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sorbed_list.hpp
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rSPECMICP SpecMiCP / ReactMiCP
sorbed_list.hpp
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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. *
============================================================================= */
#ifndef SPECMICP_DATABASE_SORBEDLIST_HPP
#define SPECMICP_DATABASE_SORBEDLIST_HPP
#include "../../types.hpp"
#ifndef SPECMICP_DATABASE_SPECIES_HPP
#include "species.hpp"
#endif
#include "aqueous_list.hpp"
//! \file aqueous_list.hpp
//! \brief The list of sorbed species
//!
//! This list stores the informations about sorbed species.
namespace
specmicp
{
namespace
database
{
//! \struct SorbedValues
//! \brief Struct to initialize a sorbed species in the sorbed species list
//!
//! \ingroup database_species
struct
SorbedValues
{
std
::
string
label
;
scalar_t
logk
;
index_t
sorption_site_occupied
;
};
//! \class SorbedList
//! \brief The sorbed species
//!
//! This is the list of sorbed species in the database
//!
//! \ingroup database_species
class
SorbedList
:
public
ReactiveSpeciesList
{
public
:
//! Initialize an empty list
SorbedList
()
{}
//! Initialize a list of 'size' sorbed species with 'nb_components' components
SorbedList
(
index_t
size
,
index_t
nb_components
)
:
ReactiveSpeciesList
(
size
,
nb_components
),
m_sorption_site
(
size
)
{}
//! \name Size
//! \brief Manage the size of the list
// --------
//! @{
//! \brief Resize the list
void
resize
(
index_t
size
)
override
{
ReactiveSpeciesList
::
resize
(
size
);
m_sorption_site
.
resize
(
size
);
}
//! \brief Resize the list, adjust the number of components
void
resize
(
index_t
size
,
index_t
nb_components
)
override
{
ReactiveSpeciesList
::
resize
(
size
,
nb_components
);
m_sorption_site
.
resize
(
size
);
}
//! @}
//! \name Getter
//! \brief Return values
// ----------------------
//! @{
//! \brief Return the ionic size of component 'k'
const
scalar_t
&
nb_sorption_site_occupied
(
index_t
k
)
const
{
return
m_sorption_site
(
k
);
}
//! @}
//! \name Setter
//! \brief Set values
// -------------
//! @{
//! \brief Set the values
//! \warning Do no set stoichiometric coefficients
void
set_values
(
index_t
k
,
const
SorbedValues
&
values
)
{
set_label
(
k
,
values
.
label
);
set_logk
(
k
,
values
.
logk
);
m_sorption_site
.
set_value
(
k
,
values
.
sorption_site_occupied
);
}
//! \brief Set the values
//! \warning Do no set stoichiometric coefficients
void
set_values
(
index_t
k
,
SorbedValues
&&
values
)
{
set_label
(
k
,
std
::
move
(
values
.
label
));
set_logk
(
k
,
values
.
logk
);
m_sorption_site
.
set_value
(
k
,
values
.
sorption_site_occupied
);
}
//! @}
//! \name Move
//! \brief Move species inside the list or to other lists
// ------------
//! @{
//! \brief Move component 'old_ind' to 'new_ind'
void
move_erase
(
index_t
old_ind
,
index_t
new_ind
)
override
{
m_sorption_site
.
move_erase
(
old_ind
,
new_ind
);
ReactiveSpeciesList
::
move_erase
(
old_ind
,
new_ind
);
}
//! \brief Move component 'old_ind' to 'new_ind'
void
move_erase
(
index_t
old_ind
,
index_t
new_ind
,
const
std
::
vector
<
index_t
>&
is_reactants_to_remove
)
override
{
m_sorption_site
.
move_erase
(
old_ind
,
new_ind
);
ReactiveSpeciesList
::
move_erase
(
old_ind
,
new_ind
,
is_reactants_to_remove
);
}
//! \brief move the species at index 'old' to 'other_ind' in 'other'
void
move_erase_to
(
index_t
old
,
SorbedList
&
other
,
index_t
other_ind
);
//! @}
//! \brief Add the aqueous species 'other_species' to 'k', to obtain a canonical system
void
canonicalize
(
index_t
ind
,
const
AqueousList
&
aqueous
,
index_t
aqueous_ind
,
scalar_t
coeff
)
{
add_alien_species_to
(
ind
,
aqueous
,
aqueous_ind
,
coeff
);
}
//! \brief Append the species in this list to the other list
void
append_to
(
SorbedList
&
other
);
private
:
VectorSpeciesWrapper
m_sorption_site
;
};
}
// end namespace database
}
// end namespace specmicp
#endif
//SPECMICP_DATABASE_SORBEDLIST_HPP
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