diff --git a/src/database/CMakeLists.txt b/src/database/CMakeLists.txt
index c7a66b2..fbf1ae5 100644
--- a/src/database/CMakeLists.txt
+++ b/src/database/CMakeLists.txt
@@ -1,141 +1,142 @@
 # The database
 # ============
 
 # database libraries
 # ------------------
 
 add_custom_target(database_incl
     SOURCES
     config_database.hpp
 
     species/ionic_parameters.hpp
     species/component_list.hpp
     species/aqueous_list.hpp
 
     section_name.hpp
 
     database_holder.hpp
     errors.hpp
     module.hpp
     database_fwd.hpp
 )
 
 set(DATABASE_LIBFILE
     species/species.cpp
     species/base_wrapper.cpp
     species/mineral_list.cpp
     species/gas_list.cpp
     species/sorbed_list.cpp
     species/compounds_list.cpp
     species/element_list.cpp
 
 
     data_container.cpp
     module.cpp
     database.cpp
     reader_common.cpp
     yaml_reader.cpp
     selector.cpp
     appender.cpp
     mineral_selector.cpp
     aqueous_selector.cpp
     oxydo_selector.cpp
     switch_basis.cpp
     yaml_writer.cpp
     unknown_class.cpp
 
 
     io/configuration.cpp
 )
 
 
 if (HDF5_FOUND)
     list(APPEND DATABASE_LIBFILE
         io/hdf5_database.cpp
     )
 
-    include_directories(HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(
         io/hdf5_database.cpp
         PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS
     )
 endif()
 
 
 set_visibility_flag(${DATABASE_LIBFILE})
 set_pgo_flag(${DATABASE_LIBFILE})
 #set_property(SOURCE ${DATABASE_LIBFILE} APPEND PROPERTY COMPILE_FLAGS -fvisibility-inlines-hidden)
 
 
 add_library(objspecmicp_database OBJECT ${DATABASE_LIBFILE})
 set_property(TARGET objspecmicp_database PROPERTY POSITION_INDEPENDENT_CODE 1)
 
 add_library(specmicp_database SHARED $<TARGET_OBJECTS:objspecmicp_database>)
 install(TARGETS specmicp_database
     LIBRARY DESTINATION ${LIBRARY_INSTALL_DIR}
 )
 
 # export includes
 # ----------------
 
 set(DATABASE_SPECIES_INCLUDE_LIST
     species/species.hpp
     species/base_wrapper.hpp
     species/ionic_parameters.hpp
     species/component_list.hpp
     species/aqueous_list.hpp
     species/mineral_list.hpp
     species/gas_list.hpp
     species/sorbed_list.hpp
     species/compounds_list.hpp
     species/element_list.hpp
 )
 
 set(DATABASE_INCLUDE_LIST
     errors.hpp
     module.hpp
 
     data_container.hpp
     database.hpp
     selector.hpp
     appender.hpp
     mineral_selector.hpp
     aqueous_selector.hpp
     oxydo_selector.hpp
     switch_basis.hpp
     unknown_class.hpp
     database_holder.hpp
 
     database_fwd.hpp
 )
 
 install(FILES ${DATABASE_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/database/
 )
 
 install(FILES ${DATABASE_SPECIES_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/database/species/
 )
 
 install(FILES io/configuration.hpp
     DESTINATION ${INCLUDE_INSTALL_DIR}/database/io/
 )
 
 
 # static libraries
 # ----------------
 
 if(SPECMICP_BUILD_STATIC)
     add_library(specmicp_database_static STATIC  $<TARGET_OBJECTS:objspecmicp_database>)
 
     install(TARGETS specmicp_database_static
         ARCHIVE DESTINATION ${STATIC_LIBRARY_INSTALL_DIR}
     )
 else()
     add_library(specmicp_database_static EXCLUDE_FROM_ALL STATIC  $<TARGET_OBJECTS:objspecmicp_database>)
 endif()
 
     set_target_properties(specmicp_database_static  PROPERTIES OUTPUT_NAME specmicp_database)
     add_dependencies(specmicp_database_static database_incl)
 
 
diff --git a/src/dfpm/CMakeLists.txt b/src/dfpm/CMakeLists.txt
index ca65c76..8d918f1 100644
--- a/src/dfpm/CMakeLists.txt
+++ b/src/dfpm/CMakeLists.txt
@@ -1,92 +1,93 @@
 #   DFPM
 # ========
 
 add_custom_target(dfpm_incl SOURCES
     types.hpp
 
     1dtransport/diffusion_parameters.hpp
 
     mesh.hpp
     meshes/mesh1dfwd.hpp
     meshes/mesh1d.hpp
     meshes/uniform_mesh1d.hpp
     meshes/generic_mesh1d.hpp
     meshes/axisymmetric_uniform_mesh1d.hpp
     meshes/axisymmetric_mesh1d.hpp
 )
 
 set(DFPMLIB
     io/meshes.cpp
     io/configuration.cpp
     meshes/axisymmetric_mesh1d.cpp
     meshes/generic_mesh1d.cpp
     1dtransport/diffusion.cpp
 )
 
 # hdf5
 # ----
 if (HDF5_FOUND)
     list(APPEND DFPMLIB
         io/hdf5_mesh.cpp
     )
 
-    include_directories(HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(
         io/hdf5_mesh.cpp
         PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS
     )
 endif()
 
 set_visibility_flag(${DFPMLIB})
 set_pgo_flag(${DFPMLIB})
 
 add_library(dfpm SHARED ${DFPMLIB})
 
 target_link_libraries(dfpm specmicp_common)
 install(TARGETS dfpm
     LIBRARY DESTINATION ${LIBRARY_INSTALL_DIR}
 )
 
 # includes
 # --------
 
 set(DFPM_MESH_INCLUDE_LIST
     meshes/mesh1dfwd.hpp
     meshes/mesh1d.hpp
     meshes/uniform_mesh1d.hpp
     meshes/generic_mesh1d.hpp
     meshes/axisymmetric_uniform_mesh1d.hpp
     meshes/axisymmetric_mesh1d.hpp
 )
 
 install(FILES types.hpp mesh.hpp
     DESTINATION ${INCLUDE_INSTALL_DIR}/dfpm
 )
 
 install(FILES 1dtransport/diffusion_parameters.hpp 1dtransport/diffusion.hpp
     DESTINATION ${INCLUDE_INSTALL_DIR}/dfpm/1dtransport
 )
 
 install(FILES io/meshes.hpp io/configuration.hpp
     DESTINATION ${INCLUDE_INSTALL_DIR}/dfpm/io
 )
 
 install(FILES ${DFPM_MESH_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/dfpm/meshes
 )
 
 
 # static libraries
 # ----------------
 
 if(SPECMICP_BUILD_STATIC)
     add_library(dfpm_static STATIC ${DFPMLIB})
     install(TARGETS dfpm_static
         ARCHIVE DESTINATION ${STATIC_LIBRARY_INSTALL_DIR}
     )
 else()
     add_library(dfpm_static EXCLUDE_FROM_ALL STATIC ${DFPMLIB})
 endif()
 
 set_target_properties(dfpm_static  PROPERTIES OUTPUT_NAME dfpm)
 target_link_libraries(dfpm_static specmicp_common_static)
diff --git a/src/reactmicp/CMakeLists.txt b/src/reactmicp/CMakeLists.txt
index 621ee4e..dc67cb8 100644
--- a/src/reactmicp/CMakeLists.txt
+++ b/src/reactmicp/CMakeLists.txt
@@ -1,190 +1,191 @@
 #   ReactMiCP
 # =============
 
 set(REACTMICP_SOLVER_DIR solver)
 set(REACTMICP_SYSTEMS_DIR systems)
 set(REACTMICP_EQUILIBRIUMCURVE equilibrium_curve)
 set(REACTMICP_IO io)
 
 add_custom_target(reactmicp_incl SOURCES
 
     ${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}/unsaturated/types_fwd.hpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/variables_sub.hpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/variables_box.hpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/transport_constraints.hpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/fv_1dof_equation.hpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/fv_1dof_equation.inl
 )
 
 set(REACTMICP_LIBFILES
 
     ${REACTMICP_EQUILIBRIUMCURVE}/chemistry.cpp
     ${REACTMICP_EQUILIBRIUMCURVE}/eqcurve_extractor.cpp
     ${REACTMICP_EQUILIBRIUMCURVE}/eqcurve_coupler.cpp
     ${REACTMICP_EQUILIBRIUMCURVE}/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/kinetic_stagger.cpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/react_solver.cpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/init_variables.cpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/diffusive_upscaling_stagger.cpp
 
 
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/variables.cpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/saturation_equation.cpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/saturation_pressure_equation.cpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/pressure_equation.cpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/aqueous_equation.cpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/transport_stagger.cpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/equilibrium_stagger.cpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/variables_interface.cpp
     ${REACTMICP_SYSTEMS_DIR}/unsaturated/equilibrium_constraints.cpp
 
     ${REACTMICP_IO}/reactive_transport.cpp
     ${REACTMICP_IO}/saturated_react.cpp
     ${REACTMICP_IO}/configuration.cpp
 )
 
 # hdf5
 # -----
 if (HDF5_FOUND)
     list(APPEND REACTMICP_LIBFILES ${REACTMICP_IO}/hdf5_unsaturated.cpp)
 
-    include_directories(HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(
         ${REACTMICP_IO}/hdf5_unsaturated.cpp
         PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS
     )
 endif()
 
 set_visibility_flag(${REACTMICP_LIBFILES})
 set_pgo_flag(${REACTMICP_LIBFILES})
 
 if(OPENMP_FOUND)
 if(SPECMICP_USE_OPENMP)
     set_source_files_properties(${REACTMICP_SYSTEMS_DIR}/saturated_react/equilibrium_stagger.cpp
          PROPERTIES COMPILE_DEFINITIONS "SPECMICP_USE_OPENMP"
     )
     set_source_files_properties(${REACTMICP_SYSTEMS_DIR}/saturated_react/kinetic_stagger.cpp
          PROPERTIES COMPILE_DEFINITIONS "SPECMICP_USE_OPENMP"
     )
     set_source_files_properties(${REACTMICP_SYSTEMS_DIR}/unsaturated/transport_stagger.cpp
          PROPERTIES COMPILE_DEFINITIONS "SPECMICP_USE_OPENMP"
     )
     set_source_files_properties(${REACTMICP_SYSTEMS_DIR}/unsaturated/equilibrium_stagger.cpp
          PROPERTIES COMPILE_DEFINITIONS "SPECMICP_USE_OPENMP"
     )
 endif()
 endif()
 
 add_library(objreactmicp OBJECT ${REACTMICP_LIBFILES})
 set_property(TARGET objreactmicp PROPERTY POSITION_INDEPENDENT_CODE 1)
 
 add_library(reactmicp SHARED $<TARGET_OBJECTS:objreactmicp>)
 
 target_link_libraries(reactmicp dfpm)
 install(TARGETS reactmicp
     LIBRARY DESTINATION ${LIBRARY_INSTALL_DIR}
 )
 
 # include files
 # -------------
 
 set(REACTMICP_STAGGERBASE_INCLUDE_LIST
     ${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
 )
 
 set(REACTMICP_SOLVER_INCLUDE_LIST
     ${REACTMICP_SOLVER_DIR}/reactive_transport_solver_structs.hpp
     ${REACTMICP_SOLVER_DIR}/reactive_transport_solver.hpp
     ${REACTMICP_SOLVER_DIR}/timestepper.hpp
     ${REACTMICP_SOLVER_DIR}/runner.hpp
 )
 
 set(REACTMICP_SATURATEDREACT_INCLUDE_LIST
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/variablesfwd.hpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/variables.hpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/transport_program.hpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/transport_stagger.hpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/equilibrium_stagger.hpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/kinetic_stagger.hpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/react_solver.hpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/init_variables.hpp
     ${REACTMICP_SYSTEMS_DIR}/saturated_react/diffusive_upscaling_stagger.hpp
 )
 
 set(REACTMICP_EQUILIBRIUMCURVE_INCLUDE_LIST
     ${REACTMICP_EQUILIBRIUMCURVE}/chemistry.cpp
     ${REACTMICP_EQUILIBRIUMCURVE}/eqcurve_extractor.cpp
     ${REACTMICP_EQUILIBRIUMCURVE}/eqcurve_coupler.cpp
     ${REACTMICP_EQUILIBRIUMCURVE}/eqcurve_solid_transport.cpp
 
 )
 
 set(REACTMICP_IO_INCLUDE_LIST
     io/reactive_transport.hpp
     io/saturated_react.hpp
     io/configuration.hpp
 )
 
 install(FILES ${REACTMICP_STAGGERBASE_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/reactmicp/solver/staggers_base
 )
 install(FILES ${REACTMICP_SOLVER_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/reactmicp/solver
 )
 install(FILES ${REACTMICP_SATURATEDREACT_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/reactmicp/systems/saturated_react
 )
 install(FILES ${REACTMICP_EQUILIBRIUMCURVE_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/reactmicp/equilibrium_curve
 )
 install(FILES ${REACTMICP_IO_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/reactmicp/io
 )
 
 
 
 # static libraries
 # ----------------
 
 if(SPECMICP_BUILD_STATIC)
     add_library(reactmicp_static STATIC $<TARGET_OBJECTS:objreactmicp>)
     install(TARGETS reactmicp_static
         ARCHIVE DESTINATION ${STATIC_LIBRARY_INSTALL_DIR}
     )
 else()
     add_library(reactmicp_static EXCLUDE_FROM_ALL STATIC $<TARGET_OBJECTS:objreactmicp>)
 endif()
 
 set_target_properties(reactmicp_static  PROPERTIES OUTPUT_NAME reactmicp)
 target_link_libraries(reactmicp_static dfpm_static)
 
diff --git a/src/specmicp/CMakeLists.txt b/src/specmicp/CMakeLists.txt
index 93fae3e..fa3d5a1 100644
--- a/src/specmicp/CMakeLists.txt
+++ b/src/specmicp/CMakeLists.txt
@@ -1,143 +1,144 @@
 # The speciation solver
 # =====================
 
 # Directories
 set(ADIMENSIONAL_DIR adimensional)
 set(ADIMKINETICS_DIR adimensional_kinetics)
 set(PROBLEM_SOLVER_DIR problem_solver)
 set(IO_DIR io)
 
 # Headers file without a source file
 add_custom_target(specmicp_incl SOURCES
     ${ADIMENSIONAL_DIR}/adimensional_system_structs.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solution.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_numbering.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_pcfm_structs.hpp
 
     ${ADIMENSIONAL_DIR}/config_solution_output_format.h
     ${ADIMENSIONAL_DIR}/config_default_options_solver.h
 
 
     ${PROBLEM_SOLVER_DIR}/formulation.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
 
     ${ADIMENSIONAL_DIR}/adimensional_system.cpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solver.cpp
 
     ${ADIMENSIONAL_DIR}/adimensional_system_solver_structs.cpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solution_extractor.cpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solution_saver.cpp
     ${ADIMENSIONAL_DIR}/adimensional_system_pcfm.cpp
     ${ADIMENSIONAL_DIR}/equilibrium_curve.cpp
 
     ${PROBLEM_SOLVER_DIR}/dissolver.cpp
 
     ${IO_DIR}/configuration.cpp
     ${IO_DIR}/print.cpp
 
     # kinetic
     ${ADIMKINETICS_DIR}/kinetic_system.cpp
     ${ADIMKINETICS_DIR}/kinetic_system_solver.cpp
     ${ADIMKINETICS_DIR}/kinetic_system_euler_solver.cpp
 )
 
 if (HDF5_FOUND)
     list(APPEND SPECMICP_LIBFILE
         ${IO_DIR}/hdf5_adimensional.cpp
     )
 
-    include_directories(HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(
         ${IO_DIR}/hdf5_adimensional.cpp
         PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS
     )
 endif()
 
 
 set_visibility_flag(${SPECMICP_LIBFILE})
 set_pgo_flag(${SPECMICP_LIBFILE})
 
 
 if(SPECMICP_DEBUG_EQUATION_FD_JACOBIAN)
    set_source_files_properties(${ADIMENSIONAL_DIR}/adimensional_system.cpp
         PROPERTIES COMPILE_DEFINITIONS "SPECMICP_DEBUG_EQUATION_FD_JACOBIAN"
     )
 endif()
 
 add_library(specmicp SHARED ${SPECMICP_LIBFILE})
 install(TARGETS specmicp
     LIBRARY DESTINATION ${LIBRARY_INSTALL_DIR}
 )
 
 # include files
 # --------------
 
 set(SPECMICP_ADIMENSIONAL_INCLUDES
     ${ADIMENSIONAL_DIR}/adimensional_system_structs.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solution.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solution_saver.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solver_structs.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_numbering.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_pcfm_structs.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solver.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_solution_extractor.hpp
     ${ADIMENSIONAL_DIR}/adimensional_system_pcfm.hpp
     ${ADIMENSIONAL_DIR}/equilibrium_curve.hpp
 
 )
 set(SPECMICP_PROBLEM_SOLVER_INCLUDES
     ${PROBLEM_SOLVER_DIR}/dissolver.hpp
     ${PROBLEM_SOLVER_DIR}/formulation.hpp
 )
 set(SPECMICP_ADIMENSIONAL_KINETICS_INCLUDES
     ${ADIMKINETICS_DIR}/kinetic_model.hpp
     ${ADIMKINETICS_DIR}/kinetic_variables.hpp
     ${ADIMKINETICS_DIR}/kinetic_system_solver_structs.hpp
     ${ADIMKINETICS_DIR}/kinetic_system.hpp
     ${ADIMKINETICS_DIR}/kinetic_system_solver.hpp
     ${ADIMKINETICS_DIR}/kinetic_system_euler_solver.hpp
 )
 
 set(SPECMICP_IO_INCLUDES
     ${IO_DIR}/configuration.hpp
     ${IO_DIR}/print.hpp
 )
 
 install(FILES ${SPECMICP_ADIMENSIONAL_INCLUDES}
     DESTINATION ${INCLUDE_INSTALL_DIR}/specmicp/adimensional
 )
 install(FILES ${SPECMICP_PROBLEM_SOLVER_INCLUDES}
     DESTINATION ${INCLUDE_INSTALL_DIR}/specmicp/problem_solver
 )
 install(FILES ${SPECMICP_ADIMENSIONAL_KINETICS_INCLUDES}
     DESTINATION ${INCLUDE_INSTALL_DIR}/specmicp/adimensional_kinetics
 )
 
 install(FILES ${SPECMICP_IO_INCLUDES}
     DESTINATION ${INCLUDE_INSTALL_DIR}/specmicp/io
 )
 
 # static libraries
 # ----------------
 
 if(SPECMICP_BUILD_STATIC)
     add_library(specmicp_static STATIC ${SPECMICP_LIBFILE})
 
     install(TARGETS specmicp_static
         ARCHIVE DESTINATION ${STATIC_LIBRARY_INSTALL_DIR}
     )
 else()
     add_library(specmicp_static EXCLUDE_FROM_ALL STATIC ${SPECMICP_LIBFILE})
 
 endif()
     set_target_properties(specmicp_static  PROPERTIES OUTPUT_NAME specmicp)
 
diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt
index d49e26b..03f9af1 100644
--- a/src/utils/CMakeLists.txt
+++ b/src/utils/CMakeLists.txt
@@ -1,127 +1,128 @@
 # headers only module
 # -------------------
 add_custom_target(utils_inc SOURCES
     #log.hpp
 
     # sparse solvers
     # --------------
     sparse_solvers/sparse_solver_base.hpp
     sparse_solvers/sparse_solver.hpp
     sparse_solvers/sparse_solver_structs.hpp
     sparse_solvers/sparse_qr.hpp
     sparse_solvers/sparse_lu.hpp
     sparse_solvers/sparse_bicgstab.hpp
     sparse_solvers/sparse_gmres.hpp
 
     options_handler.hpp
     perfs_handler.hpp
 
     compat.hpp
 
     value_checker.hpp
 )
 
 set(SPECMICP_COMMON_LIBRARY_FILES
     log.cpp
     dateandtime.cpp
     timer.cpp
     moving_average.cpp
 
     ../physics/laws.cpp
     ../physics/units.cpp
     ../physics/io/units.cpp
 
     io/format.cpp
     io/csv_formatter.cpp
     io/yaml.cpp
 )
 
 # hdf5
 # -----
 if (HDF5_FOUND)
     list(APPEND SPECMICP_COMMON_LIBRARY_FILES
         io/specmicp_hdf5.cpp
 )
 
-    include_directories(HDF5_INCLUDE_DIRS)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(io/specmicp_hdf5.cpp PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS)
 
     add_custom_target(utils_io_hdf5_inc SOURCES
         io/hdf5_eigen.hpp
         io/hdf5_eigen.inl
         )
 endif()
 
 set_pgo_flag(${SPECMICP_COMMON_LIBRARY_FILES})
 add_library(objspecmicp_common OBJECT ${SPECMICP_COMMON_LIBRARY_FILES})
 set_property(TARGET objspecmicp_common PROPERTY POSITION_INDEPENDENT_CODE 1)
 
 
 add_library(specmicp_common SHARED $<TARGET_OBJECTS:objspecmicp_common>)
 if (HDF5_FOUND)
     target_link_libraries(specmicp_common ${HDF5_LIBRARIES})
 endif()
 
 install(TARGETS specmicp_common
     LIBRARY DESTINATION ${LIBRARY_INSTALL_DIR}
 )
 
 set(UTILS_INCLUDE_LIST
     log.hpp
     options_handler.hpp
     perfs_handler.hpp
     moving_average.hpp
     timer.hpp
     dateandtime.hpp
     compat.hpp
 )
 
 set(UTILS_SPARSE_INCLUDE_LIST
     # sparse solvers
     # --------------
     sparse_solvers/sparse_solver.hpp
     sparse_solvers/sparse_solver_base.hpp
     sparse_solvers/sparse_solver_structs.hpp
     sparse_solvers/sparse_qr.hpp
     sparse_solvers/sparse_lu.hpp
     sparse_solvers/sparse_bicgstab.hpp
     sparse_solvers/sparse_gmres.hpp
 )
 
 set(UTILS_IO_INCLUDE_LIST
     io/format.hpp
     io/csv_formatter.hpp
     io/yaml.hpp
 )
 
 install(FILES ${UTILS_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/utils
 )
 
 install(FILES ${UTILS_SPARSE_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/utils/sparse_solvers
 )
 
 
 install(FILES ${UTILS_IO_INCLUDE_LIST}
     DESTINATION ${INCLUDE_INSTALL_DIR}/utils/io
 )
 
 # static libraries
 # ----------------
 
 if(SPECMICP_BUILD_STATIC)
     add_library(specmicp_common_static STATIC $<TARGET_OBJECTS:objspecmicp_common>)
 
     install(TARGETS specmicp_common_static
         ARCHIVE DESTINATION ${STATIC_LIBRARY_INSTALL_DIR}
     )
 else()
     add_library(specmicp_common_static EXCLUDE_FROM_ALL STATIC $<TARGET_OBJECTS:objspecmicp_common>)
 
 endif()
     set_target_properties(specmicp_common_static  PROPERTIES OUTPUT_NAME specmicp_common)
 
 if (HDF5_FOUND)
     target_link_libraries(specmicp_common_static ${HDF5_LIBRARIES})
 endif()
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index f683a33..03693c6 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -1,81 +1,82 @@
 ################## Tests ########################################
 
 include(CatchTest)
 
 
 set(PROJECT_TEST_DIR ${CMAKE_CURRENT_SOURCE_DIR})
 include_directories(${PROJECT_TEST_DIR})
 
 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND}) # make check is also valid
 
 
 # Catch test
 #===========
 
 #common
 
 set( COMMON_TEST_DIR common )
 
 set(SPECMICP_COMMON_TEST_FILES
     ${COMMON_TEST_DIR}/test_common.cpp
     ${COMMON_TEST_DIR}/units.cpp
     ${COMMON_TEST_DIR}/laws.cpp
     ${COMMON_TEST_DIR}/misc.cpp
     ${COMMON_TEST_DIR}/value_checker.cpp
     ${COMMON_TEST_DIR}/sparse_solvers.cpp
 )
 
 if (HDF5_FOUND)
     list(APPEND SPECMICP_COMMON_TEST_FILES
         ${COMMON_TEST_DIR}/hdf5_eigen.cpp
     )
 
-    include_directories(HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(${COMMON_TEST_DIR}/hdf5_eigen.cpp PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS)
 endif()
 
 add_catch_test(NAME common SOURCES
     ${SPECMICP_COMMON_TEST_FILES}
     LINK_LIBRARIES specmicp_common_static
 )
 
 # MiCPSolver
 # ----------
 
 set(MICPSOLVER_TEST_DIR micpsolver)
 
 add_catch_test(NAME micpsolver SOURCES
     ${MICPSOLVER_TEST_DIR}/test_micpsolver.cpp
     ${MICPSOLVER_TEST_DIR}/condition_number.cpp
     ${MICPSOLVER_TEST_DIR}/ncp_functions.cpp
     ${MICPSOLVER_TEST_DIR}/micpsolver.cpp
 
     LINK_LIBRARIES specmicp_common_static
 )
 
 # ODEInt
 # ----------
 
 set(ODEINT_TEST_DIR odeint)
 
 add_catch_test(NAME odeint SOURCES
     ${ODEINT_TEST_DIR}/test_odeint.cpp
     ${ODEINT_TEST_DIR}/butchertableau.cpp
     ${ODEINT_TEST_DIR}/embeddedrungekutta.cpp
 )
 
 # Database
 # --------
 
 add_subdirectory(database)
 
 
 # Specmicp
 # --------
 
 add_subdirectory( specmicp )
 
 # Reactmicp
 # ---------
 
 add_subdirectory( reactmicp )
diff --git a/tests/database/CMakeLists.txt b/tests/database/CMakeLists.txt
index 3bc3e35..c89c3ec 100644
--- a/tests/database/CMakeLists.txt
+++ b/tests/database/CMakeLists.txt
@@ -1,57 +1,58 @@
 # test for the database
 # =====================
 
 # databases used in the tests
 add_custom_target(test_database_inc SOURCES
     str_database.hpp
     db_test.yaml
 )
 
 file(COPY db_test.yaml DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
 
 # basic set of test
 # -----------------
 set(test_specmicp_database_files
     test_database.cpp
     database_species.cpp
     database_reader.cpp
     database_selector.cpp
     database_switch.cpp
     database_cemdata.cpp
     database_appender.cpp
     database_writer.cpp
     database_configuration.cpp
     database_unknown.cpp
 )
 
 # test the cemdata database => need the path
 set(TEST_CEMDATA_PATH \"../../data/cemdata.yaml\")
 set(TEST_MOMAS_PATH \"../../data/momas_benchmark.yaml\")
 
 set_source_files_properties(
     database_cemdata.cpp
     PROPERTIES COMPILE_DEFINITIONS
     "TEST_CEMDATA_PATH=${TEST_CEMDATA_PATH};TEST_MOMAS_PATH=${TEST_MOMAS_PATH}"
 )
 
 # hdf5 test
 # ---------
 if (HDF5_FOUND)
     list(APPEND test_specmicp_database_files
         io_hdf5_database.cpp
     )
 
-    include_directories(HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(
         adim/io_hdf5_database.cpp
         PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS
     )
 endif()
 
 # The test
 # --------
 add_catch_test(NAME database SOURCES
     ${test_specmicp_database_files}
     LINK_LIBRARIES specmicp_database_static specmicp_common_static ${YAML_LIBRARIES}
 )
 
diff --git a/tests/reactmicp/CMakeLists.txt b/tests/reactmicp/CMakeLists.txt
index 69bb8c1..516ba46 100644
--- a/tests/reactmicp/CMakeLists.txt
+++ b/tests/reactmicp/CMakeLists.txt
@@ -1,90 +1,91 @@
 # Mesh
 # ----
 
 set(test_meshes_files
     meshes/test_meshes.cpp
     meshes/test_uniform_mesh_1d.cpp
     meshes/test_generic1d.cpp
     meshes/test_axisymmetric_uniform_mesh_1d.cpp
     meshes/test_configuration.cpp
 )
 
 # hdf5
 if (HDF5_FOUND)
     list(APPEND test_meshes_files
         meshes/io_hdf5_meshes.cpp
 )
 
-    include_directories(HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(
         meshes/io_hdf5_meshes.cpp
         PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS
     )
 
 endif()
 
 add_catch_test(NAME meshes SOURCES "${test_meshes_files}"
     LINK_LIBRARIES dfpm_static specmicp_common_static ${YAML_LIBRARIES})
 
 FILE(COPY
           meshes/unif_mesh.yaml
           meshes/ramp_mesh.yaml
           meshes/unif_axisym.yaml
 
      DESTINATION ${CMAKE_CURRENT_BINARY_DIR}
 )
 
 # Reactmicp : Reactive transport solver
 # -------------------------------------
 
 set(test_reactmicp_files
     solver/test_reactive_transport_solver.cpp
     solver/test_coupling.cpp
 )
 add_catch_test(NAME reactmicp SOURCES ${test_reactmicp_files}
  LINK_LIBRARIES ${REACTMICP_STATIC_LIBS})
 
 
 # Saturated diffusion using new reactive transport solver
 # -------------------------------------------------------
 
 set(test_reactmicp_saturated_files
     systems/saturated_react/test_reactmicp_saturated_react.cpp
     systems/saturated_react/speciation_system.cpp
     systems/saturated_react/variables.cpp
     systems/saturated_react/transport_program.cpp
     systems/saturated_react/equilibrium_stagger.cpp
 )
 add_catch_test(
     NAME reactmicp_saturated_react
     SOURCES ${test_reactmicp_saturated_files}
     LINK_LIBRARIES ${REACTMICP_STATIC_LIBS}
 )
 
 # Unsaturated reactive transport system
 # -------------------------------------
 
 set(UNSATURATED_DIR systems/unsaturated)
 
 set(test_reactmicp_unsaturated_files
     ${UNSATURATED_DIR}/test_reactmicp_unsaturated.cpp
     ${UNSATURATED_DIR}/variables.cpp
     ${UNSATURATED_DIR}/saturation_equation.cpp
     ${UNSATURATED_DIR}/saturation_pressure_equation.cpp
     ${UNSATURATED_DIR}/pressure_equation.cpp
     ${UNSATURATED_DIR}/aqueous_equation.cpp
     ${UNSATURATED_DIR}/transport_stagger.cpp
     ${UNSATURATED_DIR}/equilibrium_stagger.cpp
 )
 
 set(TEST_CEMDATA_PATH \"../../data/cemdata.yaml\")
 set_source_files_properties(
     ${test_reactmicp_unsaturated_files}
      PROPERTIES COMPILE_DEFINITIONS "TEST_CEMDATA_PATH=${TEST_CEMDATA_PATH}"
 )
 
 add_catch_test(
     NAME reactmicp_unsaturated
     SOURCES ${test_reactmicp_unsaturated_files}
     LINK_LIBRARIES ${REACTMICP_STATIC_LIBS}
 )
diff --git a/tests/specmicp/CMakeLists.txt b/tests/specmicp/CMakeLists.txt
index 7376c95..51695be 100644
--- a/tests/specmicp/CMakeLists.txt
+++ b/tests/specmicp/CMakeLists.txt
@@ -1,74 +1,75 @@
 # Specmicp : Adim system
 # ----------------------
 
 set(test_specmicp_adim_files
    adim/test_specmicp_adim.cpp
 
     adim/adimensional_system.cpp
     adim/adimensional_system_solver.cpp
     adim/adimensional_system_conditions.cpp
     adim/adimensional_system_problem_solver.cpp
     adim/adimensional_system_water_pressure.cpp
     adim/adimensional_system_thermocarbo.cpp
     adim/adimensional_system_carboalu.cpp
     adim/adimensional_system_pcfm.cpp
     adim/adimensional_system_oxydoreduc.cpp
     adim/adimensional_system_configuration.cpp
 )
 
 
 if (HDF5_FOUND)
     list(APPEND test_specmicp_adim_files
         adim/io_hdf5_adimensional.cpp
     )
 
-    include_directories(HDF5_C_INCLUDE_DIR HDF5_CXX_INCLUDE_DIR)
+    include_directories(${HDF5_C_INCLUDE_DIR})
+    include_directories(${HDF5_CXX_INCLUDE_DIR})
     set_source_files_properties(
         adim/io_hdf5_adimensional.cpp
         PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS
     )
 endif()
 
 set(TEST_CEMDATA_PATH \"../../data/cemdata.yaml\")
 set_source_files_properties(${test_specmicp_adim_files} PROPERTIES COMPILE_DEFINITIONS
     "TEST_CEMDATA_PATH=${TEST_CEMDATA_PATH}"
 )
 
 add_catch_test(NAME specmicp_adim SOURCES
     ${test_specmicp_adim_files}
 
     LINK_LIBRARIES  ${SPECMICP_STATIC_LIBS}
 )
 
 file(COPY adim/specmicp_conf_test.yaml
     DESTINATION ${CMAKE_CURRENT_BINARY_DIR}
 )
 
 # Specmicp : Adim Kinetics
 # ------------------------
 
 set(ADIMKINETICS_TEST_DIR ${PROJECT_TEST_DIR}/specmicp/adim_kinetics)
 
 set(test_specmicp_adim_kinetics_files
     ${ADIMKINETICS_TEST_DIR}/test_specmicp_adim_kinetics.cpp
     ${ADIMKINETICS_TEST_DIR}/kinetics_variables.cpp
     ${ADIMKINETICS_TEST_DIR}/set_mineral_kinetic.cpp
 
 )
 
 set_source_files_properties(${test_specmicp_adim_kinetics_files} PROPERTIES COMPILE_DEFINITIONS
     "TEST_CEMDATA_PATH=${TEST_CEMDATA_PATH}"
 )
 
 
 add_catch_test(NAME specmicp_adim_kinetics SOURCES
     ${test_specmicp_adim_kinetics_files}
 
     LINK_LIBRARIES  ${SPECMICP_STATIC_LIBS}
 )
 
 
 # Specmicp : Binary
 # -----------------
 
 add_subdirectory( binary )