ParallelTracker.cpp

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//
// Class ParallelTracker
//   OPAL-T tracker.
//   The visitor class for tracking particles with time as independent
//   variable.
//
// Copyright (c) 200x - 2014, Christof Kraus, Paul Scherrer Institut, Villigen PSI, Switzerland
//               2015 - 2016, Christof Metzger-Kraus, Helmholtz-Zentrum Berlin, Germany
//               2017 - 2020, Christof Metzger-Kraus
// All rights reserved
//
// This file is part of OPAL.
//
// OPAL is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// You should have received a copy of the GNU General Public License
// along with OPAL. If not, see <https://www.gnu.org/licenses/>.
//
#include "Algorithms/ParallelTracker.h"
 
#include <cfloat>
#include <cmath>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <limits>
#include <sstream>
#include <string>
 
#include <boost/numeric/ublas/io.hpp>
 
#include "AbstractObjects/OpalData.h"
#include "Algorithms/CavityAutophaser.h"
#include "Algorithms/OrbitThreader.h"
#include "BasicActions/Option.h"
 
#include "Beamlines/Beamline.h"
#include "Beamlines/FlaggedBeamline.h"
#include "Distribution/Distribution.h"
#include "Physics/Units.h"
 
#include "Structure/BoundaryGeometry.h"
#include "Structure/BoundingBox.h"
#include "Utilities/OpalException.h"
#include "Utilities/Options.h"
#include "Utilities/Timer.h"
#include "Utilities/Util.h"
#include "ValueDefinitions/RealVariable.h"
 
#include "AbsBeamline/Offset.h"
#include "AbsBeamline/PluginElement.h"
#include "AbsBeamline/VerticalFFAMagnet.h"
 
extern Inform* gmsg;
 
class PartData;
 
ParallelTracker::ParallelTracker(
    const Beamline& beamline, const PartData& reference, bool revBeam, bool revTrack)
    : Tracker(beamline, reference, revBeam, revTrack),
      itsDataSink_m(nullptr),
      itsOpalBeamline_m(beamline.getOrigin3D(), beamline.getInitialDirection()),
      opalRing_m(nullptr),
      globalEOL_m(false),
      wakeStatus_m(false),
      wakeFunction_m(nullptr),
      pathLength_m(0.0),
      zstart_m(0.0),
      dtCurrentTrack_m(0.0),
      minStepforReBin_m(-1),
      repartFreq_m(0),
      emissionSteps_m(std::numeric_limits<unsigned int>::max()),
      numParticlesInSimulation_m(0),
      timeIntegrationTimer1_m(IpplTimings::getTimer("TIntegration1")),
      timeIntegrationTimer2_m(IpplTimings::getTimer("TIntegration2")),
      fieldEvaluationTimer_m(IpplTimings::getTimer("External field eval")),
      PluginElemTimer_m(IpplTimings::getTimer("PluginElements")),
      BinRepartTimer_m(IpplTimings::getTimer("Binaryrepart")),
      OrbThreader_m(IpplTimings::getTimer("OrbThreader")) {
}
 
ParallelTracker::ParallelTracker(
    const Beamline& beamline, PartBunch_t* bunch, DataSink& ds, const PartData& reference,
    bool revBeam, bool revTrack, const std::vector<unsigned long long>& maxSteps, double zstart,
    const std::vector<double>& zstop, const std::vector<double>& dt)
    : Tracker(beamline, bunch, reference, revBeam, revTrack),
      itsDataSink_m(&ds),
      itsOpalBeamline_m(beamline.getOrigin3D(), beamline.getInitialDirection()),
      opalRing_m(nullptr),
      globalEOL_m(false),
      wakeStatus_m(false),
      wakeFunction_m(nullptr),
      pathLength_m(0.0),
      zstart_m(zstart),
      dtCurrentTrack_m(0.0),
      minStepforReBin_m(-1),
      repartFreq_m(0),
      emissionSteps_m(std::numeric_limits<unsigned int>::max()),
      numParticlesInSimulation_m(0),
      timeIntegrationTimer1_m(IpplTimings::getTimer("TIntegration1")),
      timeIntegrationTimer2_m(IpplTimings::getTimer("TIntegration2")),
      fieldEvaluationTimer_m(IpplTimings::getTimer("External field eval")),
      BinRepartTimer_m(IpplTimings::getTimer("Binaryrepart")),
      OrbThreader_m(IpplTimings::getTimer("OrbThreader")) {
    
      for (unsigned int i = 0; i < zstop.size(); ++i) {
          stepSizes_m.push_back(dt[i], zstop[i], maxSteps[i]);
      }
 
      stepSizes_m.sortAscendingZStop();
      stepSizes_m.resetIterator();
}
 
ParallelTracker::~ParallelTracker() {
}
 
void ParallelTracker::visitScalingFFAMagnet(const ScalingFFAMagnet& bend) {
    *gmsg << "Adding ScalingFFAMagnet" << endl;
    /*
    if (opalRing_m != nullptr) {
        ScalingFFAMagnet* newBend = bend.clone(); // setup the end field, if required
        newBend->setupEndField();
        opalRing_m->appendElement(*newBend);
    } else {
        throw OpalException("ParallelCyclotronTracker::visitScalingFFAMagnet",
                            "Need to define a RINGDEFINITION to use ScalingFFAMagnet element");
    }
    */
}
 
void ParallelTracker::buildupFieldList(
    double BcParameter[], ElementType 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.
    if (elementType == ElementType::RING) {
        sindex = FieldDimensions.begin();
    } else {
        sindex = FieldDimensions.end();
    }
    FieldDimensions.insert(sindex, localpair);
}
 
/*
 * @param ring
 */
 
void ParallelTracker::visitRing(const Ring& ring) {
    *gmsg << "* ----------------------------- Ring ------------------------------------- *" << endl;
 
    delete opalRing_m;
 
    opalRing_m = dynamic_cast<Ring*>(ring.clone());
 
    myElements.push_back(opalRing_m);
 
    opalRing_m->initialise(itsBunch_m);
 
    referenceR     = opalRing_m->getBeamRInit();
    referencePr    = opalRing_m->getBeamPRInit();
    referenceTheta = opalRing_m->getBeamPhiInit();
 
    if (referenceTheta <= -180.0 || referenceTheta > 180.0) {
        throw OpalException(
            "Error in ParallelTracker::visitRing", "PHIINIT is out of [-180, 180)!");
    }
 
    referenceZ  = 0.0;
    referencePz = 0.0;
 
    referencePtot = itsReference.getGamma() * itsReference.getBeta();
    referencePt   = std::sqrt(referencePtot * referencePtot - referencePr * referencePr);
 
    if (referencePtot < 0.0)
        referencePt *= -1.0;
 
    sinRefTheta_m = std::sin(referenceTheta * Units::deg2rad);
    cosRefTheta_m = std::cos(referenceTheta * Units::deg2rad);
 
    double BcParameter[8] = {};  // zero initialise array
 
    buildupFieldList(BcParameter, ElementType::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 << " [beta gamma]" << endl;
    *gmsg << "* Reference azimuthal momentum  = " << referencePt << " [beta gamma]" << endl;
    *gmsg << "* Reference radial momentum     = " << referencePr << " [beta gamma]" << endl;
    *gmsg << "* " << opalRing_m->getSymmetry() << " fold field symmetry " << endl;
    *gmsg << "* Harmonic number h = " << opalRing_m->getHarmonicNumber() << " " << endl;
}
 
void ParallelTracker::visitVerticalFFAMagnet(const VerticalFFAMagnet& mag) {
    *gmsg << "Adding Vertical FFA Magnet" << endl;
    if (opalRing_m != nullptr)
        opalRing_m->appendElement(mag);
    else
        throw OpalException(
            "ParallelCyclotronTracker::visitVerticalFFAMagnet",
            "Need to define a RINGDEFINITION to use VerticalFFAMagnet element");
}
 
void ParallelTracker::visitBeamline(const Beamline& bl) {
    const FlaggedBeamline* fbl = static_cast<const FlaggedBeamline*>(&bl);
    if (fbl->getRelativeFlag()) {
        OpalBeamline stash(fbl->getOrigin3D(), fbl->getInitialDirection());
        stash.swap(itsOpalBeamline_m);
        fbl->iterate(*this, false);
        itsOpalBeamline_m.prepareSections();
        itsOpalBeamline_m.compute3DLattice();
        stash.merge(itsOpalBeamline_m);
        stash.swap(itsOpalBeamline_m);
    } else {
        fbl->iterate(*this, false);
    }
}
 
void ParallelTracker::visitOffset(const Offset& off) {
    if (opalRing_m == nullptr)
        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);
}
 
void ParallelTracker::updateRFElement(std::string elName, double maxPhase) {
    FieldList cavities       = itsOpalBeamline_m.getElementByType(ElementType::RFCAVITY);
    FieldList travelingwaves = itsOpalBeamline_m.getElementByType(ElementType::TRAVELINGWAVE);
    cavities.insert(cavities.end(), travelingwaves.begin(), travelingwaves.end());
 
    for (FieldList::iterator fit = cavities.begin(); fit != cavities.end(); ++fit) {
        if ((*fit).getElement()->getName() == elName) {
            RFCavity* element = static_cast<RFCavity*>((*fit).getElement().get());
 
            element->setPhasem(maxPhase);
            element->setAutophaseVeto();
 
            *ippl::Info << "Restored cavity phase from the h5 file. Name: " << element->getName()
                        << ", phase: " << maxPhase << " rad" << endl;
            return;
        }
    }
}
 
bool ParallelTracker::applyPluginElements(const double dt) {
    IpplTimings::startTimer(PluginElemTimer_m);
 
    bool flag = false;
    for (PluginElement* element : pluginElements_m) {
        bool tmp = element->check(itsBunch_m, turnnumber_m, itsBunch_m->getT(), dt);
        flag |= tmp;
 
        if (tmp) {
            itsBunch_m->updateNumTotal();
            *gmsg << "* Total number of particles after PluginElement= "
                  << itsBunch_m->getTotalNum() << endl;
        }
    }
 
    IpplTimings::stopTimer(PluginElemTimer_m);
    return flag;
}
 
void ParallelTracker::saveCavityPhases() {
    itsDataSink_m->storeCavityInformation();
}
 
void ParallelTracker::restoreCavityPhases() {
    typedef std::vector<MaxPhasesT>::iterator iterator_t;
 
    if (OpalData::getInstance()->hasPriorTrack() || OpalData::getInstance()->inRestartRun()) {
        iterator_t it  = OpalData::getInstance()->getFirstMaxPhases();
        iterator_t end = OpalData::getInstance()->getLastMaxPhases();
        for (; it < end; ++it) {
            updateRFElement((*it).first, (*it).second);
        }
    }
}
 
void ParallelTracker::execute() {
    Inform msg("ParallelTracker ", *gmsg);
    OpalData::getInstance()->setInPrepState(true);
    bool back_track = false;
 
    BorisPusher pusher(itsReference);
    const double globalTimeShift =
        itsBunch_m->weHaveEnergyBins() ? OpalData::getInstance()->getGlobalPhaseShift() : 0.0;
    OpalData::getInstance()->setGlobalPhaseShift(0.0);
 
    // the time step needs to be positive in the setup
    itsBunch_m->setdT(std::abs(itsBunch_m->getdT()));
    dtCurrentTrack_m = itsBunch_m->getdT();
 
    if (OpalData::getInstance()->hasPriorTrack() || OpalData::getInstance()->inRestartRun()) {
        OpalData::getInstance()->setOpenMode(OpalData::OpenMode::APPEND);
    }
 
    prepareSections();
 
    double minTimeStep = stepSizes_m.getMinTimeStep();
 
    itsOpalBeamline_m.activateElements();
 
    CoordinateSystemTrafo beamlineToLab = itsOpalBeamline_m.getCSTrafoLab2Local().inverted();
 
    itsBunch_m->toLabTrafo_m = beamlineToLab;
 
    itsBunch_m->RefPartR_m = beamlineToLab.transformTo(itsBunch_m->getParticleContainer()->getMeanR());
    itsBunch_m->RefPartP_m = beamlineToLab.rotateTo(itsBunch_m->getParticleContainer()->getMeanP());
 
    if (itsBunch_m->getTotalNum() > 0) {
        if (zstart_m > pathLength_m) {
            findStartPosition(pusher);
        }
 
        itsBunch_m->set_sPos(pathLength_m);
    }
 
    stepSizes_m.advanceToPos(zstart_m);
 
    Vector_t<double, 3> rmin(0.0), rmax(0.0);
    if (itsBunch_m->getTotalNum() > 0) {
        itsBunch_m->get_bounds(rmin, rmax);
    }
 
    *gmsg << "ParallelTrack: momentum=  " << itsBunch_m->getParticleContainer()->getMeanP()(2) << endl;
    *gmsg << "itsBunch_m->RefPartR_m= " << itsBunch_m->RefPartR_m << endl;
    *gmsg << "itsBunch_m->RefPartP_m= " << itsBunch_m->RefPartP_m << endl;
 
    IpplTimings::startTimer(OrbThreader_m);
 
    bool const psDump0 = 0;
    bool const statDump0 = 0;
 
    writePhaseSpace(0, psDump0, statDump0);
    msg << level2 << "Dump initial phase space" << endl;
 
 
    OrbitThreader oth(
        itsReference, itsBunch_m->RefPartR_m, itsBunch_m->RefPartP_m, pathLength_m, -rmin(2),
        itsBunch_m->getT(), (back_track ? -minTimeStep : minTimeStep), stepSizes_m,
        itsOpalBeamline_m);
 
    oth.execute();
    IpplTimings::stopTimer(OrbThreader_m);
    
    BoundingBox globalBoundingBox = oth.getBoundingBox();
 
    numParticlesInSimulation_m = itsBunch_m->getTotalNum();
 
    setTime();
 
    double time = itsBunch_m->getT() - globalTimeShift;
    itsBunch_m->setT(time);
 
    unsigned long long step = itsBunch_m->getGlobalTrackStep();
    OPALTimer::Timer myt1;
    *gmsg << "* Track start at: " << myt1.time() << ", t= " << Util::getTimeString(time) << "; "
          << "zstart at: " << Util::getLengthString(pathLength_m) << endl;
    *gmsg << "* Executing ParallelTracker\n"
          << "* Initial dt = " << Util::getTimeString(itsBunch_m->getdT()) << "\n"
          << "* Max integration steps = " << stepSizes_m.getMaxSteps() << ", next step = " << step
          << endl
          << endl;
 
    setOptionalVariables();
 
    globalEOL_m        = false;
    wakeStatus_m       = false;
    deletedParticles_m = false;
    OpalData::getInstance()->setInPrepState(false);
 
    stepSizes_m.printDirect(*gmsg);
    
    this->itsBunch_m->performBunchSanityChecks();
    
    while (!stepSizes_m.reachedEnd()) {
 
        unsigned long long trackSteps = stepSizes_m.getNumSteps() + step;
        dtCurrentTrack_m              = stepSizes_m.getdT();
        changeDT(back_track);
 
        for (; step < trackSteps; ++step) {
            Vector_t<double, 3> rmin(0.0), rmax(0.0);
            if (itsBunch_m->getTotalNum() > 0) {
                itsBunch_m->get_bounds(rmin, rmax);
                {
                    *gmsg << "* Bunch bounds at step " << step + 1 << ": "
                        << " x[" << Util::getLengthString(rmin(0)) << ", "
                        << Util::getLengthString(rmax(0)) << "] "
                        << " y[" << Util::getLengthString(rmin(1)) << ", "
                        << Util::getLengthString(rmax(1)) << "] "
                        << " z[" << Util::getLengthString(rmin(2)) << ", "
                        << Util::getLengthString(rmax(2)) << "] " << endl;
                }
                {
                    // Print out mass and charge per particle
                    *gmsg << "* Particle mass at step " << step + 1 << ": " << itsBunch_m->getMassPerParticle() << endl;
                    *gmsg << "* Charge mass at step " << step + 1 << ": " << itsBunch_m->getChargePerParticle() << endl;
                }
            }
            // ADA
            timeIntegration1(pusher);
            
            computeSpaceChargeFields(step);
            
            // \todo for a drift we can neglect that 
            // computeExternalFields(oth);
 
            timeIntegration2(pusher);
 
            /*
            The following lines contain debugging output that was needed to fix units.
            \todo I (Github @aliemen) will remove it once everything is correct.
            At the moment, some units are better, but the self fields still seem off.
            */
            /*
            {
                // Calculate bunch size: rms in position
                Vector_t<double, 3> meanR = itsBunch_m->getParticleContainer()->getMeanR();
                Vector_t<double, 3> sumR2(0.0);
                unsigned long long numParticles = itsBunch_m->getTotalNum();
                auto Rview = itsBunch_m->getParticleContainer()->R.getView();
                Kokkos::parallel_reduce(
                                     "bunchSizeCalc", numParticles,
                                     KOKKOS_LAMBDA(const size_t i, Vector_t<double,3>& localSumR2) {
                                         Vector_t<double, 3> diff = Rview(i) - meanR;
                                         localSumR2 += diff * diff;
                                     }, sumR2);
                ippl::Comm->allreduce(sumR2, 1, std::plus<Vector_t<double, 3>>());
                Vector_t<double, 3> rmsSize = sqrt( sumR2 / static_cast<double>(numParticles) );
                *gmsg << "* After step " << step + 1 << ": Bunch RMS size (x,y,z) = ("
                      << Util::getLengthString(rmsSize(0)) << ", "
                      << Util::getLengthString(rmsSize(1)) << ", "
                      << Util::getLengthString(rmsSize(2)) << ") " << endl;
            }
 
            {
                // Output sum of particle charges
                double localChargeSum = 0.0;
                unsigned long long numParticles = itsBunch_m->getTotalNum();
                auto chargeView = itsBunch_m->getParticleContainer()->Q.getView();
                Kokkos::parallel_reduce(
                                     "chargeSumCalc", numParticles,
                                     KOKKOS_LAMBDA(const size_t i, double& localSum) {
                                         localSum += chargeView(i);
                                     }, localChargeSum);
                double globalChargeSum = 0.0;
                ippl::Comm->allreduce(&localChargeSum, &globalChargeSum, 1, std::plus<double>());
                *gmsg << "* After step " << step + 1 << ": Total bunch charge = "
                      << globalChargeSum << endl; // Util::getChargeString(
            }
            {
                // Extract charge of first particle for debugging
                double firstParticleCharge = 0.0;
                auto chargeView = itsBunch_m->getParticleContainer()->Q.getView();
                Kokkos::parallel_reduce(
                                     "firstParticleCharge", 1,
                                     KOKKOS_LAMBDA(const size_t i, double& localCharge) {
                                         localCharge = chargeView(0);
                                     }, firstParticleCharge);
                *gmsg << "* After step " << step + 1 << ": First particle charge = "
                      << firstParticleCharge << endl;
            }
            {
                // Calculate mean electric field in x/y/z for debugging
                Vector_t<double, 3> localSumE(0.0);
                unsigned long long numParticles = itsBunch_m->getTotalNum();
                auto Eview = itsBunch_m->getParticleContainer()->E.getView();
                Kokkos::parallel_reduce(
                                     "meanECalc", numParticles,
                                     KOKKOS_LAMBDA(const size_t i, Vector_t<double,3>& localSum) {
                                         localSum += Eview(i);
                                     }, localSumE);
                ippl::Comm->allreduce(localSumE, 1, std::plus<Vector_t<double, 3>>());
                Vector_t<double, 3> meanE = localSumE / static_cast<double>(numParticles);
                *gmsg << "* After step " << step + 1 << ": Mean electric field (x,y,z) = ("
                      << meanE(0) << ", "
                      << meanE(1) << ", "
                      << meanE(2) << ")" << endl;
            }
            {
                // Compute mean z position for debugging
                double localSumZ = 0.0;
                unsigned long long numParticles = itsBunch_m->getTotalNum();
                auto Rview = itsBunch_m->getParticleContainer()->R.getView();
                Kokkos::parallel_reduce(
                    "meanZCalc", numParticles,
                    KOKKOS_LAMBDA(const size_t i, double& localSum) {
                        localSum += Rview(i)[2];
                    }, localSumZ);
                double globalSumZ = 0.0;
                ippl::Comm->allreduce(&localSumZ, &globalSumZ, 1, std::plus<double>());
                double meanZ = globalSumZ / static_cast<double>(numParticles);
                *gmsg << "* Mean z position at step " << step << ": " << Util::getLengthString(meanZ) << endl;
            }
            {
                // Look at the first mass and the first charge in the bunch (deep copy)
                double firstMass = 0.0;
                double firstCharge = 0.0;
                auto massView = itsBunch_m->getParticleContainer()->M.getView();
                auto chargeView = itsBunch_m->getParticleContainer()->Q.getView();
                Kokkos::parallel_reduce(
                                     "firstMassCharge", 1,
                                     KOKKOS_LAMBDA(const size_t i, double& localMass, double& localCharge) {
                                         localMass = massView(0);
                                         localCharge = chargeView(0);
                                     }, firstMass, firstCharge);
                *gmsg << "* After step " << step + 1 << ": First particle mass = "
                      << firstMass << ", charge = " << firstCharge << endl;
            }
            */
            
            selectDT(back_track);
            // \todo emitParticles(step);
            //selectDT(back_track);
 
            itsBunch_m->incrementT();
 
            if (itsBunch_m->getT() > 0.0 || itsBunch_m->getdT() < 0.0) {
                updateReference(pusher);
            }
 
            if (deletedParticles_m) {
                // \todo doDelete
                deletedParticles_m = false;
            }
 
            itsBunch_m->set_sPos(pathLength_m);
 
            // if (hasEndOfLineReached(globalBoundingBox)) break;
  
            bool const psDump =
                ((itsBunch_m->getGlobalTrackStep() % Options::psDumpFreq) + 1
                 == Options::psDumpFreq);
            bool const statDump =
                ((itsBunch_m->getGlobalTrackStep() % Options::statDumpFreq) + 1
                 == Options::statDumpFreq);
            dumpStats(step, psDump, statDump);
 
            itsBunch_m->incTrackSteps();
 
            ippl::Vector<double,3> pdivg = itsBunch_m->RefPartP_m / Util::getGamma(itsBunch_m->RefPartP_m);
            double beta = euclidean_norm(pdivg);
            double driftPerTimeStep = std::abs(itsBunch_m->getdT()) * Physics::c * beta;
 
            // Output driftPerTimeStep for debugging
            *gmsg << "* Drift per time step: " << Util::getLengthString(driftPerTimeStep) << endl;
 
            if (std::abs(stepSizes_m.getZStop() - pathLength_m) < 0.5 * driftPerTimeStep) {
                break;
            }
        }
 
        if (globalEOL_m)
            break;
        ++stepSizes_m;    
     }
    itsBunch_m->set_sPos(pathLength_m);
 
    numParticlesInSimulation_m = itsBunch_m->getTotalNum();
 
    bool const psDump =
        (((itsBunch_m->getGlobalTrackStep() - 1) % Options::psDumpFreq) + 1 != Options::psDumpFreq);
    bool const statDump =
        (((itsBunch_m->getGlobalTrackStep() - 1) % Options::statDumpFreq) + 1
         != Options::statDumpFreq);
 
    writePhaseSpace((step + 1), psDump, statDump);
 
    *gmsg << "* Dump phase space of last step" << endl;
 
    itsOpalBeamline_m.switchElementsOff();
 
    OPALTimer::Timer myt3;
    *gmsg << endl << "* Done executing ParallelTracker at " << myt3.time() << endl << endl;
}
    /*
    OpalData::getInstance()->setPriorTrack();
    */
 
void ParallelTracker::prepareSections() {
    itsBeamline_m.accept(*this);
    itsOpalBeamline_m.prepareSections();
    itsOpalBeamline_m.compute3DLattice();
    itsOpalBeamline_m.save3DLattice();
    itsOpalBeamline_m.save3DInput();
}
 
void ParallelTracker::timeIntegration1(BorisPusher& pusher) {
    IpplTimings::startTimer(timeIntegrationTimer1_m);
    pushParticles(pusher);
    IpplTimings::stopTimer(timeIntegrationTimer1_m);
}
 
void ParallelTracker::timeIntegration2(BorisPusher& pusher) {
    /*
      transport and emit particles
      that passed the cathode in the first
      half-step or that would pass it in the
      second half-step.
 
      to make IPPL and the field solver happy
      make sure that at least 10 particles are emitted
 
      also remember that node 0 has
      all the particles to be emitted
 
      this has to be done *after* the calculation of the
      space charges! thereby we neglect space charge effects
      in the very first step of a new-born particle.
 
    */
 
    IpplTimings::startTimer(timeIntegrationTimer2_m);
    kickParticles(pusher);
    // switchElements();
    pushParticles(pusher);
 
    
    auto dtview  = itsBunch_m->getParticleContainer()->dt.getView();
    double newdT = itsBunch_m->getdT();
 
    Kokkos::parallel_for(
        "changeDT", ippl::getRangePolicy(dtview),
        KOKKOS_LAMBDA(const size_t i) {
            dtview(i) = newdT;
        });                     
    
    IpplTimings::stopTimer(timeIntegrationTimer2_m);
}
 
void ParallelTracker::selectDT(bool backTrack) {
    double dt = dtCurrentTrack_m;
    itsBunch_m->setdT(dt);
 
    if (backTrack) {
        itsBunch_m->setdT(-std::abs(itsBunch_m->getdT()));
    }
}
 
void ParallelTracker::changeDT(bool backTrack) {
 
    selectDT(backTrack);
 
    auto dtview  = itsBunch_m->getParticleContainer()->dt.getView();
    double newdT = itsBunch_m->getdT();
 
    Kokkos::parallel_for(
        "changeDT", ippl::getRangePolicy(dtview),
        KOKKOS_LAMBDA(const size_t i) {
            dtview(i) = newdT;
        });                     
    
}
 
void ParallelTracker::emitParticles(long long step) {
 
}
 
void ParallelTracker::computeSpaceChargeFields(unsigned long long step) {
 
    if (!itsBunch_m->hasFieldSolver()) {
        *gmsg << "no solver avaidable " << endl;
        return;
    }
        
    itsBunch_m->calcBeamParameters();
 
    Quaternion alignment = getQuaternion(itsBunch_m->get_pmean(), Vector_t<double, 3>(0, 0, 1));
 
    CoordinateSystemTrafo beamToReferenceCSTrafo(
        Vector_t<double, 3>(0, 0, pathLength_m), alignment.conjugate());
 
    CoordinateSystemTrafo referenceToBeamCSTrafo = beamToReferenceCSTrafo.inverted();
 
    const matrix_t                rot = referenceToBeamCSTrafo.getRotationMatrix();
    const ippl::Vector<double, 3> org = referenceToBeamCSTrafo.getOrigin();
 
 
    typedef Kokkos::View<double**>  ViewMatrixType;
    ViewMatrixType Rot("Rot", 3, 3);
    ViewMatrixType::HostMirror h_Rot = Kokkos::create_mirror_view(Rot);
 
    // Initialize M matrix on host.
    for ( int i = 0; i < 3; ++i ) {
        for ( int j = 0; j < 3; ++j ) {
            h_Rot( i, j ) = rot(i, j);
        }
    }
    
    Kokkos::deep_copy(Rot, h_Rot);
 
    // Reset fields to zero
    itsBunch_m->getParticleContainer()->E = 0;
    itsBunch_m->getParticleContainer()->B = 0;
 
    auto Rview  = itsBunch_m->getParticleContainer()->R.getView();
 
    Kokkos::parallel_for(
        "referenceToBeamCSTrafo", ippl::getRangePolicy(Rview),
        KOKKOS_LAMBDA(const size_t k) {
            ippl::Vector<double, 3> x = Rview(k); // x({Rview(i)[0],Rview(i)[1],Rview(i)[2]});
                x = x - org;
                for (size_t i = 0; i < 3; ++i ) {
                    Rview(k)[i] = 0.0;
                    for (size_t j = 0; j < 3; ++j ) {
                        Rview(k)[i] += Rot(i, j) * x(j);
                    }
                }
        });         
 
    itsBunch_m->boundp();
 
    if (step % repartFreq_m + 1 == repartFreq_m) {
        doBinaryRepartition();
    }
 
    itsBunch_m->setGlobalMeanR(itsBunch_m->get_centroid());
 
    itsBunch_m->computeSelfFields();
 
    auto Eview  = itsBunch_m->getParticleContainer()->E.getView();
    auto Bview  = itsBunch_m->getParticleContainer()->B.getView();
    Kokkos::parallel_for(
        "beamToReferenceCSTrafo", ippl::getRangePolicy(Rview),
        KOKKOS_LAMBDA(const size_t k) {                           
            ippl::Vector<double, 3> x = Rview(k); // ({Rview(k)[0],Rview(k)[1],Rview(k)[2]});
            ippl::Vector<double, 3> e = Eview(k); // ({Eview(k)[0],Eview(k)[1],Eview(k)[2]});
            ippl::Vector<double, 3> b = Bview(k); // ({Bview(k)[0],Bview(k)[1],Bview(k)[2]});
            
            // beamToReferenceCSTrafo.rotateTo
            for (size_t i = 0; i < 3; ++i ) {
                Eview(k)[i] = 0.0;
                Bview(k)[i] = 0.0;
                for (size_t j = 0; j < 3; ++j ) {
                    Eview(k)[i] += Rot(j,i) * e(j);
                    Bview(k)[i] += Rot(j,i) * b(j);
                }
            }
            // beamToReferenceCSTrafo.transformTo
            x = x + org;
            for (size_t i = 0; i < 3; ++i ) {
                Rview(k)[i] = 0.0;
                for (size_t j = 0; j < 3; ++j ) {
                    Rview(k)[i] += Rot(j,i) * x(j);
                }
            }
        });         
 
}
 
void ParallelTracker::computeExternalFields(OrbitThreader& oth) {
    IpplTimings::startTimer(fieldEvaluationTimer_m);
    Inform msg("ParallelTracker ", *gmsg);
    const unsigned int localNum = itsBunch_m->getLocalNum();
    bool locPartOutOfBounds = false, globPartOutOfBounds = false;
    Vector_t<double, 3> rmin(0.0), rmax(0.0);
    if (itsBunch_m->getTotalNum() > 0)
        itsBunch_m->get_bounds(rmin, rmax);
    IndexMap::value_t elements;
 
    try {
        elements = oth.query(pathLength_m + 0.5 * (rmax(2) + rmin(2)), rmax(2) - rmin(2));
    } catch (IndexMap::OutOfBounds& e) {
        globalEOL_m = true;
        return;
    }
 
    IndexMap::value_t::const_iterator it        = elements.begin();
    const IndexMap::value_t::const_iterator end = elements.end();
 
    for (; it != end; ++it) {
 
        CoordinateSystemTrafo refToLocalCSTrafo = (itsOpalBeamline_m.getMisalignment((*it)) 
                                                   * (itsOpalBeamline_m.getCSTrafoLab2Local((*it)) 
                                                   * itsBunch_m->toLabTrafo_m));
 
        CoordinateSystemTrafo localToRefCSTrafo = refToLocalCSTrafo.inverted();
 
        (*it)->setCurrentSCoordinate(pathLength_m + rmin(2));
 
        for (unsigned int i = 0; i < localNum; ++i) {
            // \todo if (itsBunch_m->Bin[i] < 0)
            //     continue;
 
            // \todo itsBunch_m->R[i] = refToLocalCSTrafo.transformTo(itsBunch_m->R[i]);
            // \todo itsBunch_m->P[i] = refToLocalCSTrafo.rotateTo(itsBunch_m->P[i]);
            double dt = 1.0;  // \todo itsBunch_m->dt[i];
 
            Vector_t<double, 3> localE(0.0), localB(0.0);
 
            if ((*it)->apply(i, itsBunch_m->getT() + 0.5 * dt, localE, localB)) {
                // itsBunch_m->R[i]   = localToRefCSTrafo.transformTo(itsBunch_m->R[i]);
                // itsBunch_m->P[i]   = localToRefCSTrafo.rotateTo(itsBunch_m->P[i]);
                // itsBunch_m->Bin[i] = -1;
                locPartOutOfBounds = true;
 
                continue;
            }
 
            // itsBunch_m->R[i] = localToRefCSTrafo.transformTo(itsBunch_m->R[i]);
            // itsBunch_m->P[i] = localToRefCSTrafo.rotateTo(itsBunch_m->P[i]);
            // itsBunch_m->Ef[i] += localToRefCSTrafo.rotateTo(localE);
            // itsBunch_m->Bf[i] += localToRefCSTrafo.rotateTo(localB);
        }
    }
 
    IpplTimings::stopTimer(fieldEvaluationTimer_m);
 
    // \todo reduce(locPartOutOfBounds, globPartOutOfBounds, OpOrAssign());
    ippl::Comm->reduce(locPartOutOfBounds, globPartOutOfBounds, 1, std::logical_or<bool>());
 
    size_t ne = 0;
    if (globPartOutOfBounds) {
        if (itsBunch_m->hasFieldSolver()) {
            ne = itsBunch_m->boundp_destroyT();
        }
 
        // \todo
        // else {
        //    ne = itsBunch_m->destroyT();
        // }
        numParticlesInSimulation_m = itsBunch_m->getTotalNum();
        deletedParticles_m = true;
    }
 
    size_t totalNum            = itsBunch_m->getTotalNum();
    numParticlesInSimulation_m = totalNum;
 
    if (ne > 0) {
        msg << level1 << "* Deleted " << ne << " particles, "
            << "remaining " << numParticlesInSimulation_m << " particles" << endl;
    }
}
 
void ParallelTracker::doBinaryRepartition() {
    if (itsBunch_m->hasFieldSolver()) {
        *ippl::Info << "*****************************************************************" << endl;
        *ippl::Info << "do repartition because of repartFreq_m" << endl;
        *ippl::Info << "*****************************************************************" << endl;
        itsBunch_m->do_binaryRepart();
        ippl::Comm->barrier();
        IpplTimings::stopTimer(BinRepartTimer_m);
        *ippl::Info << "*****************************************************************" << endl;
        *ippl::Info << "do repartition done" << endl;
        *ippl::Info << "*****************************************************************" << endl;
    }
}
 
void ParallelTracker::dumpStats(long long step, bool psDump, bool statDump) {
    OPALTimer::Timer myt2;
 
    /*
    if (itsBunch_m->getGlobalTrackStep() % 1000 + 1 == 1000) {
        *gmsg << level1;
    } else if (itsBunch_m->getGlobalTrackStep() % 100 + 1 == 100) {
        *gmsg << level2;
    } else {
        *gmsg << level3;
    }
    */
    
    if (numParticlesInSimulation_m == 0) {
        *gmsg << "* " << myt2.time() << " "
            << "Step " << std::setw(6) << itsBunch_m->getGlobalTrackStep() << "; "
            << "   -- no emission yet --     "
            << "t= " << Util::getTimeString(itsBunch_m->getT()) << endl;
        return;
    }
 
    // \todo itsBunch_m->calcEMean();
    //    size_t totalParticles_f = numParticlesInSimulation_m;
    if (std::isnan(pathLength_m) || std::isinf(pathLength_m)) {
        throw OpalException(
            "ParallelTracker::dumpStats()",
            "there seems to be something wrong with the position of the bunch!");
    } else {
        *gmsg << "* " << myt2.time() << " "
            << "Step " << std::setw(6) << itsBunch_m->getGlobalTrackStep() << " "
            << "at " << Util::getLengthString(pathLength_m) << ", "
            << "t= " << Util::getTimeString(itsBunch_m->getT()) << ", "
            << "E=" << Util::getEnergyString(itsBunch_m->get_meanKineticEnergy()) << endl;
 
        writePhaseSpace(step, psDump, statDump);
    }
}
 
void ParallelTracker::setOptionalVariables() {
 
    /*
    minStepforReBin_m = Options::minStepForRebin;
    RealVariable* br =
        dynamic_cast<RealVariable*>(OpalData::getInstance()->find("MINSTEPFORREBIN"));
    if (br)
        minStepforReBin_m = static_cast<int>(br->getReal());
    msg << level2 << "MINSTEPFORREBIN " << minStepforReBin_m << endl;
    */
 
    // there is no point to do repartitioning with one node
    if (ippl::Comm->size() == 1) {
        repartFreq_m = std::numeric_limits<unsigned long long>::max();
    } else {
        repartFreq_m = Options::repartFreq * 100;
        RealVariable* rep =
            dynamic_cast<RealVariable*>(OpalData::getInstance()->find("REPARTFREQ"));
        if (rep)
            repartFreq_m = static_cast<int>(rep->getReal());
        *gmsg  << "* REPARTFREQ " << repartFreq_m << endl;
    }
}
 
bool ParallelTracker::hasEndOfLineReached(const BoundingBox& globalBoundingBox) {
    // \todo check in IPPL 1.0 it was OpBitwiseAndAssign()
    ippl::Comm->reduce(globalEOL_m,  globalEOL_m, 1, std::logical_and<bool>());
    globalEOL_m = globalEOL_m || globalBoundingBox.isOutside(itsBunch_m->RefPartR_m);
    return globalEOL_m;
}
 
void ParallelTracker::setTime() {
 
    auto dtview  = itsBunch_m->getParticleContainer()->dt.getView();
    double newdT = itsBunch_m->getdT();
 
    Kokkos::parallel_for(
                         "changeDT", ippl::getRangePolicy(dtview),
                         KOKKOS_LAMBDA(const int i) {
                             dtview(i) = newdT;
                         });                     
}
 
void ParallelTracker::writePhaseSpace(const long long /*step*/, bool psDump, bool statDump) {
    Vector_t<double, 3> externalE, externalB;
    Vector_t<double, 3> FDext[2];  // FDext = {BHead, EHead, BRef, ERef, BTail, ETail}.
 
    // Sample fields at (xmin, ymin, zmin), (xmax, ymax, zmax) and the centroid location. We
    // are sampling the electric and magnetic fields at the back, front and
    // center of the beam.
    Vector_t<double, 3> rmin, rmax;
    itsBunch_m->get_bounds(rmin, rmax);
 
    if (psDump || statDump) {
        externalB = Vector_t<double, 3>(0.0);
        externalE = Vector_t<double, 3>(0.0);
        itsOpalBeamline_m.getFieldAt(
            itsBunch_m->RefPartR_m, itsBunch_m->RefPartP_m,
            itsBunch_m->getT() - 0.5 * itsBunch_m->getdT(), externalE, externalB);
        FDext[0] = externalB;  // \todo itsBunch_m->toLabTrafo_m.rotateFrom(externalB);
        FDext[1] =
            (externalE * Units::Vpm2MVpm);  // \todo itsBunch_m->toLabTrafo_m.rotateFrom(externalE *
                                            // Units::Vpm2MVpm);
    }
 
    if (statDump) {
        itsDataSink_m->dumpSDDS(itsBunch_m, FDext, -1.0);
        *gmsg << "* Wrote beam statistics." << endl;
    }
 
    if (psDump && (itsBunch_m->getTotalNum() > 0)) {
        // Write bunch to .h5 file.
        itsDataSink_m->dumpH5(itsBunch_m, FDext);
 
        /*
        // Write fields to .h5 file.
        const size_t localNum    = itsBunch_m->getLocalNum();
        double distToLastStop    = stepSizes_m.getFinalZStop() - pathLength_m;
        Vector_t<double, 3> beta = itsBunch_m->RefPartP_m / Util::getGamma(itsBunch_m->RefPartP_m);
        Vector_t<double, 3> driftPerTimeStep =
            itsBunch_m->getdT()
            * Physics::c;  // \todo  * itsBunch_m->toLabTrafo_m.rotateFrom(beta);
        bool driftToCorrectPosition =
            std::abs(distToLastStop) < 0.5 * euclidean_norm(driftPerTimeStep);
        // \todo Ppos_t stashedR;
        Vector_t<double, 3> stashedR;
        Vector_t<double, 3> stashedRefPartR;
 
        if (driftToCorrectPosition) {
            const double tau =
                distToLastStop / euclidean_norm(driftPerTimeStep) * itsBunch_m->getdT();
 
            if (localNum > 0) {
 
                stashedR.create(localNum);
                stashedR        = itsBunch_m->R;
                stashedRefPartR = itsBunch_m->RefPartR_m;
 
                for (size_t i = 0; i < localNum; ++i) {
                    itsBunch_m->R[i] +=
                        tau
                        * (Physics::c * itsBunch_m->P[i] / Util::getGamma(itsBunch_m->P[i])
                           - driftPerTimeStep / itsBunch_m->getdT());
                }
 
            }
 
            driftPerTimeStep = itsBunch_m->toLabTrafo_m.rotateTo(driftPerTimeStep);
            itsBunch_m->RefPartR_m =
                itsBunch_m->RefPartR_m + tau * driftPerTimeStep / itsBunch_m->getdT();
            CoordinateSystemTrafo update(
                tau * driftPerTimeStep / itsBunch_m->getdT(), Quaternion(1.0, 0.0, 0.0, 0.0));
            itsBunch_m->toLabTrafo_m = itsBunch_m->toLabTrafo_m * update.inverted();
 
            itsBunch_m->set_sPos(stepSizes_m.getFinalZStop());
 
            itsBunch_m->calcBeamParameters();
        }
        if (!statDump && !driftToCorrectPosition)
            itsBunch_m->calcBeamParameters();
 
            msg << *itsBunch_m << endl;
        
        itsDataSink_m->dumpH5(itsBunch_m, FDext);
        */
        
        /*
        
        if (driftToCorrectPosition) {
            if (localNum > 0) {
                itsBunch_m->R = stashedR;
                stashedR.destroy(localNum, 0);
            }
 
            itsBunch_m->RefPartR_m = stashedRefPartR;
            itsBunch_m->set_sPos(pathLength_m);
 
            itsBunch_m->calcBeamParameters();
        }
 
        */
        
        *gmsg << level2 << "* Wrote beam phase space." << endl;
    }
}
 
void ParallelTracker::updateReference(const BorisPusher& pusher) {
    updateReferenceParticle(pusher);
    updateRefToLabCSTrafo();
}
 
void ParallelTracker::updateReferenceParticle(const BorisPusher& pusher) {
    const double direction = back_track ? -1 : 1;
    const double dt = direction * std::min(itsBunch_m->getT(), direction * itsBunch_m->getdT());
    const double scaleFactor = Physics::c * dt;
    Vector_t<double, 3> Ef(0.0), Bf(0.0);
 
    itsBunch_m->RefPartR_m /= scaleFactor;
    pusher.push(itsBunch_m->RefPartR_m, itsBunch_m->RefPartP_m, dt);
    itsBunch_m->RefPartR_m *= scaleFactor;
 
    IndexMap::value_t elements           = itsOpalBeamline_m.getElements(itsBunch_m->RefPartR_m);
    IndexMap::value_t::const_iterator it = elements.begin();
    const IndexMap::value_t::const_iterator end = elements.end();
 
    for (; it != end; ++it) {
        const CoordinateSystemTrafo& refToLocalCSTrafo =
            itsOpalBeamline_m.getCSTrafoLab2Local((*it));
 
        Vector_t<double, 3> localR = refToLocalCSTrafo.transformTo(itsBunch_m->RefPartR_m);
        Vector_t<double, 3> localP = refToLocalCSTrafo.rotateTo(itsBunch_m->RefPartP_m);
        Vector_t<double, 3> localE(0.0), localB(0.0);
 
        if ((*it)->applyToReferenceParticle(
                localR, localP, itsBunch_m->getT() - 0.5 * dt, localE, localB)) {
            *gmsg << level1 << "The reference particle hit an element" << endl;
            globalEOL_m = true;
        }
 
        Ef += refToLocalCSTrafo.rotateFrom(localE);
        Bf += refToLocalCSTrafo.rotateFrom(localB);
    }
 
    pusher.kick(itsBunch_m->RefPartR_m, itsBunch_m->RefPartP_m, Ef, Bf, dt);
 
    itsBunch_m->RefPartR_m /= scaleFactor;
    pusher.push(itsBunch_m->RefPartR_m, itsBunch_m->RefPartP_m, dt);
    itsBunch_m->RefPartR_m *= scaleFactor;
}
 
void ParallelTracker::transformBunch(const CoordinateSystemTrafo& trafo) {
    //const unsigned int localNum = itsBunch_m->getLocalNum();
    //for (unsigned int i = 0; i < localNum; ++i) {
        /* \todo host device .... 
        itsBunch_m->R[i]  = trafo.transformTo(itsBunch_m->R[i]);
        itsBunch_m->P[i]  = trafo.rotateTo(itsBunch_m->P[i]);
        itsBunch_m->Ef[i] = trafo.rotateTo(itsBunch_m->Ef[i]);
        itsBunch_m->Bf[i] = trafo.rotateTo(itsBunch_m->Bf[i]);
        */
    //}
    *gmsg << "* ParallelTracker::transformBunch() is not implemented." << endl;
}
 
void ParallelTracker::updateRefToLabCSTrafo() {
    /*
    Inform m("updateRefToLabCSTrafo ");
    m << " initial RefPartR: " << itsBunch_m->RefPartR_m << endl;
    m << " RefPartR after transformFrom( " << itsBunch_m->RefPartR_m << endl;
    itsBunch_m->toLabTrafo_m.rotateFrom(itsBunch_m->RefPartP_m);
    Vector_t<double, 3> P = itsBunch_m->RefPartP_m;
    m << " CS " << itsBunch_m->toLabTrafo_m << endl;
    m << " rotMat= " << itsBunch_m->toLabTrafo_m.getRotationMatrix() << endl;
    m << " initial: path Lenght= " << pathLength_m << endl;
    m << " dt= " << itsBunch_m->getdT() << " R=" << R << endl;
    */
 
    // std::cout << "Before updateRefToLabCSTrafo(): RefPartP_m: " << itsBunch_m->RefPartP_m << std::endl;
    //std::cout << "Rotation matrix = " << itsBunch_m->toLabTrafo_m.getRotationMatrix() << std::endl;
 
    Vector_t<double, 3> R = itsBunch_m->toLabTrafo_m.transformFrom(itsBunch_m->RefPartR_m);
    
    //*gmsg << "* updateRefToLabCSTrafo(): P before transformFrom: " << itsBunch_m->RefPartP_m << endl;
    Vector_t<double, 3> P = itsBunch_m->toLabTrafo_m.transformFrom(itsBunch_m->RefPartP_m);
    //*gmsg << "* updateRefToLabCSTrafo(): P after transformFrom: " << P << endl;
    
    pathLength_m += std::copysign(1, itsBunch_m->getdT()) * euclidean_norm(R);
 
    /*
    This will produce a NaN Quaternion if P is parallel to the z axis because the cross product
    of two parallel vectors is zero, leading to a zero norm when normalizing the axis of rotation.
    The fix is to check if P is parallel to the z axis and not rotate in that case.
    */
 
    // First normalize P
    double normP = euclidean_norm(P);
    if (normP < 1e-12) {
        pathLength_m += 0.0;
        return;
    }
    P /= normP;
 
    // After normalizing, we can check alignment with z-axis
    Vector_t<double, 3> target(0, 0, 1);
    double dot = P.dot(target);
    bool aligned = std::abs(std::abs(dot) - 1.0) < 1e-6;
    Quaternion Q = aligned ? Quaternion(0, 0, 0, 1.0) : getQuaternion(P, target);
 
    if (aligned) {
        *gmsg << "* Warning: Reference particle momentum is aligned with z-axis; no quaternion rotation applied." << endl;
    }
 
    CoordinateSystemTrafo update(R, Q);
 
    transformBunch(update);
 
    itsBunch_m->toLabTrafo_m = itsBunch_m->toLabTrafo_m * update.inverted(); 
}
 
void ParallelTracker::applyFractionalStep(const BorisPusher& pusher, double tau) {
    double t = itsBunch_m->getT();
    t += tau;
    itsBunch_m->setT(t);
 
    // the push method below pushes for half a time step. Hence the ref particle
    // should be pushed for 2 * tau
    itsBunch_m->RefPartR_m /= (Physics::c * 2 * tau);
    pusher.push(itsBunch_m->RefPartR_m, itsBunch_m->RefPartP_m, tau);
    itsBunch_m->RefPartR_m *= (Physics::c * 2 * tau);
 
    pathLength_m = zstart_m;
    itsBunch_m->toLabTrafo_m.transformFrom(itsBunch_m->RefPartR_m);
    Vector_t<double, 3> R = itsBunch_m->RefPartR_m;
    itsBunch_m->toLabTrafo_m.rotateFrom(itsBunch_m->RefPartP_m);
    Vector_t<double, 3> P = itsBunch_m->RefPartP_m;
    CoordinateSystemTrafo update(R, getQuaternion(P, Vector_t<double, 3>(0, 0, 1)));
    itsBunch_m->toLabTrafo_m = itsBunch_m->toLabTrafo_m * update.inverted();
}
 
void ParallelTracker::findStartPosition(const BorisPusher& pusher) {
    StepSizeConfig stepSizesCopy(stepSizes_m);
    if (back_track) {
        stepSizesCopy.shiftZStopLeft(zstart_m);
    }
 
    double t = 0.0;
    itsBunch_m->setT(t);
 
    dtCurrentTrack_m = stepSizesCopy.getdT();
    selectDT();
 
    while (true) {
        autophaseCavities(pusher);
 
        t += itsBunch_m->getdT();
        itsBunch_m->setT(t);
 
        Vector_t<double, 3> oldR = itsBunch_m->RefPartR_m;
        updateReferenceParticle(pusher);
 
        // \todo should not need the tmp
        Vector_t<double, 3> tmp = itsBunch_m->RefPartR_m - oldR;
        pathLength_m += euclidean_norm(tmp);
 
        tmp = itsBunch_m->RefPartP_m * Physics::c / Util::getGamma(itsBunch_m->RefPartP_m);
        double speed = euclidean_norm(tmp);
                                      
 
        if (pathLength_m > stepSizesCopy.getZStop()) {
            ++stepSizesCopy;
 
            if (stepSizesCopy.reachedEnd()) {
                --stepSizesCopy;
                double tau = (stepSizesCopy.getZStop() - pathLength_m) / speed;
                applyFractionalStep(pusher, tau);
 
                break;
            }
 
            dtCurrentTrack_m = stepSizesCopy.getdT();
            selectDT();
        }
 
        if (std::abs(pathLength_m - zstart_m) <= 0.5 * itsBunch_m->getdT() * speed) {
            double tau = (zstart_m - pathLength_m) / speed;
            applyFractionalStep(pusher, tau);
 
            break;
        }
    }
 
    changeDT();
}
 
void ParallelTracker::autophaseCavities(const BorisPusher& pusher) {
    double t                  = itsBunch_m->getT();
    Vector_t<double, 3> nextR = itsBunch_m->RefPartR_m / (Physics::c * itsBunch_m->getdT());
    pusher.push(nextR, itsBunch_m->RefPartP_m, itsBunch_m->getdT());
    nextR *= Physics::c * itsBunch_m->getdT();
 
    auto elementSet = itsOpalBeamline_m.getElements(nextR);
    for (auto element : elementSet) {
        if (element->getType() == ElementType::TRAVELINGWAVE) {
            const TravelingWave* TWelement = static_cast<const TravelingWave*>(element.get());
            if (!TWelement->getAutophaseVeto()) {
                CavityAutophaser ap(itsReference, element);
                ap.getPhaseAtMaxEnergy(
                    itsOpalBeamline_m.transformToLocalCS(element, itsBunch_m->RefPartR_m),
                    itsOpalBeamline_m.rotateToLocalCS(element, itsBunch_m->RefPartP_m), t,
                    itsBunch_m->getdT());
            }
 
        } else if (element->getType() == ElementType::RFCAVITY) {
            const RFCavity* RFelement = static_cast<const RFCavity*>(element.get());
            if (!RFelement->getAutophaseVeto()) {
                CavityAutophaser ap(itsReference, element);
                ap.getPhaseAtMaxEnergy(
                    itsOpalBeamline_m.transformToLocalCS(element, itsBunch_m->RefPartR_m),
                    itsOpalBeamline_m.rotateToLocalCS(element, itsBunch_m->RefPartP_m), t,
                    itsBunch_m->getdT());
            }
        }
    }
}
 
struct DistributionInfo {
    unsigned int who;
    unsigned int whom;
    unsigned int howMany;
};