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specmicp/src/reactmicp/io/hdf5_unsaturated.cpp
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/* =============================================================================
Copyright (c) 2014 - 2016
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. *
============================================================================= */
#include "hdf5_unsaturated.hpp"
#include "reactmicp/systems/unsaturated/variables.hpp"
#include "specmicp_common/io/hdf5/file.hpp"
#include "specmicp_common/io/hdf5/group.hpp"
#include "specmicp_common/io/hdf5/dataset.hpp"
#include "specmicp_common/io/hdf5_timesteps.hpp"
#include "specmicp/io/hdf5_adimensional.hpp"
#include "dfpm/io/hdf5_mesh.hpp"
#include "specmicp_database/io/hdf5_database.hpp"
#include "specmicp_common/physics/units.hpp"
#include "specmicp_database/data_container.hpp"
#include "specmicp_common/compat.hpp"
#include "specmicp_common/log.hpp"
#include <functional>
#include <iostream>
#include <array>
using namespace specmicp::reactmicp::systems::unsaturated;
#define MESH_GRPNAME "mesh"
#define DATABASE_GRPNAME "database"
#define UNIT_ATTRIBUTE "unit"
#define MAIN_VARIABLES_GRPNAME "main_variables"
#define CHEMISTRY_SOLUTION_GRPNAME "chemistry_solution"
#define TRANSPORT_PROPERTIES_GRPNAME "transport_properties"
#define LIQUID_SATURATION_DSET "liquid_saturation"
#define AQUEOUS_CONC_DSET "aqueous_concentration"
#define SOLID_CONC_DSET "solid_concentration"
#define PRESSURE_DSET "partial_pressure"
#define CAP_PRESSURE_DSET "capillary_pressure"
#define POROSITY_DSET "porosity"
#define LIQUID_DIFFUSIVITY_DSET "liquid_diffusivity"
#define REL_LIQUID_DIFFUSIVITY_DSET "relative_liquid_diffusivity"
#define LIQUID_PERMEABILITY_DSET "liquid_permeability"
#define REL_LIQUID_PERMEABILITY_DSET "relative_liquid_permeability"
#define RESISTANCE_GAS_DIFFUSIVITY_DSET "resistance_gas_diffusivity"
#define REL_GAS_DIFFUSIVITY_DSET "relative_gas_diffusivity"
namespace specmicp {
namespace io {
//! \brief Implementation of the UnsaturatedHDF5Saver
//!
//! \internal
struct SPECMICP_DLL_LOCAL UnsaturatedHDF5Saver::UnsaturatedHDF5SaverImpl
{
public:
std::string m_filepath;
std::shared_ptr<UnsaturatedVariables> m_vars; //!< the variables
database::RawDatabasePtr m_database; //!< the database
UnsaturatedHDF5SaverImpl(
const std::string& filename,
std::shared_ptr<UnsaturatedVariables> vars,
const units::UnitsSet the_units):
m_filepath(filename),
m_vars(vars),
m_database(vars->get_database())
{
init_file(the_units);
}
//! \brief Save a timestep
void save_timestep(
const std::string& name
);
//! \brief Save the main variables
void save_main_variables(
hdf5::Group& timestep_grp
);
//! \brief Save the chemical solution
void save_chemical_solution(
hdf5::Group& timestep_grp
);
//! \brief Save the transport properties
void save_transport_properties(
hdf5::Group& timestep_grp
);
//! \brief create the file and save common values (mesh, db, units)
void init_file(const units::UnitsSet& the_units);
};
//
UnsaturatedHDF5Saver::UnsaturatedHDF5Saver(
const std::string& filename,
std::shared_ptr<UnsaturatedVariables> vars,
const units::UnitsSet& the_units
):
m_impl(make_unique<UnsaturatedHDF5SaverImpl>(filename, vars, the_units))
{}
UnsaturatedHDF5Saver::~UnsaturatedHDF5Saver() = default;
void UnsaturatedHDF5Saver::save_timestep(scalar_t timestep)
{
return m_impl->save_timestep(std::to_string(timestep));
}
// Implementation
// ==============
//! \brief Save a timestep
void UnsaturatedHDF5Saver::UnsaturatedHDF5SaverImpl::save_timestep(
const std::string& name
)
{
hdf5::File the_file = hdf5::File::open(m_filepath, hdf5::OpenMode::OpenReadWrite);
hdf5::Group timestep_grp = the_file.create_group(name);
save_main_variables(timestep_grp);
save_chemical_solution(timestep_grp);
save_transport_properties(timestep_grp);
}
// ugly, but more readable at the end
#define uvars(var_name) \
m_vars->get_ ## var_name ().variable
#define uvarsi(var_name, index) \
m_vars->get_ ## var_name (index).variable
void UnsaturatedHDF5Saver::UnsaturatedHDF5SaverImpl::save_main_variables(
hdf5::Group& timestep_grp
)
{
hdf5::Group main_vars_grp = timestep_grp.create_group(MAIN_VARIABLES_GRPNAME);
// water
{
auto water_group = main_vars_grp.create_group(m_database->get_label_component(0));
water_group.create_vector_dataset(LIQUID_SATURATION_DSET,
uvars(liquid_saturation));
water_group.create_vector_dataset(AQUEOUS_CONC_DSET,
uvars(water_aqueous_concentration));
water_group.create_vector_dataset(SOLID_CONC_DSET,
uvarsi(solid_concentration, 0));
if (m_vars->component_has_gas(0))
{
water_group.create_vector_dataset(PRESSURE_DSET,
uvarsi(pressure_main_variables, 0));
}
water_group.create_vector_dataset(CAP_PRESSURE_DSET,
uvars(capillary_pressure));
}
for (index_t aq_component: m_database->range_aqueous_component())
{
auto aqcomp_group = main_vars_grp.create_group(m_database->get_label_component(aq_component));
aqcomp_group.create_vector_dataset(AQUEOUS_CONC_DSET,
uvarsi(aqueous_concentration, aq_component));
aqcomp_group.create_vector_dataset(SOLID_CONC_DSET,
uvarsi(solid_concentration, aq_component));
if (m_vars->component_has_gas(aq_component))
{
aqcomp_group.create_vector_dataset(PRESSURE_DSET,
uvarsi(pressure_main_variables, aq_component));
}
}
}
void UnsaturatedHDF5Saver::UnsaturatedHDF5SaverImpl::save_chemical_solution(
hdf5::Group& timestep_grp
)
{
auto chem_grp = timestep_grp.create_group(CHEMISTRY_SOLUTION_GRPNAME);
for (auto node: m_vars->get_mesh()->range_nodes())
{
if (m_vars->get_adim_solution(node).is_valid)
{
save_adimensional_system_solution(chem_grp,
std::to_string(node),
m_vars->get_adim_solution(node));
}
}
}
// time to get ugly and use macro
// this is simply a quick wrapper that call the save_eigen matrix function
// It avoids all the boilerplate
#define save_transport_property(name, var) \
transport_grp.create_vector_dataset(name, uvars(var))
void UnsaturatedHDF5Saver::UnsaturatedHDF5SaverImpl::save_transport_properties(
hdf5::Group& timestep_grp
)
{
auto transport_grp = timestep_grp.create_group(TRANSPORT_PROPERTIES_GRPNAME);
save_transport_property(POROSITY_DSET, porosity);
save_transport_property(LIQUID_DIFFUSIVITY_DSET,
liquid_diffusivity);
save_transport_property(REL_LIQUID_DIFFUSIVITY_DSET,
relative_liquid_diffusivity);
save_transport_property(LIQUID_PERMEABILITY_DSET,
liquid_permeability);
save_transport_property(REL_LIQUID_PERMEABILITY_DSET,
relative_liquid_permeability);
save_transport_property(RESISTANCE_GAS_DIFFUSIVITY_DSET,
resistance_gas_diffusivity);
save_transport_property(REL_GAS_DIFFUSIVITY_DSET,
relative_gas_diffusivity);
}
#undef save_transport_property // we remove the ugly macro, no one saws anything :)
#undef uvars
#undef uvarsi
void
UnsaturatedHDF5Saver::UnsaturatedHDF5SaverImpl::init_file(
const units::UnitsSet& the_units
)
{
hdf5::File the_file = hdf5::File::open(m_filepath, hdf5::OpenMode::CreateTruncate);
save_mesh(the_file, MESH_GRPNAME, m_vars->get_mesh());
save_database_labels(the_file, DATABASE_GRPNAME, m_vars->get_database());
std::array<double, 3> units_values = {
units::scaling_factor(the_units.length),
units::scaling_factor(the_units.mass),
units::scaling_factor(the_units.quantity)
};
the_file.create_scalar_attribute(UNIT_ATTRIBUTE, units_values);
}
// ===========================================================================
// ===========================================================================
// Reader
// =======
struct SPECMICP_DLL_LOCAL UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl
{
UnsaturatedHDF5ReaderImpl(const std::string& name):
m_file(hdf5::File::open(name, hdf5::OpenMode::OpenReadOnly)),
m_timesteps(m_file)
{
}
units::UnitsSet get_units();
AdimensionalSystemSolution get_adim_solution(
scalar_t timestep,
index_t node
);
AdimensionalSystemSolution get_adim_solution(
std::string timestep,
index_t node
);
void initialize_variables(
scalar_t timestep,
reactmicp::systems::unsaturated::UnsaturatedVariables* vars
);
void read_main_variables(
const hdf5::GroupPath& timestep_group,
reactmicp::systems::unsaturated::UnsaturatedVariables* vars
);
void read_chemical_solutions(
const hdf5::GroupPath& timestep_group,
reactmicp::systems::unsaturated::UnsaturatedVariables* vars
);
void read_transport_properties(
const hdf5::GroupPath& timestep_group,
reactmicp::systems::unsaturated::UnsaturatedVariables* vars
);
//! \brief Return a main variable against x
Vector main_variable_vs_x(
const std::string& timestep,
const std::string& component,
const std::string& variable
);
//! \brief Return a main variable against t
Vector main_variable_vs_t(
index_t node,
const std::string& component,
const std::string& variable
);
//! \brief Open a timestep group
hdf5::Group open_timestep(const std::string& timestep);
//! \brief Open a timestep group
hdf5::Group open_timestep(const scalar_t& timestep);
//! \brief Open the main variables group
hdf5::Group open_main_variables(const std::string& timestep);
//! \brief Open the main variables group for a component
hdf5::Group open_main_variables_component(
const std::string& timestep,
const std::string& component
);
//! \brief Open the transport variables group
hdf5::Group open_transport_variables(const std::string& timestep);
//! \brief Return a main variable against x
Vector transport_variable_vs_x(
const std::string& timestep,
const std::string& variable
);
//! \brief Return a main variable against t
Vector transport_variable_vs_t(
index_t node,
const std::string& variable
);
hdf5::Group open_chemistry_solutions(const std::string& timestep);
hdf5::File m_file;
HDF5Timesteps m_timesteps;
};
UnsaturatedHDF5Reader::UnsaturatedHDF5Reader(
const std::string &filepath
):
m_impl(utils::make_pimpl<UnsaturatedHDF5ReaderImpl>(filepath))
{
}
UnsaturatedHDF5Reader::~UnsaturatedHDF5Reader() = default;
//! \brief Initialize variables from a saved timestep
//!
//! The Mesh and the database must already be ok
void UnsaturatedHDF5Reader::initialize_variables(
scalar_t timestep,
reactmicp::systems::unsaturated::UnsaturatedVariables* vars
)
{
return m_impl->initialize_variables(timestep, vars);
}
const HDF5Timesteps& UnsaturatedHDF5Reader::get_timesteps() const
{
return m_impl->m_timesteps;
}
units::UnitsSet UnsaturatedHDF5Reader::get_units()
{
return m_impl->get_units();
}
AdimensionalSystemSolution UnsaturatedHDF5Reader::get_adim_solution(
scalar_t timestep,
index_t node
)
{
return m_impl->get_adim_solution(timestep, node);
}
AdimensionalSystemSolution UnsaturatedHDF5Reader::get_adim_solution(
std::string timestep,
index_t node
)
{
return m_impl->get_adim_solution(timestep, node);
}
Vector UnsaturatedHDF5Reader::main_variable_vs_x(
const std::string& timestep,
const std::string& component,
const std::string& variable
)
{
return m_impl->main_variable_vs_x(timestep, component, variable);
}
Vector UnsaturatedHDF5Reader::main_variable_vs_x(
scalar_t timestep,
const std::string& component,
const std::string& variable
)
{
const std::string str_timestep = m_impl->m_timesteps.get_string(timestep);
return m_impl->main_variable_vs_x(str_timestep, component, variable);
}
Vector UnsaturatedHDF5Reader::main_variable_vs_t(
index_t node,
const std::string& component,
const std::string& variable
)
{
return m_impl->main_variable_vs_t(node, component, variable);
}
Vector UnsaturatedHDF5Reader::transport_variable_vs_x(
const std::string& timestep,
const std::string& variable
)
{
return m_impl->transport_variable_vs_x(timestep, variable);
}
Vector UnsaturatedHDF5Reader::transport_variable_vs_x(
scalar_t timestep,
const std::string& variable
)
{
const std::string str_timestep = m_impl->m_timesteps.get_string(timestep);
return m_impl->transport_variable_vs_x(str_timestep, variable);
}
Vector UnsaturatedHDF5Reader::transport_variable_vs_t(
index_t node,
const std::string& variable
)
{
return m_impl->transport_variable_vs_t(node, variable);
}
// =========== Implementation ===============================
units::UnitsSet UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::get_units()
{
units::UnitsSet the_units;
// quantity conversion factor was not solved in early version
// really early, can probably be simplified at some point
std::vector<double> conversion_factor = m_file.read_scalar_attribute(UNIT_ATTRIBUTE);
the_units.length = units::from_scaling_factor<units::LengthUnit>(conversion_factor[0]);
the_units.mass = units::from_scaling_factor<units::MassUnit>(conversion_factor[1]);
if (conversion_factor.size() == 2)
{
WARNING << "Units for quantity of matter was not recorded, assuming moles.";
}
else
{
the_units.quantity = units::from_scaling_factor<units::QuantityUnit>(conversion_factor[2]);
}
return the_units;
}
void
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::initialize_variables(
scalar_t timestep,
reactmicp::systems::unsaturated::UnsaturatedVariables *vars
)
{
auto name_group = m_timesteps.get_string(timestep);
auto timestep_group = m_file.open_group(name_group);
read_main_variables(timestep_group, vars);
read_chemical_solutions(timestep_group, vars);
read_transport_properties(timestep_group, vars);
}
// ugly, but more readable at the end
#define uvars(var_name) \
vars->get_ ## var_name ().variable
#define uvarsi(var_name, index) \
vars->get_ ## var_name (index).variable
void
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::read_main_variables(
const hdf5::GroupPath& timestep_group,
reactmicp::systems::unsaturated::UnsaturatedVariables* vars
)
{
hdf5::Group main_vars_grp = timestep_group.open_group(MAIN_VARIABLES_GRPNAME);
database::RawDatabasePtr raw_database = vars->get_database();
{ // Water
auto group = main_vars_grp.open_group(raw_database->get_label_component(0));
uvars(liquid_saturation) = group.read_vector_dataset(LIQUID_SATURATION_DSET);
uvars(water_aqueous_concentration) = group.read_vector_dataset(AQUEOUS_CONC_DSET);
uvarsi(solid_concentration, 0) = group.read_vector_dataset(SOLID_CONC_DSET);
uvars(capillary_pressure) = group.read_vector_dataset(CAP_PRESSURE_DSET);
if (vars->component_has_gas(0))
{
uvarsi(pressure_main_variables, 0)
= group.read_vector_dataset(PRESSURE_DSET);
}
}
for (auto component: raw_database->range_aqueous_component())
{
auto group = main_vars_grp.open_group(
raw_database->get_label_component(component));
uvarsi(aqueous_concentration, component) = group.read_vector_dataset(AQUEOUS_CONC_DSET);
uvarsi(solid_concentration, component) = group.read_vector_dataset(SOLID_CONC_DSET);
if (vars->component_has_gas(component))
{
uvarsi(pressure_main_variables, component)
= group.read_vector_dataset(PRESSURE_DSET);
}
}
}
void
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::read_chemical_solutions(
const hdf5::GroupPath& timestep_group,
reactmicp::systems::unsaturated::UnsaturatedVariables* vars
)
{
hdf5::Group chem_group = timestep_group.open_group(CHEMISTRY_SOLUTION_GRPNAME);
database::RawDatabasePtr raw_database = vars->get_database();
mesh::Mesh1DPtr the_mesh = vars->get_mesh();
for (auto node: the_mesh->range_nodes())
{
vars->set_adim_solution(node,
read_adimensional_system_solution(chem_group, std::to_string(node)));
}
}
// time to get ugly and use macro
// this is simply a quick wrapper that call the read_eigen_matrix function
// It avoids all the boilerplate
#define read_transport_property(name, var) \
uvars(var) = trans_group.read_vector_dataset(name);
void
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::read_transport_properties(
const hdf5::GroupPath& timestep_group,
reactmicp::systems::unsaturated::UnsaturatedVariables* vars
)
{
hdf5::Group trans_group = timestep_group.open_group(TRANSPORT_PROPERTIES_GRPNAME);
read_transport_property(POROSITY_DSET, porosity);
read_transport_property(LIQUID_DIFFUSIVITY_DSET, liquid_diffusivity);
read_transport_property(REL_LIQUID_DIFFUSIVITY_DSET,
relative_liquid_diffusivity);
read_transport_property(LIQUID_PERMEABILITY_DSET,
liquid_permeability);
read_transport_property(REL_LIQUID_PERMEABILITY_DSET,
relative_liquid_permeability);
read_transport_property(RESISTANCE_GAS_DIFFUSIVITY_DSET,
resistance_gas_diffusivity);
read_transport_property(REL_GAS_DIFFUSIVITY_DSET,
relative_gas_diffusivity);
}
#undef read_transport_property // we remove the ugly macro, no one saws anything :)
#undef uvars
#undef uvarsi
hdf5::Group
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::open_timestep(
const scalar_t& timestep
)
{
auto str_timestep = m_timesteps.get_string(timestep);
return m_file.open_group(str_timestep);
}
hdf5::Group
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::open_timestep(
const std::string& timestep
)
{
return m_file.open_group(timestep);
}
hdf5::Group
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::open_main_variables(
const std::string& timestep
)
{
auto timestep_grp = open_timestep(timestep);
return timestep_grp.open_group(MAIN_VARIABLES_GRPNAME);
}
hdf5::Group
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::open_main_variables_component(
const std::string& timestep,
const std::string& component
)
{
auto main_vars_grp = open_main_variables(timestep);
return main_vars_grp.open_group(component);
}
//! \brief Return a main variable against x
Vector
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::main_variable_vs_x(
const std::string& timestep,
const std::string& component,
const std::string& variable
)
{
auto comp_grp = open_main_variables_component(timestep, component);
return comp_grp.read_vector_dataset(variable);
}
//! \brief Return a main variable against t
Vector
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::main_variable_vs_t(
index_t node,
const std::string& component,
const std::string& variable
)
{
Vector data(m_timesteps.size());
index_t cnt = 0;
for (auto it: m_timesteps)
{
Vector timestep_vector = main_variable_vs_x(it.second, component, variable);
data(cnt) = timestep_vector(node);
++cnt;
}
return data;
}
hdf5::Group
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::open_transport_variables(
const std::string& timestep
)
{
auto timestep_grp = open_timestep(timestep);
return timestep_grp.open_group(TRANSPORT_PROPERTIES_GRPNAME);
}
Vector
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::transport_variable_vs_x(
const std::string& timestep,
const std::string& variable
)
{
auto grp = open_transport_variables(timestep);
return grp.read_vector_dataset(variable);
}
Vector
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::transport_variable_vs_t(
index_t node,
const std::string& variable
)
{
Vector data(m_timesteps.size());
index_t cnt = 0;
for (auto it: m_timesteps)
{
Vector timestep_vector = transport_variable_vs_x(it.second, variable);
data(cnt) = timestep_vector(node);
++cnt;
}
return data;
}
hdf5::Group
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::open_chemistry_solutions(
const std::string& timestep
)
{
auto timestep_grp = open_timestep(timestep);
return timestep_grp.open_group(CHEMISTRY_SOLUTION_GRPNAME);
}
AdimensionalSystemSolution
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::get_adim_solution(
scalar_t timestep,
index_t node
)
{
auto str_timestep = m_timesteps.get_string(timestep);
return get_adim_solution(str_timestep, node);
}
AdimensionalSystemSolution
UnsaturatedHDF5Reader::UnsaturatedHDF5ReaderImpl::get_adim_solution(
std::string timestep,
index_t node
)
{
auto chem_grp = open_chemistry_solutions(timestep);
return read_adimensional_system_solution(chem_grp, std::to_string(node));
}
} //end namespace io
} //end namespace specmicp
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