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database.hpp
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rSPECMICP SpecMiCP / ReactMiCP
database.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_DATABASE_HPP
#define SPECMICP_DATABASE_DATABASE_HPP
//! \file specmicp_database/database.hpp
//! \brief Database management
#include "module.hpp"
#include <map>
namespace
specmicp
{
//! \namespace specmicp::database
//! \brief Database management
namespace
database
{
//! \brief Prepare the database for the simulation.
//!
//! This is the class that should be used to handle the database.
//! It does not contain the data, only the algorithms.
//!
//! \ingroup specmicp_api
class
SPECMICP_DLL_PUBLIC
Database:
public
DatabaseModule
{
public
:
//! \brief Default constructor
//!
//! the method parse_database must be called to parse the json database
Database
()
{}
//! \brief Initialise the database py parsing 'filepath'
Database
(
std
::
string
filepath
,
bool
check_compo
=
true
)
{
parse_database
(
filepath
,
check_compo
);
}
//! \brief initialise the database with the raw database
Database
(
std
::
shared_ptr
<
DataContainer
>
raw_data
)
:
DatabaseModule
(
raw_data
)
{}
//! \brief Parse the database 'filepath'
void
parse_database
(
std
::
string
filepath
,
bool
check_compo
=
true
);
//! \brief Parse the database from a stream
void
parse_database
(
std
::
istream
&
input
,
bool
check_compo
=
true
);
//! \brief Return the database
//!
//! Return a smart pointer of a DataCotnainer instance
//! Note : this is a read write access, be careful
std
::
shared_ptr
<
DataContainer
>
get_database
()
{
return
data
;}
//! \brief Change the basis
//!
//! @param new_basis list of id of the new basis
//!
//! The new basis is a list of id, id = id_component for no swapping
//! or id = id_aqueous + nb_component for swapping a secondary species
void
switch_basis
(
std
::
vector
<
index_t
>&
new_basis
);
//! \brief Swap some component in the basis
//! \param swap_to_make a map where the keys are the current
//! component and the values are the new component
void
swap_components
(
const
std
::
map
<
std
::
string
,
std
::
string
>&
swap_to_make
);
//! \brief Remove components not present in the system
//!
//! "H2O" and "E[-]" cannot be removed from the database.
//!
//! \param labels_components_to_remove list of labels of the component to remove from the basis
void
remove_components
(
const
std
::
vector
<
std
::
string
>&
labels_components_to_remove
);
//! \brief Remove components not present in the system
//!
//! "H2O" and "E[-]" cannot be removed from the database.
//!
//! \param id_components_to_remove list of id of the component to remove from the basis
void
remove_components
(
const
std
::
vector
<
index_t
>&
id_components_to_remove
);
//! \brief Keep only components in the id_components_to_keep list
//!
//! "H2O" and "E[-]" will always be kept in the database.
//!
//! \param id_components_to_keep list of id of the component to keep in the basis
void
keep_only_components
(
const
std
::
vector
<
index_t
>&
id_components_to_keep
);
//! \brief Keep only components in the labels_components_to_keep list
//!
//! "H2O" and "E[-]" will always be kept in the database.
//!
//! \param labels_components_to_keep list of labels of the component to keep in the basis
void
keep_only_components
(
const
std
::
vector
<
std
::
string
>&
labels_components_to_keep
);
//! \brief Keep only some minerals at equilibrium
//!
//! The effect is to flag all the other minerals as "kinetic"
void
minerals_keep_only
(
const
std
::
vector
<
std
::
string
>&
minerals_to_keep
);
//! \brief Keep only some minerals at equilibrium
//!
//! The effect is to flag all the other minerals as "kinetic"
void
minerals_keep_only
(
const
std
::
vector
<
index_t
>&
minerals_to_keep
);
//! \brief Remove all gas species
void
remove_gas_phases
();
//! \brief Add gas phases into the database
//!
//! The input is a JSON list of gas (formated like the database)
void
add_gas_phases
(
const
std
::
string
&
gas_input
,
bool
check_compo
=
true
);
//! \brief Remove all solid phases
void
remove_solid_phases
();
//! \brief Add some solid phases into the database
//!
//! The input is a JSON list of minerals (formated like the database)
void
add_solid_phases
(
const
std
::
string
&
solid_phases_input
,
bool
check_compo
=
true
);
//! \brief Remove all sorbed species
void
remove_sorbed_species
();
//! \brief Add sorbed species into the database
//!
//! The input is a JSON list of sorbed species (formated like the database)
void
add_sorbed_species
(
const
std
::
string
&
sorbed_species_input
,
bool
check_compo
=
true
);
//! \brief Remove the compounds
void
remove_compounds
();
//! \brief Add some compounds into the database
//!
//! The input is a JSON list of compounds (formated like the database)
void
add_compounds
(
const
std
::
string
&
solid_phases_input
,
bool
check_compo
=
true
);
//! \brief Remove all the half-cells reactions
void
remove_half_cell_reactions
();
//! \brief Remove the half-cells reactions for components in 'list_components'
void
remove_half_cell_reactions
(
const
std
::
vector
<
std
::
string
>&
list_components
);
//! \brief Remove the half-cells reactions for components in 'list_id_components'
void
remove_half_cell_reactions
(
const
std
::
vector
<
index_t
>&
list_id_components
);
//! \brief Freeze the database
void
freeze
()
{
data
->
freeze_db
();}
//! \brief Save the database on disk
void
save
(
const
std
::
string
&
filename
);
};
}
// end namespace database
}
// end namespace specmicp
#endif
// SPECMICP_DATABASE_DATABASE_HPP
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