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diffusion_secondary.hpp
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rSPECMICP SpecMiCP / ReactMiCP
diffusion_secondary.hpp
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/*-------------------------------------------------------
- Module : reactmicp/systems/diffusion
- File : diffusion_secondary.hpp
- 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.
---------------------------------------------------------*/
#ifndef SPECMICP_REACTMICP_SYSTEMS_DIFFUSION_SECONDARY_HPP
#define SPECMICP_REACTMICP_SYSTEMS_DIFFUSION_SECONDARY_HPP
#include <memory>
#include "database/data_container.hpp"
#include "reactmicp/common.hpp"
#include "diffusion_numbering.hpp"
namespace
specmicp
{
namespace
reactmicp
{
namespace
systems
{
namespace
diffusion
{
//! \brief handle secondary variables for the diffusion system
class
DiffusionSecondaryVariables
{
public
:
using
Variables
=
ParabolicVariables
;
DiffusionSecondaryVariables
(
int
nb_nodes
,
std
::
shared_ptr
<
database
::
DataContainer
>
thedatabase
,
DiffusionNumbering
&
numberer
)
:
m_data
(
thedatabase
),
m_ideq
(
numberer
),
m_secondary_variables
(
Eigen
::
MatrixXd
(
thedatabase
->
nb_component
+
thedatabase
->
nb_aqueous
+
1
,
nb_nodes
)),
m_secondary_concentration
(
Eigen
::
MatrixXd
(
thedatabase
->
nb_aqueous
,
nb_nodes
))
{
m_secondary_variables
.
setZero
();
m_secondary_concentration
.
setZero
();
}
// Secondary variables
// ===================
// Algorithms
// ----------
//! \brief Set secondary concentrations
void
compute_secondary_concentrations
(
const
Variables
&
variable
);
//! \brief Set secondary concentrations for node 'node'
void
nodal_secondary_concentrations
(
ind_t
node
,
const
Variables
&
variable
);
//! \brief Solve for secondary variables
int
solve_secondary_variables
(
const
Variables
&
variable
);
//! \brief Solve for secondary variables in one node
int
nodal_solve_secondary_variables
(
ind_t
node
,
const
Variables
&
variable
);
//! \brief Compute secondary variables
void
compute_secondary_variables
(
const
Variables
&
variable
);
//! \brief Compute the secondary variables at node 'node'
void
nodal_secondary_variables
(
ind_t
node
,
const
Variables
&
variable
);
//! \brief compute the ionic strengths
void
compute_ionic_strength
(
const
Variables
&
variable
);
//! \brief compute the ionic strength for node 'node'
void
nodal_ionic_strength
(
ind_t
node
,
const
Variables
&
variable
);
//! \brief compute the activity coefficients
void
compute_loggamma
();
//! \brief compute the logarithm of the activity coefficients for node 'node'
void
nodal_loggamma
(
ind_t
node
);
//! \brief compute the activity coefficient for the components of node 'node'
void
nodal_loggamma_component
(
ind_t
node
);
//! \brief compute the activity coefficient for the aqueous species of node 'node'
void
nodal_loggamma_aqueous
(
ind_t
node
);
// Getters and setters
// -------------------
//! \brief Secondary species concentration
double
&
secondary_concentration
(
ind_t
node
,
ind_t
aqueous
)
{
assert
(
aqueous
>=
0
and
aqueous
<
m_data
->
nb_aqueous
);
return
m_secondary_concentration
.
coeffRef
(
aqueous
,
node
);
}
//! \brief Secondary species concentration
double
secondary_concentration
(
ind_t
node
,
ind_t
aqueous
)
const
{
assert
(
aqueous
>=
0
and
aqueous
<
m_data
->
nb_aqueous
);
return
m_secondary_concentration
.
coeff
(
aqueous
,
node
);
}
//! \brief Return the loggamma of a component
double
&
loggamma_component
(
ind_t
node
,
ind_t
component
)
{
assert
(
component
>=
1
and
component
<
m_data
->
nb_component
);
return
m_secondary_variables
.
coeffRef
(
component
,
node
);
}
//! \brief Return the loggamma of a component
double
loggamma_component
(
ind_t
node
,
ind_t
component
)
const
{
assert
(
component
>=
1
and
component
<
m_data
->
nb_component
);
return
m_secondary_variables
.
coeff
(
component
,
node
);
}
//! \brief Return the loggamma of a secondary species
double
&
loggamma_secondary
(
ind_t
node
,
ind_t
aqueous
)
{
assert
(
aqueous
>=
0
and
aqueous
<
m_data
->
nb_aqueous
);
return
m_secondary_variables
.
coeffRef
(
m_data
->
nb_component
+
aqueous
,
node
);
}
//! \brief Return the loggamma of a secondary species
double
loggamma_secondary
(
ind_t
node
,
ind_t
aqueous
)
const
{
assert
(
aqueous
>=
0
and
aqueous
<
m_data
->
nb_aqueous
);
return
m_secondary_variables
.
coeff
(
m_data
->
nb_component
+
aqueous
,
node
);
}
//! \brief Return ionic strength
double
&
ionic_strength
(
ind_t
node
)
{
return
m_secondary_variables
.
coeffRef
(
m_data
->
nb_component
+
m_data
->
nb_aqueous
,
node
);
}
//! \brief Return ionic strength
double
ionic_strength
(
ind_t
node
)
const
{
return
m_secondary_variables
.
coeff
(
m_data
->
nb_component
+
m_data
->
nb_aqueous
,
node
);
}
//! \brief Return norm of the loggamma
double
loggamma_norm
()
const
{
return
m_secondary_variables
.
norm
();
}
private
:
// Return the norm used to check the convergence of the fixed-point iterations
double
norm_secondary_variables
();
double
nodal_norm_secondary_variables
(
ind_t
node
);
std
::
shared_ptr
<
database
::
DataContainer
>
m_data
;
DiffusionNumbering
&
m_ideq
;
Eigen
::
MatrixXd
m_secondary_variables
;
Eigen
::
MatrixXd
m_secondary_concentration
;
};
}
// end namespace diffusion
}
// end namespace systems
}
// end namespace reactmicp
}
// end namespace specmicp
#endif
// SPECMICP_REACTMICP_SYSTEMS_DIFFUSION_SECONDARY_HPP
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