common_def.hpp
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	/*-------------------------------------------------------

	- Module : database
	- File : common_def.hpp
	- Author : Fabien Georget

	Copyright (c) 2014, Fabien Georget, Princeton University

	---------------------------------------------------------*/

	#ifndef SPECMICP_DATABASE_COMMONDEF_HPP
	#define SPECMICP_DATABASE_COMMONDEF_HPP

	#include <vector>
	#include <Eigen/Core>
	#include <exception>

	//! \file common_def.hpp common type definitions

	namespace specmicp {
	namespace database {


	//! ID of a species
	using id_species_t = unsigned int;
	//! Vector containing a list of species (by ID)
	using list_species_t = std::vector<id_species_t>;
	//! Vector containing each strings
	using vector_labels_t = std::vector<std::string>;
	//! Stoechiometric coefficients for the reactions
	using reaction_mat_t = Eigen::Matrix<double, Eigen::Dynamic, Eigen::Dynamic>;
	//! Vector containing logK values
	using logK_vector_t = Eigen::Matrix<double, Eigen::Dynamic, 1>;



	//! \brief This error is thrown when a bad syntax is detected in the database
	class db_invalid_syntax : public std::invalid_argument
	{
	public:
	db_invalid_syntax (const std::string &msg):
	std::invalid_argument("Invalid syntax : " + msg)
	{}
	};


	//! \brief This error is thrown when the database is not as expected
	class invalid_database : public std::invalid_argument
	{

	public:
	invalid_database (const std::string &msg):
	std::invalid_argument("Invalid Database : " + msg)
	{}
	};
	} // end namespace database
	} // end namespace specmicp

	#endif // SPECMICP_DATABASE_COMMONDEF_HPP