project(specmicp)
cmake_minimum_required(VERSION 2.8.8)


#######################  External Package #####################################
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake/")
find_package(Eigen3 REQUIRED)  # This module comes from the Eigen3 Package
find_package(CxxTest)          # Necessary if you want the tests

# catch for unit testing
include(ExternalProject)
find_package(Git REQUIRED)

ExternalProject_Add(
    catch
    PREFIX ${CMAKE_BINARY_DIR}/catch
    GIT_REPOSITORY https://github.com/philsquared/Catch.git
    TIMEOUT 10
    UPDATE_COMMAND ${GIT_EXECUTABLE} pull
    CONFIGURE_COMMAND ""
    BUILD_COMMAND ""
    INSTALL_COMMAND ""
    LOG_DOWNLOAD ON
   )


########################  Compilation flags #################################
if(UNIX)
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -std=c++11")
   SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -pedantic")
   SET(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -DNDEBUG")
   message(STATUS "c++ flags ${CMAKE_CXX_FLAGS}")
else()
    message(WARNING "not tested !")
endif()


################ Directories #####################

set(PROJECT_TEST_DIR ${PROJECT_SOURCE_DIR}/tests)
ExternalProject_Get_Property(catch source_dir)
set(CATCH_INCLUDE_DIR ${source_dir}/include CACHE INTERNAL "Path to include folder for Catch")

set(PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
# include
include_directories(${EIGEN3_INCLUDE_DIR})
include_directories(${PROJECT_SOURCE_DIR})
include_directories(${CATCH_INCLUDE_DIR})
include_directories(${PROJECT_TEST_DIR})

################ Modules ##########################

# -------- MiCPSolver ----------------

set(MICPSOLVER_DIR ${PROJECT_SOURCE_DIR}/micpsolver)

add_custom_target(specmisolver_inc SOURCES
    ${MICPSOLVER_DIR}/micpsolver_base.hpp
    ${MICPSOLVER_DIR}/micpsolver_base.inl
    ${MICPSOLVER_DIR}/micpsolver.hpp
    ${MICPSOLVER_DIR}/micpsolver.inl
    ${MICPSOLVER_DIR}/micpsolver_min.hpp
    ${MICPSOLVER_DIR}/micpsolver_min.inl
    ${MICPSOLVER_DIR}/micpsolverold.hpp
    ${MICPSOLVER_DIR}/micpsolverold.inl
    ${MICPSOLVER_DIR}/micpsolver_structs.hpp
    ${MICPSOLVER_DIR}/micpprog.hpp
    ${MICPSOLVER_DIR}/ncp_function.hpp
    ${MICPSOLVER_DIR}/estimate_cond_number.hpp
)

# ------- SpecMiCP ---------------

set(SPECMICP_DIR ${PROJECT_SOURCE_DIR}/specmicp)

add_custom_target(specmic_inc SOURCES
    #${SPECMICP_DIR}/.hpp
    ${SPECMICP_DIR}/simulation_box.hpp
)

set(SPECMICP_LIBFILE
    ${SPECMICP_DIR}/equilibrium_data.cpp
    ${SPECMICP_DIR}/reduced_system.cpp
    ${SPECMICP_DIR}/reduced_system_solver.cpp
    ${SPECMICP_DIR}/reaction_path.cpp
    ${SPECMICP_DIR}/speciation_solver.cpp
    ${SPECMICP_DIR}/simple_composition.cpp
)

add_library(specmicp ${SPECMICP_LIBFILE})

# -------- Database ----------------

set(DATABASE_DIR ${PROJECT_SOURCE_DIR}/database)

set(DATABASE_LIBFILE
    ${DATABASE_DIR}/data_container.cpp
    ${DATABASE_DIR}/database.cpp
    ${DATABASE_DIR}/reader.cpp
    ${DATABASE_DIR}/selector.cpp
    ${DATABASE_DIR}/mineral_selector.cpp
    ${DATABASE_DIR}/canonicalizer.cpp
    ${DATABASE_DIR}/switch_basis.cpp
)

add_custom_target(data_incl SOURCES
    ${DATABASE_DIR}/common_def.hpp
    ${DATABASE_DIR}/module.hpp
)

add_library(specmicp_database ${DATABASE_LIBFILE})

# --------- ODE int ------------------

set(ODEINT_DIR ${PROJECT_SOURCE_DIR}/odeint)


add_custom_target(odeint_incl SOURCES
    ${ODEINT_DIR}/odeint_types.hpp
    ${ODEINT_DIR}/butcher_tableau.hpp
    ${ODEINT_DIR}/runge_kutta_step.hpp
    ${ODEINT_DIR}/runge_kutta_step.inl
)

# --------- DFPMSolver -----------------

set(DFPMSOLVER_DIR ${PROJECT_SOURCE_DIR}/dfpmsolver)

add_custom_target(dfpmsolver_incl SOURCES
    ${DFPMSOLVER_DIR}/driver.hpp
    ${DFPMSOLVER_DIR}/driver.inl
    ${DFPMSOLVER_DIR}/driver_structs.hpp
    ${DFPMSOLVER_DIR}/dfpm_program.hpp
    #
    ${DFPMSOLVER_DIR}/sparse_solver.hpp
    ${DFPMSOLVER_DIR}/sparse_solver_structs.hpp
    # Parabolic solver
    ${DFPMSOLVER_DIR}/parabolic_driver.hpp
    ${DFPMSOLVER_DIR}/parabolic_driver.inl
    ${DFPMSOLVER_DIR}/parabolic_program.hpp
    ${DFPMSOLVER_DIR}/parabolic_structs.hpp
)

# --------- ReactMiCP -----------------

set(REACTMICP_DIR ${PROJECT_SOURCE_DIR}/reactmicp)

add_custom_target(reactmicp_incl SOURCES
    ${REACTMICP_DIR}/common.hpp
    #
    ${REACTMICP_DIR}/micpsolvers/parabolicprogram.hpp
    ${REACTMICP_DIR}/micpsolvers/micpsolver_structs.hpp
    ${REACTMICP_DIR}/micpsolvers/micpsolver.hpp
    ${REACTMICP_DIR}/micpsolvers/micpsolver.inl
    #
    ${REACTMICP_DIR}/meshes/mesh1d.hpp


    ${REACTMICP_DIR}/systems/secondary_variables/secondary.hpp
    ${REACTMICP_DIR}/systems/secondary_variables/secondary.inl

    ${REACTMICP_DIR}/systems/saturated_diffusion/options.hpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/variables.hpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/transport_parameters.hpp
)

set(REACTMICP_LIBFILES
    ${REACTMICP_DIR}/systems/diffusion/diffusion.cpp
    ${REACTMICP_DIR}/systems/diffusion/diffusion_numbering.cpp
    ${REACTMICP_DIR}/systems/diffusion/diffusion_secondary.cpp

    ${REACTMICP_DIR}/systems/saturated_diffusion/reactive_transport_solver.cpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/equation_numbering.cpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/transport_program.cpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/speciation_program.cpp
)

add_library(reactmicp ${REACTMICP_LIBFILES})

# ------- Utils ------------------

set(UTILS_DIR ${PROJECT_SOURCE_DIR}/utils)

add_custom_target(utils_inc SOURCES
    ${UTILS_DIR}/log.hpp
)

# ------- Physics ----------------

set(PHYSICS_DIR ${PROJECT_SOURCE_DIR}/physics)

add_custom_target(physics_inc SOURCES
    ${PHYSICS_DIR}/constants.hpp
    ${PHYSICS_DIR}/laws.hpp
    ${PHYSICS_DIR}/units.hpp
)

# ------- Data -------------------

set(DATA_DIR ${CMAKE_CURRENT_SOURCE_DIR}/data)

set(DATABASE_LIST
        ${DATA_DIR}/specmicp_database.js
        ${DATA_DIR}/cemdata_specmicp.js
)

add_custom_target(data SOURCES ${DATABASE_LIST})

file(INSTALL ${DATABASE_LIST}
     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/data/)

# ------ Documentation -----------

set(
    DOCS_LIST
    ${CMAKE_CURRENT_SOURCE_DIR}/README.md
    ${CMAKE_CURRENT_SOURCE_DIR}/INSTALL
    ${CMAKE_CURRENT_SOURCE_DIR}/TODO
    ${CMAKE_CURRENT_SOURCE_DIR}/COPYING
)

add_custom_target(docs SOURCES ${DOCS_LIST})

# add a target to generate API documentation with Doxygen
find_package(Doxygen)
if(DOXYGEN_FOUND)
configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile @ONLY)
add_custom_target(doc
${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
COMMENT "Generating API documentation with Doxygen" VERBATIM
)
add_custom_target(citations SOURCES ${CMAKE_CURRENT_SOURCE_DIR}/doc/citations.bib)
file(INSTALL ${CMAKE_CURRENT_SOURCE_DIR}/doc/citations.bib
     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/doc/)
endif(DOXYGEN_FOUND)

# --------- Python interface ----------


add_subdirectory( cython )



# --------- Test ----------------------

enable_testing(true)

# CXX Test
# ========

if(CXXTEST_FOUND)
    set(CXXTEST_USE_PYTHON TRUE)
    include_directories(${CXXTEST_INCLUDE_DIR})
    enable_testing()

    # MiCP Solver
    # ------------
    CXXTEST_ADD_TEST(test_cond_number
                     test_cond_number.cpp
                     ${PROJECT_TEST_DIR}/micpsolver/test_cond_number.hpp)

    CXXTEST_ADD_TEST(test_ncp_funtion
                     test_ncp_function.cpp
                     ${PROJECT_TEST_DIR}/micpsolver/test_ncp_function.hpp)

    CXXTEST_ADD_TEST(test_micpsolver
                     test_micpsolver.cpp
                     ${PROJECT_TEST_DIR}/micpsolver/test_micpsolver.hpp)

    # Database
    # --------

    CXXTEST_ADD_TEST(test_data_reader
                    test_data_reader.cpp
                    ${PROJECT_TEST_DIR}/database/test_data_reader.hpp)
    target_link_libraries(test_data_reader specmicp_database jsoncpp)


    CXXTEST_ADD_TEST(test_data_selector
                    test_data_selector.cpp
                    ${PROJECT_TEST_DIR}/database/test_data_selector.hpp)
    target_link_libraries(test_data_selector specmicp_database jsoncpp)

    # Odeint
    # ------

    CXXTEST_ADD_TEST(test_butchertableau
                     test_butchertableau.cpp
                     ${PROJECT_TEST_DIR}/odeint/test_butchertableau.hpp)


    CXXTEST_ADD_TEST(test_embeddedrungekutta
                     test_embeddedrungekutta.cpp
                     ${PROJECT_TEST_DIR}/odeint/test_embeddedrungekutta.hpp)

endif()

# Test 'Perso'
# ============

add_executable(thermocarbo ${PROJECT_TEST_DIR}/specmicp/thermocarbo.cpp)
target_link_libraries(thermocarbo specmicp specmicp_database jsoncpp)

add_executable(carboalu ${PROJECT_TEST_DIR}/specmicp/carboalu.cpp)
target_link_libraries(carboalu specmicp specmicp_database jsoncpp)

add_executable(alkaliactivated ${PROJECT_TEST_DIR}/specmicp/alkaliactivated.cpp)
target_link_libraries(alkaliactivated specmicp specmicp_database jsoncpp)

add_executable(rate_nicoleau ${PROJECT_TEST_DIR}/specmicp/rate_nicoleau.cpp)
target_link_libraries(rate_nicoleau specmicp specmicp_database jsoncpp)

add_executable(kinetics ${PROJECT_TEST_DIR}/specmicp/kinetics.cpp)
target_link_libraries(kinetics specmicp specmicp_database jsoncpp)


set(DATA_TEST ${PROJECT_TEST_DIR}/specmicp/data_test/data_nicoleau_c3sm.csv
              ${PROJECT_TEST_DIR}/specmicp/data_test/data_nicoleau_c3st1.csv
              ${PROJECT_TEST_DIR}/specmicp/data_test/data_nicoleau_c3st2.csv
)

add_custom_target(data_nicoleau SOURCES ${DATA_TEST})

file(INSTALL ${DATA_TEST}
     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/data_test/)

# Catch test
#===========

add_custom_target(catch_header SOURCES
    ${PROJECT_TEST_DIR}/test_database.hpp
)

add_executable(test_reactmicp_diffusion
    ${PROJECT_TEST_DIR}/reactmip/systems/diffusion/test_reactmicp_diffusion.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/diffusion/diffusion.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/diffusion/numbering.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/diffusion/secondary.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/diffusion/solving.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/diffusion/utils.cpp
)
target_link_libraries(test_reactmicp_diffusion reactmicp specmicp specmicp_database jsoncpp)

add_executable(test_reactmicp_saturated_diffusion
    ${PROJECT_TEST_DIR}/reactmip/systems/saturated_diffusion/test_reactmicp_saturated_diffusion.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/saturated_diffusion/variables.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/saturated_diffusion/solver.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/saturated_diffusion/transport_program.cpp
    ${PROJECT_TEST_DIR}/reactmip/systems/saturated_diffusion/utils.cpp
)
target_link_libraries(test_reactmicp_saturated_diffusion reactmicp specmicp specmicp_database jsoncpp)