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adimensional_system_pcfm.cpp
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rSPECMICP SpecMiCP / ReactMiCP
adimensional_system_pcfm.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 "adimensional_system_pcfm.hpp"
#include "adimensional_system.hpp"
#include "specmicp_common/log.hpp"
#include <iostream>
namespace
specmicp
{
// AdimensionalSystemPCFM
AdimensionalSystemPCFM
::
AdimensionalSystemPCFM
(
std
::
shared_ptr
<
AdimensionalSystem
>
program
)
:
m_data
(
program
->
get_database
()),
m_program
(
program
)
{
check_validity
();
}
AdimensionalSystemPCFM
::
AdimensionalSystemPCFM
(
std
::
shared_ptr
<
AdimensionalSystem
>
program
,
const
PCFMOptions
&
options
)
:
OptionsHandler
<
PCFMOptions
>
(
options
),
m_data
(
program
->
get_database
()),
m_program
(
program
)
{
check_validity
();
}
bool
AdimensionalSystemPCFM
::
check_validity
()
{
bool
is_valid
=
true
;
if
(
m_program
->
water_equation_type
()
!=
WaterEquationType
::
NoEquation
)
{
ERROR
<<
"The implementation of the positive continuous fraction method does not compute the conservation of water"
;
is_valid
=
false
;
}
if
(
m_program
->
get_database
()
->
nb_mineral
()
!=
0.0
)
{
WARNING
<<
"The implementation of the positive continuous fraction method does not compute the solid phase assemblage"
;
is_valid
=
false
;
}
return
is_valid
;
}
PCFMReturnCode
AdimensionalSystemPCFM
::
solve
(
Vector
&
x
)
{
index_t
cnt
=
0
;
m_errors
.
setZero
(
m_program
->
total_variables
());
while
(
cnt
<
get_options
().
max_iterations
)
{
one_iteration
(
x
);
scalar_t
error
=
m_errors
.
lpNorm
<
Eigen
::
Infinity
>
();
DEBUG
<<
"PCFM error : "
<<
error
<<
" ?< "
<<
get_options
().
tolerance
;
if
(
not
std
::
isfinite
(
error
))
return
PCFMReturnCode
::
Error
;
if
(
error
<
get_options
().
tolerance
)
return
PCFMReturnCode
::
Success
;
++
cnt
;
}
if
(
cnt
==
get_options
().
max_iterations
)
return
PCFMReturnCode
::
MaxIterationsReached
;
return
PCFMReturnCode
::
NotConvergedYet
;
}
void
AdimensionalSystemPCFM
::
one_iteration
(
Vector
&
x
)
{
m_program
->
set_secondary_concentration
(
x
);
m_program
->
set_sorbed_concentrations
(
x
);
for
(
index_t
component:
m_data
->
range_aqueous_component
())
{
if
(
m_program
->
ideq_paq
(
component
)
!=
no_equation
)
{
solve_component
(
component
,
x
);
}
}
if
(
m_program
->
ideq_surf
()
!=
no_equation
)
{
solve_surface
(
x
);
}
}
void
AdimensionalSystemPCFM
::
solve_component
(
index_t
component
,
Vector
&
x
)
{
specmicp_assert
(
component
>
0
and
component
<
m_data
->
nb_component
()
and
"Must be an aqueous component"
);
specmicp_assert
(
m_program
->
ideq_paq
(
component
)
!=
no_equation
and
"No corresponding equation for this component"
);
specmicp_assert
(
m_program
->
aqueous_component_equation_type
(
component
)
==
AqueousComponentEquationType
::
MassConservation
);
const
scalar_t
total_concentration
=
m_program
->
total_concentration_bc
(
component
);
scalar_t
conc_w
=
m_program
->
density_water
()
*
m_program
->
volume_fraction_water
(
x
);
scalar_t
sum_reac
=
conc_w
*
m_program
->
component_molality
(
x
,
component
);
scalar_t
sum_prod
=
0.0
;
// compute the lhs and rhs of the mass balance so that every contribution is positive
if
(
total_concentration
>=
0
)
{
sum_prod
+=
total_concentration
;
}
else
{
sum_reac
-=
total_concentration
;
}
for
(
index_t
aqueous:
m_data
->
range_aqueous
())
{
if
(
m_data
->
nu_aqueous
(
aqueous
,
component
)
>
0
)
sum_reac
+=
conc_w
*
m_data
->
nu_aqueous
(
aqueous
,
component
)
*
m_program
->
secondary_molality
(
aqueous
);
else
sum_prod
-=
conc_w
*
m_data
->
nu_aqueous
(
aqueous
,
component
)
*
m_program
->
secondary_molality
(
aqueous
);
}
for
(
index_t
sorbed:
m_data
->
range_sorbed
())
{
if
(
m_data
->
nu_sorbed
(
sorbed
,
component
)
>
0
)
sum_reac
+=
m_data
->
nu_sorbed
(
sorbed
,
component
)
*
m_program
->
sorbed_species_concentration
(
sorbed
);
else
sum_prod
-=
m_data
->
nu_sorbed
(
sorbed
,
component
)
*
m_program
->
sorbed_species_concentration
(
sorbed
);
}
specmicp_assert
(
std
::
isfinite
(
sum_reac
));
specmicp_assert
(
sum_reac
>
0.0
&&
"Sum of reactants concentration should be positive"
);
specmicp_assert
(
sum_prod
>
0.0
&&
"Sum of products should be positive"
);
// compute the step size
scalar_t
theta
;
const
scalar_t
factor
=
(
sum_prod
/
sum_reac
);
if
(
sum_reac
>
sum_prod
)
theta
=
0.9
-
0.8
*
factor
;
else
theta
=
0.9
-
0.8
/
factor
;
//
theta
*=
get_options
().
theta_factor
;
scalar_t
new_conc
=
(
1
-
theta
+
theta
*
factor
)
*
m_program
->
component_molality
(
x
,
component
);
x
(
m_program
->
ideq_paq
(
component
))
=
std
::
log10
(
new_conc
);
m_errors
(
m_program
->
ideq_paq
(
component
))
=
std
::
abs
(
sum_reac
-
sum_prod
)
/
(
sum_reac
+
sum_prod
);
}
void
AdimensionalSystemPCFM
::
solve_surface
(
Vector
&
x
)
{
specmicp_assert
(
m_program
->
ideq_surf
()
!=
no_equation
);
specmicp_assert
(
m_program
->
surface_total_concentration
()
>
0
);
scalar_t
sum_prod
=
m_program
->
surface_total_concentration
();
scalar_t
sum_reac
=
m_program
->
free_sorption_site_concentration
(
x
);
for
(
index_t
sorbed:
m_data
->
range_sorbed
())
{
sum_reac
+=
m_data
->
nb_sorption_sites
(
sorbed
)
*
m_program
->
sorbed_species_concentration
(
sorbed
);
}
specmicp_assert
(
std
::
isfinite
(
sum_reac
));
specmicp_assert
(
sum_reac
>
0.0
&&
"Sum of reactants concentration should be positive"
);
specmicp_assert
(
sum_prod
>
0.0
&&
"Sum of products should be positive"
);
scalar_t
theta
;
const
scalar_t
factor
=
(
sum_prod
/
sum_reac
);
if
(
sum_reac
>
sum_prod
)
theta
=
0.9
-
0.8
*
factor
;
else
theta
=
0.9
-
0.8
/
factor
;
//
theta
*=
get_options
().
theta_factor
;
scalar_t
new_conc
=
(
1
-
theta
+
theta
*
factor
)
*
m_program
->
free_sorption_site_concentration
(
x
);
x
(
m_program
->
ideq_surf
())
=
std
::
log10
(
new_conc
);
m_errors
(
m_program
->
ideq_surf
())
=
std
::
abs
(
sum_reac
-
sum_prod
)
/
(
sum_reac
+
sum_prod
);
}
}
// end namespace specmicp
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