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hdf5_chloride.cpp
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hdf5_chloride.cpp
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/* =============================================================================
Copyright (c) 2014-2017 F. Georget <fabieng@princeton.edu> Princeton University
Copyright (c) 2017-2018 F. Georget <fabien.georget@epfl.ch> EPFL
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_chloride.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_common/io/hdf5/dataspace.hpp"
#include "H5Ppublic.h"
#include "specmicp/io/hdf5_adimensional.hpp"
#include "dfpm/io/hdf5_mesh.hpp"
#include "specmicp_database/io/hdf5_database.hpp"
#include "reactmicp/systems/chloride/variables.hpp"
#include "reactmicp/systems/chloride/dof_numbering.hpp"
#include "specmicp_common/log.hpp"
#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 MAIN_VARS_VALNAME "main_variables"
#define TOTAL_IMMOBILE_CONC_VALNAME "total_immobile_concentration"
#define CURRENT_VALNAME "current"
#define FLUID_VELOCITY_VALNAME "fluid_velocity"
#define POROSITY_VALNAME "porosity"
#define RESISTANCE_FACTOR_VALNAME "resistance_factor"
namespace specmicp {
namespace io {
using namespace specmicp::reactmicp::systems::chloride;
// ================================ //
// //
// Saver //
// //
// ================================ //
// Implementation declaration
// ==========================
struct SPECMICP_DLL_LOCAL ChlorideHDF5Saver::ChlorideHDF5SaverImpl
{
std::string m_filepath;
std::shared_ptr<ChlorideVariables> m_vars;
ChlorideHDF5SaverImpl(
const std::string& filepath,
std::shared_ptr<ChlorideVariables> vars
):
m_filepath(filepath),
m_vars(vars)
{
init_file();
}
//! \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();
};
// Main interface
// ==============
ChlorideHDF5Saver::ChlorideHDF5Saver(
const std::string& filepath,
std::shared_ptr<specmicp::reactmicp::systems::chloride::ChlorideVariables> vars
):
m_impl(utils::make_pimpl<ChlorideHDF5SaverImpl>(filepath, vars))
{
}
ChlorideHDF5Saver::~ChlorideHDF5Saver() = default;
void ChlorideHDF5Saver::save_timestep(scalar_t timestep)
{
m_impl->save_timestep(std::to_string(timestep));
}
// Implementation
// ==============
void ChlorideHDF5Saver::ChlorideHDF5SaverImpl::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);
}
void ChlorideHDF5Saver::ChlorideHDF5SaverImpl::init_file()
{
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());
auto the_units = m_vars->get_units();
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);
}
void ChlorideHDF5Saver::ChlorideHDF5SaverImpl::save_main_variables(
hdf5::Group& timestep_grp
)
{
hdf5::Group main_vars_grp = timestep_grp.create_group(MAIN_VARIABLES_GRPNAME);
main_vars_grp.create_vector_dataset(MAIN_VARS_VALNAME, m_vars->main_variables());
main_vars_grp.create_vector_dataset(TOTAL_IMMOBILE_CONC_VALNAME, m_vars->total_immobile_concentrations());
main_vars_grp.create_vector_dataset(CURRENT_VALNAME, m_vars->current());
main_vars_grp.create_scalar_attribute<1>(FLUID_VELOCITY_VALNAME, {m_vars->fluid_velocity(),});
}
void ChlorideHDF5Saver::ChlorideHDF5SaverImpl::save_chemical_solution(
hdf5::Group& timestep_grp
)
{
hdf5::Group chem_grp = timestep_grp.create_group(CHEMISTRY_SOLUTION_GRPNAME);
for (auto node: m_vars->get_mesh()->range_nodes())
{
if (m_vars->adim_solution(node).is_valid)
{
save_adimensional_system_solution(chem_grp,
std::to_string(node),
m_vars->adim_solution(node));
}
}
}
void ChlorideHDF5Saver::ChlorideHDF5SaverImpl::save_transport_properties(
hdf5::Group& timestep_grp
)
{
hdf5::Group trans_grp = timestep_grp.create_group(TRANSPORT_PROPERTIES_GRPNAME);
trans_grp.create_vector_dataset(POROSITY_VALNAME, m_vars->porosity());
trans_grp.create_vector_dataset(RESISTANCE_FACTOR_VALNAME, m_vars->resistance_factor());
}
// ================================ //
// //
// Reader //
// //
// ================================ //
// Implementation declaration
// ==========================
struct ChlorideHDF5Reader::ChlorideHDF5ReaderImpl
{
ChlorideHDF5ReaderImpl(const std::string& filepath,RawDatabasePtr t_database):
m_file(hdf5::File::open(filepath, hdf5::OpenMode::OpenReadOnly)),
m_timesteps(m_file),
m_numbering(t_database->nb_component()),
m_rawdata(t_database)
{
m_mesh = get_mesh();
}
units::UnitsSet get_units();
AdimensionalSystemSolution get_adim_solution(
std::string timestep,
index_t node
);
mesh::Mesh1DPtr get_mesh() {
return read_mesh(m_file, MESH_GRPNAME);
}
Vector main_variable_vs_x(
const std::string& timestep,
index_t ndof,
const std::string& variable
);
Vector main_variable_vs_t(
index_t node,
index_t ndof,
const std::string& variables
);
Vector current_vs_t(index_t node);
hdf5::Group open_timestep(const std::string& timestep);
hdf5::Group open_main_variables(const std::string& timestep);
hdf5::Group open_chemistry_solutions(const std::string& timestep);
hdf5::Group open_transport_properties(const std::string& timestep);
hdf5::File m_file;
HDF5Timesteps m_timesteps;
reactmicp::systems::chloride::DofNumbering m_numbering;
database::RawDatabasePtr m_rawdata;
mesh::Mesh1DPtr m_mesh;
};
// Main interface
// ==============
ChlorideHDF5Reader::ChlorideHDF5Reader(
const std::string& filepath,
RawDatabasePtr t_database
):
m_impl(utils::make_pimpl<ChlorideHDF5ReaderImpl>(filepath, t_database))
{}
ChlorideHDF5Reader::~ChlorideHDF5Reader() = default;
const HDF5Timesteps& ChlorideHDF5Reader::get_timesteps() const {
return m_impl->m_timesteps;
}
units::UnitsSet ChlorideHDF5Reader::get_units() {
return m_impl->get_units();
}
mesh::Mesh1DPtr ChlorideHDF5Reader::get_mesh() {
return read_mesh(m_impl->m_file, MESH_GRPNAME);
}
AdimensionalSystemSolution ChlorideHDF5Reader::get_adim_solution(
std::string timestep,
index_t node
)
{
return m_impl->get_adim_solution(timestep, node);
}
//! \brief Return a SpecMiCP solution
AdimensionalSystemSolution ChlorideHDF5Reader::get_adim_solution(
scalar_t timestep,
index_t node
)
{
auto str_timestep = m_impl->m_timesteps.get_string(timestep);
return m_impl->get_adim_solution(str_timestep, node);
}
Vector ChlorideHDF5Reader::total_mobile_concentration_vs_x(
scalar_t timestep,
const std::string& component
)
{
const auto str_timestep = m_impl->m_timesteps.get_string(timestep);
const auto ndof = m_impl->m_numbering.nodal_dof_component(m_impl->m_rawdata->get_id_component(component));
return m_impl->main_variable_vs_x(str_timestep, ndof, MAIN_VARS_VALNAME);
}
Vector ChlorideHDF5Reader::potential_vs_x(scalar_t timestep)
{
const auto str_timestep = m_impl->m_timesteps.get_string(timestep);
const auto ndof = m_impl->m_numbering.nodal_dof_psi();
return m_impl->main_variable_vs_x(str_timestep, ndof, MAIN_VARS_VALNAME);
}
Vector ChlorideHDF5Reader::main_variable_vs_x(
scalar_t timestep,
index_t ndof,
const std::string& variables
)
{
const std::string tmstep = m_impl->m_timesteps.get_string(timestep);
return main_variable_vs_x(tmstep, ndof, variables);
}
Vector ChlorideHDF5Reader::main_variable_vs_x(
const std::string& timestep,
index_t ndof,
const std::string& variables
)
{
return m_impl->main_variable_vs_x(timestep, ndof, variables);
}
Vector ChlorideHDF5Reader::main_variable_vs_t(
index_t node,
index_t ndof,
const std::string& variables
)
{
return m_impl->main_variable_vs_t(ndof, node, variables);
}
Vector ChlorideHDF5Reader::total_mobile_concentration_vs_t(
index_t node,
const std::string& component
)
{
const auto ndof = m_impl->m_numbering.nodal_dof_component(m_impl->m_rawdata->get_id_component(component));
return m_impl->main_variable_vs_t(node, ndof, MAIN_VARS_VALNAME);
}
Vector ChlorideHDF5Reader::potential_vs_t(
index_t node
)
{
const auto ndof = m_impl->m_numbering.nodal_dof_psi();
return m_impl->main_variable_vs_t(node, ndof, MAIN_VARS_VALNAME);
}
Vector ChlorideHDF5Reader::current_vs_t(index_t node)
{
return m_impl->main_variable_vs_t(node, 0, CURRENT_VALNAME);
}
// Implementation
// ==============
units::UnitsSet ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::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;
}
AdimensionalSystemSolution ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::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));
}
hdf5::Group ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::open_timestep(
const std::string &timestep)
{
return m_file.open_group(timestep);
}
hdf5::Group ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::open_main_variables(
const std::string& timestep)
{
auto timestep_grp = open_timestep(timestep);
return timestep_grp.open_group(MAIN_VARIABLES_GRPNAME);
}
hdf5::Group ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::open_chemistry_solutions(
const std::string& timestep)
{
auto timestep_grp = open_timestep(timestep);
return timestep_grp.open_group(CHEMISTRY_SOLUTION_GRPNAME);
}
hdf5::Group ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::open_transport_properties(
const std::string& timestep)
{
auto timestep_grp = open_timestep(timestep);
return timestep_grp.open_group(TRANSPORT_PROPERTIES_GRPNAME);
}
Vector ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::main_variable_vs_x(
const std::string& timestep,
index_t ndof,
const std::string& variables
)
{
auto main_var_grp = open_main_variables(timestep);
Vector out = main_var_grp.read_partial_vector_dataset(
variables,
ndof, m_numbering.ndof(), m_mesh->nb_nodes(), 1);
return out;
}
Vector ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::main_variable_vs_t(
index_t node,
index_t ndof,
const std::string& variables
)
{
Vector out(m_timesteps.size());
// get dataspace
const hsize_t nb_dofs = static_cast<hsize_t>(m_mesh->nb_nodes()*m_numbering.ndof());
const hsize_t start = static_cast<hsize_t>(m_numbering.dof(node, ndof));
hdf5::Dataspace file_space = hdf5::Dataspace::create_hyperslab(
1, {nb_dofs,}, {start,}, {1,}, {1,}, {1,});
hdf5::Dataspace mem_space = hdf5::Dataspace::create_simple(1, {1,});
for (size_t ind=0; ind<m_timesteps.size();++ind)
{
hdf5::Group grp = open_main_variables(m_timesteps(ind));
hdf5::Dataset data = grp.open_dataset(variables);
herr_t status = H5Dread(data.get_id(), H5T_NATIVE_DOUBLE,
mem_space.get_id(), file_space.get_id(), H5P_DEFAULT,
&(out[ind]));
if (status < 0)
{
throw std::runtime_error("Error while reading dataset "
+ data.get_path() + ".");
}
}
return out;
}
Vector ChlorideHDF5Reader::ChlorideHDF5ReaderImpl::current_vs_t(
index_t node
)
{
Vector out(m_timesteps.size());
// get dataspace
hdf5::Dataspace file_space = hdf5::Dataspace::create_hyperslab(
1, {1,}, {static_cast<hsize_t>(node),}, {1,}, {1,}, {1,});
hdf5::Dataspace mem_space = hdf5::Dataspace::create_simple(1, {1,});
for (size_t ind=0; ind<m_timesteps.size();++ind)
{
hdf5::Group grp = open_main_variables(m_timesteps(ind));
hdf5::Dataset data = grp.open_dataset(CURRENT_VALNAME);
herr_t status = H5Dread(data.get_id(), H5T_NATIVE_DOUBLE,
mem_space.get_id(), file_space.get_id(), H5P_DEFAULT,
&(out[ind]));
if (status < 0)
{
throw std::runtime_error("Error while reading dataset "
+ data.get_path() + ".");
}
}
return out;
}
} // namespace io
} // namespace specmicp

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