Add C++ API

.gitignore

@@ -104,3 +104,45 @@ ENV/
 .DS_Store
 
 *.prof
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+/build
+/parallel_build
+/serial_build
+
+# Vim temp files
+*.swp
+
+mpiflag.h
+

gasol/CMakeLists.txt

@@ -0,0 +1,46 @@
+# CMake script to build GASol
+
+cmake_minimum_required(VERSION 3.0)
+
+project(GASol)
+
+# Enable verbose output.
+#set(CMAKE_VERBOSE_MAKEFILE ON)
+
+# Use C++11 standard.
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+# Find OpenMP.
+find_package(OpenMP)
+if (OPENMP_FOUND)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS} -fPIC -Wall -Wextra -Werror -pedantic")
+else()
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -Wall -Wextra -Werror -pedantic")
+endif()
+
+if (COV)
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+endif()
+
+# MPI.
+if (MPI)
+    message(STATUS "-- This is a parallel MPI build --")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_CXX_COMPILER_FLAGS}")
+    include_directories(${MPI_CXX_INCLUDE_DIRS})
+    file(WRITE ${PROJECT_SOURCE_DIR}/src/mpiflag.h "#define RUNMPI true\n")
+else()
+    message(STATUS "-- This is a serial build --")
+    file(WRITE ${PROJECT_SOURCE_DIR}/src/mpiflag.h "#define RUNMPI false\n")
+endif()
+
+# GASol source dir.
+add_subdirectory(src)
+
+# GASol test dir.
+add_subdirectory(unittest)
+
+# GASol run dir.
+add_subdirectory(example)
+

gasol/README.md

@@ -0,0 +1,108 @@
+# GASol
+
+A general **G**enetic **A**lgorithm **Sol**ver in C++ 
+
+[![Build Status](https://api.travis-ci.org/PytLab/GASol.svg?branch=master)](https://travis-ci.org/PytLab/GASol)
+[![codecov](https://img.shields.io/codecov/c/github/PytLab/GASol/master.svg)](https://codecov.io/gh/PytLab/GASol)
+[![License](https://img.shields.io/badge/license-GPLv3-blue.svg)](https://github.com/PytLab/GASol/blob/master/LICENSE)
+
+## Build
+
+#### Clone GASol
+
+``` shell
+git clone --recursive [email protected]:PytLab/GASol.git
+```
+
+#### Create dir for building.
+
+``` shell
+cd GASol
+mkdir build
+cd build
+```
+#### Build GASol
+
+- Serial version
+``` shell
+cmake ..
+make
+```
+
+- MPI parallel version
+```
+export CXX=/<mpi_path>/mpicxx
+cmake -DMPI=true ..
+make
+```
+
+#### Run test
+``` shell
+make unittest
+./unittest/unittest
+```
+#### Run example
+
+``` shell
+make example
+./example/example
+```
+
+## Quick start
+
+#### Find the maxima of f(x) = x + 10sin(5x) + 7cos(4x)
+
+``` cpp
+#include "mpiutils.h"
+#include "engine.h"
+
+#include <cmath>
+#include <vector>
+#include <utility>
+
+using namespace gasol;
+
+// Define fitness function. 
+double fitness(const Individual & indv)
+{
+    double x = indv.solution()[0];
+    return x + 10*std::sin(5*x) + 7*std::cos(4*x);
+}
+
+int main()
+{
+    // Initialize MPI environment.
+    MPIUtils::init();
+    // Variable range.
+    std::vector<std::pair<double, double>> ranges {{0.0, 10.0}};
+    // Decrete precision.
+    std::vector<double> precisions {0.001};
+
+    // Create population.
+    size_t size = 50;
+    std::vector<Individual> individuals;
+    for (size_t i = 0; i < size; i++)
+    {
+        gasol::Individual indv(ranges, precisions);
+        individuals.push_back(indv);
+    }
+    Population population(individuals, &fitness);
+
+    // Genetic operators.
+    RouletteWheelSelection selection;
+    UniformCrossover crossover(0.8, 0.5);
+    FlipBitMutation mutation(0.1);
+
+    // Create engine.
+    Engine engine(population, selection, crossover, mutation);
+
+    // Run 1000 generations.
+    engine.run(1000);
+
+    // Finalize MPI env.
+    MPIUtils::finalize();
+
+    return 0;
+}
+```
+

gasol/example/1d_search.cpp

@@ -0,0 +1,71 @@
+/*! \brief GASol example for searching the maxima of f(x) = x + 10sin(5x) + 7cos(4x)
+ */
+
+#include "mpiutils.h"
+#include "engine.h"
+
+#include <iostream>
+#include <cmath>
+#include <vector>
+#include <utility>
+#include <ctime>
+
+using namespace gasol;
+
+// Define fitness function. 
+double fitness(const Individual & indv)
+{
+    double x = indv.solution()[0];
+    return x + 10*std::sin(5*x) + 7*std::cos(4*x);
+}
+
+int main()
+{
+    MPIUtils::init();
+    if (MPIUtils::isMaster())
+    {
+        std::cout << "Process number: " << MPIUtils::size() << std::endl;
+    }
+    // Variable range.
+    std::vector<std::pair<double, double>> ranges {{0.0, 100.0}};
+    // Decrete precision.
+    std::vector<double> precisions {0.001};
+
+    // Create population.
+    size_t size = 1000;
+    std::vector<Individual> individuals;
+    for (size_t i = 0; i < size; i++)
+    {
+        gasol::Individual indv(ranges, precisions);
+        individuals.push_back(indv);
+    }
+    Population population(individuals, &fitness);
+
+    // Genetic operators.
+    RouletteWheelSelection selection;
+    UniformCrossover crossover(0.8, 0.5);
+    FlipBitMutation mutation(0.1);
+
+    // Create engine.
+    Engine engine(population, selection, crossover, mutation);
+
+    // Run 100 generations.
+    time_t start = time(NULL);
+    engine.run(100);
+    time_t end = time(NULL);
+
+    const Individual & best_indv = engine.population().bestIndv();
+    double best_fitness = engine.population().fitness()(best_indv);
+    double solution = best_indv.solution()[0];
+
+    if (MPIUtils::isMaster())
+    {
+        std::cout << "Solution: " << solution << ", fitness: " << best_fitness << std::endl;
+        std::cout << "Time used: " << end - start << "s" << std::endl;
+    }
+
+    MPIUtils::finalize();
+
+    return 0;
+}
+

gasol/example/CMakeLists.txt

@@ -0,0 +1,8 @@
+# CMake script for gasol run executable program building.
+
+include_directories(${PROJECT_SOURCE_DIR}/src)
+link_directories(${CMAKE_BINARY_DIR}/../src/)
+file(GLOB RUN_SRC *.cpp)
+add_executable(example EXCLUDE_FROM_ALL ${RUN_SRC})
+target_link_libraries(example GASol)
+

gasol/src/CMakeLists.txt

@@ -0,0 +1,3 @@
+file(GLOB GASol_SRC *.cpp)
+add_library(GASol STATIC ${GASol_SRC})
+

gasol/src/crossover.cpp

@@ -0,0 +1,46 @@
+/*! \brief Implementations of uniform crossover operator.
+ */
+
+#include "individual.h"
+#include "crossover.h"
+
+#include <random>
+#include <cstddef>
+
+namespace gasol {
+
+    //--------------------------------------------------------------------------
+    //
+    std::pair<Individual, Individual> UniformCrossover::cross(Parents & parents) const
+    {
+        const Individual *father = parents.first;
+        const Individual *mother = parents.second;
+
+        // Children to return.
+        Individual child1(*father);
+        Individual child2(*mother);
+
+        // Create a random number generator.
+        std::mt19937 gen(seed());
+        std::uniform_real_distribution<double> dis(0.0, 1.0);
+
+        double rnd = dis(gen);
+        if (rnd > pc())
+        {
+            return std::pair<Individual, Individual>(child1, child2);
+        }
+        else
+        {
+            for (size_t i = 0; i < child1.chromsome().size(); i++)
+            {
+                if (child1.chromsome()[i] != child2.chromsome()[i])
+                {
+                    child1.flipGeneBit(i);
+                    child2.flipGeneBit(i);
+                }
+            }
+            return std::pair<Individual, Individual>(child1, child2);
+        }
+    }
+}
+