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specmicp/CMakeLists.txt
abe3dbcbe88dkinetics

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)

			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})
			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}/reactive_transport.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 )

specmicp/CMakeLists.txtabe3dbcbe88dkinetics

CMakeLists.txtView Options

specmicp/CMakeLists.txt
abe3dbcbe88dkinetics

CMakeLists.txt
View Options