVAL > 0)
+            checkpoint = new eoCheckPoint<DTLZ>(*(new eoEvalContinue<DTLZ>(evalFunc, NB_EVAL)));
+        else {
+            cout << "ERROR!!! : TIME or NB_EVAL must be > 0 : used option --time or --nbEval\n";
+            return EXIT_FAILURE;
+        }
+
+        checkpoint->add(term);
+
+        /*moeoArchiveObjectiveVectorSavingUpdater < DTLZ > updater(arch, OUTPUT_FILE);
+        checkpoint->add(updater);*/
+
+        // algorithm
+
+        moeoSPEA2<DTLZ> algo(*checkpoint, evalFunc ,xover, P_CROSS, mutation, EXT_P_MUT, arch, K, false);
+        /* eoSGAGenOp < DTLZ > op(xover, 1.0, mutation, 1/12);
+
+          moeoArchiveUpdater < DTLZ > up(arch, pop);
+                checkpoint.add(up);
+
+                moeoNSGAII<DTLZ> algo(checkpoint, eval ,op);
+
+                 /*moeoAdditiveEpsilonBinaryMetric < DTLZObjectiveVector > metric;
+        moeoIBEA<DTLZ> algo(checkpoint, eval ,op, metric);*/
+
+
+        /*** Go ! ***/
+
+        // help ?
+
+        eoPop<DTLZ>& pop = do_make_pop(parser, state, init);
+        // run the algo
+        make_help(parser);
+
+        do_run(algo, pop);
+
+        moeoUnboundedArchive<DTLZ> finalArchive;
+        finalArchive(arch);
+
+
+        // printing of the final population
+        //cout << "Final Archive \n";
+        //finalArchive.sortedPrintOn(outfile);
+
+        ofstream outfile(OUTPUT_FILE.c_str(), ios::app);
+        if ((unsigned int)outfile.tellp() != 0)
+            outfile << endl;
+
+        for (unsigned int i=0 ; i < finalArchive.size(); i++) {
+            for (unsigned int j=0 ; j<NB_OBJ; j++) {
+                outfile << finalArchive[i].objectiveVector()[j];
+                if (j != NB_OBJ -1)
+                    outfile << " ";
+            }
+            outfile << endl;
+        }
+
+        outfile.close();
+
+    }
+    catch (exception& e)
+    {
+        cout << e.what() << endl;
+    }
+    return EXIT_SUCCESS;
+}

problems/DTLZ/application/IBEA.param

@@ -0,0 +1,28 @@
+
+######                 General    ######
+# --help=0                                 # -h : Prints this message
+# --stopOnUnknownParam=1                   # Stop if unkown param entered
+# --seed=1238424544                        # -S : Random number seed
+
+######    Evolution Engine        ######
+# --popSize=20                             # -P : Population Size
+
+######    Output                  ######
+--outputFile=IBEA.out                    # -o : Path of the output file
+
+######    Param                   ######
+# --maxGen=10000                           # -G : Maximum number of generations
+--pCross=1                               # -C : Crossover probability
+--extPMut=1                              # -E : External Mutation probability
+--intPMut=0.083333                       # -I : Internal Mutation probability
+--vecSize=30                             # -V : Genotype Size
+--nbObj=3                                # -N : Number of Objective
+--eval=1                                 # -F : Number of the DTLZ evaluation fonction
+--dtlz4_param=100                        # -P : Parameter of the DTLZ4 evaluation fonction
+--nbEval=500                             # -P : Number of evaluation before Stop
+--time=0                                 # -T : Time(seconds) before Stop
+
+######    Persistence             ######
+# --Load=                                  # -L : A save file to restart from
+# --recomputeFitness=0                     # -r : Recompute the fitness after re-loading the pop.?
+# --status=./build/application/DTLZ_IBEA.status # Status file

problems/DTLZ/application/NSGAII.param

@@ -0,0 +1,28 @@
+
+######                 General    ######
+# --help=0                                 # -h : Prints this message
+# --stopOnUnknownParam=1                   # Stop if unkown param entered
+# --seed=1238424545                        # -S : Random number seed
+
+######    Evolution Engine        ######
+# --popSize=20                             # -P : Population Size
+
+######    Output                  ######
+--outputFile=NSGAII.out                  # -o : Path of the output file
+
+######    Param                   ######
+# --maxGen=10000                           # -G : Maximum number of generations
+--pCross=1                               # -C : Crossover probability
+--extPMut=1                              # -E : External Mutation probability
+--intPMut=0.083333                       # -I : Internal Mutation probability
+--vecSize=30                             # -V : Genotype Size
+--nbObj=3                                # -N : Number of Objective
+--eval=1                                 # -F : Number of the DTLZ evaluation fonction
+--dtlz4_param=100                        # -P : Parameter of the DTLZ4 evaluation fonction
+--nbEval=500                             # -P : Number of evaluation before Stop
+--time=0                                 # -T : Time(seconds) before Stop
+
+######    Persistence             ######
+# --Load=                                  # -L : A save file to restart from
+# --recomputeFitness=0                     # -r : Recompute the fitness after re-loading the pop.?
+# --status=./build/application/DTLZ_NSGAII.status # Status file

problems/DTLZ/application/SPEA2.param

@@ -0,0 +1,30 @@
+
+######                 General    ######
+# --help=0                                 # -h : Prints this message
+# --stopOnUnknownParam=1                   # Stop if unkown param entered
+# --seed=1238424543                        # -S : Random number seed
+
+######    Evolution Engine        ######
+# --popSize=20                             # -P : Population Size
+
+######    Output                  ######
+--outputFile=SPEA2.out                   # -o : Path of the output file
+
+######    Param                   ######
+--arcSize=100                            # -A : Archive size
+# --maxGen=10000                           # -G : Maximum number of generations
+--pCross=1                               # -C : Crossover probability
+--extPMut=1                              # -E : External Mutation probability
+--intPMut=0.083333                       # -I : Internal Mutation probability
+--vecSize=30                             # -V : Genotype Size
+--nbObj=3                                # -N : Number of Objective
+--k=10                                   # -K : k-th nearest neighbor
+--eval=1                                 # -F : Number of the DTLZ evaluation fonction
+--dtlz4_param=100                        # -P : Parameter of the DTLZ4 evaluation fonction
+--nbEval=500                             # -P : Number of evaluation before Stop
+--time=0                                 # -T : Time(seconds) before Stop
+
+######    Persistence             ######
+# --Load=                                  # -L : A save file to restart from
+# --recomputeFitness=0                     # -r : Recompute the fitness after re-loading the pop.?
+# --status=./build/application/DTLZ_SPEA2.status # Status file

problems/DTLZ/doc/CMakeLists.txt

@@ -0,0 +1,26 @@
+
+##########################################################################################
+### MOEO Doc generation using Doxygen
+##########################################################################################
+
+IF (DOXYGEN_FOUND)
+
+	SET(DOC_DIR ${CMAKE_BINARY_DIR}/doc CACHE PATH "MOEO documentation directory")
+	SET(MOEO_DOC_CONFIG_FILE "moeo.doxyfile" CACHE PATH "MOEO documentation configuration file")
+		# define the doc target
+	IF (DOXYGEN_EXECUTABLE)
+	    	ADD_CUSTOM_TARGET(doc
+	        COMMAND ${DOXYGEN_EXECUTABLE} ${MOEO_DOC_CONFIG_FILE}
+	        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+	    )
+	ENDIF (DOXYGEN_EXECUTABLE)
+	
+	# configure doxyfile file
+	CONFIGURE_FILE("${CMAKE_SOURCE_DIR}/doc/${MOEO_DOC_CONFIG_FILE}.cmake"
+	               "${CMAKE_BINARY_DIR}/doc/${MOEO_DOC_CONFIG_FILE}")
+
+ELSE (DOXYGEN_FOUND)
+	MESSAGE(STATUS "Unable to generate the documentation, Doxygen package not found")	
+ENDIF (DOXYGEN_FOUND)
+
+##########################################################################################

problems/DTLZ/doc/html/doxygen.css

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+	font-family: sans-serif;
+	margin:0.5em;
+}
+.directory { 
+	font-size: 9pt; 
+	font-weight: bold; 
+}
+.directory h3 { 
+	margin: 0px; 
+	margin-top: 1em; 
+	font-size: 11pt; 
+}
+.directory > h3 { 
+	margin-top: 0; 
+}
+.directory p { 
+	margin: 0px; 
+	white-space: nowrap; 
+}
+.directory div { 
+	display: none; 
+	margin: 0px; 
+}
+.directory img { 
+	vertical-align: -30%; 
+}
+