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specmicp/CMakeLists.txt
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CMakeLists.txt
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####################################################
# #
# SpecMiCP : CMakeLists.txt #
# #
####################################################
project(specmicp)
cmake_minimum_required(VERSION 2.8.8)
# For an explanation of the options see the INSTALL file
option(SPECMICP_USE_OPENMP "Thread parallelisation of specmicp instances if available" ON)
# 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
#########################################################################
# OpenMP
# ------
include(CheckCXXCompilerFlag)
check_cxx_compiler_flag("-fopenmp" HAS_OPENMP)
# c++11
# -----
check_cxx_compiler_flag("-std=c++11" HAS_CXX11)
if(NOT HAS_CXX11)
message(FATAL_ERROR "A c++11 compatible compiler is necessary")
endif()
if(UNIX)
# Use ld.gold if it is available and isn't disabled explicitly
# Ref : https://bugs.webkit.org/show_bug.cgi?id=137953
option(USE_LD_GOLD "Use GNU gold linker" ON)
if (USE_LD_GOLD)
execute_process(COMMAND ${CMAKE_C_COMPILER} -fuse-ld=gold -Wl,--version ERROR_QUIET OUTPUT_VARIABLE LD_VERSION)
if ("${LD_VERSION}" MATCHES "GNU gold")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fuse-ld=gold")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fuse-ld=gold")
else ()
message(WARNING "GNU gold linker isn't available, using the default system linker.")
endif ()
endif ()
# Generic options
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
if (HAS_OPENMP)
SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
endif()
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()
# 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)
add_custom_target(database_incl SOURCES
${DATABASE_DIR}/species/ionic_parameters.hpp
${DATABASE_DIR}/species/component_list.hpp
${DATABASE_DIR}/species/aqueous_list.hpp
${DATABASE_DIR}/species/gas_list.hpp
${DATABASE_DIR}/species/sorbed_list.hpp
${DATABASE_DIR}/species/mineral_list.hpp
${DATABASE_DIR}/errors.hpp
${DATABASE_DIR}/module.hpp
)
set(DATABASE_LIBFILE
${DATABASE_DIR}/species/species.cpp
${DATABASE_DIR}/species/base_wrapper.cpp
${DATABASE_DIR}/data_container.cpp
${DATABASE_DIR}/database.cpp
${DATABASE_DIR}/reader.cpp
${DATABASE_DIR}/selector.cpp
${DATABASE_DIR}/mineral_selector.cpp
${DATABASE_DIR}/switch_basis.cpp
${JSONCPP_DIR}/jsoncpp.cpp
)
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_SOLVER_DIR}/runner.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})
if(HAS_OPENMP)
if(SPECMICP_USE_OPENMP)
SET_TARGET_PROPERTIES(reactmicp PROPERTIES COMPILE_DEFINITIONS "SPECMICP_USE_OPENMP")
endif()
endif()
# Utils
# =========
# Stuff that may be used by the other modules
set(UTILS_DIR ${PROJECT_SOURCE_DIR}/utils)
set(IO_DIR ${UTILS_DIR}/io)
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
${UTILS_DIR}/timer.hpp
# input/output
${IO_DIR}/units.hpp
${IO_DIR}/meshes.hpp
${IO_DIR}/reactive_transport.hpp
${IO_DIR}/saturated_react.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 )
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