ParallelCyclotronTracker.cpp

// ------------------------------------------------------------------------
// $RCSfile: ParallelCyclotronTracker.cpp,v $
// ------------------------------------------------------------------------
// $Revision: 1.1 $initialLocalNum_m
// ------------------------------------------------------------------------
// Copyright: see Copyright.readme
// ------------------------------------------------------------------------
//
// Class: ParallelCyclotronTracker
//   The class for tracking particles with 3D space charge in Cyclotrons and FFAG's
//
// ------------------------------------------------------------------------
//
// $Date: 2007/10/17 04:00:08 $
// $Author: adelmann, yang, winklehner $
//
// ------------------------------------------------------------------------

#include <Algorithms/Ctunes.hpp>
#include "Algorithms/ParallelCyclotronTracker.h"
#include "Algorithms/PolynomialTimeDependence.h"
#include "Elements/OpalPolynomialTimeDependence.h"

#include <cfloat>
#include <iostream>
#include <fstream>
#include <vector>
#include "AbstractObjects/OpalData.h"

#include "AbsBeamline/Collimator.h"
#include "AbsBeamline/Corrector.h"
#include "AbsBeamline/Cyclotron.h"
#include "AbsBeamline/Degrader.h"
#include "AbsBeamline/Diagnostic.h"
#include "AbsBeamline/Drift.h"
#include "AbsBeamline/ElementBase.h"
#include "AbsBeamline/Lambertson.h"
#include "AbsBeamline/Offset.h"
#include "AbsBeamline/Marker.h"
#include "AbsBeamline/Monitor.h"
#include "AbsBeamline/Multipole.h"
#include "AbsBeamline/Probe.h"
#include "AbsBeamline/RBend.h"
#include "AbsBeamline/RFCavity.h"
#include "AbsBeamline/RFQuadrupole.h"
#include "AbsBeamline/SBend.h"
#include "AbsBeamline/SBend3D.h"
#include "AbsBeamline/Separator.h"
#include "AbsBeamline/Septum.h"
#include "AbsBeamline/Solenoid.h"
#include "AbsBeamline/CyclotronValley.h"
#include "AbsBeamline/Stripper.h"
#include "AbsBeamline/VariableRFCavity.h"

#include "AbstractObjects/Element.h"

#include "Elements/OpalBeamline.h"
#include "AbsBeamline/Ring.h"

#include "BeamlineGeometry/Euclid3D.h"
#include "BeamlineGeometry/PlanarArcGeometry.h"
#include "BeamlineGeometry/RBendGeometry.h"
#include "Beamlines/Beamline.h"

#include "Fields/BMultipoleField.h"
#include "FixedAlgebra/FTps.h"
#include "FixedAlgebra/FTpsMath.h"
#include "FixedAlgebra/FVps.h"

#include "Physics/Physics.h"

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

#include "BasicActions/DumpFields.h"
#include "BasicActions/DumpEMFields.h"

#include "Structure/H5PartWrapperForPC.h"
#include "Structure/BoundaryGeometry.h"
#include "Utilities/Options.h"

#include "Ctunes.h"
#include <cassert>

#include <hdf5.h>
#include "H5hut.h"

class Beamline;
class PartData;

using Physics::pi;
using Physics::q_e;

const double c_mmtns = Physics::c * 1.0e-6; // m/s --> mm/ns

Vector_t const ParallelCyclotronTracker::xaxis = Vector_t(1.0, 0.0, 0.0);
Vector_t const ParallelCyclotronTracker::yaxis = Vector_t(0.0, 1.0, 0.0);
Vector_t const ParallelCyclotronTracker::zaxis = Vector_t(0.0, 0.0, 1.0);

#define PSdim 6

extern Inform *gmsg;

// typedef FVector<double, PSdim> Vector;

/**
 * Constructor ParallelCyclotronTracker
 *
 * @param beamline
 * @param reference
 * @param revBeam
 * @param revTrack
 */
ParallelCyclotronTracker::ParallelCyclotronTracker(const Beamline &beamline,
                                                   const PartData &reference,
                                                   bool revBeam, bool revTrack):
    Tracker(beamline, reference, revBeam, revTrack),
    lastDumpedStep_m(0),
    eta_m(0.01),
    myNode_m(Ippl::myNode()),
    initialLocalNum_m(0),
    initialTotalNum_m(0),
    opalRing_m(NULL),
    itsStepper_mp(nullptr),
    mode_m(MODE::UNDEFINED),
    stepper_m(stepper::INTEGRATOR::UNDEFINED) {
    itsBeamline = dynamic_cast<Beamline *>(beamline.clone());
}

/**
 * Constructor ParallelCyclotronTracker
 *
 * @param beamline
 * @param bunch
 * @param ds
 * @param reference
 * @param revBeam
 * @param revTrack
 * @param maxSTEPS
 * @param timeIntegrator
 */
ParallelCyclotronTracker::ParallelCyclotronTracker(const Beamline &beamline,
                                                   PartBunch &bunch,
                                                   DataSink &ds,
                                                   const PartData &reference,
                                                   bool revBeam, bool revTrack,
                                                   int maxSTEPS, int timeIntegrator):
    Tracker(beamline, reference, revBeam, revTrack),
    maxSteps_m(maxSTEPS),
    lastDumpedStep_m(0),
    eta_m(0.01),
    myNode_m(Ippl::myNode()),
    initialLocalNum_m(bunch.getLocalNum()),
    initialTotalNum_m(bunch.getTotalNum()),
    opalRing_m(NULL),
    itsStepper_mp(nullptr) {
    itsBeamline = dynamic_cast<Beamline *>(beamline.clone());
    itsBunch = &bunch;
    itsDataSink = &ds;
    //  scaleFactor_m = itsBunch->getdT() * c;
    scaleFactor_m = 1;
    multiBunchMode_m = 0;

    IntegrationTimer_m = IpplTimings::getTimer("Integration");
    TransformTimer_m   = IpplTimings::getTimer("Frametransform");
    DumpTimer_m        = IpplTimings::getTimer("Dump");
    BinRepartTimer_m   = IpplTimings::getTimer("Binaryrepart");
    
    // FIXME Change track command
    if ( initialTotalNum_m == 1 ) {
        mode_m = MODE::SINGLE;
    } else if ( initialTotalNum_m == 2 ) {
        mode_m = MODE::SEO;
    } else if ( initialTotalNum_m > 2 ) {
        mode_m = MODE::BUNCH;
    } else
        mode_m = MODE::UNDEFINED;
    
    if ( timeIntegrator == 0 ) {
        stepper_m = stepper::INTEGRATOR::RK4;
    } else if ( timeIntegrator == 1) {
        stepper_m = stepper::INTEGRATOR::LF2;
    } else if ( timeIntegrator == 2) {
        stepper_m = stepper::INTEGRATOR::MTS;
    } else
        stepper_m = stepper::INTEGRATOR::UNDEFINED;
}

/**
 * Destructor ParallelCyclotronTracker
 *
 */
ParallelCyclotronTracker::~ParallelCyclotronTracker() {
    for(Component* component : myElements) {
        delete(component);
    }
    for(auto fd : FieldDimensions) {
        delete(fd);
    }
    delete itsBeamline;
    // delete opalRing_m;
}

/**
 * AAA
 *
 * @param none
 */
void ParallelCyclotronTracker::initializeBoundaryGeometry() {
    for(Component * component : myElements) {
        bgf_m = dynamic_cast<ElementBase *>(component)->getBoundaryGeometry();
        if(!bgf_m)
            continue;
        else
            break;
    }
    if (bgf_m) {
        itsDataSink->writeGeomToVtk(*bgf_m, std::string("data/testGeometry-00000.vtk"));
        OpalData::getInstance()->setGlobalGeometry(bgf_m);
        *gmsg << "* Boundary geometry initialized " << endl;
    }
}

/**
 *
 *
 * @param fn Base file name
 */
void ParallelCyclotronTracker::bgf_main_collision_test() {
    if(!bgf_m) return;

    Inform msg("bgf_main_collision_test ");

    /**
     *Here we check if a particles is outside the domain, flag it for deletion
     */

    Vector_t intecoords = 0.0;

    // This has to match the dT in the rk4 pusher
    double dtime = itsBunch->getdT() * getHarmonicNumber();

    int triId = 0;
    for(size_t i = 0; i < itsBunch->getLocalNum(); i++) {
        int res = bgf_m->partInside(itsBunch->R[i], itsBunch->P[i], dtime, itsBunch->PType[i], itsBunch->Q[i], intecoords, triId);
        //int res = bgf_m->partInside(itsBunch->R[i]*1.0e-3, itsBunch->P[i], dtime, itsBunch->PType[i], itsBunch->Q[i], intecoords, triId);
        if(res >= 0) {
            itsBunch->Bin[i] = -1;
        }
    }
}


/**
 *
 *
 * @param fn Base file name
 */
void ParallelCyclotronTracker::openFiles(std::string SfileName) {

    std::string  SfileName2 = SfileName + std::string("-Angle0.dat");
    outfTheta0_m.precision(8);
    outfTheta0_m.setf(std::ios::scientific, std::ios::floatfield);
    outfTheta0_m.open(SfileName2.c_str());
    outfTheta0_m << "#  r [mm]      beta_r*gamma       "
                 << "theta [mm]      beta_theta*gamma        "
                 << "z [mm]          beta_z*gamma" << std::endl;

    SfileName2 = SfileName + std::string("-Angle1.dat");
    outfTheta1_m.precision(8);
    outfTheta1_m.setf(std::ios::scientific, std::ios::floatfield);
    outfTheta1_m.open(SfileName2.c_str());
    outfTheta1_m << "#  r [mm]      beta_r*gamma       "
                 << "theta [mm]      beta_theta*gamma        "
                 << "z [mm]          beta_z*gamma"  << std::endl;

    SfileName2 = SfileName + std::string("-Angle2.dat");
    outfTheta2_m.precision(8);
    outfTheta2_m.setf(std::ios::scientific, std::ios::floatfield);
    outfTheta2_m.open(SfileName2.c_str());
    outfTheta2_m << "#  r [mm]      beta_r*gamma       "
                 << "theta [mm]      beta_theta*gamma        "
                 << "z [mm]          beta_z*gamma"  << std::endl;

    // for single Particle Mode, output after each turn, to define matched initial phase ellipse.

    SfileName2 = SfileName + std::string("-afterEachTurn.dat");

    outfThetaEachTurn_m.precision(8);
    outfThetaEachTurn_m.setf(std::ios::scientific, std::ios::floatfield);

    outfThetaEachTurn_m.open(SfileName2.c_str());
    outfTheta2_m << "#  r [mm]      beta_r*gamma       "
                 << "theta [mm]      beta_theta*gamma        "
                 << "z [mm]          beta_z*gamma"  << std::endl;
}

/**
 * Close all files related to
 * special output in the Cyclotron
 * mode.
 */
void ParallelCyclotronTracker::closeFiles() {

    outfTheta0_m.close();
    outfTheta1_m.close();
    outfTheta2_m.close();
    outfThetaEachTurn_m.close();
}

/**
 *
 * @param ring
 */
void ParallelCyclotronTracker::visitRing(const Ring &ring) {

    *gmsg << "* ----------------------------- Adding Ring ------------------------------ *" << endl;

    if (opalRing_m != NULL)
        delete opalRing_m;

    opalRing_m = dynamic_cast<Ring*>(ring.clone());

    myElements.push_back(opalRing_m);

    opalRing_m->initialise(itsBunch);

    referenceR = opalRing_m->getBeamRInit();
    referencePr = opalRing_m->getBeamPRInit();
    referenceTheta = opalRing_m->getBeamPhiInit();

    if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
        throw OpalException("Error in ParallelCyclotronTracker::visitRing",
                            "PHIINIT is out of [-180, 180)!");
    }

    referenceZ = 0.0;
    referencePz = 0.0;

    referencePtot = itsReference.getGamma() * itsReference.getBeta();
    referencePt = sqrt(referencePtot * referencePtot - referencePr * referencePr);

    if(referencePtot < 0.0)
        referencePt *= -1.0;

    sinRefTheta_m = sin(referenceTheta * Physics::deg2rad);
    cosRefTheta_m = cos(referenceTheta * Physics::deg2rad);

    double BcParameter[8];

    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;

    buildupFieldList(BcParameter, ElementBase::RING, opalRing_m);

    // Finally print some diagnostic
    *gmsg << "* Initial beam radius = " << referenceR << " [mm] " << endl;
    *gmsg << "* Initial gamma = " << itsReference.getGamma() << endl;
    *gmsg << "* Initial beta = " << itsReference.getBeta() << endl;
    *gmsg << "* Total reference momentum   = " << referencePtot * 1000.0
          << " [MCU]" << endl;
    *gmsg << "* Reference azimuthal momentum  = " << referencePt * 1000.0
          << " [MCU]" << endl;
    *gmsg << "* Reference radial momentum     = " << referencePr * 1000.0
          << " [MCU]" << endl;
    *gmsg << "* " << opalRing_m->getSymmetry() << " fold field symmetry "
          << endl;
    *gmsg << "* Harmonic number h= " << opalRing_m->getHarmonicNumber() << " "
          << endl;
}

/**
 *
 *
 * @param cycl
 */
void ParallelCyclotronTracker::visitCyclotron(const Cyclotron &cycl) {

    *gmsg << "* -------------------------- Adding Cyclotron ---------------------------- *" << endl;

    Cyclotron *elptr = dynamic_cast<Cyclotron *>(cycl.clone());
    myElements.push_back(elptr);

    // Is this a Spiral Inflector Simulation? If yes, we'll give the user some
    // useful information
    spiral_flag = elptr->getSpiralFlag();

    if(spiral_flag) {

        *gmsg << endl << "* This is a Spiral Inflector Simulation! This means the following:" << endl;
        *gmsg         << "* 1.) It is up to the user to provide appropriate geometry, electric and magnetic fields!" << endl;
        *gmsg         << "*     (Use BANDRF type cyclotron and use RFMAPFN to load both magnetic" << endl;
        *gmsg         << "*     and electric fields, setting SUPERPOSE to an array of TRUE values.)" << endl;
        *gmsg         << "* 2.) For high currentst is strongly recommended to use the SAAMG fieldsolver," << endl;
        *gmsg         << "*     FFT does not give the correct results (boundaty conditions are missing)." << endl;
        *gmsg         << "* 3.) The whole geometry will be meshed and used for the fieldsolve." << endl;
        *gmsg         << "*     There will be no transformations of the bunch into a local frame und consequently," << endl;
        *gmsg         << "*     the problem will be treated non-relativistically!" << endl;
        *gmsg         << "*     (This is not an issue for spiral inflectors as they are typically < 100 keV/amu.)" << endl;
        *gmsg << endl << "* Note: For now, multi-bunch mode (MBM) needs to be de-activated for spiral inflector" << endl;
        *gmsg         << "* and space charge needs to be solved every time-step. numBunch_m and scSolveFreq are reset." << endl;
        numBunch_m = 1;

    }

    // Fresh run (no restart):
    if(!OpalData::getInstance()->inRestartRun()) {

        // Get reference values from cyclotron element 
        // For now, these are still stored in mm. should be the only ones. -DW
        referenceR     = elptr->getRinit();
        referenceTheta = elptr->getPHIinit();
        referenceZ     = elptr->getZinit();
        referencePr    = elptr->getPRinit();
        referencePz    = elptr->getPZinit();

        if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
            throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron",
                                "PHIINIT is out of [-180, 180)!");
        }

        referencePtot =  itsReference.getGamma() * itsReference.getBeta();

        // Calculate reference azimuthal (tangential) momentum from total-, z- and radial momentum:
        float insqrt = referencePtot * referencePtot - \
            referencePr * referencePr - referencePz * referencePz;

        if(insqrt < 0) {

            if(insqrt > -1.0e-10) {

	        referencePt = 0.0;

            } else {

	        throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron",
                                    "Pt imaginary!");
            }

        } else {

            referencePt = sqrt(insqrt);
        }

        if(referencePtot < 0.0)
            referencePt *= -1.0;
        // End calculate referencePt

        // Restart a run:
    } else {

        // If the user wants to save the restarted run in local frame,
        // make sure the previous h5 file was local too
      if (Options::psDumpLocalFrame != Options::GLOBAL) {
        if (!previousH5Local) {
                throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron",
                                    "You are trying a local restart from a global h5 file!");
        }
            // Else, if the user wants to save the restarted run in global frame,
            // make sure the previous h5 file was global too
      } else {
        if (previousH5Local) {
                throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron",
                                    "You are trying a global restart from a local h5 file!");
            }
        }

        // Adjust some of the reference variables from the h5 file
        referencePhi *= Physics::deg2rad;
        referencePsi *= Physics::deg2rad;
        referencePtot = bega;
        if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
            throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron",
                                "PHIINIT is out of [-180, 180)!");
        }
    }

    sinRefTheta_m = sin(referenceTheta * Physics::deg2rad);
    cosRefTheta_m = cos(referenceTheta * Physics::deg2rad);

    *gmsg << endl;
    *gmsg << "* Bunch global starting position:" << endl;
    *gmsg << "* RINIT = " << referenceR  << " [mm]" << endl;
    *gmsg << "* PHIINIT = " << referenceTheta << " [deg]" << endl;
    *gmsg << "* ZINIT = " << referenceZ << " [mm]" << endl;
    *gmsg << endl;
    *gmsg << "* Bunch global starting momenta:" << endl;
    *gmsg << "* Initial gamma = " << itsReference.getGamma() << endl;
    *gmsg << "* Initial beta = " << itsReference.getBeta() << endl;
    *gmsg << "* Reference total momentum (beta * gamma) = " << referencePtot * 1000.0 << " [MCU]" << endl;
    *gmsg << "* Reference azimuthal momentum (Pt) = " << referencePt * 1000.0 << " [MCU]" << endl;
    *gmsg << "* Reference radial momentum (Pr) = " << referencePr * 1000.0 << " [MCU]" << endl;
    *gmsg << "* Reference axial momentum (Pz) = " << referencePz * 1000.0 << " [MCU]" << endl;
    *gmsg << endl;

    double sym = elptr->getSymmetry();
    *gmsg << "* " << sym << "-fold field symmerty " << endl;

    // ckr: this just returned the default value as defined in Component.h
    // double rff = elptr->getRfFrequ();
    // *gmsg << "* Rf frequency= " << rff << " [MHz]" << endl;

    std::string fmfn = elptr->getFieldMapFN();
    *gmsg << "* Field map file name = " << fmfn << " " << endl;

    std::string type = elptr->getCyclotronType();
    *gmsg << "* Type of cyclotron = " << type << " " << endl;

    double rmin = elptr->getMinR();
    double rmax = elptr->getMaxR();
    *gmsg << "* Radial aperture = " << rmin << " ... " << rmax<<" [mm] "<< endl;

    double zmin = elptr->getMinZ();
    double zmax = elptr->getMaxZ();
    *gmsg << "* Vertical aperture = " << zmin << " ... " << zmax<<" [mm]"<< endl;

    double h = elptr->getCyclHarm();
    *gmsg << "* Number of trimcoils = " << elptr->getNumberOfTrimcoils() << endl;
    *gmsg << "* Harmonic number h = " << h << " " << endl;

    /**
     * To ease the initialise() function, set a integral parameter fieldflag internally.
     * Its value is  by the option "TYPE" of the element  "CYCLOTRON"
     * fieldflag = 1, readin PSI format measured field file (default)
     * fieldflag = 2, readin carbon cyclotron field file created by Jianjun Yang, TYPE=CARBONCYCL
     * fieldflag = 3, readin ANSYS format file for CYCIAE-100 created by Jianjun Yang, TYPE=CYCIAE
     * fieldflag = 4, readin AVFEQ format file for Riken cyclotrons
     * fieldflag = 5, readin FFAG format file for MSU/FNAL FFAG
     * fieldflag = 6, readin both median plane B field map and 3D E field map of RF cavity for compact cyclotron
     * fieldflag = 7, read in fields for Daniel's synchrocyclotron simulations
     */
    int  fieldflag;
    if(type == std::string("CARBONCYCL")) {
        fieldflag = 2;
    } else if(type == std::string("CYCIAE")) {
        fieldflag = 3;
    } else if(type == std::string("AVFEQ")) {
        fieldflag = 4;
    } else if(type == std::string("FFAG")) {
        fieldflag = 5;
    } else if(type == std::string("BANDRF")) {
        fieldflag = 6;
    } else if(type == std::string("SYNCHROCYCLOTRON")) {
	fieldflag = 7;
    } else //(type == "RING")
        fieldflag = 1;

    // Read in cyclotron field maps (midplane + 3D fields if desired).
    elptr->initialise(itsBunch, fieldflag, elptr->getBScale());

    double BcParameter[8];

    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;

    BcParameter[0] = 0.001 * elptr->getRmin();
    BcParameter[1] = 0.001 * elptr->getRmax();

    // Store inner radius and outer radius of cyclotron field map in the list
    buildupFieldList(BcParameter, ElementBase::CYCLOTRON, elptr);
}

/**
 * Not implemented and most probable never used
 *
 */
void ParallelCyclotronTracker::visitBeamBeam(const BeamBeam &) {
    *gmsg << "In BeamBeam tracker is missing " << endl;
}

/**
 *
 *
 * @param coll
 */
void ParallelCyclotronTracker::visitCollimator(const Collimator &coll) {

    *gmsg << "* --------- Collimator -----------------------------" << endl;

    Collimator* elptr = dynamic_cast<Collimator *>(coll.clone());
    myElements.push_back(elptr);

    double xstart = elptr->getXStart();
    *gmsg << "* Xstart= " << xstart << " [mm]" << endl;

    double xend = elptr->getXEnd();
    *gmsg << "* Xend= " << xend << " [mm]" << endl;

    double ystart = elptr->getYStart();
    *gmsg << "* Ystart= " << ystart << " [mm]" << endl;

    double yend = elptr->getYEnd();
    *gmsg << "* Yend= " << yend << " [mm]" << endl;

    double zstart = elptr->getZStart();
    *gmsg << "* Zstart= " << zstart << " [mm]" << endl;

    double zend = elptr->getZEnd();
    *gmsg << "* Zend= " << zend << " [mm]" << endl;

    double width = elptr->getWidth();
    *gmsg << "* Width= " << width << " [mm]" << endl;

    elptr->initialise(itsBunch);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;

    BcParameter[0] = 0.001 * xstart ;
    BcParameter[1] = 0.001 * xend;
    BcParameter[2] = 0.001 * ystart ;
    BcParameter[3] = 0.001 * yend;
    BcParameter[4] = 0.001 * width ;

    buildupFieldList(BcParameter, ElementBase::COLLIMATOR, elptr);
}

/**
 *
 *
 * @param corr
 */
void ParallelCyclotronTracker::visitCorrector(const Corrector &corr) {
    *gmsg << "In Corrector; L= " << corr.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Corrector *>(corr.clone()));
}

/**
 *
 *
 * @param degrader
 */
void ParallelCyclotronTracker::visitDegrader(const Degrader &deg) {
    *gmsg << "In Degrader; L= " << deg.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Degrader *>(deg.clone()));

}


/**
 *
 *
 * @param diag
 */
void ParallelCyclotronTracker::visitDiagnostic(const Diagnostic &diag) {
    *gmsg << "In Diagnostic; L= " << diag.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Diagnostic *>(diag.clone()));
}

/**
 *
 *
 * @param drift
 */
void ParallelCyclotronTracker::visitDrift(const Drift &drift) {
    *gmsg << "In drift L= " << drift.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Drift *>(drift.clone()));
}

/**
 *
 *
 * @param lamb
 */
void ParallelCyclotronTracker::visitLambertson(const Lambertson &lamb) {
    *gmsg << "In Lambertson; L= " << lamb.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Lambertson *>(lamb.clone()));
}

void ParallelCyclotronTracker::visitOffset(const Offset & off) {
    if (opalRing_m == NULL)
        throw OpalException(
                            "ParallelCylcotronTracker::visitOffset",
                            "Attempt to place an offset when Ring not defined");
    Offset* offNonConst = const_cast<Offset*>(&off);
    offNonConst->updateGeometry(opalRing_m->getNextPosition(),
                                opalRing_m->getNextNormal());
    opalRing_m->appendElement(off);
}

/**
 *
 *
 * @param marker
 */
void ParallelCyclotronTracker::visitMarker(const Marker &marker) {
    //   *gmsg << "In Marker; L= " << marker.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Marker *>(marker.clone()));
    // Do nothing.
}

/**
 *
 *
 * @param corr
 */
void ParallelCyclotronTracker::visitMonitor(const Monitor &corr) {
    //   *gmsg << "In Monitor; L= " << corr.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Monitor *>(corr.clone()));
    //   applyDrift(flip_s * corr.getElementLength());
}


/**
 *
 *
 * @param mult
 */
void ParallelCyclotronTracker::visitMultipole(const Multipole &mult) {
    *gmsg << "In Multipole; L= " << mult.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<Multipole *>(mult.clone()));
}

/**
 *
 *
 * @param prob
 */
void ParallelCyclotronTracker::visitProbe(const Probe &prob) {
    *gmsg << "* -----------  Probe -------------------------------" << endl;
    Probe *elptr = dynamic_cast<Probe *>(prob.clone());
    myElements.push_back(elptr);

    double xstart = elptr->getXstart();
    *gmsg << "XStart= " << xstart << " [mm]" << endl;

    double xend = elptr->getXend();
    *gmsg << "XEnd= " << xend << " [mm]" << endl;

    double ystart = elptr->getYstart();
    *gmsg << "YStart= " << ystart << " [mm]" << endl;

    double yend = elptr->getYend();
    *gmsg << "YEnd= " << yend << " [mm]" << endl;

    double width = elptr->getWidth();
    *gmsg << "Width= " << width << " [mm]" << endl;


    // initialise, do nothing
    elptr->initialise(itsBunch);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;

    BcParameter[0] = 0.001 * xstart ;
    BcParameter[1] = 0.001 * xend;
    BcParameter[2] = 0.001 * ystart ;
    BcParameter[3] = 0.001 * yend;
    BcParameter[4] = 0.001 * width ;

    // store probe parameters in the list
    buildupFieldList(BcParameter, ElementBase::PROBE, elptr);
}

/**
 *
 *
 * @param bend
 */
void ParallelCyclotronTracker::visitRBend(const RBend &bend) {
    *gmsg << "In RBend; L= " << bend.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<RBend *>(bend.clone()));
}

void ParallelCyclotronTracker::visitSBend3D(const SBend3D &bend) {
    *gmsg << "Adding SBend3D" << endl;
    if (opalRing_m != NULL)
        opalRing_m->appendElement(bend);
    else
        throw OpalException("ParallelCyclotronTracker::visitSBend3D",
                            "Need to define a RINGDEFINITION to use SBend3D element");
}

void ParallelCyclotronTracker::visitVariableRFCavity(const VariableRFCavity &cav) {
    *gmsg << "Adding Variable RF Cavity" << endl;
    if (opalRing_m != NULL)
        opalRing_m->appendElement(cav);
    else
        throw OpalException("ParallelCyclotronTracker::visitVariableRFCavity",
                            "Need to define a RINGDEFINITION to use VariableRFCavity element");
}

/**
 *
 *
 * @param as
 */
void ParallelCyclotronTracker::visitRFCavity(const RFCavity &as) {

    *gmsg << "* --------- RFCavity ------------------------------" << endl;

    RFCavity *elptr = dynamic_cast<RFCavity *>(as.clone());
    myElements.push_back(elptr);

    if((elptr->getComponentType() != "SINGLEGAP") && (elptr->getComponentType() != "DOUBLEGAP")) {
        *gmsg << (elptr->getComponentType()) << endl;
        throw OpalException("ParallelCyclotronTracker::visitRFCavity",
                            "The ParallelCyclotronTracker can only play with cyclotron type RF system currently ...");
    }

    double rmin = elptr->getRmin();
    *gmsg << "* Minimal radius of cavity= " << rmin << " [mm]" << endl;

    double rmax = elptr->getRmax();
    *gmsg << "* Maximal radius of cavity= " << rmax << " [mm]" << endl;

    double rff = elptr->getCycFrequency();
    *gmsg << "* RF frequency (2*pi*f)= " << rff << " [rad/s]" << endl;

    std::string fmfn = elptr->getFieldMapFN();
    *gmsg << "* RF Field map file name= " << fmfn << endl;

    double angle = elptr->getAzimuth();
    *gmsg << "* Cavity azimuth position= " << angle << " [deg] " << endl;

    double gap = elptr->getGapWidth();
    *gmsg << "* Cavity gap width= " << gap << " [mm] " << endl;

    double pdis = elptr->getPerpenDistance();
    *gmsg << "* Cavity Shift distance= " << pdis << " [mm] " << endl;

    double phi0 = elptr->getPhi0();
    *gmsg << "* Initial RF phase (t=0)= " << phi0 << " [deg] " << endl;

    /*
      Setup time dependence and in case of no
      timedependence use a polynom with  a_0 = 1 and a_k = 0, k = 1,2,3.
    */

    std::shared_ptr<AbstractTimeDependence> freq_atd = nullptr;
    std::shared_ptr<AbstractTimeDependence> ampl_atd = nullptr;
    std::shared_ptr<AbstractTimeDependence> phase_atd = nullptr;

    dvector_t  unityVec;
    unityVec.push_back(1.);
    unityVec.push_back(0.);
    unityVec.push_back(0.);
    unityVec.push_back(0.);

    if (elptr->getFrequencyModelName() != "") {
        freq_atd = AbstractTimeDependence::getTimeDependence(elptr->getFrequencyModelName());
        *gmsg << "* Variable frequency RF Model name " << elptr->getFrequencyModelName() << endl;
    }
    else
        freq_atd = std::shared_ptr<AbstractTimeDependence>(new PolynomialTimeDependence(unityVec));

    if (elptr->getAmplitudeModelName() != "") {
        ampl_atd = AbstractTimeDependence::getTimeDependence(elptr->getAmplitudeModelName());
        *gmsg << "* Variable amplitude RF Model name " << elptr->getAmplitudeModelName() << endl;
    }
    else
        ampl_atd = std::shared_ptr<AbstractTimeDependence>(new PolynomialTimeDependence(unityVec));

    if (elptr->getPhaseModelName() != "") {
        phase_atd = AbstractTimeDependence::getTimeDependence(elptr->getPhaseModelName());
        *gmsg << "* Variable phase RF Model name " << elptr->getPhaseModelName() << endl;
    }
    else
        phase_atd = std::shared_ptr<AbstractTimeDependence>(new PolynomialTimeDependence(unityVec));

    // read cavity voltage profile data from file.
    elptr->initialise(itsBunch, freq_atd, ampl_atd, phase_atd);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;

    BcParameter[0] = 0.001 * rmin;
    BcParameter[1] = 0.001 * rmax;
    BcParameter[2] = 0.001 * pdis;
    BcParameter[3] = angle;

    buildupFieldList(BcParameter, ElementBase::RFCAVITY, elptr);
}

/**
 *
 *
 * @param rfq
 */
void ParallelCyclotronTracker::visitRFQuadrupole(const RFQuadrupole &rfq) {
    *gmsg << "In RFQuadrupole; L = " << rfq.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<RFQuadrupole *>(rfq.clone()));
}

/**
 *
 *
 * @param bend
 */
void ParallelCyclotronTracker::visitSBend(const SBend &bend) {
    *gmsg << "In SBend; L = " << bend.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<SBend *>(bend.clone()));
}

/**
 *
 *
 * @param sep
 */
void ParallelCyclotronTracker::visitSeparator(const Separator &sep) {
    *gmsg << "In Seapator L= " << sep.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<Separator *>(sep.clone()));
}

/**
 *
 *
 * @param sept
 */
void ParallelCyclotronTracker::visitSeptum(const Septum &sept) {

    *gmsg << endl << "* -----------------------------  Septum ------------------------------- *" << endl;

    Septum *elptr = dynamic_cast<Septum *>(sept.clone());
    myElements.push_back(elptr);

    double xstart = elptr->getXstart();
    *gmsg << "XStart = " << xstart << " [mm]" << endl;

    double xend = elptr->getXend();
    *gmsg << "XEnd = " << xend << " [mm]" << endl;

    double ystart = elptr->getYstart();
    *gmsg << "YStart = " << ystart << " [mm]" << endl;

    double yend = elptr->getYend();
    *gmsg << "YEnd = " << yend << " [mm]" << endl;

    double width = elptr->getWidth();
    *gmsg << "Width = " << width << " [mm]" << endl;


    // initialise, do nothing
    elptr->initialise(itsBunch);

    double BcParameter[8];
    for(