semchem_interface.hh

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#ifndef interfaceH
    #define interfaceH

#include "mesh/elements.h"
#include "la/distribution.hh"
#include <string.h>
#include <./input/input_type.hh>
#include "fields/field.hh"
//#include "fields/field_values.hh"

class Distribution;


enum type_of_reaction{kinetics = 1, slow_kinetics, equilibrium};

class Specie
{
    public:
    /*
    * Static variable for new input data types input
    */
    static Input::Type::Record input_type;
    /*
    * Constructor.
    */
    Specie();
    private:
    /*
    * Identifier.
    */
    int id;
    /*
    * Electrical charge.
    */
    double el_charge;
    /*
    * Partial Gib's energy.
    */
    double dGf;
    /*
    * Partial free enthalpy.
    */
    double dHf;
    /*
    * Molar mass.
    */
    double molar_mass;
    /*
    * Activity.
    */
    double activity;
};

class General_reaction
{
    public:
    /*
    * Static variable for new input data types input
    */
    static Input::Type::Record input_type;
    /*
     * Constructor.
     */
    General_reaction();
    private:
    /*
    * Specification of type of reaction.
    */
    type_of_reaction type;
    /*
    * Defines species participating reaction.
    */
    Specie *species;
    /*
    * Stechiometric coeficients describing reaction under consideration.
    */
    int *stoichiometry;
    /*
    * Reaction orders of all the reactants.
    */
    double *order_of_reaction;
    /*
    * Kinetic constant describing reaction rate.
    */
    double kinetic_constant;
    /*
    * Appropriate constant describing chemical equilibrium.
    */
    double equilibrim_constant;

};

class Semchem_interface
{
    public:
        /*
        * Static variable for new input data types input
        */
        static Input::Type::AbstractRecord input_type;
        /**
        *   Semchem interface is the tool to call a simulation of chemical reactions as a part of transport model. timeStep defines the length of time step for simulation of chemical reactions. nrOfSpecies is the number of transported species. dualPorosity defines type of porosity in examinated soil.
        */
        Semchem_interface(double timeStep, Mesh * mesh, int nrOfSpecies, bool dualPorosity); //(int nrOfElements, double ***ConcentrationMatrix, Mesh *mesh);
        /** 
     * @brief Sets pointer to data of other equations. 
     * @param cross_section is pointer to cross_section data of Darcy flow equation
     */
    void set_cross_section(Field<3, FieldValue<3>::Scalar> *cross_section);

    void set_sorption_fields(Field<3, FieldValue<3>::Scalar> *por_m_,
            Field<3, FieldValue<3>::Scalar> *por_imm_,
            Field<3, FieldValue<3>::Scalar> *phi_);
        /**
        *   This method has been prepared to enable simulation of chemical reactions via Semchem. porTyp defines type of porosity. ppelm is a pointer to element we want to simulate chemistry in. poradi is ID of such element. conc is a pointer to threedimensional array full of doubles.
        */
        void compute_reaction(bool porTyp, ElementIter ppelm, int poradi, double ***conc);
        /**
        *   The function update_solution(..) calls compute_reaction(..) for every single element in the mesh.
        */
        void update_solution(void);
        /**
        *   This method reads from ini-file the information if a simulation of chemical raections is switched on.
        */
        void set_chemistry_computation(void);
        /**
        *   This method enables to change the length of time step for simulation of chemical reactions.
        */
        void set_timestep(double new_timestep);
        /**
        *   This method reads from ini-file an information if dual porosity is considered in examinated soil.
        */
        void set_dual_porosity(void);
        /**
        *   This method sets the number of elements contained in mesh.
        */
        void set_nr_of_elements(int nrOfElements);
        /**
        *   This method sets the pointer to a three dimensional array of doubles.
        */
        void set_concentration_matrix(double ***ConcentrationsMatrix, Distribution *conc_distr, int *el_4_loc);
        /**
        *   This method sets the pointer to a one dimensional array for converting IDs from local to global.
        */
        void set_el_4_loc(int *el_for_loc);
        /**
        *   This method sets a pointer to mesh describing examinated area.
        */
        void set_mesh_(Mesh *mesh);
        /**
        *   function to set  path to an outputfile for semchem-module.
        */
        void set_fw_chem(std::string semchem_output_file); //(const char* semchem_output_file);
        /**
        *   It containes an information if the simulation of chemical reactions is switched on.
        */
        bool semchem_on;
        /**
        *   It containes an information if the dual porosity is switched on.
        */
        bool dual_porosity_on;
        /**
        *   It containes an information about how many elements are contained in mesh.
        */
        int nr_of_elements;
        /**
        *   It is a pointer on three dimensional matrix full of doubles.
        */
        double ***concentration_matrix;
        /**
        *   It is name of an output file for semchem.
        */
        char *fw_chem;
    private:
        /**
        *   It holds an information about the length of time step for chemical reaction simulation.
        */
        double time_step;
        /**
        *   It is a pointer on mesh.
        */
        Mesh *mesh_;
        /**
        *   It describes partitioning of elements between processors.
        */
        Distribution *distribution;
        /**
        *   It enables to change local IDs of elements in mesh into global IDs.
        */
        int *el_4_loc;
    /**
     * pointer to cross_section data (gets from flow->transport->semchem), for computing element volume
     */
    Field<3, FieldValue<3>::Scalar > *cross_section;

    /// pointers to sorption fields from transport
    Field<3, FieldValue<3>::Scalar > *por_m, *por_imm, *phi;
};
#endif