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specmicp/src/database/database.hpp
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database.hpp
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/*-------------------------------------------------------
- Module : database
- File : database.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_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):
DatabaseModule(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<index_t>& new_basis);
//! \brief Swap some component in the basis
void swap_components(std::map<std::string, std::string>& swap_to_make);
//! \brief Remove components not present in the system
void remove_components(const std::vector<index_t>& id_components_to_remove);
//! \brief Keep only components in the id_components to keep
void keep_only_components(const std::vector<index_t>& id_components_to_keep);
//! \brief Keep only components in the id_components to keep
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);
};
} // end namespace database
} // end namespace specmicp
#endif // SPECMICP_DATABASE_DATABASE_HPP
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