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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)
####################### 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/transport_parameters.hpp
${REACTMICP_DIR}/systems/saturated_diffusion/boundary_conditions.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/transport_program.cpp
${REACTMICP_DIR}/systems/saturated_diffusion/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
)
# ------- 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/reactive_transport.cpp
${PROJECT_TEST_DIR}/reactmip/systems/saturated_diffusion/utils.cpp
)
target_link_libraries(test_reactmicp_saturated_diffusion reactmicp specmicp specmicp_database jsoncpp)
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