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selector.cpp
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Fri, May 31, 05:38
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rSPECMICP SpecMiCP / ReactMiCP
selector.cpp
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/*-------------------------------------------------------------------------------
Copyright (c) 2014,2015 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 "selector.hpp"
#include "aqueous_selector.hpp"
namespace
specmicp
{
namespace
database
{
void
DatabaseSelector
::
remove_component
(
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
// Find which components are to be removed
analyse_component
(
id_component_to_remove
);
// Select the ...
// Aqueous secondary species
select_aqueous
(
id_component_to_remove
);
// Minerals
select_minerals
(
id_component_to_remove
);
select_minerals_kinetic
(
id_component_to_remove
);
// Gas
if
(
data
->
nb_gas
()
>
0
)
select_gas
(
id_component_to_remove
);
// Sorbed species
if
(
data
->
nb_sorbed
()
>
0
)
select_sorbed
(
id_component_to_remove
);
// Compounds !
if
(
data
->
nb_compounds
()
>
0
)
select_compounds
(
id_component_to_remove
);
// Elements
data
->
elements
.
remove_components
(
m_is_component_to_remove
);
// and finally the components
select_components
();
}
void
DatabaseSelector
::
analyse_component
(
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
for
(
auto
it:
id_component_to_remove
)
{
if
(
it
==
DataContainer
::
water_index
())
{
throw
std
::
invalid_argument
(
"Water cannot be removed from the database"
);
}
else
if
(
it
==
DataContainer
::
electron_index
())
{
throw
std
::
invalid_argument
(
"The electron cannot be removed from the database"
);
}
m_is_component_to_remove
[
it
]
=
no_species
;
}
auto
new_ind
=
0
;
for
(
auto
component:
data
->
range_component
())
{
if
(
m_is_component_to_remove
[
component
]
!=
no_species
)
{
m_is_component_to_remove
[
component
]
=
new_ind
;
++
new_ind
;
}
}
m_nb_component_to_keep
=
new_ind
;
specmicp_assert
(
static_cast
<
std
::
size_t
>
(
data
->
nb_component
())
-
id_component_to_remove
.
size
()
==
new_ind
);
}
// This is the main algorithm to remove secondary species
void
DatabaseSelector
::
select_secondary
(
ReactiveSpeciesList
*
toselect
,
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
// first we select which aqueous species we should remove
std
::
vector
<
bool
>
to_remove
(
toselect
->
size
(),
false
);
for
(
index_t
j:
toselect
->
range
())
{
for
(
const
auto
&
it:
id_component_to_remove
)
{
if
(
toselect
->
nu_ji
(
j
,
it
)
!=
0.0
)
{
to_remove
[
j
]
=
true
;
break
;
}
}
}
// then we remove them, in two steps
const
auto
nb_to_keep
=
std
::
count
(
to_remove
.
cbegin
(),
to_remove
.
cend
(),
false
);
auto
new_j
=
0
;
// 1) first we copy data in the beginning of the arrays
for
(
index_t
j:
toselect
->
range
())
{
if
(
to_remove
[
j
])
continue
;
toselect
->
move_erase
(
j
,
new_j
,
m_is_component_to_remove
);
++
new_j
;
}
specmicp_assert
(
new_j
==
nb_to_keep
);
// 2) then we resize the arrays
toselect
->
resize
(
nb_to_keep
,
nb_component_to_keep
());
toselect
->
set_valid
();
// By doing in this order, we avoid bulk copy of arrays
}
void
DatabaseSelector
::
select_aqueous
(
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
select_secondary
(
&
(
data
->
aqueous
),
id_component_to_remove
);
}
void
DatabaseSelector
::
select_minerals
(
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
select_secondary
(
&
(
data
->
minerals
),
id_component_to_remove
);
}
void
DatabaseSelector
::
select_minerals_kinetic
(
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
select_secondary
(
&
(
data
->
minerals_kinetic
),
id_component_to_remove
);
}
void
DatabaseSelector
::
select_gas
(
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
select_secondary
(
&
(
data
->
gas
),
id_component_to_remove
);
}
void
DatabaseSelector
::
select_sorbed
(
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
select_secondary
(
&
(
data
->
sorbed
),
id_component_to_remove
);
}
void
DatabaseSelector
::
select_compounds
(
const
std
::
vector
<
index_t
>&
id_component_to_remove
)
{
select_secondary
(
&
(
data
->
compounds
),
id_component_to_remove
);
}
void
DatabaseSelector
::
select_components
()
{
for
(
index_t
i:
data
->
range_component
())
{
index_t
new_index
=
m_is_component_to_remove
[
i
];
if
(
new_index
==
no_species
)
continue
;
data
->
components
.
move_erase
(
i
,
new_index
);
}
data
->
components
.
resize
(
nb_component_to_keep
());
data
->
components
.
set_valid
();
}
void
DatabaseSelector
::
keep_only_component
(
const
std
::
vector
<
index_t
>&
id_to_keep
)
{
// First build the list of components to remove
std
::
vector
<
index_t
>
id_to_remove
;
id_to_remove
.
reserve
(
data
->
nb_component
()
-
id_to_keep
.
size
());
for
(
index_t
id:
data
->
range_aqueous_component
())
// avoid removing H2O and E[-]
{
auto
search
=
std
::
find
(
id_to_keep
.
cbegin
(),
id_to_keep
.
cend
(),
id
);
if
(
search
==
id_to_keep
.
end
())
id_to_remove
.
push_back
(
id
);
}
// Then remove them
remove_component
(
id_to_remove
);
}
void
DatabaseSelector
::
remove_all_gas
()
{
data
->
gas
=
GasList
(
0
,
data
->
nb_component
());
data
->
gas
.
set_valid
();
}
void
DatabaseSelector
::
remove_all_sorbed
()
{
data
->
sorbed
=
SorbedList
(
0
,
data
->
nb_component
());
data
->
sorbed
.
set_valid
();
}
void
DatabaseSelector
::
remove_all_compounds
()
{
data
->
compounds
=
CompoundList
(
0
,
data
->
nb_component
());
data
->
compounds
.
set_valid
();
}
//! \brief Remove some specific aqueous species
void
DatabaseSelector
::
remove_aqueous
(
const
std
::
vector
<
index_t
>&
id_aqueous
)
{
AqueousSelector
(
data
).
remove_aqueous
(
id_aqueous
);
}
}
// end namespace database
}
// end namespace specmicp
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