#ifndef SIMULATION_H
#define SIMULATION_H
#include <iostream>
#include <iomanip>
#include <fstream>
#include <sstream>
#include <vector>
#include <algorithm>
#include <string>

#include <unistd.h>
#include <signal.h>
#include <assert.h>

#if defined(FLUKA)
#include "FlukaIO.h"
#endif

#include "lattice.h"
using namespace std;
/*
##########################################################################################################

This class contains all the tools that are necessary to run a simulation. It is called in the main.
It is also where the link is made with Fluka when the lattice contains a Fluka Collimator.

##########################################################################################################
 */


class Simulation
{


public:

    //========================Constructors, destructor=====================

    Simulation() {};

    Simulation(int size_bunch, int nbre_elts, string genere = "standard");

    virtual ~Simulation();

    //=============================== Other methods ===============================


    //base method simulating a run, it is called in the main and it calls the other functions

    void run(string inputfile, string outputpath);


    //method used to read the parameters in the collimator file

    void readInputFile(string inputfile, double& Apr, double& Zpr, double& mass, double& energyPerIon, double& emix, double& emiy, long int& npart, int& kbunch, double& sigdpp, int& taubeam, long int& nparti, string& partdistr, double& r1r2skin, long int& nrev1, int& nrev2, double& blowup2, int& blowupperiod, string& stoplineartracking, int& scaleorbit, double& wecolli, double& nsigi, string& opticsFile, double& thicknessmagneticfield, double& Bmax, double& deltaGap, int& beamflag, int& RunWithFluka, int& RunWithCrystal, double& freqrf, double& rfvoltage, double& rfharmonic, int& RunningFlag, int& idpart, int& idelt, int& outcoord, double& momentum, string& plotflag, string& inputpath, int& RFflag);


    //method used to extract the parameters of the lattice in the optics file

    void extractOpticsParameters(string opticsFile, const int& beamflag);


    //method used to end a connection with an external server (e.g. Fluka)

    void die(const char* msg);


    //method used to initialize most of the parameters read in the input files

    void defineParameters(string opticsFile, const int& beamflag,  int& JohnJaperFlag);


    //method to read the parameters of a particles from a file

    void readParticle(const double& Apr, const double& Zpr, string inputfile);


    //linear interpolation method

    double interp1(double x1, double y1, double x2, double y2, double x);


    //method generating an initial bunch of particles

    void genbunch(const int& i0, const int& npart, const string& partdistr, const double& r1r2skin, const double& emx, const double& emy, const double& sigdpp, const double& bx, const double& ax, const double& dx, const double& dpx, const double& by, const double& ay, const double& dy, const double& dpy, const double& nsigi);


    //method used to display the coordinates of all particles in a bunch at a precise time (mostly used for tests)

    void affichebunch();


    //method used to write the file output_<inputfile>.txt

    void writeoutput(string outputfile, const double& emix, const double& emiy, const double& Apr, const double& Zpr, const double& nparti, const double& beamflag, const double& PlossPb, const int& i0, const int& im, const int& npart, const int& kbunch, const vector <int>& asumrem, const vector <int>& asumhitcolli, const vector <int>& asumhits, const int& taubeam, vector <double>& hitso, const vector <int>& nhitcollio, vector <double>& Aphito, vector <double>& Zphito, const int& ibeg, const int& iend, vector <vector <double> >& xco, vector <vector <double> >& yco, const string& plotflag, string outputpath, string inputpath);


    //method making three plots illustrating the result of an ICOSIM run:
    // 1) the power load on each collimator (averagely during the beam lifetime)
    // 2) the power loss in the ring as a function of s
    // 3) how many particles there are left in the beam, how many particles that
    // have been lost on a collimator, and how many particles that have been
    // lost on the aperture, as a function of the number of revolutions.

    void PlotRunSummary(const vector <int>& asumrem, const vector <int>& asumhitcolli, const vector <int>& asumhits, const vector <int>& nhitcollio, vector <double>& hitso, const double& PlossPb, string outputpath);


    //makes plots that shows particle trajectories, trajectory of the reference particle, the beam envelope, the aperture and the collimators.

    void PlotTrajectory(const double& emix, const double& emiy, const int& ibeg, const int& iend, vector <vector <double> >& xco, vector <vector <double> >& yco, string outputpath);


    //makes a histogram that shows the losses on the aperture along the ring

    void PlotLossSpectra(const double& beamflag, const double& nparti, const vector <int>& asumrem, const double& Apr, const double& Zpr, vector <double>& hitso, vector <double>& Aphito, vector <double>& Zphito, const double& PlossPb, const int& npart, const int& kbunch, const int& taubeam, const vector <int>& nhitcollio, string outputpath, string inputpath);


    //====================================== Attributs  ======================================================

private:

    int sizeBunch; // size of the bunch
    vector <Particle> bunch; //bunch of particles
    vector <Particle> bunchhit; //contains the particles that hit a primary collimator during the linear tracking; input bunch for the non-linear tracking
    int nbre_elts; //number of elements in the lattice
    Lattice lat; //lattice (see class lattice)


};

#endif