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database.hpp
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Sat, Jul 20, 03:15
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rSPECMICP SpecMiCP / ReactMiCP
database.hpp
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/*-------------------------------------------------------
- Module : database
- File : database.hpp
- Author : Fabien Georget
Copyright (c) 2014, Fabien Georget, Princeton University
---------------------------------------------------------*/
#ifndef SPECMICP_DATABASE_DATABASE_HPP
#define SPECMICP_DATABASE_DATABASE_HPP
//! \file database.hpp Database management
#include "module.hpp"
namespace
specmicp
{
//! \namespace database Database management
namespace
database
{
//! \brief Database management
//!
//! Prepare the database for the computation.
//! This class is a proxy for one-tasked modules.
class
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
)
{
parse_database
(
filepath
);
make_canonical
();
}
//! \brief initialise the database with the raw database
Database
(
std
::
shared_ptr
<
DataContainer
>
raw_data
)
:
data
(
raw_data
)
{}
//! \brief Parse the database 'filepath'
void
parse_database
(
std
::
string
filepath
);
//! \brief Transform the database into canonical form
//!
//! This process is necessary before any computation
void
make_canonical
();
//! \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
change_basis
(
std
::
vector
<
int
>&
new_basis
);
//! \brief Swap some component in the basis
void
swap_components
(
std
::
map
<
std
::
string
,
std
::
string
>&
swap_to_make
);
//! \brief Remove components non present in the system
void
remove_components
(
const
std
::
vector
<
int
>&
id_components_to_remove
);
//! \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
);
private
:
std
::
shared_ptr
<
DataContainer
>
data
;
//!< The data
};
}
// end namespace database
}
// end namespace specmicp
#endif
// SPECMICP_DATABASE_DATABASE_HPP
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