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adimensional_system_solution_extractor.cpp
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Wed, Jul 3, 10:23
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rSPECMICP SpecMiCP / ReactMiCP
adimensional_system_solution_extractor.cpp
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#include "adimensional_system_solution_extractor.hpp"
#include "physics/laws.hpp"
#include "database/database.hpp"
namespace
specmicp
{
scalar_t
AdimensionalSystemSolutionExtractor
::
density_water
()
const
{
return
laws
::
density_water
(
units
::
celsius
(
25.0
),
length_unit
(),
mass_unit
());
}
scalar_t
AdimensionalSystemSolutionExtractor
::
mass_concentration_water
()
const
{
return
density_water
()
*
total_saturation_water
();
}
scalar_t
AdimensionalSystemSolutionExtractor
::
pH
()
const
{
// find species responsible for pH
specmicp
::
database
::
Database
db_handler
(
m_data
);
index_t
id
=
db_handler
.
component_label_to_id
(
"HO[-]"
);
if
(
id
!=
no_species
)
{
return
14
+
log_activity_component
(
id
);
}
else
{
id
=
db_handler
.
component_label_to_id
(
"H[+]"
);
if
(
id
!=
no_species
)
return
-
log_activity_component
(
id
);
throw
std
::
runtime_error
(
"No component corresponding to the dissociation of water !"
);
}
}
scalar_t
AdimensionalSystemSolutionExtractor
::
total_saturation_minerals
()
const
{
return
m_solution
.
main_variables
.
segment
(
m_data
->
nb_component
,
m_data
->
nb_mineral
).
sum
();
}
scalar_t
AdimensionalSystemSolutionExtractor
::
mole_concentration_mineral
(
index_t
mineral
)
const
{
return
total_saturation_mineral
(
mineral
)
/
m_data
->
molar_volume_mineral
(
mineral
,
length_unit
());
}
scalar_t
AdimensionalSystemSolutionExtractor
::
mass_concentration_mineral
(
index_t
mineral
)
const
{
return
mole_concentration_mineral
(
mineral
)
*
m_data
->
molar_mass_mineral
(
mineral
,
mass_unit
());
}
//! \brief Return the total aqueous concentration
scalar_t
AdimensionalSystemSolutionExtractor
::
total_aqueous_concentration
(
index_t
component
)
const
{
scalar_t
conc
=
molality_component
(
component
);
for
(
index_t
aqueous:
m_data
->
range_aqueous
())
{
if
(
m_data
->
nu_aqueous
(
aqueous
,
component
)
!=
0.0
)
{
conc
+=
m_data
->
nu_aqueous
(
aqueous
,
component
)
*
molality_aqueous
(
aqueous
);
}
}
return
conc
;
}
//! \brief Return the total solid concentration
scalar_t
AdimensionalSystemSolutionExtractor
::
total_solid_concentration
(
index_t
component
)
const
{
scalar_t
conc
=
0
;
for
(
index_t
mineral:
m_data
->
range_mineral
())
{
if
(
m_data
->
nu_mineral
(
mineral
,
component
)
!=
0.0
)
{
conc
+=
m_data
->
nu_mineral
(
mineral
,
component
)
*
total_saturation_mineral
(
mineral
)
/
m_data
->
molar_volume_mineral
(
mineral
,
length_unit
());
}
}
return
conc
;
}
//! \brief Return the total immobile concentration
scalar_t
AdimensionalSystemSolutionExtractor
::
total_immobile_concentration
(
index_t
component
)
const
{
scalar_t
conc
=
total_solid_concentration
(
component
);
for
(
index_t
sorbed:
m_data
->
range_sorbed
())
{
if
(
m_data
->
nu_sorbed
(
sorbed
,
component
)
!=
0.0
)
{
conc
+=
m_data
->
nu_sorbed
(
sorbed
,
component
)
*
sorbed_species_molalities
(
sorbed
);
}
}
return
conc
;
}
//! Return the saturation index for 'mineral'
scalar_t
AdimensionalSystemSolutionExtractor
::
saturation_index
(
index_t
mineral
)
const
{
scalar_t
saturation_index
=
-
m_data
->
logk_mineral
(
mineral
);
for
(
index_t
component:
m_data
->
range_aqueous_component
())
{
saturation_index
+=
m_data
->
nu_mineral
(
mineral
,
component
)
*
log_activity_component
(
component
);
}
return
saturation_index
;
}
//! Return the saturation index for 'mineral_kinetic'
scalar_t
AdimensionalSystemSolutionExtractor
::
saturation_index_kinetic
(
index_t
mineral_kinetic
)
const
{
scalar_t
saturation_index
=
-
m_data
->
logk_mineral_kinetic
(
mineral_kinetic
);
for
(
index_t
component:
m_data
->
range_aqueous_component
())
{
saturation_index
+=
m_data
->
nu_mineral_kinetic
(
mineral_kinetic
,
component
)
*
log_activity_component
(
component
);
}
return
saturation_index
;
}
// ########################### //
// //
// Modificator //
// //
// ########################### //
void
AdimensionalSystemSolutionModificator
::
scale_total_concentration
(
index_t
component
,
scalar_t
new_value
)
{
const
scalar_t
old_value
=
total_solid_concentration
(
component
);
const
scalar_t
factor
=
new_value
/
old_value
;
m_nonconst_solution
.
main_variables
.
segment
(
dof_mineral
(
0
),
m_data
->
nb_mineral
)
*=
factor
;
}
void
AdimensionalSystemSolutionModificator
::
remove_solids
()
{
m_nonconst_solution
.
main_variables
.
segment
(
dof_mineral
(
0
),
m_data
->
nb_mineral
).
setZero
();
}
Vector
AdimensionalSystemSolutionModificator
::
set_minerals_kinetics
(
std
::
vector
<
index_t
>&
list_species
)
{
index_t
nb_kinetics
=
list_species
.
size
();
index_t
nb_new_mineral
=
m_data
->
nb_mineral
-
nb_kinetics
;
std
::
vector
<
index_t
>
minerals_to_keep
;
minerals_to_keep
.
reserve
(
nb_new_mineral
);
std
::
vector
<
index_t
>
new_kinetics_index
(
nb_kinetics
,
no_species
);
Vector
saturation_kinetics
(
nb_kinetics
);
index_t
new_ind_eq
=
m_data
->
nb_component
;
index_t
new_ind_kin
=
0
;
index_t
tot_ind_kin
=
m_data
->
nb_mineral_kinetic
;
// ###TODO optimize
for
(
index_t
mineral:
m_data
->
range_mineral
())
{
auto
is_kin
=
std
::
find
(
list_species
.
begin
(),
list_species
.
end
(),
mineral
);
// If mineral is still at equilibrium
if
(
is_kin
==
list_species
.
end
())
{
minerals_to_keep
.
push_back
(
mineral
);
m_nonconst_solution
.
main_variables
(
new_ind_eq
)
=
total_saturation_mineral
(
mineral
);
++
new_ind_eq
;
}
// If mineral is governed by kinetics
else
{
saturation_kinetics
(
new_ind_kin
)
=
total_saturation_mineral
(
mineral
);
++
new_ind_kin
;
// save the new index (index in the kinetics vector)
// The order is conserved !
new_kinetics_index
[
is_kin
-
list_species
.
begin
()]
=
tot_ind_kin
;
++
tot_ind_kin
;
}
}
specmicp_assert
(
new_ind_eq
==
m_data
->
nb_component
+
nb_new_mineral
);
// change the database
database
::
Database
dbhandler
(
m_data
);
dbhandler
.
minerals_keep_only
(
minerals_to_keep
);
// update the list of species
list_species
.
swap
(
new_kinetics_index
);
// resize
m_nonconst_solution
.
main_variables
.
conservativeResize
(
m_data
->
nb_component
+
nb_new_mineral
);
return
saturation_kinetics
;
}
}
// end namespace specmicp
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