ParallelCyclotronTracker.cpp 154 KB
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// ------------------------------------------------------------------------
// $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 $
//
// ------------------------------------------------------------------------
#include <cfloat>
#include <iostream>
#include <fstream>
#include <vector>
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#include "AbstractObjects/OpalData.h"
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#include "Algorithms/ParallelCyclotronTracker.h"

#include "AbsBeamline/Collimator.h"
#include "AbsBeamline/Corrector.h"
#include "AbsBeamline/Cyclotron.h"
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#include "AbsBeamline/Degrader.h"
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#include "AbsBeamline/Diagnostic.h"
#include "AbsBeamline/Drift.h"
#include "AbsBeamline/ElementBase.h"
#include "AbsBeamline/Lambertson.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"
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#include "AbsBeamline/SBend3D.h"
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#include "AbsBeamline/Separator.h"
#include "AbsBeamline/Septum.h"
#include "AbsBeamline/Solenoid.h"
#include "AbsBeamline/CyclotronValley.h"
#include "AbsBeamline/Stripper.h"
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#include "Elements/OpalBeamline.h"
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#include "Elements/OpalRing.h"
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#include "BeamlineGeometry/Euclid3D.h"
#include "BeamlineGeometry/PlanarArcGeometry.h"
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#include "BeamlineGeometry/RBendGeometry.h"
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#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"

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#include "Structure/BoundaryGeometry.h"
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#include "Ctunes.h"
#include "Ctunes.cc"
#include <cassert>

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

class Beamline;
class PartData;
using Physics::c;
using Physics::m_p; // GeV
using Physics::PMASS;
using Physics::PCHARGE;
using Physics::pi;
using Physics::q_e;

const double c_mmtns = c * 1.0e-6; // m/s --> mm/ns
const double mass_coeff = 1.0e18 * q_e / c / c; // from GeV/c^2 to basic unit: GV*C*s^2/m^2

#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),
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    eta_m(0.01),
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    myNode_m(Ippl::myNode()),
    initialLocalNum_m(0),
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    initialTotalNum_m(0),
    opalRing_m(NULL) {
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    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),
    timeIntegrator_m(timeIntegrator),
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    eta_m(0.01),
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    myNode_m(Ippl::myNode()),
    initialLocalNum_m(bunch.getLocalNum()),
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    initialTotalNum_m(bunch.getTotalNum()),
    opalRing_m(NULL) {
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    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");
}

/**
 * Destructor ParallelCyclotronTracker
 *
 */
ParallelCyclotronTracker::~ParallelCyclotronTracker() {
    for(list<Component *>::iterator compindex = myElements.begin(); compindex != myElements.end(); compindex++) {
        delete(*compindex);
    }
    for(beamline_list::iterator fdindex = FieldDimensions.begin(); fdindex != FieldDimensions.end(); fdindex++) {
        delete(*fdindex);
    }
    delete itsBeamline;
}

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/**
 * AAA
 *
 * @param none
 */
void ParallelCyclotronTracker::initializeBoundaryGeometry() {
  for(list<Component *>::iterator compindex = myElements.begin(); compindex != myElements.end(); compindex++) {
    bgf_m = dynamic_cast<ElementBase *>(*compindex)->getBoundaryGeometry();
    if(!bgf_m) 
      continue;
    else
      break;
  }
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  if (bgf_m) {
    itsDataSink->writeGeomToVtk(*bgf_m, string("data/testGeometry-00000.vtk"));
    OpalData::getInstance()->setGlobalGeometry(bgf_m);
    *gmsg << "* Boundary geometry initialized " << endl;
  }
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}
/**
 *
 *
 * @param fn Base file name
 */
void ParallelCyclotronTracker::bgf_main_collision_test() {
  if(!bgf_m) return;

  Inform msg("bgf_main_collision_test ");
  
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  /**                                                                                                      
   *Here we check if a particles is outside the domain, flag it for deletion
   */

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  Vector_t intecoords = bgf_m->getmaxcoords() + bgf_m->gethr();
  double dtime = 0.5 * itsBunch->getdT(); 
  int triId = 0;     
  size_t Nimpact = 0;
  for(size_t i = 0; i < itsBunch->getLocalNum(); i++) {
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    int res = bgf_m->PartInside(itsBunch->R[i]*1.0e-3, itsBunch->P[i], dtime, itsBunch->PType[i], itsBunch->Q[i], intecoords, triId);
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    if(res >= 0) { 
      itsBunch->Bin[i] = -1;
      Nimpact++;
    }               
  }
}


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

    string  SfileName2 = SfileName + string("-Angle0.dat");

    outfTheta0_m.precision(8);
    outfTheta0_m.setf(ios::scientific, ios::floatfield);
    outfTheta0_m.open(SfileName2.c_str());
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    outfTheta0_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma" << endl;
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    SfileName2 = SfileName + string("-Angle1.dat");
    outfTheta1_m.precision(8);
    outfTheta1_m.setf(ios::scientific, ios::floatfield);
    outfTheta1_m.open(SfileName2.c_str());
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    outfTheta1_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma"  << endl;
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    SfileName2 = SfileName + string("-Angle2.dat");
    outfTheta2_m.precision(8);
    outfTheta2_m.setf(ios::scientific, ios::floatfield);
    outfTheta2_m.open(SfileName2.c_str());
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    outfTheta2_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma"  << endl;
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    // for single Particle Mode, output after each turn, to define matched initial phase ellipse.

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

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

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

/**
 * 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();
}

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/** 
 *
 * @param ring
 */
void ParallelCyclotronTracker::visitOpalRing(const OpalRing &ring) {
    *gmsg << "Adding OpalRing" << endl;
    if (opalRing_m != NULL) {
        delete opalRing_m;
    }
    opalRing_m = dynamic_cast<OpalRing*>(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::visitOpalRing",
                            "PHIINIT is out of [-180, 180)!");
    }
    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 / 180.0 * pi);
    cosRefTheta_m = cos(referenceTheta / 180.0 * pi);
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    double BcParameter[8];
    for(int i = 0; i < 8; i++) BcParameter[i] = 0.0;
    buildupFieldList(BcParameter, "OPALRING", 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;
}
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/**
 *
 *
 * @param cycl
 */
void ParallelCyclotronTracker::visitCyclotron(const Cyclotron &cycl) {

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

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    Cyclotron *elptr = dynamic_cast<Cyclotron *>(cycl.clone());
    myElements.push_back(elptr);
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    if(!OpalData::getInstance()->inRestartRun()) {
      // get values from cyclotron command
      referenceR     = elptr->getRinit();
      referenceTheta = elptr->getPHIinit();
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      referenceZ     = elptr->getZinit();
      referencePr    = elptr->getPRinit();
      referencePz    = elptr->getPZinit();
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      //msg << "PRINIT= " << pri << " [CU]" << endl;
      
      if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
        throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron", "PHIINIT is out of [-180, 180)!");
      }
      referencePtot =  itsReference.getGamma() * itsReference.getBeta();
    } 
    else {
      // in case of a restart the values from the h5 file are already within this class
      if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
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        throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron", "PHIINIT is out of [-180, 180)!");
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      }
      referencePtot =  bega;
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    }
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    // TEMP for testing if we can inject a bunch vertically for inflector -DW
    // This will probably not work for long bunches, also I don't know what happens for a restart
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    //Vector_t pmean = itsBunch->get_pmean();
    //referencePz = pmean[2];
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    //referencePr = sqrt(pmean[0] * pmean[0] + pmean[1] * pmean[1]);
    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 {
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      referencePt = sqrt(insqrt);
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    }
    // End TEMP
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    // Old Pz and Pt
    //referencePz = 0.0;
    //referencePt = sqrt(referencePtot * referencePtot - referencePr * referencePr);

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

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    sinRefTheta_m = sin(referenceTheta / 180.0 * pi);
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    cosRefTheta_m = cos(referenceTheta / 180.0 * pi);   
   
    *gmsg << "" << endl;

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    *gmsg << "* Bunch global starting position:" << endl;
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    *gmsg << "* RINIT = " << referenceR  << " [mm]" << endl;
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    *gmsg << "* PHIINIT = " << referenceTheta << " [deg]" << endl;
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    *gmsg << "* ZINIT = " << referenceZ << " [mm]" << endl;

    *gmsg << "" << endl;

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    *gmsg << "* Bunch global starting momenta:" << endl;
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    *gmsg << "* Initial gamma = " << itsReference.getGamma() << endl;

    *gmsg << "* Initial beta = " << itsReference.getBeta() << endl;

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    *gmsg << "* Total reference momentum (beta * gamma) = " << referencePtot * 1000.0 << " [MCU]" << endl;
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    *gmsg << "* Reference azimuthal momentum (Pt) = " << referencePt * 1000.0 << " [MCU]" << endl;
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    *gmsg << "* Reference radial momentum (Pr) = " << referencePr * 1000.0 << " [MCU]" << endl;
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    *gmsg << "* Reference axial momentum (Pz) = " << referencePz * 1000.0 << " [MCU]" << endl;
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    *gmsg << "" << endl;

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    double sym = elptr->getSymmetry();
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    *gmsg << "* " << sym << "-fold field symmerty " << endl;
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    // ckr: this just returned the default value as defined in Component.h
    // double rff = elptr->getRfFrequ();
    // *gmsg << "* Rf frequency= " << rff << " [MHz]" << endl;
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    string fmfn = elptr->getFieldMapFN();
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    *gmsg << "* Field map file name = " << fmfn << " " << endl;
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    string type = elptr->getType();
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    *gmsg << "* Type of cyclotron = " << type << " " << endl;
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    double rmin = elptr->getMinR();
    double rmax = elptr->getMaxR();
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    *gmsg << "* Radial aperture = " << rmin << " ... " << rmax<<" [mm] "<< endl;
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    double zmin = elptr->getMinZ();
    double zmax = elptr->getMaxZ();
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    *gmsg << "* Vertical aperture = " << zmin << " ... " << zmax<<" [mm]"<< endl;
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    /**
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    bool Sflag = elptr->getSuperpose();
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    string flagsuperposed;
    if (Sflag)
      flagsuperposed="yes";
    else
      flagsuperposed="no";
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    *gmsg << "* Electric field maps are superposed? " << flagsuperposed << " " << endl;
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    */
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    double h = elptr->getCyclHarm();
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    *gmsg << "* Harmonic number h = " << h << " " << endl;
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    /**
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    if (elptr->getSuperpose())
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        *gmsg << "* Fields are superposed " << endl;
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    */
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    /**
     * 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
     */
    int  fieldflag;
    if(type == string("CARBONCYCL")) {
        fieldflag = 2;
    } else if(type == string("CYCIAE")) {
        fieldflag = 3;
    } else if(type == string("AVFEQ")) {
        fieldflag = 4;
    } else if(type == string("FFAG")) {
        fieldflag = 5;
    } else if(type == string("BANDRF")) {
        fieldflag = 6;
    } else
        fieldflag = 1;

    // read field map on the  middle plane of cyclotron.
    // currently scalefactor is set to 1.0
    elptr->initialise(itsBunch, fieldflag, 1.0);

    double BcParameter[8];
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    for(int i = 0; i < 8; i++) 
      BcParameter[i] = 0.0;
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    string ElementType = "CYCLOTRON";
    BcParameter[0] = elptr->getRmin();
    BcParameter[1] = elptr->getRmax();

    // store inner radius and outer radius of cyclotron field map in the list
    buildupFieldList(BcParameter, ElementType, 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) {

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    *gmsg << "* --------- Collimator -----------------------------" << endl;
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    Collimator* elptr = dynamic_cast<Collimator *>(coll.clone());
    myElements.push_back(elptr);
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    double xstart = elptr->getXStart();
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    *gmsg << "* Xstart= " << xstart << " [mm]" << endl;
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    double xend = elptr->getXEnd();
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    *gmsg << "* Xend= " << xend << " [mm]" << endl;
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    double ystart = elptr->getYStart();
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    *gmsg << "* Ystart= " << ystart << " [mm]" << endl;
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    double yend = elptr->getYEnd();
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    *gmsg << "* Yend= " <<yend << " [mm]" << endl;
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    double zstart = elptr->getZStart();
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    *gmsg << "* Zstart= " << zstart << " [mm]" << endl;
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    double zend = elptr->getZEnd();
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    *gmsg << "* Zend= " <<zend << " [mm]" << endl;
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    double width = elptr->getWidth();
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    *gmsg << "* Width= " << width << " [mm]" << endl;
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    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "CCOLLIMATOR";
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    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
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    BcParameter[4] = width ;
    buildupFieldList(BcParameter, ElementType, elptr);
}

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

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

}


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/**
 *
 *
 * @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()));
}

/**
 *
 *
 * @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());
}

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/**
 *
 *
 * @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) {
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    *gmsg << "* -----------  Probe -------------------------------" << endl;
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    Probe *elptr = dynamic_cast<Probe *>(prob.clone());
    myElements.push_back(elptr);
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    double xstart = elptr->getXstart();
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    *gmsg << "XStart= " << xstart << " [mm]" << endl;
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    double xend = elptr->getXend();
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    *gmsg << "XEnd= " << xend << " [mm]" << endl;
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    double ystart = elptr->getYstart();
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    *gmsg << "YStart= " << ystart << " [mm]" << endl;
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    double yend = elptr->getYend();
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    *gmsg << "YEnd= " << yend << " [mm]" << endl;
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    double width = elptr->getWidth();
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    *gmsg << "Width= " << width << " [mm]" << endl;
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    // initialise, do nothing
    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "PROBE";
    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
    BcParameter[4] = width ;

    // store probe parameters in the list
    buildupFieldList(BcParameter, ElementType, 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()));
}

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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");
}

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

    *gmsg << "* --------- RFCavity ------------------------------" << endl;
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    RFCavity *elptr = dynamic_cast<RFCavity *>(as.clone());
    myElements.push_back(elptr);
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    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 ...");
    }

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

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

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

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

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

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

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


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

    // read cavity voltage profile data from file.
    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "CAVITY";
    BcParameter[0] = rmin;
    BcParameter[1] = rmax;
    BcParameter[2] = pdis;
    BcParameter[3] = angle;

    buildupFieldList(BcParameter, ElementType, 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) {
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    *gmsg << "* -----------  Septum -------------------------------" << endl;
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    Septum *elptr = dynamic_cast<Septum *>(sept.clone());
    myElements.push_back(elptr);
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    double xstart = elptr->getXstart();
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    *gmsg << "XStart= " << xstart << " [mm]" << endl;
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    double xend = elptr->getXend();
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    *gmsg << "XEnd= " << xend << " [mm]" << endl;
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    double ystart = elptr->getYstart();
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    *gmsg << "YStart= " << ystart << " [mm]" << endl;
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    double yend = elptr->getYend();
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    *gmsg << "YEnd= " << yend << " [mm]" << endl;
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    double width = elptr->getWidth();
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    *gmsg << "Width= " << width << " [mm]" << endl;
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    // initialise, do nothing
    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "SEPTUM";
    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
    BcParameter[4] = width ;

    // store septum parameters in the list
    buildupFieldList(BcParameter, ElementType, elptr);
}

/**
 *
 *
 * @param solenoid
 */
void ParallelCyclotronTracker::visitSolenoid(const Solenoid &solenoid) {
    myElements.push_back(dynamic_cast<Solenoid *>(solenoid.clone()));
    Component *elptr = *(--myElements.end());
    if(!elptr->hasAttribute("ELEMEDGE")) {
        *gmsg << "Solenoid: no position of the element given!" << endl;
        return;
    }
}

/**
 *
 *
 * @param pplate
 */
void ParallelCyclotronTracker::visitParallelPlate(const ParallelPlate &pplate) {//do nothing

    //*gmsg << "ParallelPlate: not in use in ParallelCyclotronTracker!" << endl;

    //buildupFieldList(startField, endField, elptr);

}

/**
 *
 *
 * @param cv
 */
void ParallelCyclotronTracker::visitCyclotronValley(const CyclotronValley &cv) {
    // Do nothing here.
}
/**
 * not used
 *
 * @param angle
 * @param curve
 * @param field
 * @param scale
 */
void ParallelCyclotronTracker::applyEntranceFringe(double angle, double curve,
        const BMultipoleField &field, double scale) {

}

/**
 *
 *
 * @param stripper
 */

void ParallelCyclotronTracker::visitStripper(const Stripper &stripper) {

    *gmsg << "* ---------Stripper------------------------------" << endl;

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    Stripper *elptr = dynamic_cast<Stripper *>(stripper.clone());
    myElements.push_back(elptr);

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

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

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

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

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

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    double opcharge = elptr->getOPCharge();
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    *gmsg << "Charge of outcome particle = +e * " << opcharge << endl;

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    double opmass = elptr->getOPMass();
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    *gmsg << "* Mass of the outcome particle = " << opmass << " [GeV/c^2]" << endl;
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    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "STRIPPER";
    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
    BcParameter[4] = width ;
    BcParameter[5] = opcharge;
    BcParameter[6] = opmass;

    buildupFieldList(BcParameter, ElementType, elptr);
}


void ParallelCyclotronTracker::applyExitFringe(double angle, double curve,
        const BMultipoleField &field, double scale) {

}


/**
 *
 *
 * @param BcParameter
 * @param ElementType
 * @param elptr
 */
void ParallelCyclotronTracker::buildupFieldList(double BcParameter[], string ElementType, Component *elptr) {
    beamline_list::iterator sindex;

    type_pair *localpair = new type_pair();
    localpair->first = ElementType;

    for(int i = 0; i < 8; i++)
        *(((localpair->second).first) + i) = *(BcParameter + i);

    (localpair->second).second = elptr;

    // always put cyclotron as the first element in the list.
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    if(ElementType == "OPALRING") {
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        sindex = FieldDimensions.begin();
    } else {
        sindex = FieldDimensions.end();
    }
    FieldDimensions.insert(sindex, localpair);

}

/**
 *
 *
 * @param bl
 */
void ParallelCyclotronTracker::visitBeamline(const Beamline &bl) {
    itsBeamline->iterate(*dynamic_cast<BeamlineVisitor *>(this), false);
}

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void ParallelCyclotronTracker::checkNumPart(std::string s) {
    int nlp = itsBunch->getLocalNum();
    int minnlp = 0;
    int maxnlp = 111111;
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    reduce(nlp, minnlp, OpMinAssign());
    reduce(nlp, maxnlp, OpMaxAssign());
    *gmsg << s << " min local particle number " << minnlp << " max local particle number: " << maxnlp << endl;
}

/**
 *
 *
 */
void ParallelCyclotronTracker::execute() {

    /*
      Initialize common variables and structures
      for the integrators
    */

    step_m = 0;
    restartStep0_m = 0;
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    // record how many bunches have already been injected. ONLY FOR MPM
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    BunchCount_m = itsBunch->getNumBunch();

    // For the time being, we set bin number equal to bunch number. FixMe: not used
    BinCount_m = BunchCount_m;

    itsBeamline->accept(*this);
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    if (opalRing_m != NULL)
        opalRing_m->lockRing();
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    // display the selected elements
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    *gmsg << "* -----------------------------" << endl;
    *gmsg << "* The selected Beam line elements are :" << endl;
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    for(beamline_list::iterator sindex = FieldDimensions.begin(); sindex != FieldDimensions.end(); sindex++)
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      *gmsg << "* -> " <<  ((*sindex)->first) << endl;
    *gmsg << "* -----------------------------" << endl;
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    initializeBoundaryGeometry();

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    // external field arrays for dumping
    for(int k = 0; k < 2; k++)
        FDext_m[k] = Vector_t(0.0, 0.0, 0.0);
    extE_m = Vector_t(0.0, 0.0, 0.0);
    extB_m = Vector_t(0.0, 0.0, 0.0);

    if(timeIntegrator_m == 0) {
        *gmsg << "* 4th order Runge-Kutta integrator" << endl;
        Tracker_RK4();
    } else if(timeIntegrator_m == 1) {
        *gmsg << "* 2nd order Leap-Frog integrator" << endl;
        Tracker_LF();
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    } else if(timeIntegrator_m == 2) {
        *gmsg << "* Multiple time stepping (MTS) integrator" << endl;
        Tracker_MTS();
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    } else {
        *gmsg << "ERROR: Invalid name of TIMEINTEGRATOR in Track command" << endl;
        exit(1);
    }

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    *gmsg << "* -----------------------------" << endl;
    *gmsg << "* Finalizing i.e. write data and close files :" << endl;
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    for(beamline_list::iterator sindex = FieldDimensions.begin(); sindex != FieldDimensions.end(); sindex++) {
        (((*sindex)->second).second)->finalise();
    }
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    *gmsg << "* -----------------------------" << endl;
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}

/**
   In general the two tracker have much code in common.
   This is a great source of errors.
   Need to avoid this

*/



/**
 *
 *
 */
void ParallelCyclotronTracker::Tracker_LF() {

    BorisPusher pusher;

    // time steps interval between bunches for multi-bunch simulation.
    const int stepsPerTurn = itsBunch->getStepsPerTurn();

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    const double harm = getHarmonicNumber();
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    // load time
    const double dt = itsBunch->getdT() * 1.0e9 * harm; //[s]-->[ns]

    // find the injection time interval
    if(numBunch_m > 1) {
        *gmsg << "Time interval between neighbour bunches is set to " << stepsPerTurn *dt << "[ns]" << endl;
    }

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    initTrackOrbitFile();
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    int SteptoLastInj = itsBunch->getSteptoLastInj();

    // get data from h5 file for restart run
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    if(OpalData::getInstance()->inRestartRun()) {
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        restartStep0_m = itsBunch->getLocalTrackStep();
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        step_m = restartStep0_m;
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        if (numBunch_m > 1) itsBunch->resetPartBinID2(eta_m);
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        *gmsg << "* Restart at integration step " << restartStep0_m << endl;
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    }

    if(OpalData::getInstance()->hasBunchAllocated() && Options::scan) {
        lastDumpedStep_m = 0;
        itsBunch->setT(0.0);
    }

    *gmsg << "* Beginning of this run is at t= " << itsBunch->getT() * 1e9 << " [ns]" << endl;
    *gmsg << "* The time step is set to dt= " << dt << " [ns]" << endl;

    // for single Particle Mode, output at zero degree.
    if(initialTotalNum_m == 1)
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        openFiles(OpalData::getInstance()->getInputBasename());
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    double const initialReferenceTheta = referenceTheta / 180.0 * pi;
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    initDistInGlobalFrame();
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    //  read in some control parameters
    const int SinglePartDumpFreq = Options::sptDumpFreq;
    const int resetBinFreq = Options::rebinFreq;
    const int scSolveFreq = Options::scSolveFreq;
    const bool doDumpAfterEachTurn = Options::psDumpEachTurn;


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    int boundpDestroyFreq = 10; // TODO: Should this be treated as a control parameter? 
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    // prepare for dump after each turn
    double oldReferenceTheta = initialReferenceTheta;

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    *gmsg << "* Single particle trajectory dump frequency is set to " << SinglePartDumpFreq << endl;
    *gmsg << "* Repartition frequency is set to " << Options::repartFreq << endl;
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    if(numBunch_m > 1)
        *gmsg << "particles energy bin ID reset frequency is set to " << resetBinFreq << endl;

    // if initialTotalNum_m = 2, trigger SEO mode
    // prepare for transverse tuning calculation
    vector<double> Ttime, Tdeltr, Tdeltz;
    // prepare for transverse tuning calculation
    vector<int> TturnNumber;
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    turnnumber_m = 1;
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    // flag to determine when to transit from single-bunch to multi-bunches mode
    bool flagTransition = false;
    // step point determining the next time point of check for transition
    int stepsNextCheck = step_m + itsBunch->getStepsPerTurn();

    const  double deltaTheta = pi / (stepsPerTurn);
    // record at which angle the space charge are solved
    double angleSpaceChargeSolve = 0.0;

    if(initialTotalNum_m == 1) {
        *gmsg << "* *---------------------------- SINGLE PARTICLE MODE------ ----------------------------*** " << endl;
        *gmsg << "* Instruction: when the total particle number equal to 1, single particle mode is triggered automatically," << endl
              << "* The initial distribution file must be specified which should contain only one line for the single particle " << endl
              << "* *------------NOTE: SINGLE PARTICLE MODE ONLY WORKS SERIALLY ON SINGLE NODE ------------------*** " << endl;
        if(Ippl::getNodes() != 1)
            throw OpalException("Error in ParallelCyclotronTracker::execute", "SINGLE PARTICLE MODE ONLY WORKS SERIALLY ON SINGLE NODE!");

    } else if(initialTotalNum_m == 2) {
        *gmsg << "* *------------------------ STATIC EQUILIBRIUM ORBIT MODE ----------------------------*** " << endl;
        *gmsg << "* Instruction: when the total particle number equal to 2, SEO mode is triggered automatically." << endl
              << "* This mode does NOT include any RF cavities. The initial distribution file must be specified" << endl
              << "* In the file the first line is for reference particle and the second line is for offcenter particle." << endl
              << "* The tunes are calculated by FFT routines based on these two particles. " << endl
              << "* *------------NOTE: SEO MODE ONLY WORKS SERIALLY ON SINGLE NODE ------------------*** " << endl;
        if(Ippl::getNodes() != 1)
            throw OpalException("Error in ParallelCyclotronTracker::execute", "SEO MODE ONLY WORKS SERIALLY ON SINGLE NODE!");
    }

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    // apply the plugin elements: probe, collimator, stripper, septum
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    // make sure that we apply elements even on first step
    applyPluginElements(dt);

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    // *****************II***************
    // main integration loop
    // *****************II***************
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    *gmsg << "* ---------------------------- Start tracking ----------------------------" << endl;
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    for(; step_m < maxSteps_m; step_m++) {
        bool dumpEachTurn = false;
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        if(step_m % SinglePartDumpFreq == 0) {
            singleParticleDump();
        }
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        Ippl::Comm->barrier();

        // Push for first half step
        itsBunch->R *= Vector_t(0.001);
        push(0.5 * dt * 1e-9);
        itsBunch->R *= Vector_t(1000.0);

        // bunch injection
        if(numBunch_m > 1) {

            if((BunchCount_m == 1) && (multiBunchMode_m == 2) && (!flagTransition)) {
                if(step_m == stepsNextCheck) {
                    // under 3 conditions, following code will be execute
                    // to check the distance between two neighborring bunches
                    // 1.multi-bunch mode, AUTO sub-mode
                    // 2.After each revolution
                    // 3.only one bunch exists

                    *gmsg << "checking for automatically injecting new bunch ..." << endl;

                    itsBunch->R /= Vector_t(1000.0); // mm --> m
                    itsBunch->calcBeamParameters_cycl();
                    itsBunch->R *= Vector_t(1000.0); // m --> mm

                    Vector_t Rmean = itsBunch->get_centroid() * 1000.0; // m --> mm

                    RThisTurn_m = sqrt(pow(Rmean[0], 2.0) + pow(Rmean[1], 2.0));

                    Vector_t Rrms = itsBunch->get_rrms() * 1000.0; // m --> mm

                    double XYrms =  sqrt(pow(Rrms[0], 2.0) + pow(Rrms[1], 2.0));


                    // if the distance between two neighbour bunch is less than CoeffDBunches_m times of its 2D rms size
                    // start multi-bunch simulation, fill current phase space to initialR and initialP arrays

                    if((RThisTurn_m - RLastTurn_m) < CoeffDBunches_m * XYrms) {
                        // since next turn, start multi-bunches
                        saveOneBunch();
                        flagTransition = true;

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                        *gmsg << "*** Save beam distribution at turn #" << turnnumber_m << " ***" << endl;
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                        *gmsg << "*** After one revolution, Multi-Bunch Mode will be invoked ***" << endl;
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                    }

                    stepsNextCheck += stepsPerTurn;

                    *gmsg << "RLastTurn = " << RLastTurn_m << " [mm]" << endl;
                    *gmsg << "RThisTurn = " << RThisTurn_m << " [mm]" << endl;
                    *gmsg << "    XYrms = " << XYrms    << " [mm]" << endl;

                    RLastTurn_m = RThisTurn_m;
                }
            } else if(SteptoLastInj == stepsPerTurn - 1) {
                if(BunchCount_m < numBunch_m) {

                    // under 4 conditions, following code will be execute
                    // to read new bunch from hdf5 format file for FORCE or AUTO mode
                    // 1.multi-bunch mode
                    // 2.after each revolution
                    // 3.existing bunches is less than the specified bunches
                    // 4.FORCE mode, or AUTO mode with flagTransition = true
                    // Note: restart from 1 < BunchCount < numBunch_m must be avoided.
                    *gmsg << "step " << step_m << ", inject a new bunch... ... ..." << endl;
                    BunchCount_m++;

                    // read initial distribution from h5 file
                    if(multiBunchMode_m == 1) {
                        readOneBunch(BunchCount_m - 1);
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                        itsBunch->resetPartBinID2(eta_m);
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                    } else if(multiBunchMode_m == 2) {

                        if(OpalData::getInstance()->inRestartRun())
                            readOneBunchFromFile(BunchCount_m - 1);
                        else
                            readOneBunch(BunchCount_m - 1);

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                        itsBunch->resetPartBinID2(eta_m);
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                    }

                    SteptoLastInj = 0;

                    itsBunch->setNumBunch(BunchCount_m);

                    stepsNextCheck += stepsPerTurn;

                    // update  after injection
                    itsBunch->boundp();

                    Ippl::Comm->barrier();
                    *gmsg << BunchCount_m << "'th bunch injected, total particle number = " << itsBunch->getTotalNum() << endl;
                }
            } else if(BunchCount_m == numBunch_m) {
                // After this, numBunch_m is wrong but useless
                numBunch_m--;

            } else {
                SteptoLastInj++;
            }
        }

        // calculate self fields Space Charge effects are included only when total macropaticles number is NOT LESS THAN 1000.
        if(itsBunch->hasFieldSolver() && initialTotalNum_m >= 1000) {
            if(step_m % scSolveFreq == 0) {
                //    *gmsg << "Calculate space charge at step " << step_m<<endl;
                // Firstly reset E and B to zero before fill new space charge field data for each track step
                itsBunch->Bf = Vector_t(0.0);
                itsBunch->Ef = Vector_t(0.0);

                Vector_t const meanR = calcMeanR();
                if((itsBunch->weHaveBins()) && BunchCount_m > 1) {
                    IpplTimings::startTimer(TransformTimer_m);
                    double const binsPhi = itsBunch->calcMeanPhi() - 0.5 * pi;
                    angleSpaceChargeSolve = binsPhi;
                    globalToLocal(itsBunch->R, binsPhi, meanR);

                    //scale coordinates
                    itsBunch->R /= Vector_t(1000.0); // mm --> m

                    if((step_m + 1) % boundpDestroyFreq == 0)
                        itsBunch->boundp_destroy();
                    else
                        itsBunch->boundp();

                    IpplTimings::stopTimer(TransformTimer_m);

                    // calcualte gamma for each energy bin
                    itsBunch->calcGammas_cycl();

                    repartition();
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                    // calculate space charge field for each energy bin
                    for(int b = 0; b < itsBunch->getLastemittedBin() ; b++) {

                        if(itsBunch->pbin_m->getTotalNumPerBin(b) >= 1000) {
                            //if(itsBunch->getNumPartInBin(b) >= 1000) {
                            itsBunch->setBinCharge(b, itsBunch->getChargePerParticle());
                            //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%//
                            itsBunch->computeSelfFields_cycl(b);
                            //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%//
                            INFOMSG("Bin:" << b << ", charge per particle " <<  itsBunch->getChargePerParticle() << endl);
                        } else {
                            INFOMSG("Note: Bin " << b << ": less than 1000 particles, omit space charge fields" << endl);
                        }
                    }

                    itsBunch->Q = itsBunch->getChargePerParticle();

                    IpplTimings::startTimer(TransformTimer_m);

                    //scale coordinates back
                    itsBunch->R *= Vector_t(1000.0); // m --> mm
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                    localToGlobal(itsBunch->R, binsPhi, meanR);
                    localToGlobal(itsBunch->Ef, binsPhi);
                    localToGlobal(itsBunch->Bf, binsPhi);
                } else {
                    Vector_t const meanP = calcMeanP();
                    double const phi = calculateAngle(meanP(0), meanP(1)) - 0.5 * pi;
                    angleSpaceChargeSolve = phi;
                    globalToLocal(itsBunch->R, phi, meanR);

                    //scale coordinates
                    itsBunch->R /= Vector_t(1000.0); // mm --> m

                    if((step_m + 1) % boundpDestroyFreq == 0)
                        itsBunch->boundp_destroy();
                    else
                        itsBunch->boundp();

                    IpplTimings::stopTimer(TransformTimer_m);
                    repartition();
                    //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%//
                    double const meanGamma = sqrt(1.0 + pow(meanP(0), 2.0) + pow(meanP(1), 2.0));
                    itsBunch->computeSelfFields_cycl(meanGamma);
                    //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%//

                    IpplTimings::startTimer(TransformTimer_m);

                    //scale coordinates back
                    itsBunch->R *= Vector_t(1000.0); // m --> mm
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