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rSPECMICP SpecMiCP / ReactMiCP
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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