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diffusion_secondary.cpp
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rSPECMICP SpecMiCP / ReactMiCP
diffusion_secondary.cpp
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/*-------------------------------------------------------
- Module : reactmicp/systems/diffusion
- File : diffusion_secondary.cpp
- Author : Fabien Georget
Copyright (c) 2014, Fabien 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:
* Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
* 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.
* Neither the name of the Princeton University 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 OWNER 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 "diffusion_secondary.hpp"
#include "physics/laws.hpp"
namespace
specmicp
{
namespace
reactmicp
{
namespace
systems
{
namespace
diffusion
{
// ================================== //
// //
// Secondary variables wibbly-timey //
// //
// ================================== //
//! \brief Set secondary concentrations
void
DiffusionSecondaryVariables
::
compute_secondary_concentrations
(
const
Variables
&
variable
)
{
for
(
ind_t
node
=
0
;
node
<
m_secondary_concentration
.
cols
();
++
node
)
{
nodal_secondary_concentrations
(
node
,
variable
);
}
}
//! \brief Set secondary concentrations for node 'node'
void
DiffusionSecondaryVariables
::
nodal_secondary_concentrations
(
ind_t
node
,
const
Variables
&
variable
)
{
for
(
int
species:
m_data
->
range_aqueous
())
{
double
sum
=
-
m_data
->
logk_aqueous
(
species
)
-
loggamma_secondary
(
node
,
species
);
for
(
int
component:
m_data
->
range_aqueous_component
())
{
sum
+=
m_data
->
nu_aqueous
(
species
,
component
)
*
(
loggamma_component
(
node
,
component
)
+
m_ideq
.
component_concentration
(
node
,
component
,
variable
)
);
}
secondary_concentration
(
node
,
species
)
=
pow10
(
sum
);
}
}
double
DiffusionSecondaryVariables
::
norm_secondary_variables
()
{
return
m_secondary_variables
.
block
(
1
,
0
,
m_data
->
nb_aqueous
+
m_data
->
nb_component
,
m_secondary_concentration
.
cols
()
).
norm
();
}
double
DiffusionSecondaryVariables
::
nodal_norm_secondary_variables
(
ind_t
node
)
{
return
m_secondary_variables
.
block
(
1
,
node
,
m_data
->
nb_aqueous
+
m_data
->
nb_component
,
1
).
norm
();
}
//! \brief Solve for secondary variables
int
DiffusionSecondaryVariables
::
solve_secondary_variables
(
const
Variables
&
variable
)
{
bool
may_have_converged
=
false
;
double
previous_norm
=
norm_secondary_variables
();
for
(
int
i
=
0
;
i
<
6
;
++
i
)
{
compute_secondary_concentrations
(
variable
);
compute_secondary_variables
(
variable
);
double
new_norm
=
norm_secondary_variables
();
if
(
std
::
abs
(
previous_norm
-
new_norm
)
/
previous_norm
<
1e-6
)
{
may_have_converged
=
true
;
break
;}
previous_norm
=
new_norm
;
}
return
may_have_converged
;
}
//! \brief Solve for secondary variables
int
DiffusionSecondaryVariables
::
nodal_solve_secondary_variables
(
ind_t
node
,
const
Variables
&
variable
)
{
bool
may_have_converged
=
false
;
double
previous_norm
=
nodal_norm_secondary_variables
(
node
);
for
(
int
i
=
0
;
i
<
6
;
++
i
)
{
nodal_secondary_concentrations
(
node
,
variable
);
nodal_secondary_variables
(
node
,
variable
);
double
new_norm
=
nodal_norm_secondary_variables
(
node
);
if
(
std
::
abs
(
previous_norm
-
new_norm
)
/
previous_norm
<
1e-6
)
{
may_have_converged
=
true
;
break
;}
previous_norm
=
new_norm
;
}
return
may_have_converged
;
}
//! \brief Compute secondary variables
void
DiffusionSecondaryVariables
::
compute_secondary_variables
(
const
Variables
&
variable
)
{
for
(
ind_t
node
=
0
;
node
<
m_secondary_concentration
.
cols
();
++
node
)
{
nodal_secondary_variables
(
node
,
variable
);
}
}
void
DiffusionSecondaryVariables
::
nodal_secondary_variables
(
ind_t
node
,
const
Variables
&
variable
)
{
nodal_ionic_strength
(
node
,
variable
);
nodal_loggamma
(
node
);
}
void
DiffusionSecondaryVariables
::
compute_ionic_strength
(
const
Variables
&
variable
)
{
for
(
ind_t
node
=
0
;
node
<
m_secondary_concentration
.
cols
();
++
node
)
{
nodal_ionic_strength
(
node
,
variable
);
}
}
//! \brief compute the ionic strength for node 'node'
void
DiffusionSecondaryVariables
::
nodal_ionic_strength
(
ind_t
node
,
const
Variables
&
variable
)
{
double
ionics
=
0
;
for
(
int
component:
m_data
->
range_aqueous_component
())
{
if
(
m_data
->
param_aq
(
component
,
0
)
==
0
)
continue
;
ionics
+=
std
::
pow
(
m_data
->
param_aq
(
component
,
0
),
2
)
*
pow10
(
m_ideq
.
component_concentration
(
node
,
component
,
variable
));
}
for
(
int
aqueous:
m_data
->
range_aqueous
())
{
ind_t
idaq
=
m_data
->
nb_component
+
aqueous
;
if
(
m_data
->
param_aq
(
idaq
,
0
)
==
0
)
continue
;
ionics
+=
std
::
pow
(
m_data
->
param_aq
(
idaq
,
0
),
2
)
*
secondary_concentration
(
node
,
aqueous
);
}
ionic_strength
(
node
)
=
ionics
/
2
;
}
void
DiffusionSecondaryVariables
::
compute_loggamma
()
{
for
(
ind_t
node
=
0
;
node
<
m_secondary_concentration
.
cols
();
++
node
)
{
nodal_loggamma
(
node
);
}
}
//! \brief compute the logarithm of the activity coefficients for node 'node'
void
DiffusionSecondaryVariables
::
nodal_loggamma
(
ind_t
node
)
{
nodal_loggamma_component
(
node
);
nodal_loggamma_aqueous
(
node
);
}
//! \brief compute the logarithm of the activity coefficients for node 'node'
void
DiffusionSecondaryVariables
::
nodal_loggamma_component
(
ind_t
node
)
{
const
double
sqrti
=
std
::
sqrt
(
ionic_strength
(
node
));
for
(
int
component:
m_data
->
range_aqueous_component
())
{
loggamma_component
(
node
,
component
)
=
laws
::
extended_debye_huckel
(
ionic_strength
(
node
),
sqrti
,
m_data
->
param_aq
(
component
,
0
),
m_data
->
param_aq
(
component
,
1
),
m_data
->
param_aq
(
component
,
2
));
}
}
//! \brief compute the logarithm of the activity coefficients for node 'node'
void
DiffusionSecondaryVariables
::
nodal_loggamma_aqueous
(
ind_t
node
)
{
const
double
sqrti
=
std
::
sqrt
(
ionic_strength
(
node
));
for
(
int
aqueous:
m_data
->
range_aqueous
())
{
ind_t
idaq
=
m_data
->
nb_component
+
aqueous
;
loggamma_secondary
(
node
,
aqueous
)
=
laws
::
extended_debye_huckel
(
ionic_strength
(
node
),
sqrti
,
m_data
->
param_aq
(
idaq
,
0
),
m_data
->
param_aq
(
idaq
,
1
),
m_data
->
param_aq
(
idaq
,
2
));
}
}
}
// end namespace diffusion
}
// end namespace systems
}
// end namespace reactmicp
}
// end namespace specmicp
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