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Created: Sun, Jan 12, 06:49

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	diff --git a/CMakeLists.txt b/CMakeLists.txt
	index ba2586d..c9b240a 100644
	--- a/CMakeLists.txt
	+++ b/CMakeLists.txt
	@@ -1,222 +1,228 @@
	####################################################
	# #
	# SpecMiCP : CMakeLists.txt #
	# #
	####################################################

	project(specmicp)
	cmake_minimum_required(VERSION 2.8.8)

	# Configuration options
	# ======================

	# For an explanation of the options see the INSTALL file
	option( SPECMICP_USE_OPENMP "Thread parallelisation of specmicp instances if available" ON )
	option( SPECMICP_NO_DEBUG "Disable SpecMiCP assert" OFF )
	option( SPECMICP_BUILD_STATIC "Build static libraries" OFF )
	option( SPECMICP_BUILD_EXAMPLE "Build the examples" ON )
	option( SPECMICP_DEBUG_EQUATION_FD_JACOBIAN "Use a finite difference jacobian is specmicp" OFF )
	option( SPECMICP_BINARIES_USE_STATIC "SpecMiCP binaries use static libraries" OFF)

	# PGO sequence
	option( SPECMICP_PROFILE_GENERATE "Generate the profile for PGO optimization" OFF )
	option( SPECMICP_PROFILE_USE "Use the generated profile for PGO optimization" OFF )

	# LTO optimization
	option( SPECMICP_LTO "Use link time optimization" OFF )
	option( SPECMICP_LD_GOLD "Use GNU gold linker" ON )

	option( SPECMICP_BENCHMARK "Build benchmark" OFF )

	# global variables
	# ================

	set(SPECMICP_VERSION 0.0.3)

	# External Package
	# ================

	set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake)

	# OpenMP
	#-------
	# not required but recommended
	if(SPECMICP_USE_OPENMP)
	find_package(OpenMP)
	endif()

	# 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()

	# Yaml-cpp
	# --------

	include(FindPkgConfig)
	pkg_check_modules(YAML REQUIRED yaml-cpp>=0.5)
	include_directories(${YAML_INCLUDE_DIRS})
	link_directories(${YAML_LIBRARY_DIRS})

	+# HDF5
	+# ----
	+
	+find_package(HDF5 REQUIRED COMPONENTS C CXX)
	+# HDF5 is optional, must be checked by files that used it
	+
	# sanitizer
	include(SanitizerBuild)

	# compilation flags
	# =================

	# check the availability of :
	# c++11
	include(cxx11)
	# -fuse-ld=gold
	include(gold_linker)
	# pgo optimization
	include(pg_optimization)
	# -fvisibility-hidden
	include(visibility_flag)

	# just a friendly warning
	if(NOT UNIX)
	message(WARNING "not tested !")
	endif()

	include(lto)

	# set the flag
	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CXX11_FLAG}")
	if (OPENMP_FOUND)
	SET( CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
	SET( CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
	endif()
	SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -pedantic")

	##SET(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
	message(STATUS "c++ flags : ${CMAKE_CXX_FLAGS}")


	# Directories
	#########################################################################

	# 3rd party
	# =========

	# installation dir
	# ----------------
	# http://www.cmake.org/pipermail/cmake/2010-February/035466.html
	# compute default library install dir
	# library
	# ------
	set (_DEFAULT_LIBRARY_INSTALL_DIR lib)
	if (EXISTS "${CMAKE_INSTALL_PREFIX}/lib32/" AND CMAKE_SIZEOF_VOID_P EQUAL 4)
	set (_DEFAULT_LIBRARY_INSTALL_DIR lib32)
	elif (EXISTS "${CMAKE_INSTALL_PREFIX}/lib64/" AND CMAKE_SIZEOF_VOID_P EQUAL 8)
	set (_DEFAULT_LIBRARY_INSTALL_DIR lib64)
	endif ()
	# the library install dir
	set(LIBRARY_INSTALL_DIR "${_DEFAULT_LIBRARY_INSTALL_DIR}" CACHE PATH "Installation directory for libraries")
	set(STATIC_LIBRARY_INSTALL_DIR "${_DEFAULT_LIBRARY_INSTALL_DIR}/static" CACHE PATH "Installation directory for static libraries")
	# make the library install dir an absolute path (can be important e.g. when using CONFIGURE_FILE to embed
	# the library installation directory into a file)
	if(NOT IS_ABSOLUTE "${LIBRARY_INSTALL_DIR}")
	set(LIBRARY_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${LIBRARY_INSTALL_DIR}")
	endif()
	if(NOT IS_ABSOLUTE "${STATIC_LIBRARY_INSTALL_DIR}")
	set(STATIC_LIBRARY_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${STATIC_LIBRARY_INSTALL_DIR}")
	endif()
	# Binaries
	# --------
	set(BIN_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for the programs")
	# include
	#--------
	set(INCLUDE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/include/specmicp" CACHE PATH "Installation directory for the headers")
	# share
	#------
	set(SHARE_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/share/specmicp" CACHE PATH "Installation directory for the miscalleneous files...")

	enable_testing(true)

	# CPP API : SpecMiCP / ReactMiCP
	#########################################################################

	# the main source directory - the c++ api
	set(SPECMICP_CPP_API ${CMAKE_CURRENT_SOURCE_DIR}/src)
	include_directories(${SPECMICP_CPP_API})
	add_subdirectory( ${SPECMICP_CPP_API} )


	set(SPECMICP_LIBS specmicp specmicp_database specmicp_common ${YAML_LIBRARIES})
	set(REACTMICP_LIBS reactmicp dfpm ${SPECMICP_LIBS} )
	set(SPECMICP_STATIC_LIBS specmicp_static specmicp_database_static specmicp_common_static ${YAML_LIBRARIES})
	set(REACTMICP_STATIC_LIBS reactmicp_static dfpm_static ${SPECMICP_STATIC_LIBS})

	# Binaries
	#########################################################################

	add_subdirectory(src/bin/specmicp)


	# Database
	#########################################################################

	add_subdirectory( data )

	# Documentation
	#########################################################################

	# "common" documentation
	# -----------------------
	set(
	DOCS_LIST
	${CMAKE_CURRENT_SOURCE_DIR}/README.md
	${CMAKE_CURRENT_SOURCE_DIR}/INSTALL
	${CMAKE_CURRENT_SOURCE_DIR}/COPYING
	)

	add_custom_target(docs SOURCES ${DOCS_LIST})
	install(FILES ${DOCS_LIST}
	DESTINATION ${SHARE_INSTALL_DIR}
	)

	# scripts
	# --------

	add_subdirectory( scripts )

	# Doxygen documentation
	# ---------------------
	add_subdirectory( doc )

	# Tests
	#########################################################################
	add_subdirectory( tests )

	# Examples
	#########################################################################
	add_subdirectory( examples )

	# Benchmark
	########################################################################
	if (SPECMICP_BENCHMARK)
	add_subdirectory( benchmark )
	endif()

	# Docker
	########################################################################

	file(COPY
	docker/Dockerfile
	docker/run_tests.sh
	DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/docker
	)

	diff --git a/src/reactmicp/CMakeLists.txt b/src/reactmicp/CMakeLists.txt
	index f593534..c062a10 100644
	--- a/src/reactmicp/CMakeLists.txt
	+++ b/src/reactmicp/CMakeLists.txt
	@@ -1,174 +1,184 @@
	# 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
	)

	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/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

	- io/reactive_transport.cpp
	- io/saturated_react.cpp
	- io/configuration.cpp
	+ ${REACTMICP_IO}/reactive_transport.cpp
	+ ${REACTMICP_IO}/saturated_react.cpp
	+ ${REACTMICP_IO}/configuration.cpp
	)

	+# hdf5
	+# -----
	+if (HDF5_FOUND)
	+ list(APPEND REACTMICP_LIBFILES ${REACTMICP_IO}/saturated_react_hdf5.cpp)
	+
	+ include_directories(HDF5_INCLUDE_DIRS)
	+ set_source_files_properties(${REACTMICP_IO}/saturated_react_hdf5.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/reactmicp/io/saturated_react_hdf5.cpp b/src/reactmicp/io/saturated_react_hdf5.cpp
	new file mode 100644
	index 0000000..f590063
	--- /dev/null
	+++ b/src/reactmicp/io/saturated_react_hdf5.cpp
	@@ -0,0 +1,13 @@
	+#include "saturated_react_hdf5.hpp"
	+
	+namespace specmicp {
	+namespace io {
	+
	+SaturatedReactHDF5NodalOutput::SaturatedReactHDF5NodalOutput(const std::string &filename):
	+ HDF5File(filename, HDF5_OpenMode::create_truncate)
	+{
	+
	+}
	+
	+} //end namespace io
	+} //end namespace specmicp
	diff --git a/src/reactmicp/io/saturated_react_hdf5.hpp b/src/reactmicp/io/saturated_react_hdf5.hpp
	new file mode 100644
	index 0000000..d02b2c0
	--- /dev/null
	+++ b/src/reactmicp/io/saturated_react_hdf5.hpp
	@@ -0,0 +1,55 @@
	+/*-------------------------------------------------------------------------------
	+
	+Copyright (c) 2015 F. Georget <fabieng@princeton.edu>, Princeton University
	+All rights reserved.
	+
	+Redistribution and use in source and binary forms, with or without modification,
	+are permitted provided that the following conditions are met:
	+
	+1. Redistributions of source code must retain the above copyright notice, this
	+list of conditions and the following disclaimer.
	+
	+2. Redistributions in binary form must reproduce the above copyright notice,
	+this list of conditions and the following disclaimer in the documentation and/or
	+other materials provided with the distribution.
	+
	+3. Neither the name of the copyright holder nor the names of its contributors
	+may be used to endorse or promote products derived from this software without
	+specific prior written permission.
	+
	+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
	+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
	+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
	+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
	+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
	+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
	+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
	+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
	+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
	+
	+-----------------------------------------------------------------------------*/
	+
	+#ifndef SPECMICP_REACTMICP_IO_SATURATEDREACTHDF5
	+#define SPECMICP_REACTMICP_IO_SATURATEDREACTHDF5
	+
	+#include <memory>
	+#include "../../utils/io/specmicp_hdf5.hpp"
	+
	+namespace specmicp {
	+namespace io {
	+
	+class SaturatedReactHDF5NodalOutput: public HDF5File
	+{
	+public:
	+ SaturatedReactHDF5NodalOutput(const std::string& filename);
	+
	+private:
	+ struct SaturatedReactHDF5NodalOutputImpl;
	+ std::unique_ptr<SaturatedReactHDF5NodalOutputImpl> m_impl;
	+};
	+
	+} //end namespace io
	+} //end namespace specmicp
	+
	+#endif // SPECMICP_REACTMICP_IO_SATURATEDREACTHDF5
	diff --git a/src/utils/CMakeLists.txt b/src/utils/CMakeLists.txt
	index 308492a..a50b341 100644
	--- a/src/utils/CMakeLists.txt
	+++ b/src/utils/CMakeLists.txt
	@@ -1,100 +1,118 @@
	+# 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
	)

	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)
	+ set_source_files_properties(io/specmicp_hdf5.cpp PROPERTIES COMPILE_DEFINITIONS HDF5_DEFINITIONS)
	+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/src/utils/io/specmicp_hdf5.cpp b/src/utils/io/specmicp_hdf5.cpp
	new file mode 100644
	index 0000000..b38ee36
	--- /dev/null
	+++ b/src/utils/io/specmicp_hdf5.cpp
	@@ -0,0 +1,114 @@
	+#include "specmicp_hdf5.hpp"
	+
	+#include <H5Cpp.h>
	+
	+#include "../compat.hpp"
	+
	+namespace specmicp {
	+namespace io {
	+
	+HDF5File::HDF5File(const std::string& filename, HDF5_OpenMode mode)
	+{
	+ open(filename, mode);
	+}
	+
	+
	+HDF5File::~HDF5File() {
	+ close();
	+}
	+
	+
	+bool HDF5File::open(
	+ const std::string& filename,
	+ HDF5_OpenMode mode
	+ )
	+{
	+ if (m_file != nullptr)
	+ m_file->close();
	+
	+
	+ unsigned int flag = H5F_ACC_DEFAULT;
	+ switch (mode) {
	+ case HDF5_OpenMode::CreateTruncate:
	+ flag = H5F_ACC_TRUNC;
	+ break;
	+ case HDF5_OpenMode::CreateFailIfExist:
	+ flag = H5F_ACC_EXCL;
	+ break;
	+ case HDF5_OpenMode::OpenReadOnly:
	+ flag = H5F_ACC_RDONLY;
	+ break;
	+ case HDF5_OpenMode::OpenReadWrite:
	+ flag = H5F_ACC_RDWR;
	+ break;
	+ }
	+
	+ m_file = make_unique<H5::H5File>(filename, flag);
	+
	+ return is_open();
	+}
	+
	+bool HDF5File::is_open() {
	+ return (m_file != nullptr);
	+
	+}
	+
	+void HDF5File::close() {
	+ if (is_open()) {
	+ m_file->close();
	+ m_file.reset(nullptr);
	+ }
	+}
	+
	+std::unique_ptr<H5::DataSet> HDF5File::create_dataset(
	+ const std::string& name,
	+ const H5::DataType& type,
	+ const H5::DataSpace& data_space,
	+ const H5::DSetCreatPropList& list
	+ )
	+{
	+ return make_unique<H5::DataSet>(
	+ m_file->createDataSet(name, type, data_space, list));
	+}
	+
	+
	+std::unique_ptr<H5::DataSet> HDF5File::create_dataset(
	+ const std::string& name,
	+ const std::string& section,
	+ const H5::DataType& type,
	+ const H5::DataSpace& data_space,
	+ const H5::DSetCreatPropList& list
	+ )
	+{
	+ return create_dataset(complete_name(name, section), type, data_space, list);
	+}
	+
	+
	+std::unique_ptr<H5::Group> HDF5File::create_group(
	+ const std::string& name
	+ )
	+{
	+ return make_unique<H5::Group>(
	+ m_file->createGroup(name)
	+ );
	+}
	+
	+
	+std::string HDF5File::complete_name(
	+ const std::string& name,
	+ const std::string& section
	+ )
	+{
	+ std::string comp = section;
	+ if (comp[comp.size()-1] != '/') {
	+ comp.reserve(comp.size()+1+name.size());
	+ comp += "/"+name;
	+ }
	+ else {
	+ comp += name;
	+ }
	+ return comp;
	+}
	+
	+} //end namespace io
	+} //end namespace specmicp
	diff --git a/src/utils/io/specmicp_hdf5.hpp b/src/utils/io/specmicp_hdf5.hpp
	new file mode 100644
	index 0000000..45d71bb
	--- /dev/null
	+++ b/src/utils/io/specmicp_hdf5.hpp
	@@ -0,0 +1,126 @@
	+/*-------------------------------------------------------------------------------
	+
	+Copyright (c) 2014,2015 F. Georget <fabieng@princeton.edu>, Princeton University
	+All rights reserved.
	+
	+Redistribution and use in source and binary forms, with or without modification,
	+are permitted provided that the following conditions are met:
	+
	+1. Redistributions of source code must retain the above copyright notice, this
	+list of conditions and the following disclaimer.
	+
	+2. Redistributions in binary form must reproduce the above copyright notice,
	+this list of conditions and the following disclaimer in the documentation and/or
	+other materials provided with the distribution.
	+
	+3. Neither the name of the copyright holder nor the names of its contributors
	+may be used to endorse or promote products derived from this software without
	+specific prior written permission.
	+
	+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
	+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
	+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
	+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
	+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
	+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
	+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
	+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
	+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
	+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
	+
	+-----------------------------------------------------------------------------*/
	+
	+#ifndef SPECMICP_UTIL_SPECMICPHDF5_HPP
	+#define SPECMICP_UTIL_SPECMICPHDF5_HPP
	+
	+#include "../../macros.hpp"
	+#include <memory>
	+
	+// forward declaration
	+namespace H5 {
	+class H5File;
	+class DataSet;
	+class DataSpace;
	+class PredType;
	+class DataType;
	+class DSetCreatPropList;
	+class Group;
	+} //end namespace H5
	+
	+namespace specmicp {
	+namespace io {
	+
	+//! \brief Mode to open/create a file
	+enum class HDF5_OpenMode
	+{
	+ CreateTruncate, //!< Create a file, truncate if it exists
	+ CreateFailIfExist, //!< Create a file, fail if it exists
	+ OpenReadOnly, //!< Open a file, read only mode
	+ OpenReadWrite //!< Open a file, read write mode
	+};
	+
	+//! \brief A HDF5 file
	+//!
	+//! To be subclassed
	+class HDF5File
	+{
	+public:
	+
	+ HDF5File();
	+ HDF5File(const std::string& filename, HDF5_OpenMode mode);
	+ ~HDF5File();
	+
	+ //! \brief Open a file
	+ //!
	+ //! \param filename Name of the file to open
	+ //! \param mode Opening mode
	+ //! \return True if the file was successfully open
	+ //!
	+ bool open(const std::string& filename, HDF5_OpenMode mode);
	+
	+ //! \brief Close the file
	+ void close();
	+
	+ //! \brief Return true if the file handle is open
	+ bool is_open();
	+
	+ //! \brief Create a dataset in the root ("/")
	+ std::unique_ptr<H5::DataSet> create_dataset(
	+ const std::string& name,
	+ const H5::DataType& type,
	+ const H5::DataSpace& data_space,
	+ const H5::DSetCreatPropList& list
	+ );
	+
	+ //! \brief Create a dataset in 'section'
	+ std::unique_ptr<H5::DataSet> create_dataset(
	+ const std::string& name,
	+ const std::string& section,
	+ const H5::DataType& type,
	+ const H5::DataSpace& data_space,
	+ const H5::DSetCreatPropList& list
	+ );
	+
	+ //! \brief Create a new group
	+ std::unique_ptr<H5::Group> create_group(
	+ const std::string& name
	+ );
	+
	+ //! \brief Give the complete the name of a dataset
	+ std::string complete_name(
	+ const std::string& name,
	+ const std::string& section
	+ );
	+
	+protected:
	+ std::unique_ptr<H5::H5File> m_file {nullptr};
	+
	+private:
	+ HDF5File(const HDF5File& other) = delete;
	+ HDF5File& operator= (const HDF5File& other) = delete;
	+};
	+
	+} //end namespace io
	+} //end namespace specmicp
	+
	+#endif // SPECMICP_UTIL_SPECMICPHDF5_HPP

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