diff --git a/CMakeLists.txt b/CMakeLists.txt index eb3f260..cb63f46 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,442 +1,443 @@ #################################################### # # # 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 ${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}/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/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_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 ) diff --git a/data/momas_benchmark.js b/data/momas_benchmark.js new file mode 100644 index 0000000..d565f95 --- /dev/null +++ b/data/momas_benchmark.js @@ -0,0 +1,114 @@ +// this is the database for the MoMas benchmark +{ + "Metadata": { + "version": "0.1", + "last-modification": "02/11/2015" + }, + "Basis": [ + { + "label": "H2O", + "molar_mass": 18.015 // g/mol + }, + { + "label": "X1", + "molar_mass": 1.0 + }, + { + "label": "X2", + "molar_mass": 1.0 + }, + { + "label": "X3", + "molar_mass": 1.0 + }, + { + "label": "X4", + "molar_mass": 1.0 + }, + { + "label": "X5", + "molar_mass": 1.0 + }, + { + "label": "S", + "molar_mass": 1.0 + } + ], + "Aqueous": [ + { + "label": "C1", + "composition": "-X2", + "log_k": 12 + }, + { + "label": "C2", + "composition": "X2, X3", + "log_k": 0.0 + }, + { + "label": "C3", + "composition": "-X2, X4", + "log_k": 0.0 + }, + { + "label": "C4", + "composition": "-4 X2, X3, 3 X4", + "log_k": 1 + }, + { + "label": "C5", + "composition": "4 X2, 3 X3, 1 X4", + "log_k": -35 + }, + { + "label": "C6", + "composition": "10 X2, 3 X3", + "log_k": -32 + }, + { + "label": "C7", + "composition": "-8 X2, 2 X4", + "log_k": 4 + } + ], + "Sorbed": [ + { + "label": "CS1", + "composition": "3 X2, X3, S", + "log_k": -6 + }, + { + "label": "CS2", + "composition": "-3 X2, X4, 2 S", + "log_k": 1 + } + ], + "Minerals": [ + { + "label": "CP1", + "composition": "3 X2, X3", + "log_k": 9.0969, + "molar_volume": 1.0 + }, + { + "label": "CP2", + "composition": "X2, X5", + "log_k": -1.30, + "molar_volume": 1.0 + }, + { + "label": "Cc", + "composition": "-3 X2, X4", + "log_k": 1.0, + "molar_volume": 1.0, + "flag_kinetic": 1 + } + + ], + "References" : [ + { + "key": "Carrayrou2010", + "description": "Carrayrou, Jérôme, Kern, Michel, Knabner, Peter: Reactive transport benchmark of MoMaS, Computational Geosciences 14(3), Springer Netherlands, 385–392, 2010" + } + ] +}