pade_approximant.hh

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/*
 * pade_approximant.h
 *
 *  Created on: Apr 2, 2012
 *      Author: lukas
 */

#ifndef PADE_APPROXIMANT_H_
#define PADE_APPROXIMANT_H_

#include <vector>
#include <input/input_type.hh>
#include <input/accessors.hh>

#include "petscvec.h"
#include "petscmat.h"
#include "petscksp.h"


class Mesh;
class Distribution;
class Linear_reaction;

class Pade_approximant: public Linear_reaction
{
    public:
        /*
        * Static variable for new input data types input
        */
        static Input::Type::Record input_type;
        /*
        * Static variable gets information about particular decay step
        */
        static Input::Type::Record input_type_one_decay_substep;
        /**
         *  Constructor with parameter for initialization of a new declared class member
         *  TODO: parameter description
         */
        Pade_approximant(Mesh &mesh, Input::Record in_rec);

        /**
        *   Destructor.
        */
        ~Pade_approximant(void);

        void zero_time_step() override;

        /**
        *   For simulation of chemical reaction in just one element either inside of MOBILE or IMMOBILE pores.
        */
        double **compute_reaction(double **concentrations, int loc_el) override;

        /**
        *   Evaluates Pade approximant from Reaction_matrix.
        */
        double **modify_reaction_matrix(void) override;
        /**
        * It enables to evaluate matrix nominator and denominator present in Pade approximant.
        */
        void evaluate_matrix_polynomial(Mat *Polynomial, Mat *Reaction_matrix, PetscScalar *coef);
        
    protected:
        /**
        *       Enables to compute factorial k!.
        */
        int factorial(int k);
                
                
        /**
        *   This method reads a sequence of numbers defining an order of substances in decay chain. The string section defines where too look for indices inside of ini-file, whereas n_subst is a number of isotopes in described decay chain.
        */
        //int *set_indeces(char *section, int n_subst);
        /**
        *   This method reads an information about a number of isotopes in a decay chain described inside of ini-file in section given as an argument. This method is used for radioactive decay simulation.
        */
        //void set_nr_of_isotopes(char* section);
        /**
        *   This method sets number of isotopes for the case of first order reaction. The value should be always 2.
        */
        //void set_nr_of_isotopes(int Nr_of_isotopes);
        /**
        *   This method reads a sequence of (nr_of_isotopes - 1) halflives belonging to separate decay chain step. This information is placed in ini-file in a block starting with a string section.
        */
        //double *set_half_lives(char *section);
        /**
        *   This method reads form ini-file an information for construction of a matrix describing bifurcation of every single decay chain on one row of the reaction matrix. Informations about bifurcation are placed in a block starting with a string section. dec_nr identifies which one decay chain is handled and which row of twodimensional bifurcation matrix (double **array)should be affected.
        */
        //void set_bifurcation(char *section, int dec_nr);
        /**
        *   This method reads from ini-file an information if the bifurcation for a current decay chain is switched on in a block starting with a string section. Initialy bifurcation is switched of.
        */
        //void set_bifurcation_on(char *section);
        /**
        *   This method reads from ini-file an information if first order reactions simulation is switched on.
        */
        //void set_For_on(void);
        /**
        *   This method reads from ini-file an information if a radioactive decay simulation is switched on.
        */
        //void set_decay_on(void);
        /**
        *   This method reads from ini-file an information and prepares a vector (onedimensional double *array) containing kinetic constants of every single first order reactions. Those informations are placed in a block with a string section at the beginning. From those constants half-lives belonging to first order reactions are computed.
        */
        //void set_kinetic_constants(char *section, int reaction_nr);
        /**
        *
        */
        double **allocate_reaction_matrix(void);
        /**
        *   This method modificates reaction matrix as described in ini-file a single section [Decay_i] or [FoReact_i]. It is used when bifurcation is switched off.
        */
        //double **modify_reaction_matrix(void);
        /**
        *   For control printing of a matrix describing simple chemical reactions.
        */
        //void print_reaction_matrix(void);
        /**
        *   For printing nr_of_isotopes identifies of isotopes in a current decay chain.
        */
        //void print_indeces(int n_subst);
        /**
        * Following method releases reaction matrix to make it possible to set a new time step for chemistry.
        */
        //void release_reaction_matrix();
        /**
        *   For printing (nr_of_isotopes - 1) doubles containing half-lives belonging to particular isotopes on screen.
        */
        //void print_half_lives(int n_subst);
        /**
        *   Small (nr_of_species x nr_of_species) square matrix for realization of radioactive decay and first order reactions simulation.
        */
        //double **reaction_matrix;
        //std::vector<double> half_lives; ///< alternative to following row
        /**
        *   Sequence of (nr_of_isotopes - 1) doubles containing half-lives belonging to particular isotopes.
        */
        //double *half_lives;
        /**
        *   Sequence of integers describing an order of isotopes in decay chain or first order reaction.
        */
        //int *substance_ids;
        /**
        *   Informs about the number of isotopes in a current decay chain.
        */
        //int nr_of_isotopes;
        /**
        *   Two dimensional array contains mass percentage of every single decay bifurcation on every single row.
        */
        //std::vector<std::vector<double> > bifurcation;
        /**
        *   One dimensional array of kinetic constants belonging to considered reactions.
        */
        //std::vector<double> kinetic_constant;
        /**
        *   Boolean which enables to turn on branching of considered decay chain.
        */
        //bool bifurcation_on;
        /**
        *   Integer which informs about the order of a polynomial term in nominator of Pade approximant rational term.
        */
        int nom_pol_deg;
        /**
        *   Integer which informs about the order of a polynomial term in denominator of Pade approximant rational term.
        */
        int den_pol_deg;
        /**
        *
        */
        //void modify_reaction_matrix(void);
        /**
        *
        */
        //double **allocate_reaction_matrix(void);
        /**
        *
        */
        //double **modify_reaction_matrix(int dec_nr);
        /**
        * PETSC format of a matrix describing linear chemical reaction.
        */
        Mat Reaction_matrix;
};

#endif /* PADE_APPROXIMANT_H_ */