kinetic_model.hpp
bc9b1984b554master

kinetic_model.hpp
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			#ifndef SPECMICP_SPECMICP_KINETICS_KINETICMODEL_HPP
			#define SPECMICP_SPECMICP_KINETICS_KINETICMODEL_HPP

			#include "common.hpp"
			#include "kinetic_variables.hpp"

			namespace specmicp {
			namespace kinetics {

			// \brief Base class for a kinetic model
			class KineticModel
			{
			public:

			KineticModel()
			{}

			KineticModel(const std::vector<index_t>& list_species):
			m_list_species(list_species)
			{}

			virtual ~KineticModel() {}

			//! \brief Return the number of kinetic minerals included in the problem
			index_t get_neq() {return m_list_species.size();}

			//! \brief Compute the kinetic rates and store them in dydt
			virtual void compute_rate(
			scalar_t t,
			const Vector& y,
			KineticVariables& variables,
			Vector& dydt
			) = 0;


			void add_equation(index_t species) {m_list_species.push_back(species);}

			//! \brief Index of species corresponding to equation 'id_equation'
			index_t index_species(index_t id_equation) {return m_list_species[id_equation];}

			//! \brief Iterator over the species vector
			std::vector<index_t>::iterator species_begin() {return m_list_species.begin();}
			std::vector<index_t>::iterator species_end() {return m_list_species.end();}

			private:
			std::vector<index_t> m_list_species;
			};

			} // end namespace kinetics
			} // end namespace specmicp


			#endif //SPECMICP_SPECMICP_KINETICS_KINETICMODEL_HPP