catheter1dsim/MainSolver.hpp at develop · cesare-corrado/catheter1dsim · GitHub

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#ifndef _MAINSOLVER_HPP
#define _MAINSOLVER_HPP

#include <fstream>
#include <string>

#include "GetPot.hpp"
#include "MitchellSchaefferSolver.hpp"
#include "MonoDomainSolver.hpp"
#include "ProbesObserver.hpp"
#include "vectormatrixdef.hpp"
#include "EvalRestitution.hpp"


class MainSolver
{
  public:
    MainSolver(const GetPot & dfile);
    ~MainSolver();
    void initialize(const GetPot & dfile);
    void reset();
    void setSeqObsDir(size_t indSeq);
    void setBCL(double &newBCL);
    void setPacingTimes(Vector & thePacingTimes);
    void setOutoutController(vectorBool & theOutput_ctrl);
    void setIonicParam(const double & vcrit, const double & acrit, const double & tau_in, const double & tau_out, const double & tau_open, const double & tau_close);
    void set_vcrit(const double & vcrit);
    void set_acrit(const double & acrit);
    void set_tau_in(const double & tau_in);
    void set_tau_out(const double & tau_out);
    void set_tau_open(const double & tau_open);
    void set_tau_close(const double & tau_close);
    void setConductivity(double TheNewConductivity);
    void outInfo();
    void solve();
    int SelftestCode();
    inline void setAPDMAX(double & theAPDMAX){APDmax=theAPDMAX;};
  private:
    void setAndCreateAllOutputDir(std::string theOut_dir);
    void setSourcesAndEctoBeats();
    void setSourcesForProtocols();
    void writeParametersValues();
    void writeEctopicBeats();
    void prepareForPostProcess();
    void finalizePostProcess();
    void writeGeoFile();
    void writeVarsAtTime(double theTime);
    double evalTactiv(double & ctime);
    void setBiphasicIappStimulus(double ctime, double tact);
    void solveIonicStandard_step1(double tactiv, double time, bool stimulusIsApplied);
    void solveIonicStandard_step3(double tactiv, double time, bool stimulusIsApplied);
    void prepacing();
    void reinitForMultiple();
    int check0D(double  p_rate=300.0,int nb_of_pacing=2);

    MonoDomainSolver conductionSolver;
    std::vector<MitchellSchaefferSolver> IonicSolver;
    ProbesObserver probes;
    EvalRestitution * EvalRes;

    double conductivity;
    double lambda;
    double domain_length;
    double init_time;
    double end_time;

    double APDmax;
    double Time_period;
    double IappMod;
    double t_stim;
    bool standardStim;
    bool multiple_beats;
    unsigned nb_of_beats;
    unsigned nb_of_beats_old;
    double beats_step;
    double minimum_beats_step;
    bool basis_stimulus;
    Vector ectopic_beats_time;
    //for pre-pacing
    bool _s1fail;
    bool _prepacing;
    unsigned _nb_of_prepacing;
    double _s1_prepacing;
    bool _s12_prepacing;
    double _s2_prepacing;
    bool _pacingFromFile;
    bool _is_output_control;
    bool _dump_controller;
    bool _evalSelfActiv;
    vectorBool output_controller_flags;
    short int protocolTest;
    bool _biphasic;
    double _d1;
    double _m2m1;
    bool _splittingSolver;
    // discretiation
    double dt;
    //  double ionic_dt;
    int nsubit_ionic;
    size_t npt;
    short int verbose;

    //postprocessing
    bool  output;
    bool _outputBinary;
    bool  out_ionic;
    bool  out_extracell;
    bool _out_restitutions;
    bool _use_pre_chek_0D;
    bool _use_pre_chek_1D;
    unsigned out_freq;
    std::string output_dir;

    // observations
    unsigned obs_freq;
    std::string obs_dir;
    std::string param_dir;
    std::string BCL_dir;

    Vector ue;
    VectorRef Vm;
    VectorRef wREF;
    double mean;
    vectorBool activatedPt;

    std::ofstream datVmfile;
    std::ofstream datWfile;
    std::ofstream datUefile;
    std::ofstream datTimeFile;

};


#endif