####################################################
#                                                  #
#           SpecMiCP : CMakeLists.txt              #
#                                                  #
####################################################

project(specmicp)
cmake_minimum_required(VERSION 2.8.8)

# For an explanation of the options see the INSTALL file

#                         External Package
#########################################################################

set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake/")

# Boost
# -----
find_package(Boost REQUIRED)
include_directories(${Boost_INCLUDE_DIR})

# Eigen
# -----
find_package(Eigen3 REQUIRED)  # This module comes from the Eigen3 Package
include_directories(${EIGEN3_INCLUDE_DIR})
# Eigen unsuported
# GMRES.h is really the file we are using/looking for
# If it doesn't exist then the solver will not be included in the list of the parse solvers
if(EXISTS "${EIGEN3_INCLUDE_DIR}/unsupported/Eigen/src/IterativeSolvers/GMRES.h")
    add_definitions(-DEIGEN_UNSUPPORTED_FOUND)
    INCLUDE_DIRECTORIES("${EIGEN3_INCLUDE_DIR}/unsupported/")
endif()

#                        Compilation flags
#########################################################################

if(UNIX)
   # Generic options
   SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -std=c++11 -fuse-ld=gold")
   SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -pedantic")
   SET(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O2 -DNDEBUG")
   # OpenMP
   if(SPECMICP_USE_OPENMP)
        SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}  -fopenmp")
        add_definitions(-DSPECMICP_USE_OPENMP)
   endif()
   message(STATUS "c++ flags ${CMAKE_CXX_FLAGS}")
else()
    message(WARNING "not tested !")
endif()

# Activate this option to use finite difference jacobian
# add_definitions(-DSPECMICP_DEBUG_EQUATION_FD_JACOBIAN)


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

# 3rd party
# =========

# JsonCPP
# -------

set(JSONCPP_DIR  ${PROJECT_SOURCE_DIR}/3rdparty/jsoncpp/)

add_custom_target(3rdparty_header SOURCES
    ${JSONCPP_DIR}/json/json.h
    ${JSONCPP_DIR}/json/json-forwards.h
)
include_directories(${PROJECT_SOURCE_DIR}/3rdparty/jsoncpp/)

# Source
# =======

set(PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)

# Includes
# =========

include_directories(${PROJECT_SOURCE_DIR})

add_custom_target(common SOURCES
    ${PROJECT_SOURCE_DIR}/common.hpp
    ${PROJECT_SOURCE_DIR}/database.hpp
)

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


#   MiCPSolver
# ==============

# Mixed complementarity Solver
# include only module

set(MICPSOLVER_DIR ${PROJECT_SOURCE_DIR}/micpsolver)

add_custom_target(micpsolver_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
# ============

# The speciation solver

set(SPECMICP_DIR ${PROJECT_SOURCE_DIR}/specmicp)
set(KINETICS_DIR ${SPECMICP_DIR}/kinetics)
set(ADIMENSIONAL_DIR ${SPECMICP_DIR}/adimensional)
set(ADIMKINETICS_DIR ${SPECMICP_DIR}/adimensional_kinetics)
set(PROBLEM_SOLVER_DIR ${SPECMICP_DIR}/problem_solver)

# headers only module
add_custom_target(specmic_inc SOURCES
    ${SPECMICP_DIR}/simulation_box.hpp
    ${SPECMICP_DIR}/reduced_system_structs.hpp
    ${SPECMICP_DIR}/reduced_system_solver_structs.hpp

    ${ADIMENSIONAL_DIR}/adimensional_system_structs.hpp
    ${ADIMENSIONAL_DIR}/adimensional_system_solution.hpp
    ${ADIMENSIONAL_DIR}/adimensional_system_solver_structs.hpp
    ${ADIMENSIONAL_DIR}/adimensional_system_numbering.hpp
    ${ADIMENSIONAL_DIR}/adimensional_system_pcfm_structs.hpp

    ${PROBLEM_SOLVER_DIR}/formulation.hpp

    ${KINETICS_DIR}/kinetic_model.hpp
    ${KINETICS_DIR}/kinetic_variables.hpp
    ${KINETICS_DIR}/kinetic_system_solver_structs.hpp


    ${ADIMKINETICS_DIR}/kinetic_model.hpp
    ${ADIMKINETICS_DIR}/kinetic_variables.hpp
    ${ADIMKINETICS_DIR}/kinetic_system_solver_structs.hpp

)

# Source for the library
set(SPECMICP_LIBFILE
    ${SPECMICP_DIR}/equilibrium_data.cpp
    ${SPECMICP_DIR}/reduced_system.cpp
    ${SPECMICP_DIR}/reduced_system_solver.cpp
    ${SPECMICP_DIR}/reaction_path.cpp

    ${ADIMENSIONAL_DIR}/adimensional_system.cpp
    ${ADIMENSIONAL_DIR}/adimensional_system_solver.cpp
    ${ADIMENSIONAL_DIR}/adimensional_system_solution_extractor.cpp
    ${ADIMENSIONAL_DIR}/adimensional_system_pcfm.cpp
    ${ADIMENSIONAL_DIR}/equilibrium_curve.cpp

    ${PROBLEM_SOLVER_DIR}/dissolver.cpp

    # kinetic
    ${KINETICS_DIR}/kinetic_system.cpp
    ${KINETICS_DIR}/kinetic_system_solver.cpp

    ${ADIMKINETICS_DIR}/kinetic_system.cpp
    ${ADIMKINETICS_DIR}/kinetic_system_solver.cpp
    ${ADIMKINETICS_DIR}/kinetic_system_euler_solver.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

    ${JSONCPP_DIR}/jsoncpp.cpp
)

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

add_library(specmicp_database ${DATABASE_LIBFILE})

#   ODEint
# ==========

# ODE integration, headers-only

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
    ${ODEINT_DIR}/runge_kutta_step_structs.hpp
)

#   DFPMSolver
# ==============

## Parabolic solver for finite element problem, header only

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
    #
    # Parabolic solver
    ${DFPMSOLVER_DIR}/parabolic_driver.hpp
    ${DFPMSOLVER_DIR}/parabolic_driver.inl
    ${DFPMSOLVER_DIR}/parabolic_program.hpp
    ${DFPMSOLVER_DIR}/parabolic_structs.hpp
)

#   DFPM
# ========

# Dynaflow+- , Finite element solver, mostly headers

set (DFPM_DIR ${PROJECT_SOURCE_DIR}/dfpm)

add_custom_target(dfpm_incl SOURCES
    ${DFPM_DIR}/types.hpp

    ${DFPM_DIR}/1dtransport/diffusion_parameters.hpp

    ${DFPM_DIR}/mesh.hpp
    ${DFPM_DIR}/meshes/mesh1dfwd.hpp
    ${DFPM_DIR}/meshes/mesh1d.hpp
    ${DFPM_DIR}/meshes/uniform_mesh1d.hpp
    ${DFPM_DIR}/meshes/generic_mesh1d.hpp
    ${DFPM_DIR}/meshes/axisymmetric_uniform_mesh1d.hpp
    ${DFPM_DIR}/meshes/axisymmetric_mesh1d.hpp
)

set(DFPMLIB
    ${DFPM_DIR}/1dtransport/diffusion.cpp
)

add_library(dfpm ${DFPMLIB})

#   ReactMiCP
# =============

# Reactive transport solver

set(REACTMICP_DIR ${PROJECT_SOURCE_DIR}/reactmicp)
set(REACTMICP_SOLVER_DIR ${REACTMICP_DIR}/solver/)
set(REACTMICP_SYSTEMS_DIR ${REACTMICP_DIR}/systems/)

add_custom_target(reactmicp_incl SOURCES
    ${REACTMICP_DIR}/common.hpp
    #
    ${REACTMICP_DIR}/micpsolvers/parabolicprogram.hpp ## remove or fix
    ${REACTMICP_DIR}/micpsolvers/micpsolver_structs.hpp ## remove or fix
    ${REACTMICP_DIR}/micpsolvers/micpsolver.hpp ## remove or fix
    ${REACTMICP_DIR}/micpsolvers/micpsolver.inl ## remove or fix
    #

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

    ${REACTMICP_DIR}/systems/saturated_diffusion/reactive_transport_solver_structs.hpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/transport_parameters.hpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/transport_parameters_base.hpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/transport_neutrality_parameters.hpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/boundary_conditions.hpp

    # Flexible reactive tranport solver
    # ---------------------------------

    ${REACTMICP_SOLVER_DIR}/reactive_transport_solver_structs.hpp

    ${REACTMICP_SOLVER_DIR}/staggers_base/variables_base.hpp
    ${REACTMICP_SOLVER_DIR}/staggers_base/transport_stagger_base.hpp
    ${REACTMICP_SOLVER_DIR}/staggers_base/chemistry_stagger_base.hpp
    ${REACTMICP_SOLVER_DIR}/staggers_base/upscaling_stagger_base.hpp
    ${REACTMICP_SOLVER_DIR}/staggers_base/stagger_structs.hpp
    ${REACTMICP_SOLVER_DIR}/staggers_base/decl.inl
    ${REACTMICP_SOLVER_DIR}/staggers_base/staggers_base.hpp


    ${REACTMICP_SYSTEMS_DIR}/saturated_react/variablesfwd.hpp
)

set(REACTMICP_LIBFILES

    ${REACTMICP_DIR}/systems/saturated_diffusion/reactive_transport_solver.cpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/reactive_transport_neutrality_solver.cpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/transport_program.cpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/transport_neutrality_program.cpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/transport_neutrality_variables.cpp
    ${REACTMICP_DIR}/systems/saturated_diffusion/variables.cpp

    ${REACTMICP_DIR}/equilibrium_curve/chemistry.cpp
    ${REACTMICP_DIR}/equilibrium_curve/eqcurve_extractor.cpp
    ${REACTMICP_DIR}/equilibrium_curve/eqcurve_coupler.cpp
    ${REACTMICP_DIR}/equilibrium_curve/eqcurve_solid_transport.cpp


    # Flexible reactive transport solver
    # ----------------------------------
    ${REACTMICP_SOLVER_DIR}/reactive_transport_solver.cpp
    ${REACTMICP_SOLVER_DIR}/timestepper.cpp

    #
    ${REACTMICP_SYSTEMS_DIR}/saturated_react/variables.cpp
    ${REACTMICP_SYSTEMS_DIR}/saturated_react/transport_program.cpp
    ${REACTMICP_SYSTEMS_DIR}/saturated_react/transport_stagger.cpp
    ${REACTMICP_SYSTEMS_DIR}/saturated_react/equilibrium_stagger.cpp
    ${REACTMICP_SYSTEMS_DIR}/saturated_react/react_solver.cpp
    ${REACTMICP_SYSTEMS_DIR}/saturated_react/init_variables.cpp
)

add_library(reactmicp ${REACTMICP_LIBFILES})

#   Utils
# =========

# Stuff that may be used by the other modules


set(UTILS_DIR ${PROJECT_SOURCE_DIR}/utils)

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

    # sparse solvers
    # --------------
    ${UTILS_DIR}/sparse_solvers/sparse_solver.hpp
    ${UTILS_DIR}/sparse_solvers/sparse_solver_base.hpp
    ${UTILS_DIR}/sparse_solvers/sparse_solver_structs.hpp
    ${UTILS_DIR}/sparse_solvers/sparse_qr.hpp
    ${UTILS_DIR}/sparse_solvers/sparse_lu.hpp
    ${UTILS_DIR}/sparse_solvers/sparse_bicgstab.hpp
    ${UTILS_DIR}/sparse_solvers/sparse_gmres.hpp

    ${UTILS_DIR}/options_handler.hpp
    ${UTILS_DIR}/perfs_handler.hpp

    ${UTILS_DIR}/moving_average.hpp
)

#   Physics
# ===========

# Stuff that may be used by the other modules, but is related to 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
)

#                        Database
#########################################################################


# Not code, just necessary data

set(DATA_DIR ${CMAKE_CURRENT_SOURCE_DIR}/data)

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

add_custom_target(data SOURCES ${DATABASE_LIST})

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

#                       Documentation
#########################################################################

# "common" 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})

# Doxygen documentation
# ---------------------

# add a target to generate API documentation with Doxygen
find_package(Doxygen)

if(DOXYGEN_FOUND)
    # Configure doxygen
    configure_file(${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/doc/Doxyfile @ONLY)
    # Citations for the documentations
    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/)
    # Target to build the documentations
    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
    )
endif(DOXYGEN_FOUND)


# The following modules have their own CMakeLists.txt

#                      Python interface
#########################################################################
add_subdirectory( cython )

#                          Tests
#########################################################################
add_subdirectory( tests )

#                        Examples
#########################################################################
add_subdirectory( examples )