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/**
 * @file ClosedOrbitFinder.h
 * The algorithm is based on the paper of M. M. Gordon: "Computation of closed orbits and basic focusing properties for
 * sector-focused cyclotrons and the design of 'cyclops'" (1983)
 * As template arguments one chooses the type of the variables and the integrator for the ODEs. The supported steppers can
 * be found on
 * http://www.boost.org/ where it is part of the library Odeint.
 *
 * @author Matthias Frey
 * @version 1.0
 */

#ifndef CLOSEDORBITFINDER_H
#define CLOSEDORBITFINDER_H

#include <algorithm>
#include <array>
#include <cmath>
#include <functional>
#include <limits>
#include <numeric>
#include <string>
#include <utility>
#include <vector>

#include "Utilities/Options.h"
#include "Utilities/Options.h"
#include "Utilities/OpalException.h"

// #include "physics.h"

#include "MagneticField.h"

// include headers for integration
#include <boost/numeric/odeint/integrate/integrate_n_steps.hpp>

/// Finds a closed orbit of a cyclotron for a given energy
template<typename Value_type, typename Size_type, class Stepper>
class ClosedOrbitFinder
{
    public:
        /// Type of variables
        typedef Value_type value_type;
        /// Type for specifying sizes
        typedef Size_type size_type;
        /// Type of container for storing quantities (path length, orbit, etc.)
        typedef std::vector<value_type> container_type;
        /// Type for holding state of ODE values
        typedef std::vector<value_type> state_type;

        /// Sets the initial values for the integration and calls findOrbit().
        /*!
         * @param E is the energy [MeV] to which the closed orbit should be found
         * @param E0 is the potential energy (particle energy at rest) [MeV].
         * @param wo is the nominal orbital frequency (see paper of Dr. C. Baumgarten: "Transverse-Longitudinal
         * Coupling by Space Charge in Cyclotrons" (2012), formula (1))
         * @param N specifies the number of splits (2pi/N), i.e number of integration steps
         * @param accuracy specifies the accuracy of the closed orbit
         * @param maxit is the maximal number of iterations done. Program stops if closed orbit not found within this time.
         * @param Emin is the minimum energy [MeV] needed in cyclotron
         * @param Emax is the maximum energy [MeV] reached in cyclotron
         * @param nSector is the number of sectors (--> symmetry) of cyclotron
         * @param fmapfn is the location of the file that specifies the magnetic field
	 * @param guess value of radius for closed orbit finder
         * @param type specifies the field format (e.g. CARBONCYCL)
         * @param scaleFactor for the magnetic field (default: 1.0)
         * @param domain is a boolean (default: true). If "true" the closed orbit is computed over a single sector,
         * otherwise over 2*pi.
         */
        ClosedOrbitFinder(value_type E, value_type E0, value_type wo, size_type N,
                          value_type accuracy, size_type maxit, value_type Emin, value_type Emax,
                          size_type nSector, const std::string& fmapfn, value_type guess,
                          const std::string& type, value_type scaleFactor = 1.0,
                          bool domain = true);

        /// Returns the inverse bending radius (size of container N+1)
        container_type& getInverseBendingRadius();

        /// Returns the step lengths of the path (size of container N+1)
        container_type& getPathLength();

        /// Returns the field index (size of container N+1)
        container_type& getFieldIndex();

        /// Returns the radial and vertical tunes (in that order)
        std::pair<value_type,value_type> getTunes();

        /// Returns the closed orbit (size of container N+1) starting at specific angle (only makes sense when computing
        /// the closed orbit for a whole turn) (default value: 0°).
        /// Attention: It computes the starting index of the array. If it's not an integer it just cuts the floating point
        /// part, i.e. it takes the next starting index below. There's no interpolation of the radius.
        /*!
         * @param angle is the start angle for the output. Has to be within [0°,360°[ (default: 0°).
         */
        container_type getOrbit(value_type angle = 0);

        /// Returns the momentum of the orbit (size of container N+1)starting at specific angle (only makes sense when
        /// computing the closed orbit for a whole turn) (default value: 0°), \f$ \left[ p_{r} \right] = \si{m}\f$.
        /// Attention: It computes the starting index of the array. If it's not an integer it just cuts the floating point
        /// part, i.e. it takes the next starting index below. There's no interpolation of the momentum.
        /*!
         * @param angle is the start angle for the output. Has to be within [0°,360°[ (default: 0°).
         * @returns the momentum in \f$ \beta * \gamma \f$ units
         */
        container_type getMomentum(value_type angle = 0);

        /// Returns the relativistic factor gamma
        value_type getGamma();

        /// Returns the average orbit radius
        value_type getAverageRadius();

        /// Returns the frequency error
        value_type getFrequencyError();

        /// Returns true if a closed orbit could be found
        bool isConverged();

    private:
        /// Computes the closed orbit
        /*!
         * @param accuracy specifies the accuracy of the closed orbit
         * @param maxit is the maximal number of iterations done for finding the closed orbit
         */
        bool findOrbit(value_type, size_type);

        /// Fills in the values of h_m, ds_m, fidx_m. It gets called by in by constructor.
        void computeOrbitProperties();

        /// This function is called by the function getTunes().
        /*! Transfer matrix Y = [y11, y12; y21, y22] (see Gordon paper for more details).
         * @param y are the positions (elements y11 and y12 of Y)
         * @param py2 is the momentum of the second solution (element y22 of Y)
         * @param ncross is the number of sign changes (\#crossings of zero-line)
         */
        value_type computeTune(const std::array<value_type,2>&, value_type, size_type);

        /// This function computes nzcross_ which is used to compute the tune in z-direction and the frequency error
        void computeVerticalOscillations();

        /// Stores current position in horizontal direction for the solutions of the ODE with different initial values
        std::array<value_type,2> x_m; // x_m = [x1, x2]
        /// Stores current momenta in horizontal direction for the solutions of the ODE with different initial values
        std::array<value_type,2> px_m; // px_m = [px1, px2]
        /// Stores current position in vertical direction for the solutions of the ODE with different initial values
        std::array<value_type,2> z_m; // z_m = [z1, z2]
        /// Stores current momenta in vertical direction for the solutions of the ODE with different initial values
        std::array<value_type,2> pz_m; // pz_m = [pz1, pz2]

        /// Stores the inverse bending radius
        container_type h_m;
        /// Stores the step length
        container_type ds_m;
        /// Stores the radial orbit (size: N_m+1)
        container_type r_m;
        /// Stores the radial momentum
        container_type pr_m;
        /// Stores the field index
        container_type fidx_m;

        /// Counts the number of zero-line crossings in horizontal direction (used for computing horizontal tune)
        size_type nxcross_m;
        /// Counts the number of zero-line crossings in vertical direction (used for computing vertical tune)
        size_type nzcross_m; //#crossings of zero-line in x- and z-direction

        /// Is the energy for which the closed orbit should be found
        value_type E_m;
        
        /// Is the potential energy [MeV]
        value_type E0_m;
        
        /// Is the nominal orbital frequency
        value_type wo_m;
        /// Number of integration steps
        size_type N_m;
        /// Is the angle step size
        value_type dtheta_m;

        /// Is the relativistic factor
        value_type gamma_m;

        /// Is the average radius
        value_type ravg_m;

        /// Is the phase
        value_type phase_m;

        /**
         * Boolean which tells if a closed orbit for this configuration could be found (get set by the function findOrbit)
         */
        bool converged_m;

        /// Minimum energy needed in cyclotron
        value_type Emin_m;

        /// Maximum energy reached in cyclotron
        value_type Emax_m;

        /// Number of sectors (symmetry)
        size_type nSector_m;

        /**
         * Stores the last orbit value (since we have to return to the beginning to check the convergence in the
         * findOrbit() function. This last value is then deleted from the array but is stored in lastOrbitVal_m to
         * compute the vertical oscillations)
         */
        value_type lastOrbitVal_m;

        /**
         * Stores the last momentum value (since we have to return to the beginning to check the convergence in the
         * findOrbit() function. This last value is then deleted from the array but is stored in lastMomentumVal_m to
         * compute the vertical oscillations)
         */
        value_type lastMomentumVal_m;

        /**
         * Boolean which is true if computeVerticalOscillations() executed, otherwise false. This is used for checking in
         * getTunes() and getFrequencyError().
         */
        bool vertOscDone_m;

        /**
         * Boolean which is true by default. "true": orbit integration over one sector only, "false": integration
         * over 2*pi
         */
        bool domain_m;

        /// Defines the stepper for integration of the ODE's
        Stepper stepper_m;

	/// a guesss for the clo finder
	value_type rguess_m;
        
        /*!
         * This quantity is defined in the paper "Transverse-Longitudinal Coupling by Space Charge in Cyclotrons" 
         * of Dr. Christian Baumgarten (2012)
         * The lambda function takes the orbital frequency \f$ \omega_{o} \f$ (also defined in paper) as input argument.
         */
        std::function<double(double)> acon_m = [](double wo) { return Physics::c / wo; };
        
        /// Cyclotron unit \f$ \left[T\right] \f$ (Tesla)
        /*!
         * The lambda function takes the orbital frequency \f$ \omega_{o} \f$ as input argument.
         */
        std::function<double(double, double)> bcon_m = [](double e0, double wo) {
            return e0 * 1.0e7 / (/* physics::q0 */ 1.0 * Physics::c * Physics::c / wo);
        };
        
        MagneticField bField_m;
};

// -----------------------------------------------------------------------------------------------------------------------
// PUBLIC MEMBER FUNCTIONS
// -----------------------------------------------------------------------------------------------------------------------

template<typename Value_type, typename Size_type, class Stepper>
ClosedOrbitFinder<Value_type,
                  Size_type,
                  Stepper>::ClosedOrbitFinder(value_type E, value_type E0,
                                              value_type wo, size_type N,
                                              value_type accuracy, size_type maxit,
                                              value_type Emin, value_type Emax,
                                              size_type nSector, const std::string& fmapfn,
                                              value_type rguess, const std::string& type,
                                              value_type scaleFactor, bool domain)
: nxcross_m(0), nzcross_m(0), E_m(E), E0_m(E0), wo_m(wo), N_m(N), dtheta_m(Physics::two_pi/value_type(N)),
  gamma_m(E/E0+1.0), ravg_m(0), phase_m(0), converged_m(false), Emin_m(Emin), Emax_m(Emax), nSector_m(nSector),
  lastOrbitVal_m(0.0), lastMomentumVal_m(0.0),
  vertOscDone_m(false), domain_m(domain), stepper_m(), rguess_m(rguess), bField_m(fmapfn, nSector)
{
    
    if ( Emin_m > Emax_m )
        throw OpalException("ClosedOrbitFinder::ClosedOrbitFinder()",
                            "Incorrect cyclotron energy (MeV) bounds: Maximum cyclotron energy smaller than minimum cyclotron energy.");
    
//     // Even if the numbers are equal --> if statement is true.
//     if ( E_m < Emin_m )
//         throw OpalException("ClosedOrbitFinder::ClosedOrbitFinder()", "Kinetic energy smaller than minimum cyclotron energy");
     
    if ( E_m > Emax_m )
        throw OpalException("ClosedOrbitFinder::ClosedOrbitFinder()", "Kinetic energy exceeds cyclotron energy");

    // velocity: beta = v/c = sqrt(1-1/(gamma*gamma))
    if (gamma_m == 0)
        throw OpalException("ClosedOrbitFinder::ClosedOrbitFinder()", "Relativistic factor equal zero.");

    // if domain_m = true --> integrate over a single sector
    if (domain_m) {
        N_m /=  nSector_m;
    }

    // reserve storage for the orbit and momentum (--> size = 0, capacity = N_m+1)
    /*
     * we need N+1 storage, since dtheta = 2pi/N (and not 2pi/(N-1)) that's why we need N+1 integration steps
     * to return to the origin (but the return size is N_m)
     */
    r_m.reserve(N_m + 1);
    pr_m.reserve(N_m + 1);

    // reserve memory of N_m for the properties (--> size = 0, capacity = N_m)
    h_m.reserve(N_m);
    ds_m.reserve(N_m);
    fidx_m.reserve(N_m);
    
    // read in magnetic fieldmap
    bField_m.read(type, scaleFactor);
    
    // compute closed orbit
    converged_m = findOrbit(accuracy, maxit);

    // compute h, ds, fidx, rav (average radius)
    computeOrbitProperties();
}

template<typename Value_type, typename Size_type, class Stepper>
inline typename ClosedOrbitFinder<Value_type, Size_type, Stepper>::container_type&
    ClosedOrbitFinder<Value_type, Size_type, Stepper>::getInverseBendingRadius()
{
    return h_m;
}

template<typename Value_type, typename Size_type, class Stepper>
inline typename ClosedOrbitFinder<Value_type, Size_type, Stepper>::container_type&
    ClosedOrbitFinder<Value_type, Size_type, Stepper>::getPathLength()
{
    return ds_m;
}

template<typename Value_type, typename Size_type, class Stepper>
inline typename ClosedOrbitFinder<Value_type, Size_type, Stepper>::container_type&
    ClosedOrbitFinder<Value_type, Size_type, Stepper>::getFieldIndex()
{
    return fidx_m;
}

template<typename Value_type, typename Size_type, class Stepper>
std::pair<Value_type,Value_type> ClosedOrbitFinder<Value_type, Size_type, Stepper>::getTunes() {
    // compute radial tune
    value_type nur = computeTune(x_m,px_m[1],nxcross_m);

    // compute nzcross_m
    if (!vertOscDone_m)
        computeVerticalOscillations();

    // compute vertical tune
    value_type nuz = computeTune(z_m,pz_m[1],nzcross_m);

    return std::make_pair(nur,nuz);
}

template<typename Value_type, typename Size_type, class Stepper>
inline typename ClosedOrbitFinder<Value_type, Size_type, Stepper>::container_type
    ClosedOrbitFinder<Value_type, Size_type, Stepper>::getOrbit(value_type angle)
{
    container_type r = r_m;

    if (angle != 0.0) {
        // compute the number of steps per degree
        value_type deg_step = N_m / 360.0;

        // compute starting point
        size_type start = deg_step * angle;

        // copy end to start
        std::copy(r_m.begin() + start, r_m.end(), r.begin());

        // copy start to end
        std::copy_n(r_m.begin(), start, r.end() - start);
    }

    return r;
}

template<typename Value_type, typename Size_type, class Stepper>
inline typename ClosedOrbitFinder<Value_type, Size_type, Stepper>::container_type
    ClosedOrbitFinder<Value_type, Size_type, Stepper>::getMomentum(value_type angle)
{
    container_type pr = pr_m;

    if (angle != 0.0) {
        // compute the number of steps per degree
        value_type deg_step = N_m / 360.0;

        // compute starting point
        size_type start = deg_step * angle;
        // copy end to start
        std::copy(pr_m.begin() + start, pr_m.end(), pr.begin());

        // copy start to end
        std::copy_n(pr_m.begin(), start, pr.end() - start);
    }
    
    // change units from meters to \beta * \gamma
    /* in Gordon paper:
     * 
     * p = \gamma * \beta * a
     * 
     * where a = c / \omega_{0} with \omega_{0} = 2 * \pi * \nu_{0} = 2 * \pi * \nu_{rf} / h
     * 
     * c: speed of light
     * h: harmonic number
     * v_{rf}: nomial rf frequency
     * 
     * Units:
     * 
     * [a] = m --> [p] = m
     * 
     * The momentum in \beta * \gamma is obtained by dividing by "a"
     */
    value_type factor =  1.0 / acon_m(wo_m);
    
    
    std::for_each(pr.begin(), pr.end(), [factor](value_type p) { return p * factor; });
    
    return pr;
}

template<typename Value_type, typename Size_type, class Stepper>
inline typename ClosedOrbitFinder<Value_type, Size_type, Stepper>::value_type
    ClosedOrbitFinder<Value_type, Size_type, Stepper>::getGamma()
{
    return gamma_m;
}

template<typename Value_type, typename Size_type, class Stepper>
inline typename ClosedOrbitFinder<Value_type, Size_type, Stepper>::value_type
    ClosedOrbitFinder<Value_type, Size_type, Stepper>::getAverageRadius()
{
    return ravg_m;
}

template<typename Value_type, typename Size_type, class Stepper>
typename ClosedOrbitFinder<Value_type, Size_type, Stepper>::value_type
    ClosedOrbitFinder<Value_type, Size_type, Stepper>::getFrequencyError()
{
    // if the vertical oscillations aren't computed, we have to, since there we also compuote the frequency error.
    if(!vertOscDone_m)
        computeVerticalOscillations();

    return phase_m;
}

template<typename Value_type, typename Size_type, class Stepper>
inline bool ClosedOrbitFinder<Value_type, Size_type, Stepper>::isConverged() {
    return converged_m;
}

// -----------------------------------------------------------------------------------------------------------------------
// PRIVATE MEMBER FUNCTIONS
// -----------------------------------------------------------------------------------------------------------------------

template<typename Value_type, typename Size_type, class Stepper>
bool ClosedOrbitFinder<Value_type, Size_type, Stepper>::findOrbit(value_type accuracy, size_type maxit) {
    /* REMARK TO GORDON
     * q' = 1/b = 1/bcon
     * a' = a = acon
     */

    // READ IN MAGNETIC FIELD: ONLY FOR STAND-ALONE PROGRAM
    
    value_type bint, brint, btint;

    // resize vectors (--> size = N_m+1, capacity = N_m+1), note: we do N_m+1 integration steps
    r_m.resize(N_m+1);
    pr_m.resize(N_m+1);

    // store acon and bcon locally
    value_type acon = acon_m(wo_m);                     // [acon] = m
    value_type invbcon = 1.0 / bcon_m(E0_m, wo_m);      // [bcon] = MeV*s/(C*m^2) = 10^6 T = 10^7 kG (kilo Gauss)

    // helper constants
    value_type p2;                                      // p^2 = p*p
    value_type pr2;                                     // squared radial momentum (pr^2 = pr*pr)
    value_type ptheta, invptheta;                       // Gordon, formula (5c)
    value_type invdenom;                                // denominator for computing dr,dpr
    value_type xold = 0.0;                              // for counting nxcross

    // index for reaching next element of the arrays r and pr (no nicer way found yet)
    size_type idx = 0;
    // observer for storing the current value after each ODE step (e.g. Runge-Kutta step) into the containers of r and pr
    auto store = [&](state_type& y, const value_type t)
    {
        r_m[idx] = y[0];
        pr_m[idx] = y[1];

	// count number of crossings (excluding starting point --> idx>0)
        nxcross_m += (idx > 0) * (y[4] * xold < 0);
        xold = y[4];
        ++idx;
    };

    // define the six ODEs (using lambda function)
    std::function<void(const state_type&, state_type&, const double)> orbit_integration = [&](const state_type &y,
                                                                                              state_type &dydt,
                                                                                              const double theta)
    {
        pr2 = y[1] * y[1];
		
        if (p2 < pr2)
            throw OpalException("ClosedOrbitFinder::findOrbit()", "p_{r}^2 > p^{2} (defined in Gordon paper) --> Square root of negative number.");

        // Gordon, formula (5c)
        ptheta = std::sqrt(p2 - pr2);
        invptheta = 1.0 / ptheta;

        // interpolate values of magnetic field
        bField_m.interpolate(bint, brint, btint, y[0], theta * 180.0 / Physics::pi);

        bint *= invbcon;
        brint *= invbcon;

        // Gordon, formula (5a)
        dydt[0] = y[0] * y[1] * invptheta;
        // Gordon, formula (5b)
        dydt[1] = ptheta - y[0] * bint;
	// Gordon, formulas (9a) and (9b)
        for (size_type i = 2; i < 5; i += 2) {
            dydt[i] = (y[1] * y[i] + y[0] * p2 * y[i+1] * invptheta * invptheta) * invptheta;
            dydt[i+1] = - y[1] * y[i+1] * invptheta - (bint + y[0] * brint) * y[i];
        }
    };

    // define initial state container for integration: y = {r, pr, x1, px1, x2, px2}
    state_type y(6);

    // difference of last and first value of r (1. element) and pr (2. element)
    container_type err(2);
    // correction term for initial values: r = r + dr, pr = pr + dpr; Gordon, formula (17)
    container_type delta = {0.0, 0.0};
    // amplitude of error; Gordon, formula (18) (a = a')
    value_type error = std::numeric_limits<value_type>::max();
    // if niterations > maxit --> stop iteration
    size_type niterations = 0;

    /*
     * Christian:
     * N = 1440 ---> N = 720 ---> dtheta = 2PI/720 --> nsteps = 721
     *
     * 0, 2, 4, ... ---> jeden zweiten berechnene: 1, 3, 5, ... interpolieren --> 1440 Werte
     *
     * Matthias:
     * N = 1440 --> dtheta = 2PI/1440 --> nsteps = 1441
     *
     * 0, 1, 2, 3, 4, 5, ... --> 1440 Werte
     *
     */

    // step size of energy
    value_type dE; 

    if (Emin_m == Emax_m)
      dE = 0.0;
    else
      dE = (E_m - Emin_m) / (Emax_m - Emin_m);

    // iterate until suggested energy (start with minimum energy)
    value_type E = Emin_m;

    // energy increase not more than 0.25
    dE = (dE > 0.25) ? 0.25 : dE;

    // energy dependent values
    value_type en = E / E0_m;                      // en = E/E0 = E/(mc^2) (E0 is potential energy)
    value_type p = acon * std::sqrt(en * (2.0 + en));     // momentum [p] = m; Gordon, formula (3)
    value_type gamma2 = (1.0 + en) * (1.0 + en);          // = gamma^2
    value_type beta = std::sqrt(1.0 - 1.0 / gamma2);
    p2 = p * p;                                           // p^2 = p*p
    value_type invgamma4 = 1.0 / (gamma2 * gamma2);       // = 1/gamma^4

    // set initial values for radius and radial momentum for lowest energy Emin
    // orbit, [r] = m; Gordon, formula (20)
    // radial momentum; Gordon, formula (20)

    container_type init;
    if (rguess_m < 0)
      init = {beta * acon, 0.0};
    else
      init = {rguess_m/1000.0, 0.0};

    // store initial values for updating values for higher energies
    container_type previous_init = {0.0, 0.0};

    do {
        
        // (re-)set inital values for r and pr
        r_m[0] = init[0];
        pr_m[0] = init[1];

        // integrate until error smaller than user-define accuracy
        do {
            // (re-)set inital values
            x_m[0]  = 1.0;               // x1; Gordon, formula (10)
            px_m[0] = 0.0;               // px1; Gordon, formula (10)
            x_m[1]  = 0.0;               // x2; Gordon, formula (10)
            px_m[1] = 1.0;               // px2; Gordon, formula (10)
            nxcross_m = 0;               // counts the number of crossings of x-axis (excluding first step)
            idx = 0;                     // index for looping over r and pr arrays

            // fill container with initial states
            y = {init[0],init[1], x_m[0], px_m[0], x_m[1], px_m[1]};

            // integrate from 0 to 2*pi (one has to get back to the "origin")
            boost::numeric::odeint::integrate_n_steps(stepper_m,orbit_integration,y,0.0,dtheta_m,N_m,store);

            // write new state
            x_m[0] = y[2];
            px_m[0] = y[3];
            x_m[1] = y[4];
            px_m[1] = y[5];

            // compute error (compare values of orbit and momentum for theta = 0 and theta = 2*pi)
            // (Note: size = N_m+1 --> last entry is N_m)
            err[0] = r_m[N_m] - r_m[0];      // Gordon, formula (14)
            err[1] = pr_m[N_m] - pr_m[0];    // Gordon, formula (14)

            // correct inital values of r and pr
            invdenom = 1.0 / (x_m[0] + px_m[1] - 2.0);
            delta[0] = ((px_m[1] - 1.0) * err[0] - x_m[1] * err[1]) * invdenom; // dr; Gordon, formula (16a)
            delta[1] = ((x_m[0] - 1.0) * err[1] - px_m[0] * err[0]) * invdenom; // dpr; Gordon, formula (16b)

            // improved initial values; Gordon, formula (17) (here it's used for higher energies)
            init[0] += delta[0];
            init[1] += delta[1];

            // compute amplitude of the error
            error = std::sqrt(delta[0] * delta[0] + delta[1] * delta[1] * invgamma4) / r_m[0];
        } while (error > accuracy && niterations++ < maxit);

        // reset iteration counter
        niterations = 0;

        // reset correction term
        delta[0] = delta[1] = 0.0;

        // increase energy by dE
        if (E_m <= E + dE)
            E = E_m;
        else
            E += dE;

        // set constants for new energy E
        en = E / E0_m;                     // en = E/E0 = E/(mc^2) (E0 is potential energy)
        p = acon * std::sqrt(en * (2.0 + en));    // momentum [p] = m; Gordon, formula (3)
        p2 = p * p;                               // p^2 = p*p
        gamma2 = (1.0 + en) * (1.0 + en);
        invgamma4 = 1.0 / (gamma2 * gamma2);


    } while (E != E_m);

    /* store last entry, since it is needed in computeVerticalOscillations(), because we have to do the same
     * number of integrations steps there.
     */
    lastOrbitVal_m = r_m[N_m];           // needed in computeVerticalOscillations()
    lastMomentumVal_m = pr_m[N_m];       // needed in computeVerticalOscillations()

    // remove last entry (since we don't have to store [0,2pi], but [0,2pi[)  --> size = N_m, capacity = N_m+1
    r_m.pop_back();
    pr_m.pop_back();


    // returns true if converged, otherwise false
    return error < accuracy;
}

template<typename Value_type, typename Size_type, class Stepper>
Value_type ClosedOrbitFinder<Value_type, Size_type, Stepper>::computeTune(const std::array<value_type,2>& y,
                                                                          value_type py2, size_type ncross)
{
    // Y = [y1, y2; py1, py2]

    // cos(mu)
    value_type cos = 0.5 * (y[0] + py2);
    
    value_type mu;

    // sign of sin(mu) has to be equal to y2
    bool negative = std::signbit(y[1]);

    bool uneven = (ncross % 2);

    if (std::fabs(cos) > 1.0) {
        // store the number of crossings
        value_type n = ncross;

        if (uneven)
            n = ncross - 1;

        // Gordon, formula (36b)
        value_type muPrime = -std::acosh(std::fabs(cos));      // mu'
        mu = n * Physics::pi + muPrime;

    } else {
        value_type muPrime = (uneven) ? std::acos(-cos) : std::acos(cos);    // mu'
        /* It has to be fulfilled: 0<= mu' <= pi
        * But since |cos(mu)| <= 1, we have
        * -1 <= cos(mu) <= 1 --> 0 <= mu <= pi (using above programmed line), such
        * that condition is already fulfilled.
        */

        // Gordon, formula (36)
        mu = ncross * Physics::pi + muPrime;

        // if sign(y[1]) > 0 && sign(sin(mu)) < 0
        if (!negative && std::signbit(std::sin(mu))) {
            mu = ncross * Physics::pi - muPrime;
        } else if (negative && !std::signbit(std::sin(mu))) {
            mu = ncross * Physics::pi - muPrime + Physics::two_pi;
        }
    }

    // nu = mu/theta, where theta = integration domain

    /* domain_m = true --> only integrated over a single sector --> multiply by nSector_m to
     * get correct tune.
     */
    if (domain_m)
        mu *= nSector_m;

    return mu * Physics::u_two_pi;
}

template<typename Value_type, typename Size_type, class Stepper>
void ClosedOrbitFinder<Value_type, Size_type, Stepper>::computeOrbitProperties() {
    /*
     * The formulas for h, fidx and ds are from the paper:
     * "Tranverse-Longitudinal Coupling by Space Charge in Cyclotrons"
     * written by Dr. Christian Baumgarten (2012, PSI)
     * p. 6
     */

    // READ IN MAGNETIC FIELD: ONLY FOR STAND-ALONE PROGRAM
    value_type bint, brint, btint; // B, dB/dr, dB/dtheta

    value_type invbcon = 1.0 / bcon_m(E0_m, wo_m);
    value_type en = E_m / E0_m;                                  // en = E/E0 = E/(mc^2) (E0 is potential energy)
    value_type p = acon_m(wo_m) * std::sqrt(en * (2.0 + en));    // momentum [p] = m; Gordon, formula (3)
    value_type p2 = p * p;
    value_type theta = 0.0;                                             // angle for interpolating
    value_type ptheta;

    // resize of container (--> size = N_m, capacity = N_m)
    h_m.resize(N_m);
    fidx_m.resize(N_m);
    ds_m.resize(N_m);

    for (size_type i = 0; i < N_m; ++i) {
        // interpolate magnetic field
        bField_m.interpolate(bint, brint, btint, r_m[i], theta * 180.0 / Physics::pi);
        bint *= invbcon;
        brint *= invbcon;
        btint *= invbcon;

        // inverse bending radius
        h_m[i] = bint / p;

        // local field index
        ptheta = std::sqrt(p2 - pr_m[i] * pr_m[i]);
        fidx_m[i] = (brint * ptheta - btint * pr_m[i] / r_m[i]) / p2; //(bint*bint);

        // path length element
        ds_m[i] = std::hypot(r_m[i] * pr_m[i] / ptheta,r_m[i]) * dtheta_m; // C++11 function

        // increase angle
        theta += dtheta_m;
    }

    // compute average radius
    ravg_m = std::accumulate(r_m.begin(),r_m.end(),0.0) / value_type(r_m.size());
}

template<typename Value_type, typename Size_type, class Stepper>
void ClosedOrbitFinder<Value_type, Size_type, Stepper>::computeVerticalOscillations() {

    vertOscDone_m = true;

    // READ IN MAGNETIC FIELD: ONLY FOR STAND-ALONE PROGRAM
    value_type bint, brint, btint; // B, dB/dr, dB/dtheta

    value_type en = E_m / E0_m;                                  // en = E/E0 = E/(mc^2) with potential energy E0
    value_type p = acon_m(wo_m) * std::sqrt(en *(en + 2.0));     // Gordon, formula (3)
    value_type p2 = p * p;                                              // p^2 = p*p
    size_type idx = 0;                                                  // index for going through container
    value_type pr2;                                                     // pr^2 = pr*pr
    value_type ptheta, invptheta;                                       // Gordon, formula (5c)
    value_type zold = 0.0;                                              // for counting nzcross

    // store bcon locally
    value_type invbcon = 1.0 / bcon_m(E0_m, wo_m);     // [bcon] = MeV*s/(C*m^2) = 10^6 T = 10^7 kG (kilo Gauss)

    // define the ODEs (using lambda function)
    std::function<void(const state_type&, state_type&, const double)> vertical = [&](const state_type &y,
                                                                                     state_type &dydt,
                                                                                     const double theta)
    {
        pr2 = y[1] * y[1];
        if (p2 < pr2) {
            throw OpalException("ClosedOrbitFinder::computeVerticalOscillations()",
                                "p_{r}^2 > p^{2} (defined in Gordon paper) --> Square root of negative number.");
        }

        // Gordon, formula (5c)
        ptheta = std::sqrt(p2 - pr2);
        invptheta = 1.0 / ptheta;

        // intepolate values of magnetic field
        bField_m.interpolate(bint, brint, btint, y[0], theta * 180.0 / Physics::pi);
        
        bint *= invbcon;
        brint *= invbcon;
        btint *= invbcon;

        // We have to integrate r and pr again, otherwise we don't have the Runge-Kutta of the B-field
        // Gordon, formula (5a)
        dydt[0] = y[0] * y[1] * invptheta;
        // Gordon, formula (5b)
        dydt[1] = ptheta - y[0] * bint;

        // Gordon, formulas (22a) and (22b)
        for (size_type i = 2; i < 5; i += 2) {
            dydt[i] = y[0] * y[i+1] * invptheta;
            dydt[i+1] = (y[0] * brint - y[1] * invptheta * btint) * y[i];
        }

        // integrate phase
        dydt[6] = y[0] * invptheta * gamma_m - 1;
    };

    // to get next index for r and pr (to iterate over container)
    auto next = [&](state_type& y, const value_type t) {
        // number of times z2 changes sign
        nzcross_m += (idx > 0) * (y[4] * zold < 0);
        zold = y[4];
        ++idx;
    };

    // set initial state container for integration: y = {r, pr, z1, pz1, z2, pz2, phase}
    state_type y = {r_m[0], pr_m[0], 1.0, 0.0, 0.0, 1.0, 0.0};

    // add last element for integration (since we have to return to the initial point (--> size = N_m+1, capacity = N_m+1)
    r_m.push_back(lastOrbitVal_m);
    pr_m.push_back(lastMomentumVal_m);

    // integrate: assume no imperfections --> only integrate over a single sector (dtheta_m = 2pi/N_m)
    boost::numeric::odeint::integrate_n_steps(stepper_m,vertical,y,0.0,dtheta_m,N_m,next);

    // remove last element again (--> size = N_m, capacity = N_m+1)
    r_m.pop_back();
    pr_m.pop_back();

    // write new state
    z_m[0] = y[2];
    pz_m[0] = y[3];
    z_m[1] = y[4];
    pz_m[1] = y[5];
    phase_m = y[6] * Physics::u_two_pi; // / (2.0 * Physics::pi);

    /* domain_m = true --> only integrated over a single sector
     * --> multiply by nSector_m to get correct phase_m
     */
    if (domain_m)
        phase_m *= nSector_m;
}

#endif