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rSPECMICP SpecMiCP / ReactMiCP
variables.cpp
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/*------------------------------------------------------------------------------
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.
-----------------------------------------------------------------------------*/
#include "variables.hpp"
#include "../../../dfpm/meshes/mesh1d.hpp"
#include "variables_box.hpp"
#include "../../../utils/log.hpp"
#include <stdexcept>
namespace
specmicp
{
namespace
reactmicp
{
namespace
systems
{
namespace
unsaturated
{
// ===================
// List main variables
// ===================
ListMainVariable
::
ListMainVariable
(
index_t
nb_vars
,
index_t
nb_nodes
)
{
variables
.
reserve
(
nb_vars
);
variables
.
emplace_back
(
make_unique
<
MainVariable
>
(
nb_nodes
));
variables
.
emplace_back
(
nullptr
);
for
(
index_t
i
=
2
;
i
<
nb_vars
;
++
i
)
{
variables
.
emplace_back
(
make_unique
<
MainVariable
>
(
nb_nodes
));
}
}
ListMainVariable
::
ListMainVariable
(
index_t
nb_vars
,
index_t
nb_nodes
,
std
::
vector
<
bool
>
to_init
)
{
variables
.
reserve
(
nb_vars
);
for
(
const
auto
&
is_present:
to_init
)
{
if
(
is_present
)
{
variables
.
emplace_back
(
make_unique
<
MainVariable
>
(
nb_nodes
));
}
else
{
variables
.
emplace_back
(
nullptr
);
}
}
}
//! \brief Reset the variables
void
ListMainVariable
::
reset
()
{
variables
[
0
]
->
reset
();
for
(
vector_type
::
size_type
i
=
2
;
i
<
variables
.
size
();
++
i
)
{
if
(
variables
[
i
]
!=
nullptr
)
variables
[
i
]
->
reset
();
}
}
void
ListMainVariable
::
hard_reset
(
index_t
component
,
index_t
nb_nodes
)
{
specmicp_assert
(
component
>=
0
and
(
unsigned
)
component
<
variables
.
size
());
if
(
nb_nodes
==
0
)
variables
[
component
].
reset
(
nullptr
);
else
variables
[
component
].
reset
(
new
MainVariable
(
nb_nodes
));
}
// ==============
// Variables box
// ==============
SaturationVariableBox
::
SaturationVariableBox
(
UnsaturatedVariables
&
vars
)
:
liquid_saturation
(
vars
.
m_liquid_var
.
water
()),
solid_concentration
(
vars
.
m_solid_var
.
water
()),
vapor_pressure
(
vars
.
m_gas_var
.
water
()),
aqueous_concentration
(
vars
.
m_water_aq_concentration
),
porosity
(
vars
.
m_porosity
),
liquid_permeability
(
vars
.
m_liquid_permeability
),
liquid_diffusivity
(
vars
.
m_liquid_diffusivity
),
relative_liquid_permeability
(
vars
.
m_relative_liquid_permeability
),
relative_liquid_diffusivity
(
vars
.
m_relative_liquid_diffusivity
),
capillary_pressure
(
vars
.
m_capillary_pressure
),
advection_flux
(
vars
.
m_advection_flux
),
constants
(
vars
.
m_constants
),
capillary_pressure_f
(
vars
.
m_capillary_pressure_f
),
relative_liquid_permeability_f
(
vars
.
m_relative_liquid_permeability_f
),
relative_liquid_diffusivity_f
(
vars
.
m_relative_liquid_diffusivity_f
)
{}
SaturationPressureVariableBox
::
SaturationPressureVariableBox
(
UnsaturatedVariables
&
vars
)
:
binary_diffusion_coefficient
(
vars
.
get_binary_gas_diffusivity
(
0
)),
liquid_saturation
(
vars
.
m_liquid_var
.
water
()),
partial_pressure
(
vars
.
get_pressure_main_variables
(
0
)),
solid_concentration
(
vars
.
m_solid_var
.
water
()),
aqueous_concentration
(
vars
.
m_water_aq_concentration
),
porosity
(
vars
.
m_porosity
),
liquid_permeability
(
vars
.
m_liquid_permeability
),
liquid_diffusivity
(
vars
.
m_liquid_diffusivity
),
relative_liquid_permeability
(
vars
.
m_relative_liquid_permeability
),
relative_liquid_diffusivity
(
vars
.
m_relative_liquid_diffusivity
),
capillary_pressure
(
vars
.
m_capillary_pressure
),
resistance_gas_diffusivity
(
vars
.
m_resistance_gas_diffusivity
),
relative_gas_diffusivity
(
vars
.
m_relative_gas_diffusivity
),
advection_flux
(
vars
.
m_advection_flux
),
constants
(
vars
.
m_constants
),
capillary_pressure_f
(
vars
.
m_capillary_pressure_f
),
relative_liquid_permeability_f
(
vars
.
m_relative_liquid_permeability_f
),
relative_liquid_diffusivity_f
(
vars
.
m_relative_liquid_diffusivity_f
),
relative_gas_diffusivity_f
(
vars
.
m_relative_gas_diffusivity_f
),
partial_pressure_f
(
vars
.
m_vapor_pressure_f
)
{}
LiquidAqueousComponentVariableBox
::
LiquidAqueousComponentVariableBox
(
UnsaturatedVariables
&
vars
,
index_t
component
)
:
aqueous_concentration
(
vars
.
m_liquid_var
.
aqueous_component
(
component
)),
solid_concentration
(
vars
.
m_solid_var
.
aqueous_component
(
component
)),
partial_pressure
(
vars
.
get_pressure_main_variables
(
component
)),
saturation
(
vars
.
m_liquid_var
.
water
()),
porosity
(
vars
.
m_porosity
),
liquid_diffusivity
(
vars
.
m_liquid_diffusivity
),
relative_liquid_diffusivity
(
vars
.
m_relative_liquid_diffusivity
),
advection_flux
(
vars
.
m_advection_flux
),
constants
(
vars
.
m_constants
)
{}
LiquidGasAqueousVariableBox
::
LiquidGasAqueousVariableBox
(
UnsaturatedVariables
&
vars
,
index_t
component
)
:
LiquidAqueousComponentVariableBox
(
vars
,
component
),
binary_diffusion_coefficient
(
vars
.
get_binary_gas_diffusivity
(
component
)),
resistance_gas_diffusivity
(
vars
.
m_resistance_gas_diffusivity
),
relative_gas_diffusivity
(
vars
.
m_relative_gas_diffusivity
)
{}
PressureVariableBox
::
PressureVariableBox
(
UnsaturatedVariables
&
vars
,
index_t
component
)
:
binary_diffusion_coefficient
(
vars
.
get_binary_gas_diffusivity
(
component
)),
partial_pressure
(
vars
.
get_pressure_main_variables
(
component
)),
liquid_saturation
(
vars
.
m_liquid_var
.
water
()),
porosity
(
vars
.
m_porosity
),
resistance_gas_diffusivity
(
vars
.
m_resistance_gas_diffusivity
),
relative_gas_diffusivity
(
vars
.
m_relative_gas_diffusivity
),
constants
(
vars
.
m_constants
)
{}
void
ConstantBox
::
scale
(
units
::
LengthUnit
length_unit
)
{
scalar_t
scaling_factor
=
units
::
scaling_factor
(
length_unit
);
//viscosity_liquid_water *= 1.0/scaling_factor;
rt
/=
std
::
pow
(
scaling_factor
,
3
);
//total_pressure *= 1.0/scaling_factor;
}
// ======================
// Unsaturated variables
// ======================
namespace
internal
{
//! \brief Find the correspond gas id for a component with gas
static
index_t
get_id_gas
(
database
::
RawDatabasePtr
the_database
,
index_t
component
)
{
index_t
id
=
no_species
;
for
(
auto
gas:
the_database
->
range_gas
())
{
const
scalar_t
nu
=
the_database
->
nu_gas
(
gas
,
component
);
if
(
nu
==
0.0
)
continue
;
if
(
nu
!=
1.0
)
{
ERROR
<<
"Database not in the good format"
<<
"; expect : gas <=> component
\n
"
<<
"component : "
<<
the_database
->
get_label_component
(
component
)
<<
"
\n
"
<<
"gas : "
<<
the_database
->
get_label_gas
(
gas
)
<<
"."
;
throw
std
::
runtime_error
(
"Badly formatted database"
);
}
else
{
id
=
gas
;
}
}
if
(
id
==
no_species
)
{
ERROR
<<
"No corresponding gas in the database for component : "
<<
the_database
->
get_label_component
(
component
);
throw
std
::
runtime_error
(
"Badly formatted database"
);
}
return
id
;
}
}
//end namespace internal
UnsaturatedVariables
::
UnsaturatedVariables
(
mesh
::
Mesh1DPtr
the_mesh
,
database
::
RawDatabasePtr
the_database
,
std
::
vector
<
bool
>
has_gas
)
:
database
::
DatabaseHolder
(
the_database
),
m_mesh
(
the_mesh
),
m_has_gas
(
has_gas
),
m_id_gas
(
the_database
->
nb_component
(),
no_species
),
// main var
m_liquid_var
(
the_database
->
nb_component
(),
the_mesh
->
nb_nodes
()),
m_gas_var
(
the_database
->
nb_component
(),
the_mesh
->
nb_nodes
(),
has_gas
),
m_solid_var
(
the_database
->
nb_component
(),
the_mesh
->
nb_nodes
()),
// chem sol
m_chem_sol
(
the_mesh
->
nb_nodes
()),
// secondary vars
m_porosity
(
the_mesh
->
nb_nodes
()),
m_water_aq_concentration
(
the_mesh
->
nb_nodes
()),
m_liquid_permeability
(
the_mesh
->
nb_nodes
()),
m_relative_liquid_permeability
(
the_mesh
->
nb_nodes
()),
m_liquid_diffusivity
(
the_mesh
->
nb_nodes
()),
m_relative_liquid_diffusivity
(
the_mesh
->
nb_nodes
()),
m_binary_gas_diffusivity
(
Vector
::
Zero
(
the_database
->
nb_component
())),
m_resistance_gas_diffusivity
(
the_mesh
->
nb_nodes
()),
m_relative_gas_diffusivity
(
the_mesh
->
nb_nodes
()),
m_capillary_pressure
(
the_mesh
->
nb_nodes
()),
m_advection_flux
(
the_mesh
->
nb_nodes
()),
m_aqueous_scaling
(
Vector
::
Ones
(
the_database
->
nb_component
())),
m_gaseous_scaling
(
Vector
::
Ones
(
the_database
->
nb_component
()))
{
specmicp_assert
(
has_gas
.
size
()
==
(
unsigned
)
the_database
->
nb_component
());
//
// trick to avoid more branching in equations :
m_gas_var
.
hard_reset
(
1
,
the_mesh
->
nb_nodes
());
for
(
auto
component:
the_database
->
range_aqueous_component
())
{
if
(
has_gas
[
component
])
{
m_id_gas
[
component
]
=
internal
::
get_id_gas
(
the_database
,
component
);
}
}
}
UnsaturatedVariables
::
UnsaturatedVariables
(
mesh
::
Mesh1DPtr
the_mesh
,
database
::
RawDatabasePtr
the_database
,
std
::
vector
<
bool
>
has_gas
,
units
::
LengthUnit
length_unit
)
:
UnsaturatedVariables
(
the_mesh
,
the_database
,
has_gas
)
{
m_constants
.
scale
(
length_unit
);
}
void
UnsaturatedVariables
::
reset_main_variables
()
{
m_liquid_var
.
reset
();
m_gas_var
.
reset
();
m_solid_var
.
reset
();
}
SaturationVariableBox
UnsaturatedVariables
::
get_saturation_variables
()
{
return
SaturationVariableBox
(
*
this
);
}
SaturationPressureVariableBox
UnsaturatedVariables
::
get_saturation_pressure_variables
()
{
return
SaturationPressureVariableBox
(
*
this
);
}
PressureVariableBox
UnsaturatedVariables
::
get_vapor_pressure_variables
()
{
return
PressureVariableBox
(
*
this
,
0
);
}
LiquidAqueousComponentVariableBox
UnsaturatedVariables
::
get_liquid_aqueous_component_variables
(
index_t
component
)
{
return
LiquidAqueousComponentVariableBox
(
*
this
,
component
);
}
LiquidGasAqueousVariableBox
UnsaturatedVariables
::
get_liquid_gas_aqueous_variables
(
index_t
component
)
{
return
LiquidGasAqueousVariableBox
(
*
this
,
component
);
}
PressureVariableBox
UnsaturatedVariables
::
get_pressure_variables
(
index_t
component
)
{
return
PressureVariableBox
(
*
this
,
component
);
}
MainVariable
&
UnsaturatedVariables
::
get_pressure_main_variables
(
index_t
component
)
{
if
(
component_has_gas
(
component
))
{
specmicp_assert
(
m_gas_var
(
component
)
!=
nullptr
);
return
*
m_gas_var
(
component
);
}
else
return
*
m_gas_var
(
1
);
// a zero var..., this is a trick to always get a valid info
}
index_t
UnsaturatedVariables
::
nb_gas
()
{
return
std
::
count
(
m_has_gas
.
begin
(),
m_has_gas
.
end
(),
true
);
}
void
UnsaturatedVariables
::
set_relative_variables
(
index_t
node
)
{
const
scalar_t
saturation
=
m_liquid_var
.
water
().
variable
(
node
);
m_relative_liquid_diffusivity
(
node
)
=
m_relative_liquid_diffusivity_f
(
node
,
saturation
);
m_relative_gas_diffusivity
(
node
)
=
m_relative_gas_diffusivity_f
(
node
,
saturation
);
m_relative_liquid_permeability
(
node
)
=
m_relative_liquid_permeability_f
(
node
,
saturation
);
m_capillary_pressure
(
node
)
=
m_capillary_pressure_f
(
node
,
saturation
);
}
void
UnsaturatedVariables
::
set_relative_variables
()
{
for
(
index_t
node:
m_mesh
->
range_nodes
())
{
set_relative_variables
(
node
);
}
}
void
UnsaturatedVariables
::
set_vapor_pressure
(
index_t
node
)
{
if
(
component_has_gas
(
0
))
{
const
scalar_t
saturation
=
m_liquid_var
.
water
().
variable
(
node
);
m_gas_var
(
0
)
->
variable
(
node
)
=
m_vapor_pressure_f
(
node
,
saturation
);
}
}
}
//end namespace unsatura
}
//end namespace systems
}
//end namespace reactmicp
}
//end namespace specmicp
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