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specmicp/CMakeLists.txt
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CMakeLists.txt
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project(specmicp)
cmake_minimum_required(VERSION 2.8.8)
# Options :
# - SPECMICP_USE_OPENMP : bool : use openmp to parallelize code
#
#
####################### External Package #####################################
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${PROJECT_SOURCE_DIR}/cmake/")
find_package(Boost REQUIRED)
include_directories(${Boost_INCLUDE_DIR})
find_package(Eigen3 REQUIRED) # This module comes from the Eigen3 Package
include_directories(${EIGEN3_INCLUDE_DIR})
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)
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 "${CMAKE_CXX_FLAGS_RELEASE} -O2 -DNDEBUG")
if(SPECMICP_USE_OPENMP)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
add_definitions(-DSPECMICP_USE_OPENMP)
endif()
message(STATUS "c++ flags ${CMAKE_CXX_FLAGS}")
else()
message(WARNING "not tested !")
endif()
################ Directories #####################
# 3rd party
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/)
set(PROJECT_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src)
# include
include_directories(${PROJECT_SOURCE_DIR})
add_custom_target(common SOURCES
${PROJECT_SOURCE_DIR}/common.hpp
${PROJECT_SOURCE_DIR}/database.hpp
)
################ 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)
set(KINETICS_DIR ${SPECMICP_DIR}/kinetics)
set(ADIMENSIONAL_DIR ${SPECMICP_DIR}/adimensional)
set(PROBLEM_SOLVER_DIR ${SPECMICP_DIR}/problem_solver)
add_custom_target(specmic_inc SOURCES
#${SPECMICP_DIR}/.hpp
${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
${PROBLEM_SOLVER_DIR}/formulation.hpp
${KINETICS_DIR}/kinetic_model.hpp
${KINETICS_DIR}/kinetic_variables.hpp
${KINETICS_DIR}/kinetic_system_solver_structs.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
${ADIMENSIONAL_DIR}/adimensional_system.cpp
${ADIMENSIONAL_DIR}/adimensional_system_solver.cpp
${ADIMENSIONAL_DIR}/adimensional_system_solution_extractor.cpp
${ADIMENSIONAL_DIR}/equilibrium_curve.cpp
${PROBLEM_SOLVER_DIR}/dissolver.cpp
# kinetic
${KINETICS_DIR}/kinetic_system.cpp
${KINETICS_DIR}/kinetic_system_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})
# --------- 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
${ODEINT_DIR}/runge_kutta_step_structs.hpp
)
# --------- 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
#
# Parabolic solver
${DFPMSOLVER_DIR}/parabolic_driver.hpp
${DFPMSOLVER_DIR}/parabolic_driver.inl
${DFPMSOLVER_DIR}/parabolic_program.hpp
${DFPMSOLVER_DIR}/parabolic_structs.hpp
)
# -------- DFPM ------------------------
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/axisymmetric_uniform_mesh1d.hpp
)
set(DFPMLIB
${DFPM_DIR}/1dtransport/diffusion.cpp
)
add_library(dfpm ${DFPMLIB})
# --------- ReactMiCP -----------------
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
${REACTMICP_DIR}/micpsolvers/micpsolver_structs.hpp
${REACTMICP_DIR}/micpsolvers/micpsolver.hpp
${REACTMICP_DIR}/micpsolvers/micpsolver.inl
#
${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
${REACTMICP_SYSTEMS_DIR}/saturated_react/input_data.hpp
)
set(REACTMICP_LIBFILES
#${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/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_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 ------------------
set(UTILS_DIR ${PROJECT_SOURCE_DIR}/utils)
add_custom_target(utils_inc SOURCES
${UTILS_DIR}/log.hpp
${UTILS_DIR}/sparse_solver.hpp
${UTILS_DIR}/sparse_solver_structs.hpp
${UTILS_DIR}/options_handler.hpp
${UTILS_DIR}/perfs_handler.hpp
${UTILS_DIR}/moving_average.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 ----------------------
add_subdirectory( tests )
# --------- Examples ------------------
add_subdirectory( examples )
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