Distribution.cpp

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//
// Class Distribution
//   This class defines the initial beam that is injected or emitted into the simulation.
//
// Copyright (c) 2008 - 2022, Paul Scherrer Institut, Villigen PSI, Switzerland
// 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 "Distribution/Distribution.h"
 
#include "AbsBeamline/SpecificElementVisitor.h"
#include "AbstractObjects/BeamSequence.h"
#include "AbstractObjects/Expressions.h"
#include "AbstractObjects/OpalData.h"
#include "Algorithms/PartBins.h"
#include "Algorithms/PartBinsCyc.h"
#include "Algorithms/PartBunchBase.h"
#include "BasicActions/Option.h"
#include "DataSource/DataConnect.h"
#include "Distribution/ClosedOrbitFinder.h"
#include "Distribution/LaserProfile.h"
#include "Elements/OpalBeamline.h"
#include "Physics/Physics.h"
#include "Physics/Units.h"
#include "Structure/H5PartWrapper.h"
#include "Structure/H5PartWrapperForPC.h"
#include "Utilities/EarlyLeaveException.h"
#include "Utilities/Options.h"
#include "Utilities/Util.h"
#include "Utility/IpplTimings.h"
 
#include <gsl/gsl_histogram.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_rng.h>
#include <gsl/gsl_sf_erf.h>
 
#include <boost/filesystem.hpp>
#include <boost/regex.hpp>
#include <boost/numeric/odeint/stepper/runge_kutta4.hpp>
 
#include <sys/time.h>
 
#include <cmath>
#include <cfloat>
#include <iomanip>
#include <iostream>
#include <map>
#include <numeric>
 
extern Inform *gmsg;
 
constexpr double SMALLESTCUTOFF = 1e-12;
 
/* Increase tEmission_m by twice this percentage
 * to ensure that no particles fall on the leading edge of
 * the first emission time step or the trailing edge of the last
 * emission time step. */
const double Distribution::percentTEmission_m = 0.0005;
 
namespace {
    SymTenzor<double, 6> getUnit6x6() {
        SymTenzor<double, 6> unit6x6;
        for (unsigned int i = 0; i < 6u; ++ i) {
            unit6x6(i,i) = 1.0;
        }
        return unit6x6;
    }
}
 
 
Distribution::Distribution():
    Definition( Attrib::Legacy::Distribution::SIZE, "DISTRIBUTION",
                "The DISTRIBUTION statement defines data for the 6D particle distribution."),
    distrTypeT_m(DistributionType::NODIST),
    numberOfDistributions_m(1),
    emitting_m(false),
    emissionModel_m(EmissionModel::NONE),
    tEmission_m(0.0),
    tBin_m(0.0),
    currentEmissionTime_m(0.0),
    currentEnergyBin_m(1),
    currentSampleBin_m(0),
    numberOfEnergyBins_m(0),
    numberOfSampleBins_m(0),
    energyBins_m(nullptr),
    energyBinHist_m(nullptr),
    randGen_m(nullptr),
    pTotThermal_m(0.0),
    pmean_m(0.0),
    cathodeWorkFunc_m(0.0),
    laserEnergy_m(0.0),
    cathodeFermiEnergy_m(0.0),
    cathodeTemp_m(0.0),
    emitEnergyUpperLimit_m(0.0),
    totalNumberParticles_m(0),
    totalNumberEmittedParticles_m(0),
    avrgpz_m(0.0),
    inputMoUnits_m(InputMomentumUnits::NONE),
    sigmaTRise_m(0.0),
    sigmaTFall_m(0.0),
    tPulseLengthFWHM_m(0.0),
    correlationMatrix_m(getUnit6x6()),
    sepPeaks_m(0.0),
    nPeaks_m(1),
    laserProfileFileName_m(""),
    laserImageName_m(""),
    laserIntensityCut_m(0.0),
    laserProfile_m(nullptr),
    I_m(0.0),
    E_m(0.0)
{
    setAttributes();
 
    Distribution *defaultDistribution = clone("UNNAMED_Distribution");
    defaultDistribution->builtin = true;
 
    try {
        OpalData::getInstance()->define(defaultDistribution);
    } catch(...) {
        delete defaultDistribution;
    }
 
    gsl_rng_env_setup();
    randGen_m = gsl_rng_alloc(gsl_rng_default);
}
Distribution::Distribution(const std::string &name, Distribution *parent):
    Definition(name, parent),
    distT_m(parent->distT_m),
    distrTypeT_m(DistributionType::NODIST),
    numberOfDistributions_m(parent->numberOfDistributions_m),
    emitting_m(parent->emitting_m),
    particleRefData_m(parent->particleRefData_m),
    addedDistributions_m(parent->addedDistributions_m),
    particlesPerDist_m(parent->particlesPerDist_m),
    emissionModel_m(parent->emissionModel_m),
    tEmission_m(parent->tEmission_m),
    tBin_m(parent->tBin_m),
    currentEmissionTime_m(parent->currentEmissionTime_m),
    currentEnergyBin_m(parent->currentEnergyBin_m),
    currentSampleBin_m(parent->currentSampleBin_m),
    numberOfEnergyBins_m(parent->numberOfEnergyBins_m),
    numberOfSampleBins_m(parent->numberOfSampleBins_m),
    energyBins_m(nullptr),
    energyBinHist_m(nullptr),
    randGen_m(nullptr),
    pTotThermal_m(parent->pTotThermal_m),
    pmean_m(parent->pmean_m),
    cathodeWorkFunc_m(parent->cathodeWorkFunc_m),
    laserEnergy_m(parent->laserEnergy_m),
    cathodeFermiEnergy_m(parent->cathodeFermiEnergy_m),
    cathodeTemp_m(parent->cathodeTemp_m),
    emitEnergyUpperLimit_m(parent->emitEnergyUpperLimit_m),
    totalNumberParticles_m(parent->totalNumberParticles_m),
    totalNumberEmittedParticles_m(parent->totalNumberEmittedParticles_m),
    xDist_m(parent->xDist_m),
    pxDist_m(parent->pxDist_m),
    yDist_m(parent->yDist_m),
    pyDist_m(parent->pyDist_m),
    tOrZDist_m(parent->tOrZDist_m),
    pzDist_m(parent->pzDist_m),
    xWrite_m(parent->xWrite_m),
    pxWrite_m(parent->pxWrite_m),
    yWrite_m(parent->yWrite_m),
    pyWrite_m(parent->pyWrite_m),
    tOrZWrite_m(parent->tOrZWrite_m),
    pzWrite_m(parent->pzWrite_m),
    avrgpz_m(parent->avrgpz_m),
    inputMoUnits_m(parent->inputMoUnits_m),
    sigmaTRise_m(parent->sigmaTRise_m),
    sigmaTFall_m(parent->sigmaTFall_m),
    tPulseLengthFWHM_m(parent->tPulseLengthFWHM_m),
    sigmaR_m(parent->sigmaR_m),
    sigmaP_m(parent->sigmaP_m),
    cutoffR_m(parent->cutoffR_m),
    cutoffP_m(parent->cutoffP_m),
    correlationMatrix_m(parent->correlationMatrix_m),
    sepPeaks_m(parent->sepPeaks_m),
    nPeaks_m(parent->nPeaks_m),
    laserProfileFileName_m(parent->laserProfileFileName_m),
    laserImageName_m(parent->laserImageName_m),
    laserIntensityCut_m(parent->laserIntensityCut_m),
    laserProfile_m(nullptr),
    I_m(parent->I_m),
    E_m(parent->E_m),
    tRise_m(parent->tRise_m),
    tFall_m(parent->tFall_m),
    sigmaRise_m(parent->sigmaRise_m),
    sigmaFall_m(parent->sigmaFall_m),
    cutoff_m(parent->cutoff_m)
{
    gsl_rng_env_setup();
    randGen_m = gsl_rng_alloc(gsl_rng_default);
}
 
Distribution::~Distribution() {
 
    delete energyBins_m;
    gsl_histogram_free(energyBinHist_m);
    gsl_rng_free(randGen_m);
    delete laserProfile_m;
}
 
 
size_t Distribution::getNumOfLocalParticlesToCreate(size_t n) {
 
    size_t locNumber = n / Ippl::getNodes();
 
    // make sure the total number is exact
    size_t remainder  = n % Ippl::getNodes();
    size_t myNode = Ippl::myNode();
    if (myNode < remainder)
        ++ locNumber;
 
    return locNumber;
}
 
bool Distribution::canReplaceBy(Object *object) {
    return dynamic_cast<Distribution *>(object) != 0;
}
 
Distribution *Distribution::clone(const std::string &name) {
    return new Distribution(name, this);
}
 
void Distribution::execute() {
}
 
void Distribution::update() {
}
 
void Distribution::create(size_t &numberOfParticles, double massIneV, double charge) {
 
    /*
     * If Options::cZero is true than we reflect generated distribution
     * to ensure that the transverse averages are 0.0.
     *
     * For now we just cut the number of generated particles in half.
     */
    size_t numberOfLocalParticles = numberOfParticles;
    if (Options::cZero && distrTypeT_m != DistributionType::FROMFILE) {
        numberOfLocalParticles = (numberOfParticles + 1) / 2;
    }
 
    size_t mySeed = Options::seed;
 
    if (Options::seed == -1) {
        struct timeval tv;
        gettimeofday(&tv,0);
        mySeed = tv.tv_sec + tv.tv_usec;
    }
 
    if (Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE])) {
        numberOfLocalParticles = getNumOfLocalParticlesToCreate(numberOfLocalParticles);
        *gmsg << level2 << "* Generation of distribution with seed = " << mySeed << " + core_id\n"
              << "* is scalable with number of particles and cores." << endl;
        mySeed += Ippl::myNode();
    } else {
        *gmsg << level2 << "* Generation of distribution with seed = " << mySeed << "\n"
              << "* isn't scalable with number of particles and cores." << endl;
    }
 
    gsl_rng_set(randGen_m, mySeed);
 
    switch (distrTypeT_m) {
 
    case DistributionType::MATCHEDGAUSS:
        createMatchedGaussDistribution(numberOfLocalParticles, massIneV, charge);
        break;
    case DistributionType::FROMFILE:
        createDistributionFromFile(numberOfParticles, massIneV);
        break;
    case DistributionType::GAUSS:
        createDistributionGauss(numberOfLocalParticles, massIneV);
        break;
    case DistributionType::BINOMIAL:
        createDistributionBinomial(numberOfLocalParticles, massIneV);
        break;
    case DistributionType::FLATTOP:
    case DistributionType::GUNGAUSSFLATTOPTH:
    case DistributionType::ASTRAFLATTOPTH:
        createDistributionFlattop(numberOfLocalParticles, massIneV);
        break;
    case DistributionType::MULTIGAUSS:
        createDistributionMultiGauss(numberOfLocalParticles, massIneV);
        break;
    default:
        throw OpalException("Distribution::create",
                            "Unknown \"TYPE\" of \"DISTRIBUTION\"");
    }
 
    if (emitting_m) {
 
        unsigned int numAdditionalRNsPerParticle = 0;
        if (emissionModel_m == EmissionModel::ASTRA ||
            distrTypeT_m == DistributionType::ASTRAFLATTOPTH ||
            distrTypeT_m == DistributionType::GUNGAUSSFLATTOPTH) {
 
            numAdditionalRNsPerParticle = 2;
        } else if (emissionModel_m == EmissionModel::NONEQUIL) {
            if (Options::cZero) {
                numAdditionalRNsPerParticle = 40;
            } else {
                numAdditionalRNsPerParticle = 20;
            }
        }
 
        int saveProcessor = -1;
        const int myNode = Ippl::myNode();
        const int numNodes = Ippl::getNodes();
        const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
        for (size_t partIndex = 0; partIndex < numberOfLocalParticles; ++ partIndex) {
 
            // Save to each processor in turn.
            ++ saveProcessor;
            if (saveProcessor >= numNodes)
                saveProcessor = 0;
 
            if (scalable || myNode == saveProcessor) {
                std::vector<double> rns;
                for (unsigned int i = 0; i < numAdditionalRNsPerParticle; ++ i) {
                    double x = gsl_rng_uniform(randGen_m);
                    rns.push_back(x);
                }
                additionalRNs_m.push_back(rns);
            } else {
                for (unsigned int i = 0; i < numAdditionalRNsPerParticle; ++ i) {
                    gsl_rng_uniform(randGen_m);
                }
            }
        }
    }
 
    // Scale coordinates according to distribution input.
    scaleDistCoordinates();
 
    // Now reflect particles if Options::cZero is true
    reflectDistribution(numberOfLocalParticles);
 
    adjustPhaseSpace(massIneV);
 
    if (Options::seed != -1)
        Options::seed = gsl_rng_uniform_int(randGen_m, gsl_rng_max(randGen_m));
 
    if (particlesPerDist_m.empty()) {
        particlesPerDist_m.push_back(tOrZDist_m.size());
    } else {
        particlesPerDist_m[0] = tOrZDist_m.size();
    }
}
 
void Distribution::doRestartOpalT(PartBunchBase<double, 3> *beam, size_t /*Np*/, int restartStep, H5PartWrapper *dataSource) {
 
    IpplTimings::startTimer(beam->distrReload_m);
 
    long numParticles = dataSource->getNumParticles();
    size_t numParticlesPerNode = numParticles / Ippl::getNodes();
 
    size_t firstParticle = numParticlesPerNode * Ippl::myNode();
    size_t lastParticle = firstParticle + numParticlesPerNode - 1;
    if (Ippl::myNode() == Ippl::getNodes() - 1)
        lastParticle = numParticles - 1;
    OpalData::getInstance()->addProblemCharacteristicValue("NP", numParticles);
 
    numParticles = lastParticle - firstParticle + 1;
    PAssert_GE(numParticles, 0);
 
    beam->create(numParticles);
 
    dataSource->readHeader();
    dataSource->readStep(beam, firstParticle, lastParticle);
 
    beam->boundp();
 
    double actualT = beam->getT();
    long long ltstep = beam->getLocalTrackStep();
    long long gtstep = beam->getGlobalTrackStep();
 
    IpplTimings::stopTimer(beam->distrReload_m);
 
    *gmsg << "Total number of particles in the h5 file= " << beam->getTotalNum() << "\n"
          << "Global step= " << gtstep << "; Local step= " << ltstep << "; "
          << "restart step= " << restartStep << "\n"
          << "time of restart= " << actualT << "; phishift= " << OpalData::getInstance()->getGlobalPhaseShift() << endl;
}
 
void Distribution::doRestartOpalCycl(PartBunchBase<double, 3> *beam,
                                     size_t /*Np*/,
                                     int /*restartStep*/,
                                     const int specifiedNumBunch,
                                     H5PartWrapper *dataSource) {
 
    // h5_int64_t rc;
    IpplTimings::startTimer(beam->distrReload_m);
    INFOMSG("---------------- Start reading hdf5 file----------------" << endl);
 
    long numParticles = dataSource->getNumParticles();
    size_t numParticlesPerNode = numParticles / Ippl::getNodes();
 
    size_t firstParticle = numParticlesPerNode * Ippl::myNode();
    size_t lastParticle = firstParticle + numParticlesPerNode - 1;
    if (Ippl::myNode() == Ippl::getNodes() - 1)
        lastParticle = numParticles - 1;
    OpalData::getInstance()->addProblemCharacteristicValue("NP", numParticles);
 
    numParticles = lastParticle - firstParticle + 1;
    PAssert_GE(numParticles, 0);
 
    beam->create(numParticles);
 
    dataSource->readHeader();
    dataSource->readStep(beam, firstParticle, lastParticle);
 
    beam->Q = beam->getChargePerParticle();
 
    beam->boundp();
 
    double meanE = static_cast<H5PartWrapperForPC*>(dataSource)->getMeanKineticEnergy();
 
    const int globalN = beam->getTotalNum();
    INFOMSG("Restart from hdf5 format file " << OpalData::getInstance()->getRestartFileName() << endl);
    INFOMSG("total number of particles = " << globalN << endl);
    INFOMSG("* Restart Energy = " << meanE << " (MeV), Path lenght = " << beam->get_sPos() << " (m)" <<  endl);
    INFOMSG("Tracking Step since last bunch injection is " << beam->getSteptoLastInj() << endl);
    INFOMSG(beam->getNumBunch() << " Bunches(bins) exist in this file" << endl);
 
    double gamma = 1 + meanE / (beam->getM() * Units::eV2MeV);
    double beta = std::sqrt(1.0 - (1.0 / std::pow(gamma, 2)));
 
    INFOMSG("* Gamma = " << gamma << ", Beta = " << beta << endl);
 
    if (dataSource->predecessorIsSameFlavour()) {
        INFOMSG("Restart from hdf5 file generated by OPAL-cycl" << endl);
        if (specifiedNumBunch > 1) {
            // the allowed maximal bin number is set to 1000
            energyBins_m = new PartBinsCyc(1000, beam->getNumBunch());
            beam->setPBins(energyBins_m);
        }
 
    } else {
        INFOMSG("Restart from hdf5 file generated by OPAL-t" << endl);
 
        Vector_t meanR(0.0, 0.0, 0.0);
        Vector_t meanP(0.0, 0.0, 0.0);
        unsigned long int newLocalN = beam->getLocalNum();
        for (unsigned int i = 0; i < newLocalN; ++i) {
            for (int d = 0; d < 3; ++d) {
                meanR(d) += beam->R[i](d);
                meanP(d) += beam->P[i](d);
            }
        }
        reduce(meanR, meanR, OpAddAssign());
        meanR /= Vector_t(globalN);
        reduce(meanP, meanP, OpAddAssign());
        meanP /= Vector_t(globalN);
        INFOMSG("Rmean = " << meanR << "[m], Pmean=" << meanP << endl);
 
        for (unsigned int i = 0; i < newLocalN; ++i) {
            beam->R[i] -= meanR;
            beam->P[i] -= meanP;
        }
    }
 
    INFOMSG("---------------Finished reading hdf5 file---------------" << endl);
    IpplTimings::stopTimer(beam->distrReload_m);
}
 
Distribution *Distribution::find(const std::string &name) {
    Distribution *dist = dynamic_cast<Distribution *>(OpalData::getInstance()->find(name));
 
    if (dist == 0) {
        throw OpalException("Distribution::find()", "Distribution \"" + name + "\" not found.");
    }
 
    return dist;
}
 
double Distribution::getTEmission() {
    if (tEmission_m > 0.0) {
        return tEmission_m;
    }
 
    setDistType();
 
    tPulseLengthFWHM_m = Attributes::getReal(itsAttr[Attrib::Distribution::TPULSEFWHM]);
    cutoff_m = Attributes::getReal(itsAttr[Attrib::Legacy::Distribution::CUTOFF]);
    tRise_m = Attributes::getReal(itsAttr[Attrib::Distribution::TRISE]);
    tFall_m = Attributes::getReal(itsAttr[Attrib::Distribution::TFALL]);
    double tratio = std::sqrt(2.0 * std::log(10.0)) - std::sqrt(2.0 * std::log(10.0 / 9.0));
    sigmaRise_m = tRise_m / tratio;
    sigmaFall_m = tFall_m / tratio;
 
    switch(distrTypeT_m) {
    case DistributionType::ASTRAFLATTOPTH: {
        double a = tPulseLengthFWHM_m / 2;
        double sig = tRise_m / 2;
        double inv_erf08 = 0.906193802436823; // erfinv(0.8)
        double sqr2 = std::sqrt(2.);
        double t = a - sqr2 * sig * inv_erf08;
        double tmps = sig;
        double tmpt = t;
        for (int i = 0; i < 10; ++ i) {
            sig = (t + tRise_m - a) / (sqr2 * inv_erf08);
            t = a - 0.5 * sqr2 * (sig + tmps) * inv_erf08;
            sig = (0.5 * (t + tmpt) + tRise_m - a) / (sqr2 * inv_erf08);
            tmps = sig;
            tmpt = t;
        }
        tEmission_m = tPulseLengthFWHM_m + 10 * sig;
        break;
    }
    case DistributionType::GUNGAUSSFLATTOPTH: {
        tEmission_m = tPulseLengthFWHM_m + (cutoff_m - std::sqrt(2.0 * std::log(2.0))) * (sigmaRise_m + sigmaFall_m);
        break;
    }
    default:
        tEmission_m = 0.0;
    }
    return tEmission_m;
}
 
Inform &Distribution::printInfo(Inform &os) const {
 
    os << "\n"
       << "* ************* D I S T R I B U T I O N ********************************************" << endl;
    os << "* " << endl;
    if (OpalData::getInstance()->inRestartRun()) {
        os << "* In restart. Distribution read in from .h5 file." << endl;
    } else {
        if (!addedDistributions_m.empty()) {
            os << "* Main Distribution" << endl
               << "-----------------" << endl;
        }
        if (particlesPerDist_m.empty())
            printDist(os, 0);
        else
            printDist(os, particlesPerDist_m.at(0));
 
        size_t distCount = 1;
        for (unsigned distIndex = 0; distIndex < addedDistributions_m.size(); distIndex++) {
            os << "* " << endl;
            os << "* Added Distribution #" << distCount << endl;
            os << "* ----------------------" << endl;
            addedDistributions_m.at(distIndex)->printDist(os, particlesPerDist_m.at(distCount));
            distCount++;
        }
 
        os << "* " << endl;
        if (numberOfEnergyBins_m > 0) {
            os << "* Number of energy bins    = " << numberOfEnergyBins_m << endl;
 
            //            if (numberOfEnergyBins_m > 1)
            //    printEnergyBins(os);
        }
 
        if (emitting_m) {
            os << "* Distribution is emitted. " << endl;
            os << "* Emission time            = " << tEmission_m << " [sec]" << endl;
            os << "* Time per bin             = " << tEmission_m / numberOfEnergyBins_m << " [sec]" << endl;
            os << "* Delta t during emission  = " << tBin_m / numberOfSampleBins_m << " [sec]" << endl;
            os << "* " << endl;
            printEmissionModel(os);
        } else {
            os << "* Distribution is injected." << endl;
        }
 
        if (Attributes::getBool(itsAttr[Attrib::Distribution::WRITETOFILE])) {
            os << "*\n* Write initial distribution to file '" << outFilename_m << "'" << endl;
        }
    }
    os << "* " << endl;
    os << "* **********************************************************************************" << endl;
 
    return os;
}
 
void Distribution::addDistributions() {
    /*
     * Move particle coordinates from added distributions to main distribution.
     */
 
    size_t idx = 1;
    std::vector<Distribution *>::iterator addedDistIt;
    for (addedDistIt = addedDistributions_m.begin();
         addedDistIt != addedDistributions_m.end(); ++ addedDistIt, ++ idx) {
 
        particlesPerDist_m[idx] = (*addedDistIt)->tOrZDist_m.size();
 
        for (double dist : (*addedDistIt)->getXDist()) {
            xDist_m.push_back(dist);
        }
        (*addedDistIt)->eraseXDist();
 
        for (double dist : (*addedDistIt)->getBGxDist()) {
            pxDist_m.push_back(dist);
        }
        (*addedDistIt)->eraseBGxDist();
 
        for (double dist : (*addedDistIt)->getYDist()) {
            yDist_m.push_back(dist);
        }
        (*addedDistIt)->eraseYDist();
 
        for (double dist : (*addedDistIt)->getBGyDist()) {
            pyDist_m.push_back(dist);
        }
        (*addedDistIt)->eraseBGyDist();
 
        for (double dist : (*addedDistIt)->getTOrZDist()) {
            tOrZDist_m.push_back(dist);
        }
        (*addedDistIt)->eraseTOrZDist();
 
        for (double dist : (*addedDistIt)->getBGzDist()) {
            pzDist_m.push_back(dist);
        }
        (*addedDistIt)->eraseBGzDist();
    }
}
 
void Distribution::applyEmissionModel(double lowEnergyLimit, double &px, double &py, double &pz, std::vector<double> &additionalRNs) {
 
    switch (emissionModel_m) {
 
    case EmissionModel::NONE:
        applyEmissModelNone(pz);
        break;
    case EmissionModel::ASTRA:
        applyEmissModelAstra(px, py, pz, additionalRNs);
        break;
    case EmissionModel::NONEQUIL:
        applyEmissModelNonEquil(lowEnergyLimit, px, py, pz, additionalRNs);
        break;
    default:
        break;
    }
}
 
void Distribution::applyEmissModelAstra(double &px, double &py, double &pz, std::vector<double> &additionalRNs) {
 
    double phi = 2.0 * std::acos(std::sqrt(additionalRNs[0]));
    double theta = Physics::two_pi * additionalRNs[1];
 
    px = pTotThermal_m * std::sin(phi) * std::cos(theta);
    py = pTotThermal_m * std::sin(phi) * std::sin(theta);
    pz = pTotThermal_m * std::abs(std::cos(phi));
 
}
 
void Distribution::applyEmissModelNone(double &pz) {
    pz += pTotThermal_m;
}
 
void Distribution::applyEmissModelNonEquil(double lowEnergyLimit,
                                           double &bgx,
                                           double &bgy,
                                           double &bgz,
                                           std::vector<double> &additionalRNs) {
 
    // Generate emission energy.
    double energy = 0.0;
    bool allow = false;
 
    const double expRelativeLaserEnergy = exp(laserEnergy_m / cathodeTemp_m);
    // double energyRange = emitEnergyUpperLimit_m - lowEnergyLimit;
    unsigned int counter = 0;
    while (!allow) {
        energy = lowEnergyLimit + additionalRNs[counter++] * emitEnergyUpperLimit_m;
        double randFuncValue = additionalRNs[counter++];
        double expRelativeEnergy = exp((energy - cathodeFermiEnergy_m) / cathodeTemp_m);
        double funcValue = ((1.0
                            - 1.0 / (1.0 + expRelativeEnergy * expRelativeLaserEnergy)) /
                            (1.0 + expRelativeEnergy));
 
        if (randFuncValue <= funcValue)
            allow = true;
 
        if (counter == additionalRNs.size()) {
            for (unsigned int i = 0; i < counter; ++ i) {
                additionalRNs[i] = gsl_rng_uniform(randGen_m);
            }
 
            counter = 0;
        }
    }
 
    while (additionalRNs.size() - counter < 2) {
        -- counter;
        additionalRNs[counter] = gsl_rng_uniform(randGen_m);
    }
 
    // Compute emission angles.
    double energyInternal = energy + laserEnergy_m;
    double energyExternal = energy - lowEnergyLimit; // uniformly distributed (?) value between 0 and emitEnergyUpperLimit_m
 
    double thetaInMax = std::acos(std::sqrt((lowEnergyLimit + laserEnergy_m) / (energyInternal)));
    double thetaIn = additionalRNs[counter++] * thetaInMax;
    double sinThetaOut = std::sin(thetaIn) * std::sqrt(energyInternal / energyExternal);
    double phi = Physics::two_pi * additionalRNs[counter];
 
    // Compute emission momenta.
    double betaGammaExternal
        = std::sqrt(std::pow(energyExternal / (Physics::m_e * Units::GeV2eV) + 1.0, 2) - 1.0);
 
    bgx = betaGammaExternal * sinThetaOut * std::cos(phi);
    bgy = betaGammaExternal * sinThetaOut * std::sin(phi);
    bgz = betaGammaExternal * std::sqrt(1.0 - std::pow(sinThetaOut, 2));
 
}
 
void Distribution::calcPartPerDist(size_t numberOfParticles) {
 
    if (numberOfDistributions_m == 1) {
        particlesPerDist_m.push_back(numberOfParticles);
        return;
    }
 
    std::map<unsigned int, size_t> nPartFromFiles;
    double totalWeight = 0.0;
    for (unsigned int i = 0; i <= addedDistributions_m.size(); ++ i) {
        Distribution *currDist = this;
        if (i > 0)
            currDist = addedDistributions_m[i - 1];
 
        if (currDist->distrTypeT_m == DistributionType::FROMFILE) {
            std::ifstream inputFile;
            if (Ippl::myNode() == 0) {
                std::string fileName = Attributes::getString(currDist->itsAttr[Attrib::Distribution::FNAME]);
                inputFile.open(fileName.c_str());
            }
            size_t nPart = getNumberOfParticlesInFile(inputFile);
            nPartFromFiles.insert(std::make_pair(i, nPart));
            if (nPart > numberOfParticles) {
                throw OpalException("Distribution::calcPartPerDist",
                                    "Number of particles is too small");
            }
 
            numberOfParticles -= nPart;
        } else {
            totalWeight += currDist->getWeight();
        }
    }
 
    size_t numberOfCommittedPart = 0;
    for (unsigned int i = 0; i <= addedDistributions_m.size(); ++ i) {
        Distribution *currDist = this;
        if (i > 0)
            currDist = addedDistributions_m[i - 1];
 
        if (currDist->distrTypeT_m == DistributionType::FROMFILE) {
            particlesPerDist_m.push_back(nPartFromFiles[i]);
        } else {
            size_t particlesCurrentDist = numberOfParticles * currDist->getWeight() / totalWeight;
            particlesPerDist_m.push_back(particlesCurrentDist);
            numberOfCommittedPart += particlesCurrentDist;
        }
    }
 
    // Remaining particles go into first distribution that isn't FROMFILE
    if (numberOfParticles != numberOfCommittedPart) {
        size_t diffNumber = numberOfParticles - numberOfCommittedPart;
        for (unsigned int i = 0; i <= addedDistributions_m.size(); ++ i) {
            Distribution *currDist = this;
            if (i > 0)
                currDist = addedDistributions_m[i - 1];
 
            if (currDist->distrTypeT_m != DistributionType::FROMFILE) {
                particlesPerDist_m.at(i) += diffNumber;
                diffNumber = 0;
                break;
            }
        }
        if (diffNumber != 0) {
            throw OpalException("Distribution::calcPartPerDist",
                                "Particles can't be distributed to distributions in array");
        }
    }
}
 
void Distribution::checkEmissionParameters() {
 
    // There must be at least on energy bin for an emitted beam->
    numberOfEnergyBins_m
        = std::abs(static_cast<int> (Attributes::getReal(itsAttr[Attrib::Distribution::NBIN])));
    if (numberOfEnergyBins_m == 0)
        numberOfEnergyBins_m = 1;
 
    int emissionSteps = std::abs(static_cast<int> (Attributes::getReal(itsAttr[Attrib::Distribution::EMISSIONSTEPS])));
 
    // There must be at least one emission step.
    if (emissionSteps == 0)
        emissionSteps = 1;
 
    // Set number of sample bins per energy bin from the number of emission steps.
    numberOfSampleBins_m = static_cast<int> (std::ceil(emissionSteps / numberOfEnergyBins_m));
    if (numberOfSampleBins_m <= 0)
        numberOfSampleBins_m = 1;
 
    // Initialize emission counters.
    currentEnergyBin_m = 1;
    currentSampleBin_m = 0;
 
}
 
void Distribution::checkIfEmitted() {
 
    emitting_m = Attributes::getBool(itsAttr[Attrib::Distribution::EMITTED]);
 
    switch (distrTypeT_m) {
 
    case DistributionType::ASTRAFLATTOPTH:
    case DistributionType::GUNGAUSSFLATTOPTH:
        emitting_m = true;
        break;
    default:
        break;
    }
}
 
void Distribution::checkParticleNumber(size_t &numberOfParticles) {
 
    size_t numberOfDistParticles = tOrZDist_m.size();
    reduce(numberOfDistParticles, numberOfDistParticles, OpAddAssign());
 
    if (numberOfDistParticles == 0) {
        throw OpalException("Distribution::checkParticleNumber",
                            "Zero particles in the distribution! "
                            "The number of particles needs to be specified.");
    }
 
    if (numberOfDistParticles != numberOfParticles) {
        throw OpalException("Distribution::checkParticleNumber",
                            "The number of particles in the initial\n"
                            "distribution " +
                            std::to_string(numberOfDistParticles) + "\n"
                            "is different from the number of particles\n"
                            "defined by the BEAM command\n" +
                            std::to_string(numberOfParticles) + ".\n"
                            "This often happens when using a FROMFILE type\n"
                            "distribution and not matching the number of\n"
                            "particles in the input distribution file(s) with\n"
                            "the number given in the BEAM command.");
    }
}
 
void Distribution::checkFileMomentum() {
    // If the distribution was read from a file, the file momentum pmean_m[2]
    // should coincide with the momentum given in the beam command avrgpz_m.
 
    if (std::abs(pmean_m[2] - avrgpz_m) / pmean_m[2] > 1e-2) {
        throw OpalException("Distribution::checkFileMomentum",
                            "The z-momentum of the particle distribution\n" +
                            std::to_string(pmean_m[2]) + "\n"
                            "is different from the momentum given in the \"BEAM\" command\n" +
                            std::to_string(avrgpz_m) + ".\n"
                            "When using a \"FROMFILE\" type distribution\n"
                            "the momentum in the \"BEAM\" command should be\n"
                            "the same as the momentum of the particles in the file.");
    }
}
 
void Distribution::chooseInputMomentumUnits(InputMomentumUnits inputMoUnits) {
    /*
     * Toggle what units to use for inputing momentum.
     */
    static const std::map<std::string, InputMomentumUnits> stringInputMomentumUnits_s = {
        {"NONE",    InputMomentumUnits::NONE},
        {"EVOVERC", InputMomentumUnits::EVOVERC}
    };
 
    const std::string inputUnits = Attributes::getString(itsAttr[Attrib::Distribution::INPUTMOUNITS]);
    if (inputUnits.empty()) {
        inputMoUnits_m = inputMoUnits;
    } else {
        inputMoUnits_m = stringInputMomentumUnits_s.at(inputUnits);
    }
}
 
void Distribution::createDistributionBinomial(size_t numberOfParticles, double massIneV) {
 
    setDistParametersBinomial(massIneV);
    generateBinomial(numberOfParticles);
}
 
void Distribution::createDistributionFlattop(size_t numberOfParticles, double massIneV) {
 
    setDistParametersFlattop(massIneV);
 
    if (emitting_m) {
        if (laserProfile_m == nullptr)
            generateFlattopT(numberOfParticles);
        else
            generateFlattopLaserProfile(numberOfParticles);
    } else
        generateFlattopZ(numberOfParticles);
}
 
void Distribution::createDistributionMultiGauss(size_t numberOfParticles, double massIneV) {
 
    gsl_qrng *quasiRandGen2D = selectRandomGenerator(Options::rngtype,2);
 
    setDistParametersMultiGauss(massIneV);
 
    // Generate the distribution
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
    double L = (nPeaks_m - 1) * sepPeaks_m;
 
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
        double x = 0.0, y = 0.0, tOrZ = 0.0;
        double px = 0.0, py = 0.0, pz  = 0.0;
        double r;
 
        // Transverse coordinates
        sampleUniformDisk(quasiRandGen2D, x, y);
        x *= sigmaR_m[0];
        y *= sigmaR_m[1];
 
        // Longitudinal coordinates
        bool allow = false;
        double randNums[2] = {0.0, 0.0};
        while (!allow) {
            if (quasiRandGen2D != nullptr) {
                gsl_qrng_get(quasiRandGen2D, randNums);
            } else {
                randNums[0] = gsl_rng_uniform(randGen_m);
                randNums[1] = gsl_rng_uniform(randGen_m);
            }
            r = randNums[1] * nPeaks_m;
            tOrZ = (2 * randNums[0] - 1) * (L/2 + sigmaR_m[2] * cutoffR_m[2]);
 
            double proba = 0.0;
            for (unsigned i = 0; i < nPeaks_m; i++)
                proba += exp( - .5 * std::pow( (tOrZ + L/2 - i * sepPeaks_m) / sigmaR_m[2], 2) );
            allow = (r <= proba);
        }
 
        if (!emitting_m) {
            // Momentum has non-zero spread only if bunch is being emitted
            allow = false;
            while (!allow) {
                px = gsl_ran_gaussian(randGen_m, 1.0);
                py = gsl_ran_gaussian(randGen_m, 1.0);
                pz = gsl_ran_gaussian(randGen_m, 1.0);
                allow = ( (std::pow( x / cutoffP_m[0], 2) + std::pow( y / cutoffP_m[1], 2) <= 1.0)
                    && (std::abs(pz) <= cutoffP_m[2]) );
            }
            px *= sigmaP_m[0];
            py *= sigmaP_m[1];
            pz *= sigmaP_m[2];
            pz += avrgpz_m;
        }
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            xDist_m.push_back(x);
            pxDist_m.push_back(px);
            yDist_m.push_back(y);
            pyDist_m.push_back(py);
            tOrZDist_m.push_back(tOrZ);
            pzDist_m.push_back(pz);
        }
    }
 
    gsl_qrng_free(quasiRandGen2D);
}
 
size_t Distribution::getNumberOfParticlesInFile(std::ifstream &inputFile) {
 
    size_t numberOfParticlesRead = 0;
    if (Ippl::myNode() == 0) {
        const boost::regex commentExpr("[[:space:]]*#.*");
        const std::string repl("");
        std::string line;
        std::stringstream linestream;
        long tempInt = 0;
 
        do {
            std::getline(inputFile, line);
            line = boost::regex_replace(line, commentExpr, repl);
        } while (line.length() == 0 && !inputFile.fail());
 
        linestream.str(line);
        linestream >> tempInt;
        if (tempInt <= 0) {
            throw OpalException("Distribution::getNumberOfParticlesInFile",
                                "The file '" +
                                Attributes::getString(itsAttr[Attrib::Distribution::FNAME]) +
                                "' does not seem to be an ASCII file containing a distribution.");
        }
        numberOfParticlesRead = static_cast<size_t>(tempInt);
    }
    reduce(numberOfParticlesRead, numberOfParticlesRead, OpAddAssign());
 
    return numberOfParticlesRead;
}
 
void Distribution::createDistributionFromFile(size_t /*numberOfParticles*/, double massIneV) {
    // Data input file is only read by node 0.
    std::ifstream inputFile;
    std::string fileName = Attributes::getString(itsAttr[Attrib::Distribution::FNAME]);
    if (!boost::filesystem::exists(fileName)) {
        throw OpalException(
            "Distribution::createDistributionFromFile",
            "Open file operation failed, please check if '" + fileName + "' really exists.");
    }
    if (Ippl::myNode() == 0) {
        inputFile.open(fileName.c_str());
    }
 
    size_t numberOfParticlesRead = getNumberOfParticlesInFile(inputFile);
    /*
     * We read in the particle information using node zero, but save the particle
     * data to each processor in turn.
     */
    unsigned int saveProcessor = 0;
 
    pmean_m = 0.0;
 
    unsigned int distributeFrequency = 1000;
    size_t singleDataSize            = 6;
    unsigned int dataSize            = distributeFrequency * singleDataSize;
    std::vector<double> data(dataSize);
 
    if (Ippl::myNode() == 0) {
        constexpr unsigned int bufferSize = 1024;
        char lineBuffer[bufferSize];
        unsigned int numParts                         = 0;
        std::vector<double>::iterator currentPosition = data.begin();
        while (!inputFile.eof()) {
            inputFile.getline(lineBuffer, bufferSize);
 
            Vector_t R(0.0), P(0.0);
 
            std::istringstream line(lineBuffer);
            line >> R(0);
            if (line.rdstate())
                break;
            line >> P(0);
            line >> R(1);
            line >> P(1);
            line >> R(2);
            line >> P(2);
 
            if (saveProcessor >= (unsigned)Ippl::getNodes())
                saveProcessor = 0;
 
            if (inputMoUnits_m == InputMomentumUnits::EVOVERC) {
                P(0) = Util::convertMomentumEVoverCToBetaGamma(P(0), massIneV);
                P(1) = Util::convertMomentumEVoverCToBetaGamma(P(1), massIneV);
                P(2) = Util::convertMomentumEVoverCToBetaGamma(P(2), massIneV);
            }
            pmean_m += P;
 
            if (saveProcessor > 0u) {
                currentPosition = std::copy(&(R[0]), &(R[0]) + 3, currentPosition);
                currentPosition = std::copy(&(P[0]), &(P[0]) + 3, currentPosition);
 
                if (currentPosition == data.end()) {
                    MPI_Bcast(&dataSize, 1, MPI_UNSIGNED, 0, Ippl::getComm());
                    MPI_Bcast(&(data[0]), dataSize, MPI_DOUBLE, 0, Ippl::getComm());
 
                    currentPosition = data.begin();
                }
            } else {
                xDist_m.push_back(R(0));
                yDist_m.push_back(R(1));
                tOrZDist_m.push_back(R(2));
                pxDist_m.push_back(P(0));
                pyDist_m.push_back(P(1));
                pzDist_m.push_back(P(2));
            }
 
            ++numParts;
            ++saveProcessor;
        }
 
        dataSize =
            (numberOfParticlesRead == numParts ? currentPosition - data.begin()
                                               : std::numeric_limits<unsigned int>::max());
 
        MPI_Bcast(&dataSize, 1, MPI_UNSIGNED, 0, Ippl::getComm());
        if (numberOfParticlesRead != numParts) {
            throw OpalException(
                "Distribution::createDistributionFromFile",
                "Found " + std::to_string(numParts) + " particles in file '" + fileName
                    + "' instead of " + std::to_string(numberOfParticlesRead));
        }
        MPI_Bcast(&(data[0]), dataSize, MPI_DOUBLE, 0, Ippl::getComm());
 
    } else {
        do {
            MPI_Bcast(&dataSize, 1, MPI_UNSIGNED, 0, Ippl::getComm());
            if (dataSize == std::numeric_limits<unsigned int>::max()) {
                throw OpalException(
                    "Distribution::createDistributionFromFile",
                    "Couldn't find " + std::to_string(numberOfParticlesRead)
                        + " particles in file '" + fileName + "'");
            }
            MPI_Bcast(&(data[0]), dataSize, MPI_DOUBLE, 0, Ippl::getComm());
 
            size_t i = 0;
            while (i < dataSize) {
                if (saveProcessor + 1 == (unsigned)Ippl::myNode()) {
                    const double* tmp = &(data[i]);
                    xDist_m.push_back(tmp[0]);
                    yDist_m.push_back(tmp[1]);
                    tOrZDist_m.push_back(tmp[2]);
                    pxDist_m.push_back(tmp[3]);
                    pyDist_m.push_back(tmp[4]);
                    pzDist_m.push_back(tmp[5]);
                }
                i += singleDataSize;
 
                ++saveProcessor;
                if (saveProcessor + 1 >= (unsigned)Ippl::getNodes()) {
                    saveProcessor = 0;
                }
            }
        } while (dataSize == distributeFrequency * singleDataSize);
    }
 
    pmean_m /= numberOfParticlesRead;
    reduce(pmean_m, pmean_m, OpAddAssign());
 
    if (Ippl::myNode() == 0)
        inputFile.close();
}
 
void Distribution::createMatchedGaussDistribution(size_t numberOfParticles,
                                                  double massIneV,
                                                  double charge)
{
 
    /*
      ToDo:
      - eliminate physics and error
    */
 
    std::string lineName = Attributes::getString(itsAttr[Attrib::Distribution::LINE]);
    if (lineName.empty()) return;
 
    const BeamSequence* lineSequence = BeamSequence::find(lineName);
    if (lineSequence == nullptr)
        throw OpalException("Distribution::CreateMatchedGaussDistribution",
                            "didn't find any Cyclotron element in line");
 
    SpecificElementVisitor<Cyclotron> CyclotronVisitor(*lineSequence->fetchLine());
    CyclotronVisitor.execute();
    size_t NumberOfCyclotrons = CyclotronVisitor.size();
 
    if (NumberOfCyclotrons > 1) {
        throw OpalException("Distribution::createMatchedGaussDistribution",
                            "I am confused, found more than one Cyclotron element in line");
    }
    if (NumberOfCyclotrons == 0) {
        throw OpalException("Distribution::createMatchedGaussDistribution",
                            "didn't find any Cyclotron element in line");
    }
 
    /* FIXME we need to remove const-ness otherwise we can't update the injection radius
     * and injection radial momentum. However, there should be a better solution ..
     */
    Cyclotron* CyclotronElement = const_cast<Cyclotron*>(CyclotronVisitor.front());
 
    bool full    = !Attributes::getBool(itsAttr[Attrib::Distribution::SECTOR]);
    int Nint     = (int)Attributes::getReal(itsAttr[Attrib::Distribution::NSTEPS]);
    int Nsectors = (int)Attributes::getReal(itsAttr[Attrib::Distribution::NSECTORS]);
 
    if ( Nint < 0 )
        throw OpalException("Distribution::createMatchedGaussDistribution()",
                            "Negative number of integration steps");
 
    if ( Nsectors < 0 )
        throw OpalException("Distribution::createMatchedGaussDistribution()",
                            "Negative number of sectors");
 
    if ( Nsectors > 1 && full == false )
        throw OpalException("Distribution::createMatchedGaussDistribution()",
                            "Averaging over sectors can only be done with SECTOR=FALSE");
 
    *gmsg << "* ----------------------------------------------------" << endl;
    *gmsg << "* About to find closed orbit and matched distribution " << endl;
    *gmsg << "* I= " << I_m*Units::A2mA << " (mA)  E= " << E_m*Units::eV2MeV << " (MeV)" << endl;
    *gmsg << "* EX= " << Attributes::getReal(itsAttr[Attrib::Distribution::EX])
          << "  EY= " << Attributes::getReal(itsAttr[Attrib::Distribution::EY])
          << "  ET= " << Attributes::getReal(itsAttr[Attrib::Distribution::ET]) << endl;
    if ( full ) {
        *gmsg << "* SECTOR: " << "match using all sectors, with" << endl
              << "* NSECTORS = " << Nsectors << " to average the field over" << endl;
    }
    else
        *gmsg << "* SECTOR: " << "match using single sector" << endl;
 
    *gmsg << "* NSTEPS = "    << Nint << endl
          << "* HN = "        << CyclotronElement->getCyclHarm()
          << "  PHIINIT = "   << CyclotronElement->getPHIinit()    << endl
          << "* FIELD MAP = " << CyclotronElement->getFieldMapFN() << endl
          << "* ----------------------------------------------------" << endl;
 
    if ( CyclotronElement->getFMLowE()  < 0 ||
         CyclotronElement->getFMHighE() < 0 )
    {
        throw OpalException("Distribution::createMatchedGaussDistribution()",
                            "Missing attributes 'FMLOWE' and/or 'FMHIGHE' in "
                            "'CYCLOTRON' definition.");
    }
 
    std::size_t maxitCOF =
        Attributes::getReal(itsAttr[Attrib::Distribution::MAXSTEPSCO]);
 
    double rguess =
        Attributes::getReal(itsAttr[Attrib::Distribution::RGUESS]);
 
    double denergy = Units::GeV2MeV *
        Attributes::getReal(itsAttr[Attrib::Distribution::DENERGY]);
 
    if ( denergy < 0.0 )
        throw OpalException("Distribution:createMatchedGaussDistribution()",
                            "DENERGY < 0");
 
    double accuracy =
        Attributes::getReal(itsAttr[Attrib::Distribution::RESIDUUM]);
 
    if ( Options::cloTuneOnly ) {
        *gmsg << "* Stopping after closed orbit and tune calculation" << endl;
        typedef std::vector<double> container_t;
        typedef boost::numeric::odeint::runge_kutta4<container_t> rk4_t;
        typedef ClosedOrbitFinder<double,unsigned int, rk4_t> cof_t;
 
        cof_t cof(massIneV*Units::eV2MeV, charge, Nint, CyclotronElement, full, Nsectors);
        cof.findOrbit(accuracy, maxitCOF, E_m*Units::eV2MeV, denergy, rguess, true);
 
        throw EarlyLeaveException("Distribution::createMatchedGaussDistribution()",
                                  "Do only tune calculation.");
    }
 
    bool writeMap = true;
 
    std::unique_ptr<SigmaGenerator> siggen = std::unique_ptr<SigmaGenerator>(
        new SigmaGenerator(I_m,
                           Attributes::getReal(itsAttr[Attrib::Distribution::EX])*Units::m2mm * Units::rad2mrad,
                           Attributes::getReal(itsAttr[Attrib::Distribution::EY])*Units::m2mm * Units::rad2mrad,
                           Attributes::getReal(itsAttr[Attrib::Distribution::ET])*Units::m2mm * Units::rad2mrad,
                           E_m*Units::eV2MeV,
                           massIneV*Units::eV2MeV,
                           charge,
                           CyclotronElement,
                           Nint,
                           Nsectors,
                           Attributes::getReal(itsAttr[Attrib::Distribution::ORDERMAPS]),
                           writeMap));
 
    if (siggen->match(accuracy,
                      Attributes::getReal(itsAttr[Attrib::Distribution::MAXSTEPSSI]),
                      maxitCOF,
                      CyclotronElement,
                      denergy,
                      rguess,
                      full))  {
 
        std::array<double,3> Emit = siggen->getEmittances();
 
        if (rguess > 0)
            *gmsg << "* RGUESS " << rguess << " (m) " << endl;
 
        *gmsg << "* Converged (Ex, Ey, Ez) = (" << Emit[0] << ", " << Emit[1] << ", "
              << Emit[2] << ") pi mm mrad for E= " << E_m * Units::eV2MeV << " (MeV)" << endl;
        *gmsg << "* Sigma-Matrix " << endl;
 
        for (unsigned int i = 0; i < siggen->getSigma().size1(); ++ i) {
            *gmsg << std::setprecision(4)  << std::setw(11) << siggen->getSigma()(i,0);
            for (unsigned int j = 1; j < siggen->getSigma().size2(); ++ j) {
                if (std::abs(siggen->getSigma()(i,j)) < 1.0e-15) {
                    *gmsg << " & " <<  std::setprecision(4)  << std::setw(11) << 0.0;
                }
                else{
                    *gmsg << " & " <<  std::setprecision(4)  << std::setw(11) << siggen->getSigma()(i,j);
                }
 
            }
            *gmsg << " \\\\" << endl;
        }
 
        generateMatchedGauss(siggen->getSigma(), numberOfParticles, massIneV);
 
        // update injection radius and radial momentum
        CyclotronElement->setRinit(siggen->getInjectionRadius() * Units::m2mm);
        CyclotronElement->setPRinit(siggen->getInjectionMomentum());
    }
    else {
        *gmsg << "* Not converged for " << E_m*Units::eV2MeV << " MeV" << endl;
 
        throw OpalException("Distribution::CreateMatchedGaussDistribution",
                            "didn't find any matched distribution.");
    }
}
 
void Distribution::createDistributionGauss(size_t numberOfParticles, double massIneV) {
 
    setDistParametersGauss(massIneV);
 
    if (emitting_m) {
        generateTransverseGauss(numberOfParticles);
        generateLongFlattopT(numberOfParticles);
    } else {
        generateGaussZ(numberOfParticles);
    }
}
 
void Distribution::createOpalCycl(PartBunchBase<double, 3> *beam,
                                  size_t numberOfParticles,
                                  double current, const Beamline &/*bl*/) {
 
    /*
     *  setup data for matched distribution generation
     */
    E_m = (beam->getInitialGamma() - 1.0) * beam->getM();
    I_m = current;
 
    size_t numberOfPartToCreate = numberOfParticles;
    totalNumberParticles_m = numberOfParticles;
    if (beam->getTotalNum() != 0) {
        numberOfPartToCreate = beam->getLocalNum();
    }
 
    // Setup particle bin structure.
    setupParticleBins(beam->getM(),beam);
 
    /*
     * Set what units to use for input momentum units. Default in OPAL-cycl
     * is eV/c.
     */
    chooseInputMomentumUnits(InputMomentumUnits::EVOVERC);
 
    /*
     * Determine the number of particles for each distribution. For OPAL-cycl
     * there are currently no arrays of distributions supported
     */
    calcPartPerDist(numberOfParticles);
 
    // Set distribution type.
    setDistType();
 
    // Emitting particles is not supported in OPAL-cycl.
    emitting_m = false;
 
    // Create distribution.
    create(numberOfPartToCreate, beam->getM(), beam->getQ());
 
    // this variable is needed to be compatible with OPAL-T
    particlesPerDist_m.push_back(tOrZDist_m.size());
 
    shiftDistCoordinates(beam->getM());
 
    // Setup energy bins.
    if (numberOfEnergyBins_m > 0) {
        fillParticleBins();
        beam->setPBins(energyBins_m);
    }
 
    // Check number of particles in distribution.
    checkParticleNumber(numberOfParticles);
 
    initializeBeam(beam);
    writeOutFileHeader();
 
    injectBeam(beam);
 
    OpalData::getInstance()->addProblemCharacteristicValue("NP", numberOfParticles);
}
 
void Distribution::createOpalT(PartBunchBase<double, 3> *beam,
                               std::vector<Distribution *> addedDistributions,
                               size_t &numberOfParticles) {
 
    addedDistributions_m = addedDistributions;
    createOpalT(beam, numberOfParticles);
}
 
void Distribution::createOpalT(PartBunchBase<double, 3> *beam,
                               size_t &numberOfParticles) {
 
    IpplTimings::startTimer(beam->distrCreate_m);
 
    // This is PC from BEAM
    double deltaP = Attributes::getReal(itsAttr[Attrib::Distribution::OFFSETP]);
    if (inputMoUnits_m == InputMomentumUnits::EVOVERC) {
        deltaP = Util::convertMomentumEVoverCToBetaGamma(deltaP, beam->getM());
    }
 
    avrgpz_m = beam->getP()/beam->getM() + deltaP;
 
    totalNumberParticles_m = numberOfParticles;
 
    /*
     * Set what units to use for input momentum units. Default in OPAL-T is
     * unitless (i.e. BetaXGamma, BetaYGamma, BetaZGamma).
     */
    chooseInputMomentumUnits(InputMomentumUnits::NONE);
 
    // Set distribution type(s).
    setDistType();
    for (Distribution* addedDist : addedDistributions_m)
        addedDist->setDistType();
 
    /*
     * Determine the number of particles for each distribution. Note
     * that if a distribution is generated from an input file, then
     * the number of particles in that file will override what is
     * determined here.
     */
    calcPartPerDist(numberOfParticles);
 
    // Check if this is to be an emitted beam->
    checkIfEmitted();
 
    /*
     * Force added distributions to the same emission condition as the main
     * distribution.
     */
    for (Distribution* addedDist : addedDistributions_m)
        addedDist->setDistToEmitted(emitting_m);
 
    if (emitting_m)
        setupEmissionModel(beam);
 
    // Create distributions.
    create(particlesPerDist_m.at(0), beam->getM(), beam->getQ());
 
    size_t distCount = 1;
    for (Distribution* addedDist : addedDistributions_m) {
        addedDist->create(particlesPerDist_m.at(distCount), beam->getM(), beam->getQ());
        distCount++;
    }
 
    // Move added distribution particles to main distribution.
    addDistributions();
 
    if (emitting_m && emissionModel_m == EmissionModel::NONE)
        setupEmissionModelNone(beam);
 
    // Check number of particles in distribution.
    checkParticleNumber(numberOfParticles);
 
    if (emitting_m) {
        checkEmissionParameters();
    } else {
        if (distrTypeT_m == DistributionType::FROMFILE) {
            checkFileMomentum();
        } else {
            pmean_m = Vector_t(0, 0, avrgpz_m);
        }
    }
 
    /*
     * Find max. and min. particle positions in the bunch. For the
     * case of an emitted beam these will be in time (seconds). For
     * an injected beam in z (meters).
     */
    double maxTOrZ = getMaxTOrZ();
    double minTOrZ = getMinTOrZ();
 
    /*
     * Set emission time and/or shift distributions if necessary.
     * For an emitted beam we place all particles at negative time.
     * For an injected beam we just ensure that there are no
     * particles at z < 0.
     */
 
    if (emitting_m) {
        setEmissionTime(maxTOrZ, minTOrZ);
    }
    shiftBeam(maxTOrZ, minTOrZ);
 
    shiftDistCoordinates(beam->getM());
 
    if (numberOfEnergyBins_m > 0) {
        setupEnergyBins(maxTOrZ, minTOrZ);
        fillEBinHistogram();
    }
 
    initializeBeam(beam);
    writeOutFileHeader();
 
    if (emitting_m && Options::cZero) {
        std::vector<std::vector<double> > mirrored;
        const auto end = additionalRNs_m.end();
 
        if (emissionModel_m == EmissionModel::ASTRA ||
            distrTypeT_m == DistributionType::ASTRAFLATTOPTH ||
            distrTypeT_m == DistributionType::GUNGAUSSFLATTOPTH) {
 
            for (auto it = additionalRNs_m.begin(); it != end; ++ it) {
                std::vector<double> tmp;
                tmp.push_back((*it).front());
                tmp.push_back((*it).back() + 0.5);
                mirrored.push_back(tmp);
            }
        } else {
            size_t numAdditionals = additionalRNs_m.front().size() / 2;
            for (auto it = additionalRNs_m.begin(); it != end; ++ it) {
                std::vector<double> tmp((*it).begin() + numAdditionals, (*it).end());
                mirrored.push_back(tmp);
                (*it).erase((*it).begin() + numAdditionals, (*it).end());
            }
        }
 
        additionalRNs_m.insert(additionalRNs_m.end(), mirrored.begin(), mirrored.end());
    }
 
    /*
     * If this is an injected beam, we create particles right away.
     * Emitted beams get created during the course of the simulation.
     */
    if (!emitting_m)
        injectBeam(beam);
 
    OpalData::getInstance()->addProblemCharacteristicValue("NP", numberOfParticles);
    IpplTimings::stopTimer(beam->distrCreate_m);
}
 
size_t Distribution::emitParticles(PartBunchBase<double, 3> *beam, double eZ) {
 
    // Number of particles that have already been emitted and are on this processor.
    size_t numberOfEmittedParticles = beam->getLocalNum();
    size_t oldNumberOfEmittedParticles = numberOfEmittedParticles;
 
    if (!tOrZDist_m.empty() && emitting_m) {
 
        /*
         * Loop through emission beam coordinate containers and emit particles with
         * the appropriate time coordinate. Once emitted, remove particle from the
         * "to be emitted" list.
         */
        std::vector<size_t> particlesToBeErased;
        double phiEffective = (cathodeWorkFunc_m
                               - std::sqrt(std::max(0.0, (Physics::q_e * beam->getQ() * eZ) /
                                                    (4.0 * Physics::pi * Physics::epsilon_0))));
        double lowEnergyLimit = cathodeFermiEnergy_m + phiEffective - laserEnergy_m;
 
        for (size_t particleIndex = 0; particleIndex < tOrZDist_m.size(); particleIndex++) {
 
            // Advance particle time.
            tOrZDist_m.at(particleIndex) += beam->getdT();
 
            // If particle time is now greater than zero, we emit it.
            if (tOrZDist_m.at(particleIndex) >= 0.0) {
 
                particlesToBeErased.push_back(particleIndex);
 
                beam->create(1);
                double deltaT = tOrZDist_m.at(particleIndex);
                beam->dt[numberOfEmittedParticles] = deltaT;
 
                double oneOverCDt = 1.0 / (Physics::c * deltaT);
 
                double px = pxDist_m.at(particleIndex);
                double py = pyDist_m.at(particleIndex);
                double pz = pzDist_m.at(particleIndex);
                std::vector<double> additionalRNs;
                if (additionalRNs_m.size() > particleIndex) {
                    additionalRNs = additionalRNs_m[particleIndex];
                } else {
                    throw OpalException("Distribution::emitParticles",
                                        "not enough additional particles");
                }
                applyEmissionModel(lowEnergyLimit, px, py, pz, additionalRNs);
 
                double particleGamma
                    = std::sqrt(1.0
                                + std::pow(px, 2)
                                + std::pow(py, 2)
                                + std::pow(pz, 2));
 
                beam->R[numberOfEmittedParticles]
                    = Vector_t(oneOverCDt * (xDist_m.at(particleIndex)
                                             + px * deltaT * Physics::c / (2.0 * particleGamma)),
                               oneOverCDt * (yDist_m.at(particleIndex)
                                             + py * deltaT * Physics::c / (2.0 * particleGamma)),
                               pz / (2.0 * particleGamma));
                beam->P[numberOfEmittedParticles]
                    = Vector_t(px, py, pz);
                beam->Bin[numberOfEmittedParticles] = currentEnergyBin_m - 1;
                beam->Q[numberOfEmittedParticles] = beam->getChargePerParticle();
                beam->M[numberOfEmittedParticles] = beam->getMassPerParticle();
                beam->Ef[numberOfEmittedParticles] = Vector_t(0.0);
                beam->Bf[numberOfEmittedParticles] = Vector_t(0.0);
                beam->PType[numberOfEmittedParticles] = beam->getPType();
                beam->POrigin[numberOfEmittedParticles] = ParticleOrigin::REGULAR;
                beam->TriID[numberOfEmittedParticles] = 0;
                numberOfEmittedParticles++;
 
                beam->iterateEmittedBin(currentEnergyBin_m - 1);
 
                // Save particles to vectors for writing initial distribution.
                xWrite_m.push_back(xDist_m.at(particleIndex));
                pxWrite_m.push_back(px);
                yWrite_m.push_back(yDist_m.at(particleIndex));
                pyWrite_m.push_back(py);
                tOrZWrite_m.push_back(-(beam->getdT() - deltaT + currentEmissionTime_m));
                pzWrite_m.push_back(pz);
                binWrite_m.push_back(currentEnergyBin_m);
            }
        }
 
        // Now erase particles that were emitted.
        std::vector<size_t>::reverse_iterator ptbErasedIt;
        for (ptbErasedIt = particlesToBeErased.rbegin();
             ptbErasedIt < particlesToBeErased.rend();
             ++ptbErasedIt) {
 
            /*
             * We don't use the vector class function erase because it
             * is much slower than doing a swap and popping off the end
             * of the vector.
             */
            std::swap( xDist_m.at(*ptbErasedIt),      xDist_m.back());
            std::swap(pxDist_m.at(*ptbErasedIt),     pxDist_m.back());
            std::swap( yDist_m.at(*ptbErasedIt),      yDist_m.back());
            std::swap(pyDist_m.at(*ptbErasedIt),     pyDist_m.back());
            std::swap(tOrZDist_m.at(*ptbErasedIt), tOrZDist_m.back());
            std::swap(pzDist_m.at(*ptbErasedIt),     pzDist_m.back());
            if (additionalRNs_m.size() == xDist_m.size()) {
                std::swap(additionalRNs_m.at(*ptbErasedIt), additionalRNs_m.back());
 
                additionalRNs_m.pop_back();
            }
 
            xDist_m.pop_back();
            pxDist_m.pop_back();
            yDist_m.pop_back();
            pyDist_m.pop_back();
            tOrZDist_m.pop_back();
            pzDist_m.pop_back();
 
        }
 
        /*
         * Set energy bin to emitted if all particles in the bin have been emitted.
         * However, be careful with the last energy bin. We cannot emit it until all
         * of the particles have been accounted for. So when on the last bin, keep it
         * open for the rest of the beam->
         */
        currentSampleBin_m++;
        if (currentSampleBin_m == numberOfSampleBins_m) {
 
            INFOMSG(level3 << "* Bin number: "
                    << currentEnergyBin_m
                    << " has emitted all particles (new emit)." << endl);
            currentSampleBin_m = 0;
            currentEnergyBin_m++;
 
        }
 
        /*
         * Set beam to emitted. Make sure temporary storage is cleared.
         */
        if (currentEnergyBin_m > numberOfEnergyBins_m || tOrZDist_m.empty()) {
            emitting_m = false;
 
            xDist_m.clear();
            pxDist_m.clear();
            yDist_m.clear();
            pyDist_m.clear();
            tOrZDist_m.clear();
            pzDist_m.clear();
 
            currentEnergyBin_m = numberOfEnergyBins_m;
        }
 
    }
    currentEmissionTime_m += beam->getdT();
 
    // Write emitted particles to file.
    writeOutFileEmission();
 
    size_t currentEmittedParticles = numberOfEmittedParticles - oldNumberOfEmittedParticles;
    reduce(currentEmittedParticles, currentEmittedParticles, OpAddAssign());
    totalNumberEmittedParticles_m += currentEmittedParticles;
 
    return currentEmittedParticles;
 
}
 
void Distribution::eraseXDist() {
    xDist_m.erase(xDist_m.begin(), xDist_m.end());
}
 
void Distribution::eraseBGxDist() {
    pxDist_m.erase(pxDist_m.begin(), pxDist_m.end());
}
 
void Distribution::eraseYDist() {
    yDist_m.erase(yDist_m.begin(), yDist_m.end());
}
 
void Distribution::eraseBGyDist() {
    pyDist_m.erase(pyDist_m.begin(), pyDist_m.end());
}
 
void Distribution::eraseTOrZDist() {
    tOrZDist_m.erase(tOrZDist_m.begin(), tOrZDist_m.end());
}
 
void Distribution::eraseBGzDist() {
    pzDist_m.erase(pzDist_m.begin(), pzDist_m.end());
}
 
void Distribution::sampleUniformDisk(gsl_qrng* quasiRandGen2D, double& x1, double& x2)
{
    bool allow = false;
    double randNums[2] = {0.0, 0.0};
    while (!allow) {
        if (quasiRandGen2D != nullptr)
            gsl_qrng_get(quasiRandGen2D, randNums);
        else {
            randNums[0] = gsl_rng_uniform(randGen_m);
            randNums[1] = gsl_rng_uniform(randGen_m);
        }
 
        x1 = 2 * randNums[0] - 1;
        x2 = 2 * randNums[1] - 1;
        allow = (std::pow(x1, 2) + std::pow(x2, 2) <= 1);
    }
}
 
void Distribution::fillEBinHistogram() {
    double upper = 0.0;
    double lower = 0.0;
    gsl_histogram_get_range(energyBinHist_m,
                            gsl_histogram_bins(energyBinHist_m) - 1,
                            &lower, &upper);
    const size_t numberOfParticles = tOrZDist_m.size();
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
 
        double &tOrZ = tOrZDist_m.at(partIndex);
 
        if (gsl_histogram_increment(energyBinHist_m, tOrZ) == GSL_EDOM) {
            gsl_histogram_increment(energyBinHist_m, 0.5 * (lower + upper));
        }
    }
 
    reduce(energyBinHist_m->bin, energyBinHist_m->bin + energyBinHist_m->n, energyBinHist_m->bin, OpAddAssign());
}
 
void Distribution::fillParticleBins() {
 
    for (size_t particleIndex = 0; particleIndex < tOrZDist_m.size(); particleIndex++) {
 
        std::vector<double> partCoord;
 
        partCoord.push_back(xDist_m.at(particleIndex));
        partCoord.push_back(yDist_m.at(particleIndex));
        partCoord.push_back(tOrZDist_m.at(particleIndex));
        partCoord.push_back(pxDist_m.at(particleIndex));
        partCoord.push_back(pyDist_m.at(particleIndex));
        partCoord.push_back(pzDist_m.at(particleIndex));
        partCoord.push_back(0.0);
 
        energyBins_m->fill(partCoord);
 
    }
 
    energyBins_m->sortArray();
}
 
size_t Distribution::findEBin(double tOrZ) {
 
    if (tOrZ <= gsl_histogram_min(energyBinHist_m)) {
        return 0;
    } else if (tOrZ >= gsl_histogram_max(energyBinHist_m)) {
        return numberOfEnergyBins_m - 1;
    } else {
        size_t binNumber;
        gsl_histogram_find(energyBinHist_m, tOrZ, &binNumber);
        return binNumber / numberOfSampleBins_m;
    }
}
 
void Distribution::generateAstraFlattopT(size_t numberOfParticles) {
 
    /*
     * Legacy function to support the ASTRAFLATTOPOTH
     * distribution type.
     */
    checkEmissionParameters();
 
    gsl_qrng *quasiRandGen = gsl_qrng_alloc(gsl_qrng_halton, 2);
 
    int numberOfSampleBins
        = std::abs(static_cast<int> (Attributes::getReal(itsAttr[Attrib::Legacy::Distribution::SBIN])));
    int numberOfEnergyBins
        = std::abs(static_cast<int> (Attributes::getReal(itsAttr[Attrib::Distribution::NBIN])));
 
    int binTotal = numberOfSampleBins * numberOfEnergyBins;
 
    double *distributionTable = new double[binTotal + 1];
 
    double a = tPulseLengthFWHM_m / 2.;
    double sig = tRise_m / 2.;
    double inv_erf08 = 0.906193802436823; // erfinv(0.8)
    double sqr2 = std::sqrt(2.0);
    double t = a - sqr2 * sig * inv_erf08;
    double tmps = sig;
    double tmpt = t;
 
    for (int i = 0; i < 10; ++ i) {
        sig = (t + tRise_m - a) / (sqr2 * inv_erf08);
        t = a - 0.5 * sqr2 * (sig + tmps) * inv_erf08;
        sig = (0.5 * (t + tmpt) + tRise_m - a) / (sqr2 * inv_erf08);
        tmps = sig;
        tmpt = t;
    }
 
    /*
     * Emission time is set here during distribution particle creation only for
     * the ASTRAFLATTOPTH distribution type.
     */
    tEmission_m = tPulseLengthFWHM_m + 10. * sig;
    tBin_m = tEmission_m / numberOfEnergyBins;
 
    double lo = -tBin_m / 2.0 * numberOfEnergyBins;
    double hi = tBin_m / 2.0 * numberOfEnergyBins;
    double dx = tBin_m / numberOfSampleBins;
    double x = lo;
    double tot = 0;
    double weight = 2.0;
 
    // sample the function that describes the histogram of the requested distribution
    for (int i = 0; i < binTotal + 1; ++ i, x += dx, weight = 6. - weight) {
        distributionTable[i] = gsl_sf_erf((x + a) / (sqr2 * sig)) - gsl_sf_erf((x - a) / (sqr2 * sig));
        tot += distributionTable[i] * weight;
    }
    tot -= distributionTable[binTotal] * (5. - weight);
    tot -= distributionTable[0];
 
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
    double tCoord = 0.0;
 
    int effectiveNumParticles = 0;
    int largestBin = 0;
    std::vector<int> numParticlesInBin(numberOfEnergyBins,0);
    for (int k = 0; k < numberOfEnergyBins; ++ k) {
        double loc_fraction = -distributionTable[numberOfSampleBins * k] / tot;
 
        weight = 2.0;
        for (int i = numberOfSampleBins * k; i < numberOfSampleBins * (k + 1) + 1;
            ++ i, weight = 6. - weight) {
            loc_fraction += distributionTable[i] * weight / tot;
        }
        loc_fraction -= distributionTable[numberOfSampleBins * (k + 1)]
            * (5. - weight) / tot;
        numParticlesInBin[k] = static_cast<int>(std::round(loc_fraction * numberOfParticles));
        effectiveNumParticles += numParticlesInBin[k];
        if (numParticlesInBin[k] > numParticlesInBin[largestBin]) largestBin = k;
    }
 
    numParticlesInBin[largestBin] += (numberOfParticles - effectiveNumParticles);
 
    for (int k = 0; k < numberOfEnergyBins; ++ k) {
        gsl_ran_discrete_t *table
            = gsl_ran_discrete_preproc(numberOfSampleBins,
                                       &(distributionTable[numberOfSampleBins * k]));
 
        for (int i = 0; i < numParticlesInBin[k]; i++) {
            double xx[2];
            gsl_qrng_get(quasiRandGen, xx);
            tCoord = hi * (xx[1] + static_cast<int>(gsl_ran_discrete(randGen_m, table))
                           - binTotal / 2 + k * numberOfSampleBins) / (binTotal / 2);
 
            saveProcessor++;
            if (saveProcessor >= numNodes)
                saveProcessor = 0;
 
            if (scalable || myNode == saveProcessor) {
                tOrZDist_m.push_back(tCoord);
                pzDist_m.push_back(0.0);
            }
        }
        gsl_ran_discrete_free(table);
    }
 
    gsl_qrng_free(quasiRandGen);
    delete [] distributionTable;
 
}
 
void Distribution::generateBinomial(size_t numberOfParticles) {
 
    // Calculate emittance and Twiss parameters.
    Vector_t emittance;
    Vector_t alpha, beta, gamma;
    for (unsigned int index = 0; index < 3; index++) {
        emittance(index) = sigmaR_m[index] * sigmaP_m[index]
            * std::cos(std::asin(correlationMatrix_m(2 * index + 1, 2 * index)));
 
        if (std::abs(emittance(index)) > std::numeric_limits<double>::epsilon()) {
            beta(index)  = std::pow(sigmaR_m[index], 2) / emittance(index);
            gamma(index) = std::pow(sigmaP_m[index], 2) / emittance(index);
        } else {
            beta(index)  = std::sqrt(std::numeric_limits<double>::max());
            gamma(index) = std::sqrt(std::numeric_limits<double>::max());
        }
        alpha(index) = -correlationMatrix_m(2 * index + 1, 2 * index)
                        * std::sqrt(beta(index) * gamma(index));
    }
 
    Vector_t M, PM, L, PL, X, PX;
    Vector_t CHI, COSCHI, SINCHI(0.0);
    Vector_t AMI;
    Vektor<BinomialBehaviorSplitter*, 3> splitter;
    for (unsigned int index = 0; index < 3; index++) {
        // gamma(index) *= cutoffR_m[index];
        // beta(index)  *= cutoffP_m[index];
        COSCHI[index] =  std::sqrt(1.0 / (1.0 + std::pow(alpha(index), 2)));
        SINCHI[index] = -alpha(index) * COSCHI[index];
        CHI[index]    =  std::atan2(SINCHI[index], COSCHI[index]);
        AMI[index]    =  1.0 / mBinomial_m[index];
        M[index]      =  std::sqrt(emittance(index) * beta(index));
        PM[index]     =  std::sqrt(emittance(index) * gamma(index));
        L[index]      =  std::sqrt((mBinomial_m[index] + 1.0) / 2.0) * M[index];
        PL[index]     =  std::sqrt((mBinomial_m[index] + 1.0) / 2.0) * PM[index];
 
        if (mBinomial_m[index] < 10000) {
            X[index] =  L[index];
            PX[index] = PL[index];
            splitter[index] = new MDependentBehavior(mBinomial_m[index]);
        } else {
            X[index] =  M[index];
            PX[index] = PM[index];
            splitter[index] = new GaussianLikeBehavior();
        }
    }
 
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
    double temp = 1.0 - std::pow(correlationMatrix_m(1, 0), 2);
    const double tempa = std::copysign(std::sqrt(std::abs(temp)), temp);
    const double l32 = (correlationMatrix_m(4, 1) -
                        correlationMatrix_m(1, 0) * correlationMatrix_m(4, 0)) / tempa;
    temp = 1 - std::pow(correlationMatrix_m(4, 0), 2) - l32 * l32;
    const double l33 = std::copysign(std::sqrt(std::abs(temp)), temp);
 
    const double l42 = (correlationMatrix_m(5, 1) -
                        correlationMatrix_m(1, 0) * correlationMatrix_m(5, 0)) / tempa;
    const double l43 = (correlationMatrix_m(5, 4) -
                        correlationMatrix_m(4, 0) * correlationMatrix_m(5, 0) - l42 * l32) / l33;
    temp = 1 - std::pow(correlationMatrix_m(5, 0), 2) - l42 * l42 - l43 * l43;
    const double l44 = std::copysign(std::sqrt(std::abs(temp)), temp);
 
    Vector_t x = Vector_t(0.0);
    Vector_t p = Vector_t(0.0);
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
 
        double A = 0.0;
        double AL = 0.0;
        double Ux = 0.0, U = 0.0;
        double Vx = 0.0, V = 0.0;
 
        A = splitter[0]->get(gsl_rng_uniform(randGen_m));
        AL = Physics::two_pi * gsl_rng_uniform(randGen_m);
        Ux = A * std::cos(AL);
        Vx = A * std::sin(AL);
        x[0] = X[0] * Ux;
        p[0] = PX[0] * (Ux * SINCHI[0] + Vx * COSCHI[0]);
 
        A = splitter[1]->get(gsl_rng_uniform(randGen_m));
        AL = Physics::two_pi * gsl_rng_uniform(randGen_m);
        U = A * std::cos(AL);
        V = A * std::sin(AL);
        x[1] = X[1] * U;
        p[1] = PX[1] * (U * SINCHI[1] + V * COSCHI[1]);
 
        A = splitter[2]->get(gsl_rng_uniform(randGen_m));
        AL = Physics::two_pi * gsl_rng_uniform(randGen_m);
        U = A * std::cos(AL);
        V = A * std::sin(AL);
        x[2] = X[2] *  (Ux * correlationMatrix_m(4, 0) + Vx * l32 + U * l33);
        p[2] = PX[2] * (Ux * correlationMatrix_m(5, 0) + Vx * l42 + U * l43 + V * l44);
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            xDist_m.push_back(x[0]);
            pxDist_m.push_back(p[0]);
            yDist_m.push_back(x[1]);
            pyDist_m.push_back(p[1]);
            tOrZDist_m.push_back(x[2]);
            pzDist_m.push_back(avrgpz_m + p[2]);
        }
    }
 
    for (unsigned int index = 0; index < 3; index++) {
        delete splitter[index];
    }
}
 
void Distribution::generateFlattopLaserProfile(size_t numberOfParticles) {
 
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
 
        double x = 0.0;
        double px = 0.0;
        double y = 0.0;
        double py = 0.0;
 
        laserProfile_m->getXY(x, y);
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            xDist_m.push_back(x * sigmaR_m[0]);
            pxDist_m.push_back(px);
            yDist_m.push_back(y * sigmaR_m[1]);
            pyDist_m.push_back(py);
        }
    }
 
    if (distrTypeT_m == DistributionType::ASTRAFLATTOPTH)
        generateAstraFlattopT(numberOfParticles);
    else
        generateLongFlattopT(numberOfParticles);
 
}
 
void Distribution::generateFlattopT(size_t numberOfParticles) {
 
    gsl_qrng *quasiRandGen2D = selectRandomGenerator(Options::rngtype,2);
 
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
 
        double x = 0.0;
        double px = 0.0;
        double y = 0.0;
        double py = 0.0;
 
        sampleUniformDisk(quasiRandGen2D, x, y);
        x *= sigmaR_m[0];
        y *= sigmaR_m[1];
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            xDist_m.push_back(x);
            pxDist_m.push_back(px);
            yDist_m.push_back(y);
            pyDist_m.push_back(py);
        }
 
    }
 
    gsl_qrng_free(quasiRandGen2D);
 
    if (distrTypeT_m == DistributionType::ASTRAFLATTOPTH)
        generateAstraFlattopT(numberOfParticles);
    else
        generateLongFlattopT(numberOfParticles);
 
}
 
void Distribution::generateFlattopZ(size_t numberOfParticles) {
 
    gsl_qrng *quasiRandGen1D = selectRandomGenerator(Options::rngtype,1);
    gsl_qrng *quasiRandGen2D = selectRandomGenerator(Options::rngtype,2);
 
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
 
        double x = 0.0;
        double px = 0.0;
        double y = 0.0;
        double py = 0.0;
        double z = 0.0;
        double pz = 0.0;
 
        sampleUniformDisk(quasiRandGen2D, x, y);
        x *= sigmaR_m[0];
        y *= sigmaR_m[1];
 
        if (quasiRandGen1D != nullptr)
            gsl_qrng_get(quasiRandGen1D, &z);
        else
            z = gsl_rng_uniform(randGen_m);
 
        z = (z - 0.5) * sigmaR_m[2];
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            xDist_m.push_back(x);
            pxDist_m.push_back(px);
            yDist_m.push_back(y);
            pyDist_m.push_back(py);
            tOrZDist_m.push_back(z);
            pzDist_m.push_back(avrgpz_m + pz);
        }
    }
 
    gsl_qrng_free(quasiRandGen1D);
    gsl_qrng_free(quasiRandGen2D);
}
 
void Distribution::generateGaussZ(size_t numberOfParticles) {
 
    gsl_matrix * corMat  = gsl_matrix_alloc (6, 6);
    gsl_vector * rx = gsl_vector_alloc(6);
    gsl_vector * ry = gsl_vector_alloc(6);
 
    for (unsigned int i = 0; i < 6; ++ i) {
        gsl_matrix_set(corMat, i, i, correlationMatrix_m(i, i));
        for (unsigned int j = 0; j < i; ++ j) {
            gsl_matrix_set(corMat, i, j, correlationMatrix_m(i, j));
            gsl_matrix_set(corMat, j, i, correlationMatrix_m(i, j));
        }
    }
 
#define DISTDBG1
#ifdef DISTDBG1
    *gmsg << "* m before gsl_linalg_cholesky_decomp" << endl;
    for (int i = 0; i < 6; i++) {
        for (int j = 0; j < 6; j++) {
            if (j==0)
                *gmsg << "* r(" << std::setprecision(1) << i << ", : ) = "
                      << std::setprecision(4) << std::setw(10) << gsl_matrix_get (corMat, i, j);
            else
                *gmsg << " & " << std::setprecision(4) << std::setw(10) << gsl_matrix_get (corMat, i, j);
        }
        *gmsg << " \\\\" << endl;
    }
#endif
/*
    //Sets the GSL error handler off, exception will be handled internally with a renormalization method
    gsl_set_error_handler_off();
*/
    int errcode = gsl_linalg_cholesky_decomp(corMat);
/*
    double rn = 1e-12;
 
    while (errcode == GSL_EDOM) {
 
        // Resets the correlation matrix
        for (unsigned int i = 0; i < 6; ++ i) {
            gsl_matrix_set(corMat, i, i, correlationMatrix_m(i, i));
            for (unsigned int j = 0; j < i; ++ j) {
                gsl_matrix_set(corMat, i, j, correlationMatrix_m(i, j));
                gsl_matrix_set(corMat, j, i, correlationMatrix_m(i, j));
            }
        }
        // Applying a renormalization method corMat = corMat + rn*Unitymatrix
        // This is the renormalization
        for(int i = 0; i < 6; i++){
            double corMati = gsl_matrix_get(corMat, i , i);
            gsl_matrix_set(corMat, i, i, corMati + rn);
        }
        //Just to be sure that the renormalization worked
        errcode = gsl_linalg_cholesky_decomp(corMat);
        if(errcode != GSL_EDOM) *gmsg << "* WARNING: Correlation matrix had to be renormalized"<<endl;
        else rn *= 10;
    }
    //Sets again the standard GSL error handler on
    gsl_set_error_handler(nullptr);
*/
    //Just to be sure
    if (errcode == GSL_EDOM) {
        throw OpalException("Distribution::GenerateGaussZ",
                            "gsl_linalg_cholesky_decomp failed");
    }
    // so make the upper part zero.
    for (int i = 0; i < 5; ++ i) {
        for (int j = i+1; j < 6 ; ++ j) {
            gsl_matrix_set (corMat, i, j, 0.0);
        }
    }
#define DISTDBG2
#ifdef DISTDBG2
    *gmsg << "* m after gsl_linalg_cholesky_decomp" << endl;
    for (int i = 0; i < 6; i++) {
        for (int j = 0; j < 6; j++) {
            if (j==0)
                *gmsg << "* r(" << std::setprecision(1) << i << ", : ) = "
                      << std::setprecision(4) << std::setw(10) << gsl_matrix_get (corMat, i, j);
            else
                *gmsg << " & " << std::setprecision(4) << std::setw(10) << gsl_matrix_get (corMat, i, j);
        }
        *gmsg << " \\\\" << endl;
    }
#endif
 
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
        bool allow = false;
 
        double x  = 0.0;
        double px = 0.0;
        double y  = 0.0;
        double py = 0.0;
        double z  = 0.0;
        double pz = 0.0;
 
        while (!allow) {
            gsl_vector_set(rx, 0, gsl_ran_gaussian(randGen_m, 1.0));
            gsl_vector_set(rx, 1, gsl_ran_gaussian(randGen_m, 1.0));
            gsl_vector_set(rx, 2, gsl_ran_gaussian(randGen_m, 1.0));
            gsl_vector_set(rx, 3, gsl_ran_gaussian(randGen_m, 1.0));
            gsl_vector_set(rx, 4, gsl_ran_gaussian(randGen_m, 1.0));
            gsl_vector_set(rx, 5, gsl_ran_gaussian(randGen_m, 1.0));
 
            gsl_blas_dgemv(CblasNoTrans, 1.0, corMat, rx, 0.0, ry);
 
            x  = gsl_vector_get(ry, 0);
            px = gsl_vector_get(ry, 1);
            y  = gsl_vector_get(ry, 2);
            py = gsl_vector_get(ry, 3);
            z  = gsl_vector_get(ry, 4);
            pz = gsl_vector_get(ry, 5);
 
            bool xAndYOk   = (std::pow( x / cutoffR_m[0], 2) + std::pow( y / cutoffR_m[1], 2) <= 1.0);
            bool pxAndPyOk = (std::pow(px / cutoffP_m[0], 2) + std::pow(py / cutoffP_m[1], 2) <= 1.0);
 
            bool zOk  = (std::abs(z)  <= cutoffR_m[2]);
            bool pzOk = (std::abs(pz) <= cutoffP_m[2]);
 
            allow = (xAndYOk && pxAndPyOk && zOk && pzOk);
        }
 
        x  *= sigmaR_m[0];
        y  *= sigmaR_m[1];
        z  *= sigmaR_m[2];
        px *= sigmaP_m[0];
        py *= sigmaP_m[1];
        pz *= sigmaP_m[2];
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            xDist_m.push_back(x);
            pxDist_m.push_back(px);
            yDist_m.push_back(y);
            pyDist_m.push_back(py);
            tOrZDist_m.push_back(z);
            pzDist_m.push_back(avrgpz_m + pz);
 
            //*gmsg << "x,y,z,px,py,pz " << std::setw(11) << x << std::setw(11) << y << std::setw(11) << z << std::setw(11) << px << std::setw(11) << py << std::setw(11) << avrgpz_m + pz << endl;
        }
    }
 
    gsl_vector_free(rx);
    gsl_vector_free(ry);
    gsl_matrix_free(corMat);
}
 
void Distribution::generateMatchedGauss(const SigmaGenerator::matrix_t& sigma,
                                        size_t numberOfParticles, double massIneV)
{
    /* This particle distribution generation is based on a
     * symplectic method described in
     * https://arxiv.org/abs/1205.3601
     */
 
    /* Units of the Sigma Matrix:
     *  spatial: m
     *  moment:  rad
     *
     * Attention: The vertical and longitudinal direction must be interchanged!
     */
    for (unsigned int i = 0; i < 3; ++ i) {
        if ( sigma(2 * i, 2 * i) < 0 || sigma(2 * i + 1, 2 * i + 1) < 0 )
            throw OpalException("Distribution::generateMatchedGauss()",
                                "Negative value on the diagonal of the sigma matrix.");
    }
 
    double bgam = Util::getBetaGamma(E_m, massIneV);
 
    /*
     * only used for printing
     */
 
    // horizontal
    sigmaR_m[0] = std::sqrt(sigma(0, 0));
    sigmaP_m[0] = std::sqrt(sigma(1, 1)) * bgam;
 
    // longitudinal
    sigmaR_m[1] = std::sqrt(sigma(4, 4));
    sigmaP_m[1] = std::sqrt(sigma(5, 5)) * bgam;
 
    // vertical
    sigmaR_m[2] = std::sqrt(sigma(2, 2));
    sigmaP_m[2] = std::sqrt(sigma(3, 3)) * bgam;
 
    correlationMatrix_m(1, 0) = sigma(0, 1) / (std::sqrt(sigma(0, 0) * sigma(1, 1)));
    correlationMatrix_m(3, 2) = sigma(2, 3) / (std::sqrt(sigma(2, 2) * sigma(3, 3)));
    correlationMatrix_m(5, 4) = sigma(4, 5) / (std::sqrt(sigma(4, 4) * sigma(5, 5)));
    correlationMatrix_m(4, 0) = sigma(0, 4) / (std::sqrt(sigma(0, 0) * sigma(4, 4)));
    correlationMatrix_m(4, 1) = sigma(1, 4) / (std::sqrt(sigma(1, 1) * sigma(4, 4)));
    correlationMatrix_m(5, 0) = sigma(0, 5) / (std::sqrt(sigma(0, 0) * sigma(5, 5)));
    correlationMatrix_m(5, 1) = sigma(1, 5) / (std::sqrt(sigma(1, 1) * sigma(5, 5)));
 
    inputMoUnits_m = InputMomentumUnits::NONE;
 
    /*
     * decouple horizontal and longitudinal direction
     */
 
    // extract horizontal and longitudinal directions
    RealDiracMatrix::matrix_t A(4, 4);
    A(0, 0) = sigma(0, 0);
    A(1, 1) = sigma(1, 1);
    A(2, 2) = sigma(4, 4);
    A(3, 3) = sigma(5, 5);
 
    A(0, 1) = sigma(0, 1);
    A(0, 2) = sigma(0, 4);
    A(0, 3) = sigma(0, 5);
    A(1, 0) = sigma(1, 0);
    A(2, 0) = sigma(4, 0);
    A(3, 0) = sigma(5, 0);
 
    A(1, 2) = sigma(1, 4);
    A(2, 1) = sigma(4, 1);
    A(1, 3) = sigma(1, 5);
    A(3, 1) = sigma(5, 1);
    A(2, 3) = sigma(4, 5);
    A(3, 2) = sigma(5, 4);
 
 
    RealDiracMatrix rdm;
    RealDiracMatrix::sparse_matrix_t R1 = rdm.diagonalize(A);
 
    RealDiracMatrix::vector_t variances(8);
    for (int i = 0; i < 4; ++i) {
        variances(i) = std::sqrt(A(i, i));
    }
 
    /*
     * decouple vertical direction
     */
    A *= 0.0;
    A(0, 0) = 1;
    A(1, 1) = 1;
    A(2, 2) = sigma(2, 2);
    A(3, 3) = sigma(3, 3);
    A(2, 3) = sigma(2, 3);
    A(3, 2) = sigma(3, 2);
 
    RealDiracMatrix::sparse_matrix_t R2 = rdm.diagonalize(A);
 
    for (int i = 0; i < 4; ++i) {
        variances(4 + i) = std::sqrt(A(i, i));
    }
 
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
    RealDiracMatrix::vector_t p1(4), p2(4);
    for (size_t i = 0; i < numberOfParticles; i++) {
        for (int j = 0; j < 4; j++) {
            p1(j) = gsl_ran_gaussian(randGen_m, 1.0) * variances(j);
            p2(j) = gsl_ran_gaussian(randGen_m, 1.0) * variances(4 + j);
        }
 
        p1 = boost::numeric::ublas::prod(R1, p1);
        p2 = boost::numeric::ublas::prod(R2, p2);
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            xDist_m.push_back(p1(0));
            pxDist_m.push_back(p1(1) * bgam);
            yDist_m.push_back(p1(2));
            pyDist_m.push_back(p1(3) * bgam);
            tOrZDist_m.push_back(p2(2));
            pzDist_m.push_back(p2(3) * bgam);
        }
    }
}
 
void Distribution::generateLongFlattopT(size_t numberOfParticles) {
 
    double flattopTime = tPulseLengthFWHM_m
        - std::sqrt(2.0 * std::log(2.0)) * (sigmaTRise_m + sigmaTFall_m);
 
    if (flattopTime < 0.0)
        flattopTime = 0.0;
 
    double normalizedFlankArea = 0.5 * std::sqrt(Physics::two_pi) * gsl_sf_erf(cutoffR_m[2] / std::sqrt(2.0));
    double distArea = flattopTime
        + (sigmaTRise_m + sigmaTFall_m) * normalizedFlankArea;
 
    // Find number of particles in rise, fall and flat top.
    size_t numRise = numberOfParticles * sigmaTRise_m * normalizedFlankArea / distArea;
    size_t numFall = numberOfParticles * sigmaTFall_m * normalizedFlankArea / distArea;
    size_t numFlat = numberOfParticles - numRise - numFall;
 
    // Generate particles in tail.
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
    for (size_t partIndex = 0; partIndex < numFall; partIndex++) {
 
        double t = 0.0;
        double pz = 0.0;
 
        bool allow = false;
        while (!allow) {
            t = gsl_ran_gaussian_tail(randGen_m, 0, sigmaTFall_m);
            if (t <= sigmaTFall_m * cutoffR_m[2]) {
                t = -t + sigmaTFall_m * cutoffR_m[2];
                allow = true;
            }
        }
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            tOrZDist_m.push_back(t);
            pzDist_m.push_back(pz);
        }
    }
 
    /*
     * Generate particles in flat top. The flat top can also have sinusoidal
     * modulations.
     */
    double modulationAmp = Attributes::getReal(itsAttr[Attrib::Distribution::FTOSCAMPLITUDE]) / 100.0;
    if (modulationAmp > 1.0)
        modulationAmp = 1.0;
    double numModulationPeriods
        = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::FTOSCPERIODS]));
    double modulationPeriod = 0.0;
    if (numModulationPeriods != 0.0)
        modulationPeriod = flattopTime / numModulationPeriods;
 
    gsl_qrng *quasiRandGen1D = selectRandomGenerator(Options::rngtype,1);
    gsl_qrng *quasiRandGen2D = selectRandomGenerator(Options::rngtype,2);
 
    for (size_t partIndex = 0; partIndex < numFlat; partIndex++) {
 
        double t = 0.0;
        double pz = 0.0;
 
        if (modulationAmp == 0.0 || numModulationPeriods == 0.0) {
 
            if (quasiRandGen1D != nullptr)
                gsl_qrng_get(quasiRandGen1D, &t);
            else
                t = gsl_rng_uniform(randGen_m);
 
            t = flattopTime * t;
 
        } else {
 
            bool allow = false;
            double randNums[2] = {0.0, 0.0};
            while (!allow) {
                if (quasiRandGen2D != nullptr) {
                    gsl_qrng_get(quasiRandGen2D, randNums);
                } else {
                    randNums[0]= gsl_rng_uniform(randGen_m);
                    randNums[1]= gsl_rng_uniform(randGen_m);
                }
                t = randNums[0] * flattopTime;
 
                double funcValue = (1.0 + modulationAmp
                                    * std::sin(Physics::two_pi * t / modulationPeriod))
                    / (1.0 + std::abs(modulationAmp));
 
                allow = (randNums[1] <= funcValue);
            }
        }
        // Shift the uniform part of distribution behind the fall
        t += sigmaTFall_m * cutoffR_m[2];
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            tOrZDist_m.push_back(t);
            pzDist_m.push_back(pz);
        }
    }
 
    // Generate particles in rise.
    for (size_t partIndex = 0; partIndex < numRise; partIndex++) {
 
        double t = 0.0;
        double pz = 0.0;
 
        bool allow = false;
        while (!allow) {
            t = gsl_ran_gaussian_tail(randGen_m, 0, sigmaTRise_m);
            if (t <= sigmaTRise_m * cutoffR_m[2]) {
                t += sigmaTFall_m * cutoffR_m[2] + flattopTime;
                allow = true;
            }
        }
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            tOrZDist_m.push_back(t);
            pzDist_m.push_back(pz);
        }
    }
 
    gsl_qrng_free(quasiRandGen1D);
    gsl_qrng_free(quasiRandGen2D);
}
 
void Distribution::generateTransverseGauss(size_t numberOfParticles) {
 
    // Generate coordinates.
    gsl_matrix * corMat  = gsl_matrix_alloc (4, 4);
    gsl_vector * rx = gsl_vector_alloc(4);
    gsl_vector * ry = gsl_vector_alloc(4);
 
    for (unsigned int i = 0; i < 4; ++ i) {
        gsl_matrix_set(corMat, i, i, correlationMatrix_m(i, i));
        for (unsigned int j = 0; j < i; ++ j) {
            gsl_matrix_set(corMat, i, j, correlationMatrix_m(i, j));
            gsl_matrix_set(corMat, j, i, correlationMatrix_m(i, j));
        }
    }
 
    int errcode = gsl_linalg_cholesky_decomp(corMat);
 
    if (errcode == GSL_EDOM) {
        throw OpalException("Distribution::GenerateTransverseGauss",
                            "gsl_linalg_cholesky_decomp failed");
    }
 
    for (int i = 0; i < 3; ++ i) {
        for (int j = i+1; j < 4 ; ++ j) {
            gsl_matrix_set (corMat, i, j, 0.0);
        }
    }
 
    int saveProcessor = -1;
    const int myNode = Ippl::myNode();
    const int numNodes = Ippl::getNodes();
    const bool scalable = Attributes::getBool(itsAttr[Attrib::Distribution::SCALABLE]);
 
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
 
        double x = 0.0;
        double px = 0.0;
        double y = 0.0;
        double py = 0.0;
 
        bool allow = false;
        while (!allow) {
 
            gsl_vector_set(rx, 0, gsl_ran_gaussian (randGen_m,1.0));
            gsl_vector_set(rx, 1, gsl_ran_gaussian (randGen_m,1.0));
            gsl_vector_set(rx, 2, gsl_ran_gaussian (randGen_m,1.0));
            gsl_vector_set(rx, 3, gsl_ran_gaussian (randGen_m,1.0));
 
            gsl_blas_dgemv(CblasNoTrans, 1.0, corMat, rx, 0.0, ry);
            x = gsl_vector_get(ry, 0);
            px = gsl_vector_get(ry, 1);
            y = gsl_vector_get(ry, 2);
            py = gsl_vector_get(ry, 3);
 
            bool xAndYOk   = (std::pow( x / cutoffR_m[0], 2) + std::pow( y / cutoffR_m[1], 2) <= 1.0);
            bool pxAndPyOk = (std::pow(px / cutoffP_m[0], 2) + std::pow(py / cutoffP_m[1], 2) <= 1.0);
 
            allow = (xAndYOk && pxAndPyOk);
 
        }
        x *= sigmaR_m[0];
        y *= sigmaR_m[1];
        px *= sigmaP_m[0];
        py *= sigmaP_m[1];
 
        // Save to each processor in turn.
        saveProcessor++;
        if (saveProcessor >= numNodes)
            saveProcessor = 0;
 
        if (scalable || myNode == saveProcessor) {
            xDist_m.push_back(x);
            pxDist_m.push_back(px);
            yDist_m.push_back(y);
            pyDist_m.push_back(py);
        }
    }
 
    gsl_matrix_free(corMat);
    gsl_vector_free(rx);
    gsl_vector_free(ry);
}
 
void Distribution::initializeBeam(PartBunchBase<double, 3> *beam) {
 
    /*
     * Set emission time, the current beam bunch number and
     * set the beam energy bin structure, if it has one.
     */
    beam->setTEmission(tEmission_m);
    beam->setNumBunch(1);
    if (numberOfEnergyBins_m > 0)
        beam->setEnergyBins(numberOfEnergyBins_m);
}
 
void Distribution::injectBeam(PartBunchBase<double, 3> *beam) {
 
    writeOutFileInjection();
 
    std::vector<double> id1 = Attributes::getRealArray(itsAttr[Attrib::Distribution::ID1]);
    std::vector<double> id2 = Attributes::getRealArray(itsAttr[Attrib::Distribution::ID2]);
 
    bool hasID1 = !id1.empty();
    bool hasID2 = !id2.empty();
 
    if (hasID1 || hasID2)
        *gmsg << "* Use special ID1 or ID2 particle in distribution" << endl;
 
 
    size_t numberOfParticles = tOrZDist_m.size();
    beam->create(numberOfParticles);
    for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
 
        beam->R[partIndex] = Vector_t(xDist_m.at(partIndex),
                                     yDist_m.at(partIndex),
                                     tOrZDist_m.at(partIndex));
 
        beam->P[partIndex] = Vector_t(pxDist_m.at(partIndex),
                                      pyDist_m.at(partIndex),
                                      pzDist_m.at(partIndex));
 
        beam->Q[partIndex] = beam->getChargePerParticle();
        beam->M[partIndex] = beam->getMassPerParticle();
        beam->Ef[partIndex] = Vector_t(0.0);
        beam->Bf[partIndex] = Vector_t(0.0);
        beam->PType[partIndex] = beam->getPType();
        beam->POrigin[partIndex] = ParticleOrigin::REGULAR;
        beam->TriID[partIndex] = 0;
        if (numberOfEnergyBins_m > 0) {
            size_t binNumber = findEBin(tOrZDist_m.at(partIndex));
            beam->Bin[partIndex] = binNumber;
            beam->iterateEmittedBin(binNumber);
        } else
            beam->Bin[partIndex] = 0;
 
        if (hasID1) {
            if (beam->ID[partIndex] == 1) {
                beam->R[partIndex] = Vector_t(id1[0],id1[1],id1[2]);
                beam->P[partIndex] = Vector_t(id1[3],id1[4],id1[5]);
            }
        }
 
        if (hasID2) {
            if (beam->ID[partIndex] == 2) {
                beam->R[partIndex] = Vector_t(id2[0],id2[1],id2[2]);
                beam->P[partIndex] = Vector_t(id2[3],id2[4],id2[5]);
            }
        }
    }
 
    xDist_m.clear();
    pxDist_m.clear();
    yDist_m.clear();
    pyDist_m.clear();
    tOrZDist_m.clear();
    pzDist_m.clear();
 
    beam->boundp();
    beam->calcEMean();
}
 
bool Distribution::getIfDistEmitting() {
    return emitting_m;
}
 
int Distribution::getLastEmittedEnergyBin() {
    return currentEnergyBin_m;
}
 
double Distribution::getMaxTOrZ() {
 
    double maxTOrZ = std::numeric_limits<int>::min();
    for (auto tOrZ : tOrZDist_m) {
        if (maxTOrZ < tOrZ)
            maxTOrZ = tOrZ;
    }
 
    reduce(maxTOrZ, maxTOrZ, OpMaxAssign());
 
    return maxTOrZ;
}
 
double Distribution::getMinTOrZ() {
 
    double minTOrZ = std::numeric_limits<int>::max();
    for (auto tOrZ : tOrZDist_m) {
        if (minTOrZ > tOrZ)
            minTOrZ = tOrZ;
    }
 
    reduce(minTOrZ, minTOrZ, OpMinAssign());
 
    return minTOrZ;
}
 
size_t Distribution::getNumberOfEmissionSteps() {
    return static_cast<size_t> (numberOfEnergyBins_m * numberOfSampleBins_m);
}
 
int Distribution::getNumberOfEnergyBins() {
    return numberOfEnergyBins_m;
}
 
double Distribution::getEmissionDeltaT() {
    return tBin_m / numberOfSampleBins_m;
}
 
double Distribution::getEnergyBinDeltaT() {
    return tBin_m;
}
 
double Distribution::getWeight() {
    return std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::WEIGHT]));
}
 
std::vector<double>& Distribution::getXDist() {
    return xDist_m;
}
 
std::vector<double>& Distribution::getBGxDist() {
    return pxDist_m;
}
 
std::vector<double>& Distribution::getYDist() {
    return yDist_m;
}
 
std::vector<double>& Distribution::getBGyDist() {
    return pyDist_m;
}
 
std::vector<double>& Distribution::getTOrZDist() {
    return tOrZDist_m;
}
 
std::vector<double>& Distribution::getBGzDist() {
    return pzDist_m;
}
 
void Distribution::printDist(Inform &os, size_t numberOfParticles) const {
 
    if (numberOfParticles > 0) {
        size_t np = numberOfParticles * (Options::cZero && !(distrTypeT_m == DistributionType::FROMFILE)? 2: 1);
        reduce(np, np, OpAddAssign());
        os << "* Number of particles: "
           << np
           << endl
           << "* " << endl;
    }
 
    os << "* Distribution input momentum units: ";
    switch (inputMoUnits_m) {
        case InputMomentumUnits::NONE: {
            os << "[Beta Gamma]" << "\n* " << endl;
            break;
        }
        case InputMomentumUnits::EVOVERC: {
            os << "[eV/c]" << "\n* " << endl;
            break;
        }
        default:
            throw OpalException("Distribution::printDist",
                                "Unknown \"INPUTMOUNITS\" for \"DISTRIBUTION\" command");
    }
 
    switch (distrTypeT_m) {
        case DistributionType::FROMFILE:
            printDistFromFile(os);
            break;
        case DistributionType::GAUSS:
            printDistGauss(os);
            break;
        case DistributionType::BINOMIAL:
            printDistBinomial(os);
            break;
        case DistributionType::FLATTOP:
        case DistributionType::GUNGAUSSFLATTOPTH:
        case DistributionType::ASTRAFLATTOPTH:
            printDistFlattop(os);
            break;
        case DistributionType::MULTIGAUSS:
            printDistMultiGauss(os);
            break;
        case DistributionType::MATCHEDGAUSS:
            printDistMatchedGauss(os);
            break;
        default:
            throw OpalException("Distribution::printDist",
                                "Unknown \"TYPE\" of \"DISTRIBUTION\"");
    }
 
}
 
void Distribution::printDistBinomial(Inform &os) const {
 
    os << "* Distribution type: BINOMIAL" << endl;
    os << "* " << endl;
    os << "* SIGMAX   = " << sigmaR_m[0] << " [m]" << endl;
    os << "* SIGMAY   = " << sigmaR_m[1] << " [m]" << endl;
    if (emitting_m)
        os << "* SIGMAT   = " << sigmaR_m[2] << " [sec]" << endl;
    else
        os << "* SIGMAZ   = " << sigmaR_m[2] << " [m]" << endl;
    os << "* SIGMAPX  = " << sigmaP_m[0] << " [Beta Gamma]" << endl;
    os << "* SIGMAPY  = " << sigmaP_m[1] << " [Beta Gamma]" << endl;
    os << "* SIGMAPZ  = " << sigmaP_m[2] << " [Beta Gamma]" << endl;
    os << "* MX       = " << mBinomial_m[0] << endl;
    os << "* MY       = " << mBinomial_m[1] << endl;
    if (emitting_m)
        os << "* MT       = " << mBinomial_m[2] << endl;
    else
        os << "* MZ       = " << mBinomial_m[2] << endl;
    os << "* CORRX    = " << correlationMatrix_m(1, 0) << endl;
    os << "* CORRY    = " << correlationMatrix_m(3, 2) << endl;
    os << "* CORRZ    = " << correlationMatrix_m(5, 4) << endl;
    os << "* R61      = " << correlationMatrix_m(5, 0) << endl;
    os << "* R62      = " << correlationMatrix_m(5, 1) << endl;
    os << "* R51      = " << correlationMatrix_m(4, 0) << endl;
    os << "* R52      = " << correlationMatrix_m(4, 1) << endl;
}
 
void Distribution::printDistFlattop(Inform &os) const {
 
    switch (distrTypeT_m) {
 
    case DistributionType::ASTRAFLATTOPTH:
        os << "* Distribution type: ASTRAFLATTOPTH" << endl;
        break;
 
    case DistributionType::GUNGAUSSFLATTOPTH:
        os << "* Distribution type: GUNGAUSSFLATTOPTH" << endl;
        break;
 
    default:
        os << "* Distribution type: FLATTOP" << endl;
        break;
 
    }
    os << "* " << endl;
 
    if (laserProfile_m != nullptr) {
 
        os << "* Transverse profile determined by laser image: " << endl
           << endl
           << "* Laser profile: " << laserProfileFileName_m << endl
           << "* Laser image:   " << laserImageName_m << endl
           << "* Intensity cut: " << laserIntensityCut_m << endl;
 
    } else {
 
        os << "* SIGMAX                        = " << sigmaR_m[0] << " [m]" << endl;
        os << "* SIGMAY                        = " << sigmaR_m[1] << " [m]" << endl;
 
    }
 
    if (emitting_m) {
 
        if (distrTypeT_m == DistributionType::ASTRAFLATTOPTH) {
 
            os << "* Time Rise                     = " << tRise_m
               << " [sec]" << endl;
            os << "* TPULSEFWHM                    = " << tPulseLengthFWHM_m
               << " [sec]" << endl;
 
        } else {
            os << "* Sigma Time Rise               = " << sigmaTRise_m
               << " [sec]" << endl;
            os << "* TPULSEFWHM                    = " << tPulseLengthFWHM_m
               << " [sec]" << endl;
            os << "* Sigma Time Fall               = " << sigmaTFall_m
               << " [sec]" << endl;
            os << "* Longitudinal cutoff           = " << cutoffR_m[2]
               << " [units of Sigma Time]" << endl;
            os << "* Flat top modulation amplitude = "
               << Attributes::getReal(itsAttr[Attrib::Distribution::FTOSCAMPLITUDE])
               << " [Percent of distribution amplitude]" << endl;
            os << "* Flat top modulation periods   = "
               << std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::FTOSCPERIODS]))
               << endl;
        }
 
    } else
        os << "* SIGMAZ                        = " << sigmaR_m[2]
           << " [m]" << endl;
}
 
void Distribution::printDistMultiGauss(Inform &os) const {
 
    os << "* Distribution type: MULTIGAUSS" << endl;
    os << "* " << endl;
 
 
    os << "* SIGMAX                        = " << sigmaR_m[0] << " [m]" << endl;
    os << "* SIGMAY                        = " << sigmaR_m[1] << " [m]" << endl;
 
    std::string longUnits;
    if (emitting_m)
        longUnits = " [sec]";
    else
        longUnits = " [m]";
 
    os << "* SIGMAZ                        = " << sigmaR_m[2] << longUnits << endl;
    os << "* CUTOFFLONG                    = " << cutoffR_m[2] << " [units of SIGMAZ]" << endl;
    os << "* SEPPEAKS                      = " << sepPeaks_m << longUnits << endl;
    os << "* NPEAKS                        = " << nPeaks_m << endl;
 
    if (!emitting_m) {
        os << "* SIGMAPX                        = " << sigmaP_m[0] << " [Beta Gamma]" << endl;
        os << "* SIGMAPY                        = " << sigmaP_m[1] << " [Beta Gamma]" << endl;
        os << "* SIGMAPZ                        = " << sigmaP_m[2] << " [Beta Gamma]" << endl;
        os << "* CUTOFFPX                       = " << cutoffP_m[0] << " [units of SIGMAPX]" << endl;
        os << "* CUTOFFPY                       = " << cutoffP_m[1] << " [units of SIGMAPY]" << endl;
        os << "* CUTOFFPZ                       = " << cutoffP_m[2] << " [units of SIGMAPZ]" << endl;
    }
}
 
void Distribution::printDistFromFile(Inform &os) const {
    os << "* Distribution type: FROMFILE" << endl;
    os << "* " << endl;
    os << "* Input file: '"
       << Attributes::getString(itsAttr[Attrib::Distribution::FNAME]) << "'" << endl;
}
 
 
void Distribution::printDistMatchedGauss(Inform &os) const {
    os << "* Distribution type: MATCHEDGAUSS" << endl;
    os << "* SIGMAX     = " << sigmaR_m[0] << " [m]" << endl;
    os << "* SIGMAY     = " << sigmaR_m[1] << " [m]" << endl;
    os << "* SIGMAZ     = " << sigmaR_m[2] << " [m]" << endl;
    os << "* SIGMAPX    = " << sigmaP_m[0] << " [Beta Gamma]" << endl;
    os << "* SIGMAPY    = " << sigmaP_m[1] << " [Beta Gamma]" << endl;
    os << "* SIGMAPZ    = " << sigmaP_m[2] << " [Beta Gamma]" << endl;
//     os << "* AVRGPZ     = " << avrgpz_m <<    " [Beta Gamma]" << endl;
 
    os << "* CORRX      = " << correlationMatrix_m(1, 0) << endl;
    os << "* CORRY      = " << correlationMatrix_m(3, 2) << endl;
    os << "* CORRZ      = " << correlationMatrix_m(5, 4) << endl;
    os << "* R61        = " << correlationMatrix_m(5, 0) << endl;
    os << "* R62        = " << correlationMatrix_m(5, 1) << endl;
    os << "* R51        = " << correlationMatrix_m(4, 0) << endl;
    os << "* R52        = " << correlationMatrix_m(4, 1) << endl;
//     os << "* CUTOFFX    = " << cutoffR_m[0] << " [units of SIGMAX]" << endl;
//     os << "* CUTOFFY    = " << cutoffR_m[1] << " [units of SIGMAY]" << endl;
//     os << "* CUTOFFLONG = " << cutoffR_m[2] << " [units of SIGMAZ]" << endl;
//     os << "* CUTOFFPX   = " << cutoffP_m[0] << " [units of SIGMAPX]" << endl;
//     os << "* CUTOFFPY   = " << cutoffP_m[1] << " [units of SIGMAPY]" << endl;
//     os << "* CUTOFFPZ   = " << cutoffP_m[2] << " [units of SIGMAPY]" << endl;
}
 
void Distribution::printDistGauss(Inform &os) const {
    os << "* Distribution type: GAUSS" << endl;
    os << "* " << endl;
    if (emitting_m) {
        os << "* Sigma Time Rise               = " << sigmaTRise_m
           << " [sec]" << endl;
        os << "* TPULSEFWHM                    = " << tPulseLengthFWHM_m
           << " [sec]" << endl;
        os << "* Sigma Time Fall               = " << sigmaTFall_m
           << " [sec]" << endl;
        os << "* Longitudinal cutoff           = " << cutoffR_m[2]
           << " [units of Sigma Time]" << endl;
        os << "* Flat top modulation amplitude = "
           << Attributes::getReal(itsAttr[Attrib::Distribution::FTOSCAMPLITUDE])
           << " [Percent of distribution amplitude]" << endl;
        os << "* Flat top modulation periods   = "
           << std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::FTOSCPERIODS]))
           << endl;
        os << "* SIGMAX                        = " << sigmaR_m[0] << " [m]" << endl;
        os << "* SIGMAY                        = " << sigmaR_m[1] << " [m]" << endl;
        os << "* SIGMAPX                       = " << sigmaP_m[0]
           << " [Beta Gamma]" << endl;
        os << "* SIGMAPY                       = " << sigmaP_m[1]
           << " [Beta Gamma]" << endl;
        os << "* CORRX                         = " << correlationMatrix_m(1, 0) << endl;
        os << "* CORRY                         = " << correlationMatrix_m(3, 2) << endl;
        os << "* CUTOFFX                       = " << cutoffR_m[0]
           << " [units of SIGMAX]" << endl;
        os << "* CUTOFFY                       = " << cutoffR_m[1]
           << " [units of SIGMAY]" << endl;
        os << "* CUTOFFPX                      = " << cutoffP_m[0]
           << " [units of SIGMAPX]" << endl;
        os << "* CUTOFFPY                      = " << cutoffP_m[1]
           << " [units of SIGMAPY]" << endl;
    } else {
        os << "* SIGMAX     = " << sigmaR_m[0] << " [m]" << endl;
        os << "* SIGMAY     = " << sigmaR_m[1] << " [m]" << endl;
        os << "* SIGMAZ     = " << sigmaR_m[2] << " [m]" << endl;
        os << "* SIGMAPX    = " << sigmaP_m[0] << " [Beta Gamma]" << endl;
        os << "* SIGMAPY    = " << sigmaP_m[1] << " [Beta Gamma]" << endl;
        os << "* SIGMAPZ    = " << sigmaP_m[2] << " [Beta Gamma]" << endl;
        os << "* AVRGPZ     = " << avrgpz_m <<    " [Beta Gamma]" << endl;
 
        os << "* CORRX      = " << correlationMatrix_m(1, 0) << endl;
        os << "* CORRY      = " << correlationMatrix_m(3, 2) << endl;
        os << "* CORRZ      = " << correlationMatrix_m(5, 4) << endl;
        os << "* R61        = " << correlationMatrix_m(5, 0) << endl;
        os << "* R62        = " << correlationMatrix_m(5, 1) << endl;
        os << "* R51        = " << correlationMatrix_m(4, 0) << endl;
        os << "* R52        = " << correlationMatrix_m(4, 1) << endl;
        os << "* CUTOFFX    = " << cutoffR_m[0] << " [units of SIGMAX]" << endl;
        os << "* CUTOFFY    = " << cutoffR_m[1] << " [units of SIGMAY]" << endl;
        os << "* CUTOFFLONG = " << cutoffR_m[2] << " [units of SIGMAZ]" << endl;
        os << "* CUTOFFPX   = " << cutoffP_m[0] << " [units of SIGMAPX]" << endl;
        os << "* CUTOFFPY   = " << cutoffP_m[1] << " [units of SIGMAPY]" << endl;
        os << "* CUTOFFPZ   = " << cutoffP_m[2] << " [units of SIGMAPY]" << endl;
    }
}
 
void Distribution::printEmissionModel(Inform &os) const {
 
    os << "* ------------- THERMAL EMITTANCE MODEL --------------------------------------------" << endl;
 
    switch (emissionModel_m) {
 
    case EmissionModel::NONE:
        printEmissionModelNone(os);
        break;
    case EmissionModel::ASTRA:
        printEmissionModelAstra(os);
        break;
    case EmissionModel::NONEQUIL:
        printEmissionModelNonEquil(os);
        break;
    default:
        break;
    }
 
    os << "* ----------------------------------------------------------------------------------" << endl;
 
}
 
void Distribution::printEmissionModelAstra(Inform &os) const {
    os << "*  THERMAL EMITTANCE in ASTRA MODE" << endl;
    os << "*  Kinetic energy (thermal emittance) = "
       << std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::EKIN]))
       << " [eV]  " << endl;
}
 
void Distribution::printEmissionModelNone(Inform &os) const {
    os << "*  THERMAL EMITTANCE in NONE MODE" << endl;
    os << "*  Kinetic energy added to longitudinal momentum = "
       << std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::EKIN]))
       << " [eV]  " << endl;
}
 
void Distribution::printEmissionModelNonEquil(Inform &os) const {
    os << "*  THERMAL EMITTANCE in NONEQUIL MODE" << endl;
    os << "*  Cathode work function     = " << cathodeWorkFunc_m << " [eV]  " << endl;
    os << "*  Cathode Fermi energy      = " << cathodeFermiEnergy_m << " [eV]  " << endl;
    os << "*  Cathode temperature       = " << cathodeTemp_m / Physics::kB << " [K]  " << endl;
    os << "*  Photocathode laser energy = " << laserEnergy_m << " [eV]  " << endl;
}
 
void Distribution::printEnergyBins(Inform &os) const {
 
    os << "* " << endl;
    for (int binIndex = numberOfEnergyBins_m - 1; binIndex >=0; binIndex--) {
        size_t sum = 0;
        for (int sampleIndex = 0; sampleIndex < numberOfSampleBins_m; sampleIndex++)
            sum += gsl_histogram_get(energyBinHist_m,
                                     binIndex * numberOfSampleBins_m + sampleIndex);
 
        os << "* Energy Bin # " << numberOfEnergyBins_m - binIndex
           << " contains " << sum << " particles" << endl;
    }
    os << "* " << endl;
 
}
 
bool Distribution::Rebin() {
    /*
     * Allow a rebin (numberOfEnergyBins_m = 0) if all particles are emitted or
     * injected.
     */
    if (!emitting_m) {
        numberOfEnergyBins_m = 0;
        return true;
    } else {
        return false;
    }
}
 
void Distribution::reflectDistribution(size_t &numberOfParticles) {
 
    if (!Options::cZero || (distrTypeT_m == DistributionType::FROMFILE))
        return;
 
    size_t currentNumPart = tOrZDist_m.size();
    for (size_t partIndex = 0; partIndex < currentNumPart; partIndex++) {
        xDist_m.push_back(-xDist_m.at(partIndex));
        pxDist_m.push_back(-pxDist_m.at(partIndex));
        yDist_m.push_back(-yDist_m.at(partIndex));
        pyDist_m.push_back(-pyDist_m.at(partIndex));
        tOrZDist_m.push_back(tOrZDist_m.at(partIndex));
        pzDist_m.push_back(pzDist_m.at(partIndex));
    }
    numberOfParticles = tOrZDist_m.size();
    reduce(numberOfParticles, numberOfParticles, OpAddAssign());
 
    // if numberOfParticles is odd then delete last particle
    if (Ippl::myNode() == 0 &&
        (numberOfParticles + 1) / 2 != numberOfParticles / 2) {
        xDist_m.pop_back();
        pxDist_m.pop_back();
        yDist_m.pop_back();
        pyDist_m.pop_back();
        tOrZDist_m.pop_back();
        pzDist_m.pop_back();
    }
}
 
void Distribution::scaleDistCoordinates() {
    // at this point the distributions of an array of distributions are still separated
 
    const double xmult    = Attributes::getReal(itsAttr[Attrib::Distribution::XMULT]);
    const double pxmult   = Attributes::getReal(itsAttr[Attrib::Distribution::PXMULT]);
    const double ymult    = Attributes::getReal(itsAttr[Attrib::Distribution::YMULT]);
    const double pymult   = Attributes::getReal(itsAttr[Attrib::Distribution::PYMULT]);
    const double longmult = (emitting_m ?
                             Attributes::getReal(itsAttr[Attrib::Distribution::TMULT]) :
                             Attributes::getReal(itsAttr[Attrib::Distribution::ZMULT]));
    const double pzmult   = Attributes::getReal(itsAttr[Attrib::Distribution::PZMULT]);
 
    for (size_t particleIndex = 0; particleIndex < tOrZDist_m.size(); ++ particleIndex) {
        xDist_m.at(particleIndex)    *= xmult;
        pxDist_m.at(particleIndex)   *= pxmult;
        yDist_m.at(particleIndex)    *= ymult;
        pyDist_m.at(particleIndex)   *= pymult;
        tOrZDist_m.at(particleIndex) *= longmult;
        pzDist_m.at(particleIndex)   *= pzmult;
    }
}
 
gsl_qrng* Distribution::selectRandomGenerator(std::string,unsigned int dimension)
{
    gsl_qrng *quasiRandGen = nullptr;
    if (Options::rngtype != std::string("RANDOM")) {
        INFOMSG("RNGTYPE= " << Options::rngtype << endl);
        if (Options::rngtype == std::string("HALTON")) {
            quasiRandGen = gsl_qrng_alloc(gsl_qrng_halton, dimension);
        } else if (Options::rngtype == std::string("SOBOL")) {
            quasiRandGen = gsl_qrng_alloc(gsl_qrng_sobol, dimension);
        } else if (Options::rngtype == std::string("NIEDERREITER")) {
            quasiRandGen = gsl_qrng_alloc(gsl_qrng_niederreiter_2, dimension);
        } else {
            INFOMSG("RNGTYPE= " << Options::rngtype << " not known, using HALTON" << endl);
            quasiRandGen = gsl_qrng_alloc(gsl_qrng_halton, dimension);
        }
    }
    return quasiRandGen;
}
 
void Distribution::setAttributes() {
    itsAttr[Attrib::Distribution::TYPE]
        = Attributes::makePredefinedString("TYPE","Distribution type.",
                                           {"FROMFILE",
                                            "GAUSS",
                                            "BINOMIAL",
                                            "FLATTOP",
                                            "MULTIGAUSS",
                                            "GUNGAUSSFLATTOPTH",
                                            "ASTRAFLATTOPTH",
                                            "GAUSSMATCHED"});
    itsAttr[Attrib::Legacy::Distribution::DISTRIBUTION]
        = Attributes::makeString("DISTRIBUTION","This attribute isn't supported any more. Use TYPE instead");
    itsAttr[Attrib::Distribution::LINE]
        = Attributes::makeString("LINE", "Beamline that contains a cyclotron or ring ", "");
    itsAttr[Attrib::Distribution::EX]
        = Attributes::makeReal("EX", "Projected normalized emittance EX (m-rad), used to create matched distribution ", 1E-6);
    itsAttr[Attrib::Distribution::EY]
        = Attributes::makeReal("EY", "Projected normalized emittance EY (m-rad) used to create matched distribution ", 1E-6);
    itsAttr[Attrib::Distribution::ET]
        = Attributes::makeReal("ET", "Projected normalized emittance ET (m-rad) used to create matched distribution ", 1E-6);
    // itsAttr[Attrib::Distribution::E2]
    //     = Attributes::makeReal("E2", "If E2<Eb, we compute the tunes from the beams energy Eb to E2 with dE=0.25 MeV ", 0.0);
    itsAttr[Attrib::Distribution::RESIDUUM]
        = Attributes::makeReal("RESIDUUM", "Residuum for the closed orbit finder and sigma matrix generator ", 1e-8);
    itsAttr[Attrib::Distribution::MAXSTEPSCO]
        = Attributes::makeReal("MAXSTEPSCO", "Maximum steps used to find closed orbit ", 100);
    itsAttr[Attrib::Distribution::MAXSTEPSSI]
        = Attributes::makeReal("MAXSTEPSSI", "Maximum steps used to find matched distribution ",500);
    itsAttr[Attrib::Distribution::ORDERMAPS]
        = Attributes::makeReal("ORDERMAPS", "Order used in the field expansion ", 7);
    itsAttr[Attrib::Distribution::SECTOR]
        = Attributes::makeBool("SECTOR", "Match using single sector (true)"
                               " (false: using all sectors) (default: true)",
                               true);
    itsAttr[Attrib::Distribution::NSTEPS]
        = Attributes::makeReal("NSTEPS", "Number of integration steps of closed orbit finder (matched gauss)"
                               " (default: 720)", 720);
 
    itsAttr[Attrib::Distribution::RGUESS]
        = Attributes::makeReal("RGUESS", "Guess value of radius (m) for closed orbit finder ", -1);
 
    itsAttr[Attrib::Distribution::DENERGY]
        = Attributes::makeReal("DENERGY", "Energy step size for closed orbit finder [GeV]", 0.001);
 
    itsAttr[Attrib::Distribution::NSECTORS]
        = Attributes::makeReal("NSECTORS", "Number of sectors to average field, for closed orbit finder ", 1);
 
    itsAttr[Attrib::Distribution::FNAME]
        = Attributes::makeString("FNAME", "File for reading in 6D particle "
                                 "coordinates.", "");
 
 
    itsAttr[Attrib::Distribution::WRITETOFILE]
        = Attributes::makeBool("WRITETOFILE", "Write initial distribution to file.",
                               false);
 
    itsAttr[Attrib::Distribution::WEIGHT]
        = Attributes::makeReal("WEIGHT", "Weight of distribution when used in a "
                               "distribution list.", 1.0);
 
    itsAttr[Attrib::Distribution::INPUTMOUNITS]
        = Attributes::makePredefinedString("INPUTMOUNITS", "Tell OPAL what the input units are of the momentum.", {"NONE", "EVOVERC"});
 
    // Attributes for beam emission.
    itsAttr[Attrib::Distribution::EMITTED]
        = Attributes::makeBool("EMITTED", "Emitted beam, from cathode, as opposed to "
                               "an injected beam.", false);
    itsAttr[Attrib::Distribution::EMISSIONSTEPS]
        = Attributes::makeReal("EMISSIONSTEPS", "Number of time steps to use during emission.",
                               1);
    itsAttr[Attrib::Distribution::EMISSIONMODEL]
        = Attributes::makePredefinedString("EMISSIONMODEL", "Model used to emit electrons from a "
                                           "photocathode.",
                                           {"NONE", "ASTRA", "NONEQUIL"}, "NONE");
    itsAttr[Attrib::Distribution::EKIN]
        = Attributes::makeReal("EKIN", "Kinetic energy used in ASTRA thermal emittance "
                               "model (eV). (Thermal energy added in with random "
                               "number generator.)", 1.0);
    itsAttr[Attrib::Distribution::ELASER]
        = Attributes::makeReal("ELASER", "Laser energy (eV) for photocathode "
                               "emission. (Default 255 nm light.)", 4.86);
    itsAttr[Attrib::Distribution::W]
        = Attributes::makeReal("W", "Workfunction of photocathode material (eV)."
                               " (Default atomically clean copper.)", 4.31);
    itsAttr[Attrib::Distribution::FE]
        = Attributes::makeReal("FE", "Fermi energy of photocathode material (eV)."
                               " (Default atomically clean copper.)", 7.0);
    itsAttr[Attrib::Distribution::CATHTEMP]
        = Attributes::makeReal("CATHTEMP", "Temperature of photocathode (K)."
                               " (Default 300 K.)", 300.0);
    itsAttr[Attrib::Distribution::NBIN]
        = Attributes::makeReal("NBIN", "Number of energy bins to use when doing a space "
                               "charge solve.", 0.0);
 
    // Parameters for shifting or scaling initial distribution.
    itsAttr[Attrib::Distribution::XMULT] = Attributes::makeReal("XMULT", "Multiplier for x dimension.", 1.0);
    itsAttr[Attrib::Distribution::YMULT] = Attributes::makeReal("YMULT", "Multiplier for y dimension.", 1.0);
    itsAttr[Attrib::Distribution::ZMULT] = Attributes::makeReal("TMULT", "Multiplier for z dimension.", 1.0);
    itsAttr[Attrib::Distribution::TMULT] = Attributes::makeReal("TMULT", "Multiplier for t dimension.", 1.0);
 
    itsAttr[Attrib::Distribution::PXMULT] = Attributes::makeReal("PXMULT", "Multiplier for px dimension.", 1.0);
    itsAttr[Attrib::Distribution::PYMULT] = Attributes::makeReal("PYMULT", "Multiplier for py dimension.", 1.0);
    itsAttr[Attrib::Distribution::PZMULT] = Attributes::makeReal("PZMULT", "Multiplier for pz dimension.", 1.0);
 
    itsAttr[Attrib::Distribution::OFFSETX]
        = Attributes::makeReal("OFFSETX", "Average x offset of distribution.", 0.0);
    itsAttr[Attrib::Distribution::OFFSETY]
        = Attributes::makeReal("OFFSETY", "Average y offset of distribution.", 0.0);
    itsAttr[Attrib::Distribution::OFFSETZ]
        = Attributes::makeReal("OFFSETZ", "Average z offset of distribution.", 0.0);
    itsAttr[Attrib::Distribution::OFFSETT]
        = Attributes::makeReal("OFFSETT", "Average t offset of distribution.", 0.0);
 
    itsAttr[Attrib::Distribution::OFFSETPX]
        = Attributes::makeReal("OFFSETPX", "Average px offset of distribution.", 0.0);
    itsAttr[Attrib::Distribution::OFFSETPY]
        = Attributes::makeReal("OFFSETPY", "Average py offset of distribution.", 0.0);
    itsAttr[Attrib::Distribution::OFFSETPZ]
        = Attributes::makeReal("OFFSETPZ", "Average pz offset of distribution.", 0.0);
    itsAttr[Attrib::Distribution::OFFSETP]
        = Attributes::makeReal("OFFSETP", "Momentum shift relative to referenc particle.", 0.0);
 
    // Parameters for defining an initial distribution.
    itsAttr[Attrib::Distribution::SIGMAX] = Attributes::makeReal("SIGMAX", "SIGMAx (m)", 0.0);
    itsAttr[Attrib::Distribution::SIGMAY] = Attributes::makeReal("SIGMAY", "SIGMAy (m)", 0.0);
    itsAttr[Attrib::Distribution::SIGMAR] = Attributes::makeReal("SIGMAR", "SIGMAr (m)", 0.0);
    itsAttr[Attrib::Distribution::SIGMAZ] = Attributes::makeReal("SIGMAZ", "SIGMAz (m)", 0.0);
    itsAttr[Attrib::Distribution::SIGMAT] = Attributes::makeReal("SIGMAT", "SIGMAt (m)", 0.0);
    itsAttr[Attrib::Distribution::TPULSEFWHM]
        = Attributes::makeReal("TPULSEFWHM", "Pulse FWHM for emitted distribution.", 0.0);
    itsAttr[Attrib::Distribution::TRISE]
        = Attributes::makeReal("TRISE", "Rise time for emitted distribution.", 0.0);
    itsAttr[Attrib::Distribution::TFALL]
        = Attributes::makeReal("TFALL", "Fall time for emitted distribution.", 0.0);
    itsAttr[Attrib::Distribution::SIGMAPX] = Attributes::makeReal("SIGMAPX", "SIGMApx", 0.0);
    itsAttr[Attrib::Distribution::SIGMAPY] = Attributes::makeReal("SIGMAPY", "SIGMApy", 0.0);
    itsAttr[Attrib::Distribution::SIGMAPZ] = Attributes::makeReal("SIGMAPZ", "SIGMApz", 0.0);
    itsAttr[Attrib::Distribution::SEPPEAKS] = Attributes::makeReal("SEPPEAKS", "Separation between "
                                                                   "Gaussian peaks in MultiGauss "
                                                                   "distribution.", 0.0);
    itsAttr[Attrib::Distribution::NPEAKS] = Attributes::makeReal("NPEAKS", "Number of Gaussian "
                                                                 " pulses in MultiGauss "
                                                                 "distribution.", 0.0);
    itsAttr[Attrib::Distribution::MX]
        = Attributes::makeReal("MX", "Defines the binomial distribution in x, "
                               "0.0 ... infinity.", 10001.0);
    itsAttr[Attrib::Distribution::MY]
        = Attributes::makeReal("MY", "Defines the binomial distribution in y, "
                               "0.0 ... infinity.", 10001.0);
    itsAttr[Attrib::Distribution::MZ]
        = Attributes::makeReal("MZ", "Defines the binomial distribution in z, "
                               "0.0 ... infinity.", 10001.0);
    itsAttr[Attrib::Distribution::MT]
        = Attributes::makeReal("MT", "Defines the binomial distribution in t, "
                               "0.0 ... infinity.", 10001.0);
 
    itsAttr[Attrib::Distribution::CUTOFFX] = Attributes::makeReal("CUTOFFX", "Distribution cutoff x "
                                                         "direction in units of sigma.", 3.0);
    itsAttr[Attrib::Distribution::CUTOFFY] = Attributes::makeReal("CUTOFFY", "Distribution cutoff r "
                                                         "direction in units of sigma.", 3.0);
    itsAttr[Attrib::Distribution::CUTOFFR] = Attributes::makeReal("CUTOFFR", "Distribution cutoff radial "
                                                         "direction in units of sigma.", 3.0);
    itsAttr[Attrib::Distribution::CUTOFFLONG]
        = Attributes::makeReal("CUTOFFLONG", "Distribution cutoff z or t direction in "
                               "units of sigma.", 3.0);
    itsAttr[Attrib::Distribution::CUTOFFPX] = Attributes::makeReal("CUTOFFPX", "Distribution cutoff px "
                                                          "dimension in units of sigma.", 3.0);
    itsAttr[Attrib::Distribution::CUTOFFPY] = Attributes::makeReal("CUTOFFPY", "Distribution cutoff py "
                                                          "dimension in units of sigma.", 3.0);
    itsAttr[Attrib::Distribution::CUTOFFPZ] = Attributes::makeReal("CUTOFFPZ", "Distribution cutoff pz "
                                                          "dimension in units of sigma.", 3.0);
 
    itsAttr[Attrib::Distribution::FTOSCAMPLITUDE]
        = Attributes::makeReal("FTOSCAMPLITUDE", "Amplitude of oscillations superimposed "
                               "on flat top portion of emitted GAUSS "
                               "distribtuion (in percent of flat top "
                               "amplitude)",0.0);
    itsAttr[Attrib::Distribution::FTOSCPERIODS]
        = Attributes::makeReal("FTOSCPERIODS", "Number of oscillations superimposed on "
                               "flat top portion of emitted GAUSS "
                               "distribution", 0.0);
 
    /*
     * TODO: Find out what these correlations really mean and write
     * good descriptions for them.
     */
    itsAttr[Attrib::Distribution::CORRX]
        = Attributes::makeReal("CORRX", "x/px correlation, (R12 in transport "
                               "notation).", 0.0);
    itsAttr[Attrib::Distribution::CORRY]
        = Attributes::makeReal("CORRY", "y/py correlation, (R34 in transport "
                               "notation).", 0.0);
    itsAttr[Attrib::Distribution::CORRZ]
        = Attributes::makeReal("CORRZ", "z/pz correlation, (R56 in transport "
                               "notation).", 0.0);
    itsAttr[Attrib::Distribution::CORRT]
        = Attributes::makeReal("CORRT", "t/pt correlation, (R56 in transport "
                               "notation).", 0.0);
 
    itsAttr[Attrib::Distribution::R51]
        = Attributes::makeReal("R51", "x/z correlation, (R51 in transport "
                               "notation).", 0.0);
    itsAttr[Attrib::Distribution::R52]
        = Attributes::makeReal("R52", "xp/z correlation, (R52 in transport "
                               "notation).", 0.0);
 
    itsAttr[Attrib::Distribution::R61]
        = Attributes::makeReal("R61", "x/pz correlation, (R61 in transport "
                               "notation).", 0.0);
    itsAttr[Attrib::Distribution::R62]
        = Attributes::makeReal("R62", "xp/pz correlation, (R62 in transport "
                               "notation).", 0.0);
 
    itsAttr[Attrib::Distribution::R]
        = Attributes::makeRealArray("R", "r correlation");
 
    // Parameters for using laser profile to generate a distribution.
    itsAttr[Attrib::Distribution::LASERPROFFN]
        = Attributes::makeString("LASERPROFFN", "File containing a measured laser image "
                                 "profile (x,y).", "");
    itsAttr[Attrib::Distribution::IMAGENAME]
        = Attributes::makeString("IMAGENAME", "Name of the laser image.", "");
    itsAttr[Attrib::Distribution::INTENSITYCUT]
        = Attributes::makeReal("INTENSITYCUT", "For background subtraction of laser "
                               "image profile, in % of max intensity.",
                               0.0);
    itsAttr[Attrib::Distribution::FLIPX]
        = Attributes::makeBool("FLIPX", "Flip laser profile horizontally", false);
    itsAttr[Attrib::Distribution::FLIPY]
        = Attributes::makeBool("FLIPY", "Flip laser profile vertically", false);
    itsAttr[Attrib::Distribution::ROTATE90]
        = Attributes::makeBool("ROTATE90", "Rotate laser profile 90 degrees counter clockwise", false);
    itsAttr[Attrib::Distribution::ROTATE180]
        = Attributes::makeBool("ROTATE180", "Rotate laser profile 180 degrees counter clockwise", false);
    itsAttr[Attrib::Distribution::ROTATE270]
        = Attributes::makeBool("ROTATE270", "Rotate laser profile 270 degrees counter clockwise", false);
 
    /*
     *   Feature request Issue #14
     */
 
    itsAttr[Attrib::Distribution::ID1]
        = Attributes::makeRealArray("ID1", "User defined particle with ID=1");
    itsAttr[Attrib::Distribution::ID2]
        = Attributes::makeRealArray("ID2", "User defined particle with ID=2");
 
 
    itsAttr[Attrib::Distribution::SCALABLE]
        = Attributes::makeBool("SCALABLE", "If true then distribution is scalable with "
                               "respect of number of particles and number of cores", false);
 
    /*
     * Legacy attributes (or ones that need to be implemented.)
     */
 
    // Parameters for emitting a distribution.
    // itsAttr[Attrib::Legacy::Distribution::DEBIN]
    //     = Attributes::makeReal("DEBIN", "Energy band for a bin in keV that defines "
    //                            "when to combine bins. That is, when the energy "
    //                            "spread of all bins is below this number "
    //                            "combine bins into a single bin.", 1000000.0);
    itsAttr[Attrib::Legacy::Distribution::SBIN]
        = Attributes::makeReal("SBIN", "Number of sample bins to use per energy bin "
                               "when emitting a distribution.", 100.0);
    /*
     * Specific to type GAUSS and GUNGAUSSFLATTOPTH and ASTRAFLATTOPTH. These
     * last two distribution will eventually just become a subset of GAUSS.
     */
    itsAttr[Attrib::Legacy::Distribution::SIGMAPT] = Attributes::makeReal("SIGMAPT", "SIGMApt", 0.0);
 
    itsAttr[Attrib::Legacy::Distribution::CUTOFF]
        = Attributes::makeReal("CUTOFF", "Longitudinal cutoff for Gaussian in units "
                               "of sigma.", 3.0);
 
 
    // Mixed use attributes (used by more than one distribution type).
    itsAttr[Attrib::Legacy::Distribution::T]
        = Attributes::makeReal("T", "Not supported anymore");
 
    itsAttr[Attrib::Legacy::Distribution::PT]
        = Attributes::makeReal("PT", "Not supported anymore.");
 
 
    // Attributes that are not yet implemented.
    // itsAttr[Attrib::Legacy::Distribution::ALPHAX]
    //     = Attributes::makeReal("ALPHAX", "Courant Snyder parameter.", 0.0);
    // itsAttr[Attrib::Legacy::Distribution::ALPHAY]
    //     = Attributes::makeReal("ALPHAY", "Courant Snyder parameter.", 0.0);
    // itsAttr[Attrib::Legacy::Distribution::BETAX]
    //     = Attributes::makeReal("BETAX", "Courant Snyder parameter.", 1.0);
    // itsAttr[Attrib::Legacy::Distribution::BETAY]
    //     = Attributes::makeReal("BETAY", "Courant Snyder parameter.", 1.0);
 
    // itsAttr[Attrib::Legacy::Distribution::DX]
    //     = Attributes::makeReal("DX", "Dispersion in x (R16 in Transport notation).", 0.0);
    // itsAttr[Attrib::Legacy::Distribution::DDX]
    //     = Attributes::makeReal("DDX", "First derivative of DX.", 0.0);
 
    // itsAttr[Attrib::Legacy::Distribution::DY]
    //     = Attributes::makeReal("DY", "Dispersion in y (R36 in Transport notation).", 0.0);
    // itsAttr[Attrib::Legacy::Distribution::DDY]
    //     = Attributes::makeReal("DDY", "First derivative of DY.", 0.0);
 
    registerOwnership(AttributeHandler::STATEMENT);
}
 
void Distribution::setDistToEmitted(bool emitted) {
    emitting_m = emitted;
}
 
void Distribution::setDistType() {
    if (itsAttr[Attrib::Legacy::Distribution::DISTRIBUTION]) {
        throw OpalException("Distribution::setDistType()",
                            "The attribute \"DISTRIBUTION\" isn't supported any more, use \"TYPE\" instead");
    }
 
    static const std::map<std::string, DistributionType> typeStringToDistType_s = {
        {"NODIST",            DistributionType::NODIST},
        {"FROMFILE",          DistributionType::FROMFILE},
        {"GAUSS",             DistributionType::GAUSS},
        {"BINOMIAL",          DistributionType::BINOMIAL},
        {"FLATTOP",           DistributionType::FLATTOP},
        {"MULTIGAUSS",        DistributionType::MULTIGAUSS},
        {"GUNGAUSSFLATTOPTH", DistributionType::GUNGAUSSFLATTOPTH},
        {"ASTRAFLATTOPTH",    DistributionType::ASTRAFLATTOPTH},
        {"GAUSSMATCHED",      DistributionType::MATCHEDGAUSS}
    };
 
    distT_m = Attributes::getString(itsAttr[Attrib::Distribution::TYPE]);
    if (distT_m.empty()) {
        throw OpalException("Distribution::setDistType",
                            "The attribute \"TYPE\" isn't set for the \"DISTRIBUTION\"!");
    } else {
        distrTypeT_m = typeStringToDistType_s.at(distT_m);
    }
}
 
void Distribution::setSigmaR_m() {
    sigmaR_m = Vector_t(std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAX])),
                        std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAY])),
                        std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAT])));
    // SIGMAZ overrides SIGMAT
    if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAZ])) != 0)
        sigmaR_m[2] = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAZ]));
    // SIGMAR overrides SIGMAX/Y
    if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAR])) > 0.0) {
        sigmaR_m[0] = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAR]));
        sigmaR_m[1] = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAR]));
    }
}
 
void Distribution::setSigmaP_m(double massIneV) {
    sigmaP_m = Vector_t(std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAPX])),
                        std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAPY])),
                        std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAPZ])));
 
    // SIGMAPZ overrides SIGMAPT. SIGMAPT is left for legacy compatibility.
    if ((sigmaP_m[2] == 0.0) && (Attributes::getReal(itsAttr[Attrib::Legacy::Distribution::SIGMAPT]) != 0.0)) {
        sigmaP_m[2] = std::abs(Attributes::getReal(itsAttr[Attrib::Legacy::Distribution::SIGMAPT]));
        WARNMSG("The attribute SIGMAPT may be removed in a future version\n"
                << "use  SIGMAPZ instead" << endl);
    }
 
    // Check what input units we are using for momentum.
    if (inputMoUnits_m == InputMomentumUnits::EVOVERC) {
        sigmaP_m[0] = Util::convertMomentumEVoverCToBetaGamma(sigmaP_m[0], massIneV);
        sigmaP_m[1] = Util::convertMomentumEVoverCToBetaGamma(sigmaP_m[1], massIneV);
        sigmaP_m[2] = Util::convertMomentumEVoverCToBetaGamma(sigmaP_m[2], massIneV);
    }
}
 
void Distribution::setEmissionTime(double &maxT, double &minT) {
 
    if (addedDistributions_m.empty()) {
 
        switch (distrTypeT_m) {
 
        case DistributionType::FLATTOP:
        case DistributionType::GAUSS:
        case DistributionType::GUNGAUSSFLATTOPTH:
            tEmission_m = tPulseLengthFWHM_m + (cutoffR_m[2] - std::sqrt(2.0 * std::log(2.0)))
                * (sigmaTRise_m + sigmaTFall_m);
            break;
        case DistributionType::ASTRAFLATTOPTH:
            /*
             * Don't do anything. Emission time is set during the distribution
             * creation. Only this distribution type does it this way. This is
             * a legacy feature.
             */
            break;
        default:
            /*
             * Increase maxT and decrease minT by percentTEmission_m of total
             * time to ensure that no particles fall on the leading edge of
             * the first emission time step or the trailing edge of the last
             * emission time step.
             */
            double deltaT = maxT - minT;
            maxT += deltaT * percentTEmission_m;
            minT -= deltaT * percentTEmission_m;
            tEmission_m = (maxT - minT);
            break;
        }
 
    } else {
        /*
         * Increase maxT and decrease minT by percentTEmission_m of total
         * time to ensure that no particles fall on the leading edge of
         * the first emission time step or the trailing edge of the last
         * emission time step.
         */
        double deltaT = maxT - minT;
        maxT += deltaT * percentTEmission_m;
        minT -= deltaT * percentTEmission_m;
        tEmission_m = (maxT - minT);
    }
    tBin_m = tEmission_m / numberOfEnergyBins_m;
}
 
void Distribution::setDistParametersBinomial(double massIneV) {
 
    /*
     * Set Distribution parameters. Do all the necessary checks depending
     * on the input attributes.
     */
    std::vector<double> cr = Attributes::getRealArray(itsAttr[Attrib::Distribution::R]);
 
    if (!cr.empty()) {
        throw OpalException("Distribution::setDistParametersBinomial",
                            "Attribute R is not supported for binomial distribution\n"
                            "use CORR[X|Y|Z] and R51, R52, R61, R62 instead");
    }
 
    correlationMatrix_m(1, 0) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRX]);
    correlationMatrix_m(3, 2) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRY]);
    correlationMatrix_m(5, 4) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRT]);
    correlationMatrix_m(4, 0) = Attributes::getReal(itsAttr[Attrib::Distribution::R51]);
    correlationMatrix_m(4, 1) = Attributes::getReal(itsAttr[Attrib::Distribution::R52]);
    correlationMatrix_m(5, 0) = Attributes::getReal(itsAttr[Attrib::Distribution::R61]);
    correlationMatrix_m(5, 1) = Attributes::getReal(itsAttr[Attrib::Distribution::R62]);
 
    //CORRZ overrides CORRT. We initially use CORRT for legacy compatibility.
    if (!itsAttr[Attrib::Distribution::CORRZ].defaultUsed())
        correlationMatrix_m(5, 4) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRZ]);
 
    setSigmaR_m();
    setSigmaP_m(massIneV);
 
    mBinomial_m = Vector_t(std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::MX])),
                           std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::MY])),
                           std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::MT])));
 
    cutoffR_m = Vector_t(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFX]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFY]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFLONG]));
 
    cutoffP_m = Vector_t(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPX]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPY]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPZ]));
 
    if (mBinomial_m[2] == 0.0
        || Attributes::getReal(itsAttr[Attrib::Distribution::MZ]) != 0.0)
        mBinomial_m[2] = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::MZ]));
 
    if (emitting_m) {
        mBinomial_m[2] = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::MT]));
        correlationMatrix_m(5, 4) = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::CORRT]));
    }
}
 
void Distribution::setDistParametersFlattop(double massIneV) {
 
    /*
     * Set distribution parameters. Do all the necessary checks depending
     * on the input attributes.
     */
    setSigmaP_m(massIneV);
 
    cutoffR_m = Vector_t(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFX]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFY]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFLONG]));
 
    correlationMatrix_m(1, 0) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRX]);
    correlationMatrix_m(3, 2) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRY]);
    correlationMatrix_m(5, 4) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRT]);
 
    // CORRZ overrides CORRT.
    if (Attributes::getReal(itsAttr[Attrib::Distribution::CORRZ]) != 0.0)
        correlationMatrix_m(5, 4) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRZ]);
 
    setSigmaR_m();
    if (emitting_m) {
        sigmaR_m[2] = 0.0;
 
        sigmaTRise_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAT]));
        sigmaTFall_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAT]));
 
        tPulseLengthFWHM_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TPULSEFWHM]));
 
        /*
         * If TRISE and TFALL are defined > 0.0 then these attributes
         * override SIGMAT.
         */
        if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TRISE])) > 0.0
            || std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TFALL])) > 0.0) {
 
            double timeRatio = std::sqrt(2.0 * std::log(10.0)) - std::sqrt(2.0 * std::log(10.0 / 9.0));
 
            if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TRISE])) > 0.0)
                sigmaTRise_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TRISE]))
                    / timeRatio;
 
            if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TFALL])) > 0.0)
                sigmaTFall_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TFALL]))
                    / timeRatio;
 
        }
 
        // For an emitted beam, the longitudinal cutoff >= 0.
        cutoffR_m[2] = std::abs(cutoffR_m[2]);
    }
 
    // Set laser profile/
    laserProfileFileName_m = Attributes::getString(itsAttr[Attrib::Distribution::LASERPROFFN]);
    if (!(laserProfileFileName_m == std::string(""))) {
        laserImageName_m = Attributes::getString(itsAttr[Attrib::Distribution::IMAGENAME]);
        laserIntensityCut_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::INTENSITYCUT]));
        short flags = 0;
        if (Attributes::getBool(itsAttr[Attrib::Distribution::FLIPX])) flags |= LaserProfile::FLIPX;
        if (Attributes::getBool(itsAttr[Attrib::Distribution::FLIPY])) flags |= LaserProfile::FLIPY;
        if (Attributes::getBool(itsAttr[Attrib::Distribution::ROTATE90])) flags |= LaserProfile::ROTATE90;
        if (Attributes::getBool(itsAttr[Attrib::Distribution::ROTATE180])) flags |= LaserProfile::ROTATE180;
        if (Attributes::getBool(itsAttr[Attrib::Distribution::ROTATE270])) flags |= LaserProfile::ROTATE270;
 
        laserProfile_m = new LaserProfile(laserProfileFileName_m,
                                          laserImageName_m,
                                          laserIntensityCut_m,
                                          flags);
    }
 
    // Legacy for ASTRAFLATTOPTH.
    if (distrTypeT_m == DistributionType::ASTRAFLATTOPTH)
        tRise_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TRISE]));
 
}
 
void Distribution::setDistParametersMultiGauss(double massIneV) {
 
    setSigmaR_m();
    cutoffR_m[2] = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFLONG]));
 
    if (!emitting_m)
        setSigmaP_m(massIneV);
 
    cutoffP_m = Vector_t(std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPX])),
                         std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPY])),
                         std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPZ])));
 
    sepPeaks_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SEPPEAKS]));
    nPeaks_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::NPEAKS]));
}
 
void Distribution::setDistParametersGauss(double massIneV) {
 
    /*
     * Set distribution parameters. Do all the necessary checks depending
     * on the input attributes.
     * In case of DistributionType::MATCHEDGAUSS we only need to set the cutoff parameters
     */
 
 
    cutoffP_m = Vector_t(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPX]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPY]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFPZ]));
 
 
    cutoffR_m = Vector_t(Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFX]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFY]),
                         Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFLONG]));
 
    if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAR])) > 0.0) {
        cutoffR_m[0] = Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFR]);
        cutoffR_m[1] = Attributes::getReal(itsAttr[Attrib::Distribution::CUTOFFR]);
    }
 
    if  (distrTypeT_m != DistributionType::MATCHEDGAUSS) {
        setSigmaP_m(massIneV);
 
        std::vector<double> cr = Attributes::getRealArray(itsAttr[Attrib::Distribution::R]);
 
        if (!cr.empty()) {
            if (cr.size() == 15) {
                *gmsg << "* Use r to specify correlations" << endl;
                unsigned int k = 0;
                for (unsigned int i = 0; i < 5; ++ i) {
                    for (unsigned int j = i + 1; j < 6; ++ j, ++ k) {
                        correlationMatrix_m(j, i) = cr.at(k);
                    }
                }
 
            }
            else {
                throw OpalException("Distribution::SetDistParametersGauss",
                                    "Inconsistent set of correlations specified, check manual");
            }
        }
        else {
            correlationMatrix_m(1, 0) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRX]);
            correlationMatrix_m(3, 2) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRY]);
            correlationMatrix_m(5, 4) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRT]);
            correlationMatrix_m(4, 0) = Attributes::getReal(itsAttr[Attrib::Distribution::R51]);
            correlationMatrix_m(4, 1) = Attributes::getReal(itsAttr[Attrib::Distribution::R52]);
            correlationMatrix_m(5, 0) = Attributes::getReal(itsAttr[Attrib::Distribution::R61]);
            correlationMatrix_m(5, 1) = Attributes::getReal(itsAttr[Attrib::Distribution::R62]);
 
            // CORRZ overrides CORRT.
            if (Attributes::getReal(itsAttr[Attrib::Distribution::CORRZ]) != 0.0)
                correlationMatrix_m(5, 4) = Attributes::getReal(itsAttr[Attrib::Distribution::CORRZ]);
        }
    }
 
    if (distrTypeT_m != DistributionType::MATCHEDGAUSS)
        setSigmaR_m();
 
    if (emitting_m) {
        sigmaR_m[2] = 0.0;
 
        sigmaTRise_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAT]));
        sigmaTFall_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::SIGMAT]));
 
        tPulseLengthFWHM_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TPULSEFWHM]));
 
        /*
         * If TRISE and TFALL are defined then these attributes
         * override SIGMAT.
         */
        if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TRISE])) > 0.0
            || std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TFALL])) > 0.0) {
 
            double timeRatio = std::sqrt(2.0 * std::log(10.0)) - std::sqrt(2.0 * std::log(10.0 / 9.0));
 
            if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TRISE])) > 0.0)
                sigmaTRise_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TRISE]))
                    / timeRatio;
 
            if (std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TFALL])) > 0.0)
                sigmaTFall_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::TFALL]))
                    / timeRatio;
 
        }
 
        // For and emitted beam, the longitudinal cutoff >= 0.
        cutoffR_m[2] = std::abs(cutoffR_m[2]);
 
    }
 
    // if cutoff 0 then infinite cutoff (except for CUTOFFLONG)
    for (int i=0; i<3; i++) {
        if (cutoffR_m[i] < SMALLESTCUTOFF && i!=2)
            cutoffR_m[i] = std::numeric_limits<double>::max();
        if (cutoffP_m[i] < SMALLESTCUTOFF)
            cutoffP_m[i] = std::numeric_limits<double>::max();
    }
}
 
void Distribution::setupEmissionModel(PartBunchBase<double, 3> *beam) {
 
    static const std::map<std::string, EmissionModel> stringEmissionModel_s = {
        {"NONE",     EmissionModel::NONE},
        {"ASTRA",    EmissionModel::ASTRA},
        {"NONEQUIL", EmissionModel::NONEQUIL}
    };
 
    std::string model = Attributes::getString(itsAttr[Attrib::Distribution::EMISSIONMODEL]);
    if (model.empty()) {
        emissionModel_m = EmissionModel::NONE;
    } else {
        emissionModel_m = stringEmissionModel_s.at(model);
    }
 
    /*
     * The ASTRAFLATTOPTH of GUNGAUSSFLATTOPTH distributions always uses the
     * ASTRA emission model.
     */
    if (distrTypeT_m == DistributionType::ASTRAFLATTOPTH ||
        distrTypeT_m == DistributionType::GUNGAUSSFLATTOPTH) {
        emissionModel_m = EmissionModel::ASTRA;
    }
 
    switch (emissionModel_m) {
        case EmissionModel::ASTRA: {
            setupEmissionModelAstra(beam);
            break;
        }
        case EmissionModel::NONEQUIL: {
            setupEmissionModelNonEquil();
            break;
        }
        default: {
            break;
        }
    }
}
 
void Distribution::setupEmissionModelAstra(PartBunchBase<double, 3> *beam) {
 
    double wThermal = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::EKIN]));
    pTotThermal_m = Util::getBetaGamma(wThermal, beam->getM());
    pmean_m = Vector_t(0.0, 0.0, 0.5 * pTotThermal_m);
}
 
void Distribution::setupEmissionModelNone(PartBunchBase<double, 3> *beam) {
 
    double wThermal = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::EKIN]));
    pTotThermal_m = Util::getBetaGamma(wThermal, beam->getM());
    double avgPz = std::accumulate(pzDist_m.begin(), pzDist_m.end(), 0.0);
    size_t numParticles = pzDist_m.size();
    reduce(avgPz, avgPz, OpAddAssign());
    reduce(numParticles, numParticles, OpAddAssign());
    avgPz /= numParticles;
 
    pmean_m = Vector_t(0.0, 0.0, pTotThermal_m + avgPz);
}
 
void Distribution::setupEmissionModelNonEquil() {
 
    cathodeWorkFunc_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::W]));
    laserEnergy_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::ELASER]));
    cathodeFermiEnergy_m = std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::FE]));
    cathodeTemp_m = Physics::kB * std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::CATHTEMP]));
 
    /*
     * Upper limit on energy distribution theoretically goes to infinity.
     * Practically we limit to a probability of 1 part in a billion.
     */
    emitEnergyUpperLimit_m = cathodeFermiEnergy_m
        + cathodeTemp_m * std::log(1.0e9 - 1.0);
 
    // TODO: get better estimate of pmean
    pmean_m = Vector_t(0, 0, std::sqrt(std::pow(0.5 * emitEnergyUpperLimit_m / (Physics::m_e * Units::GeV2eV) + 1.0, 2) - 1.0));
}
 
void Distribution::setupEnergyBins(double maxTOrZ, double minTOrZ) {
 
    energyBinHist_m = gsl_histogram_alloc(numberOfSampleBins_m * numberOfEnergyBins_m);
 
    if (emitting_m)
        gsl_histogram_set_ranges_uniform(energyBinHist_m, -tEmission_m, 0.0);
    else
        gsl_histogram_set_ranges_uniform(energyBinHist_m, minTOrZ, maxTOrZ);
 
}
 
void Distribution::setupParticleBins(double /*massIneV*/, PartBunchBase<double, 3> *beam) {
 
    numberOfEnergyBins_m
        = static_cast<int>(std::abs(Attributes::getReal(itsAttr[Attrib::Distribution::NBIN])));
 
    if (numberOfEnergyBins_m > 0) {
        delete energyBins_m;
 
        int sampleBins = static_cast<int>(std::abs(Attributes::getReal(itsAttr[Attrib::Legacy::Distribution::SBIN])));
        energyBins_m = new PartBins(numberOfEnergyBins_m, sampleBins);
 
        if (!itsAttr[Attrib::Legacy::Distribution::PT].defaultUsed())
            throw OpalException("Distribution::setupParticleBins",
                                "PT is obsolete. The moments of the beam is defined with OFFSETPZ");
 
        // we get gamma from PC of the beam
        const double pz    = beam->getP()/beam->getM();
        double gamma = std::hypot(pz, 1.0);
        energyBins_m->setGamma(gamma);
 
    } else {
        energyBins_m = nullptr;
    }
}
 
void Distribution::shiftBeam(double &maxTOrZ, double &minTOrZ) {
 
    if (emitting_m) {
 
        if (addedDistributions_m.empty()) {
 
            if (distrTypeT_m == DistributionType::ASTRAFLATTOPTH) {
                for (double& tOrZ : tOrZDist_m)
                    tOrZ -= tEmission_m / 2.0;
 
                minTOrZ -= tEmission_m / 2.0;
                maxTOrZ -= tEmission_m / 2.0;
            } else if (distrTypeT_m == DistributionType::GAUSS
                       || distrTypeT_m == DistributionType::FLATTOP
                       || distrTypeT_m == DistributionType::GUNGAUSSFLATTOPTH) {
                for (double& tOrZ : tOrZDist_m)
                    tOrZ -= tEmission_m;
 
                minTOrZ -= tEmission_m;
                maxTOrZ -= tEmission_m;
            } else {
                for (double& tOrZ : tOrZDist_m)
                    tOrZ -= maxTOrZ;
 
                minTOrZ -= maxTOrZ;
                maxTOrZ -= maxTOrZ;
            }
 
        } else {
            for (double& tOrZ : tOrZDist_m)
                tOrZ -= maxTOrZ;
 
            minTOrZ -= maxTOrZ;
            maxTOrZ -= maxTOrZ;
        }
 
    } else if (distrTypeT_m != DistributionType::FROMFILE) {
        double avgZ[] = {0.0, 1.0 * tOrZDist_m.size()};
        for (double tOrZ : tOrZDist_m)
            avgZ[0] += tOrZ;
 
        reduce(avgZ, avgZ + 2, avgZ, OpAddAssign());
        avgZ[0] /= avgZ[1];
 
        for (double& tOrZ : tOrZDist_m)
            tOrZ -= avgZ[0];
    }
}
 
double Distribution::getEmissionTimeShift() const {
    if (emitting_m)
        return Attributes::getReal(itsAttr[Attrib::Distribution::OFFSETT]);
 
    return 0.0;
}
 
void Distribution::shiftDistCoordinates(double massIneV) {
 
    size_t startIdx = 0;
    for (unsigned int i = 0; i <= addedDistributions_m.size(); ++ i) {
        Distribution *currDist = this;
        if (i > 0)
            currDist = addedDistributions_m[i - 1];
        double deltaX = Attributes::getReal(currDist->itsAttr[Attrib::Distribution::OFFSETX]);
        double deltaY = Attributes::getReal(currDist->itsAttr[Attrib::Distribution::OFFSETY]);
 
        /*
         * OFFSETZ overrides T if it is nonzero. We initially use T
         * for legacy compatiblity. OFFSETT always overrides T, even
         * when zero, for an emitted beam.
         */
        if (currDist->itsAttr[Attrib::Legacy::Distribution::T]) {
            throw OpalException("Distribution::shiftDistCoordinates",
                                "Attribute T isn't supported anymore; use OFFSETZ instead");
        }
 
        double deltaTOrZ = 0.0;
        if (!emitting_m)
            if (Attributes::getReal(currDist->itsAttr[Attrib::Distribution::OFFSETZ]) != 0.0)
                deltaTOrZ = Attributes::getReal(currDist->itsAttr[Attrib::Distribution::OFFSETZ]);
 
        double deltaPx = Attributes::getReal(currDist->itsAttr[Attrib::Distribution::OFFSETPX]);
        double deltaPy = Attributes::getReal(currDist->itsAttr[Attrib::Distribution::OFFSETPY]);
        double deltaPz = Attributes::getReal(currDist->itsAttr[Attrib::Distribution::OFFSETPZ]);
 
        if (Attributes::getReal(currDist->itsAttr[Attrib::Legacy::Distribution::PT])!=0.0)
            WARNMSG("PT & PZ are obsolete and will be ignored. The moments of the beam is defined with PC" << endl);
 
        // Check input momentum units.
        if (inputMoUnits_m == InputMomentumUnits::EVOVERC) {
            deltaPx = Util::convertMomentumEVoverCToBetaGamma(deltaPx, massIneV);
            deltaPy = Util::convertMomentumEVoverCToBetaGamma(deltaPy, massIneV);
            deltaPz = Util::convertMomentumEVoverCToBetaGamma(deltaPz, massIneV);
        }
 
        size_t endIdx = startIdx + particlesPerDist_m[i];
        for (size_t particleIndex = startIdx; particleIndex < endIdx; ++ particleIndex) {
            xDist_m.at(particleIndex) += deltaX;
            pxDist_m.at(particleIndex) += deltaPx;
            yDist_m.at(particleIndex) += deltaY;
            pyDist_m.at(particleIndex) += deltaPy;
            tOrZDist_m.at(particleIndex) += deltaTOrZ;
            pzDist_m.at(particleIndex) += deltaPz;
        }
 
        startIdx = endIdx;
    }
}
 
void Distribution::writeOutFileHeader() {
 
    if (Attributes::getBool(itsAttr[Attrib::Distribution::WRITETOFILE]) == false) {
        return;
    }
 
    unsigned int totalNum = tOrZDist_m.size();
    reduce(totalNum, totalNum, OpAddAssign());
    if (Ippl::myNode() != 0)
        return;
 
    outFilename_m = Util::combineFilePath({
        OpalData::getInstance()->getAuxiliaryOutputDirectory(),
        OpalData::getInstance()->getInputBasename() + "_" + getOpalName() + ".dat"
    });
 
    std::ofstream outputFile(outFilename_m);
    if (outputFile.bad()) {
        *gmsg << "Unable to open output file '" << outFilename_m << "'" << endl;
    } else {
        outputFile.setf(std::ios::left);
        outputFile << "# ";
        outputFile.width(17);
        outputFile << "x [m]";
        outputFile.width(17);
        outputFile << "px [betax gamma]";
        outputFile.width(17);
        outputFile << "y [m]";
        outputFile.width(17);
        outputFile << "py [betay gamma]";
        if (emitting_m) {
            outputFile.width(17);
            outputFile << "t [s]";
        } else {
            outputFile.width(17);
            outputFile << "z [m]";
        }
        outputFile.width(17);
        outputFile << "pz [betaz gamma]" ;
        if (emitting_m) {
            outputFile.width(17);
            outputFile << "Bin Number" << std::endl;
        } else {
            if (numberOfEnergyBins_m > 0) {
                outputFile.width(17);
                outputFile << "Bin Number";
            }
            outputFile << std::endl;
 
            outputFile << "# " << totalNum << std::endl;
        }
    }
    outputFile.close();
}
 
void Distribution::writeOutFileEmission() {
 
    if (!Attributes::getBool(itsAttr[Attrib::Distribution::WRITETOFILE])) {
        xWrite_m.clear();
        pxWrite_m.clear();
        yWrite_m.clear();
        pyWrite_m.clear();
        tOrZWrite_m.clear();
        pzWrite_m.clear();
        binWrite_m.clear();
 
        return;
    }
 
    // Gather particles to be written onto node 0.
    std::vector<char> msgbuf;
    const size_t bitsPerParticle = (6 * sizeof(double) + sizeof(size_t));
    size_t totalSendBits = xWrite_m.size() * bitsPerParticle;
 
    std::vector<unsigned long> numberOfBits(Ippl::getNodes(), 0);
    numberOfBits[Ippl::myNode()] = totalSendBits;
 
    if (Ippl::myNode() == 0) {
        MPI_Reduce(MPI_IN_PLACE, &(numberOfBits[0]), Ippl::getNodes(), MPI_UNSIGNED_LONG, MPI_SUM, 0, Ippl::getComm());
    } else {
        MPI_Reduce(&(numberOfBits[0]), nullptr, Ippl::getNodes(), MPI_UNSIGNED_LONG, MPI_SUM, 0, Ippl::getComm());
    }
 
    Ippl::Comm->barrier();
    int tag = Ippl::Comm->next_tag(IPPL_APP_TAG2, IPPL_APP_CYCLE);
    if (Ippl::myNode() > 0) {
        if (totalSendBits > 0) {
            msgbuf.reserve(totalSendBits);
            const char *buffer;
            for (size_t idx = 0; idx < xWrite_m.size(); ++ idx) {
                buffer = reinterpret_cast<const char*>(&(xWrite_m[idx]));
                msgbuf.insert(msgbuf.end(), buffer, buffer + sizeof(double));
                buffer = reinterpret_cast<const char*>(&(pxWrite_m[idx]));
                msgbuf.insert(msgbuf.end(), buffer, buffer + sizeof(double));
                buffer = reinterpret_cast<const char*>(&(yWrite_m[idx]));
                msgbuf.insert(msgbuf.end(), buffer, buffer + sizeof(double));
                buffer = reinterpret_cast<const char*>(&(pyWrite_m[idx]));
                msgbuf.insert(msgbuf.end(), buffer, buffer + sizeof(double));
                buffer = reinterpret_cast<const char*>(&(tOrZWrite_m[idx]));
                msgbuf.insert(msgbuf.end(), buffer, buffer + sizeof(double));
                buffer = reinterpret_cast<const char*>(&(pzWrite_m[idx]));
                msgbuf.insert(msgbuf.end(), buffer, buffer + sizeof(double));
                buffer = reinterpret_cast<const char*>(&(binWrite_m[idx]));
                msgbuf.insert(msgbuf.end(), buffer, buffer + sizeof(size_t));
            }
 
            Ippl::Comm->raw_send(&(msgbuf[0]), totalSendBits, 0, tag);
        }
    } else {
        std::ofstream outputFile(outFilename_m, std::fstream::app);
        if (outputFile.bad()) {
            ERRORMSG(level1 << "Unable to write to file '" << outFilename_m << "'" << endl);
            for (int node = 1; node < Ippl::getNodes(); ++ node) {
                if (numberOfBits[node] == 0) continue;
                char *recvbuf = new char[numberOfBits[node]];
                Ippl::Comm->raw_receive(recvbuf, numberOfBits[node], node, tag);
                delete[] recvbuf;
            }
        } else {
 
            outputFile.precision(9);
            outputFile.setf(std::ios::scientific);
            outputFile.setf(std::ios::right);
 
            for (size_t partIndex = 0; partIndex < xWrite_m.size(); partIndex++) {
 
                outputFile << std::setw(17) << xWrite_m.at(partIndex)
                           << std::setw(17) << pxWrite_m.at(partIndex)
                           << std::setw(17) << yWrite_m.at(partIndex)
                           << std::setw(17) << pyWrite_m.at(partIndex)
                           << std::setw(17) << tOrZWrite_m.at(partIndex)
                           << std::setw(17) << pzWrite_m.at(partIndex)
                           << std::setw(17) << binWrite_m.at(partIndex) << std::endl;
            }
 
            int numSenders = 0;
            for (int i = 1; i < Ippl::getNodes(); ++ i) {
                if (numberOfBits[i] > 0) numSenders ++;
            }
 
            for (int i = 0; i < numSenders; ++ i) {
                int node = Communicate::COMM_ANY_NODE;
                char *recvbuf;
                const int bufsize = Ippl::Comm->raw_probe_receive(recvbuf, node, tag);
 
                int j = 0;
                while (j < bufsize) {
                    const double *dbuffer = reinterpret_cast<const double*>(recvbuf + j);
                    const size_t *sbuffer = reinterpret_cast<const size_t*>(recvbuf + j + 6 * sizeof(double));
                    outputFile << std::setw(17) << dbuffer[0]
                               << std::setw(17) << dbuffer[1]
                               << std::setw(17) << dbuffer[2]
                               << std::setw(17) << dbuffer[3]
                               << std::setw(17) << dbuffer[4]
                               << std::setw(17) << dbuffer[5]
                               << std::setw(17) << sbuffer[0]
                               << std::endl;
                    j += bitsPerParticle;
                }
 
                delete[] recvbuf;
 
            }
        }
        outputFile.close();
 
    }
 
    // Clear write vectors.
    xWrite_m.clear();
    pxWrite_m.clear();
    yWrite_m.clear();
    pyWrite_m.clear();
    tOrZWrite_m.clear();
    pzWrite_m.clear();
    binWrite_m.clear();
 
}
 
void Distribution::writeOutFileInjection() {
 
    if (Attributes::getBool(itsAttr[Attrib::Distribution::WRITETOFILE]) == false)
        return;
 
    // Nodes take turn writing particles to file.
    for (int nodeIndex = 0; nodeIndex < Ippl::getNodes(); nodeIndex++) {
 
        // Write to file if its our turn.
        size_t numberOfParticles = 0;
        if (Ippl::myNode() == nodeIndex) {
            std::ofstream outputFile(outFilename_m, std::fstream::app);
            if (outputFile.bad()) {
                *gmsg << "Node " << Ippl::myNode() << " unable to write"
                      << "to file '" << outFilename_m << "'" << endl;
            } else {
 
                outputFile.precision(9);
                outputFile.setf(std::ios::scientific);
                outputFile.setf(std::ios::right);
 
                numberOfParticles = tOrZDist_m.size();
                for (size_t partIndex = 0; partIndex < numberOfParticles; partIndex++) {
 
                    outputFile.width(17);
                    outputFile << xDist_m.at(partIndex);
                    outputFile.width(17);
                    outputFile << pxDist_m.at(partIndex);
                    outputFile.width(17);
                    outputFile << yDist_m.at(partIndex);
                    outputFile.width(17);
                    outputFile << pyDist_m.at(partIndex);
                    outputFile.width(17);
                    outputFile << tOrZDist_m.at(partIndex);
                    outputFile.width(17);
                    outputFile << pzDist_m.at(partIndex);
                    if (numberOfEnergyBins_m > 0) {
                        size_t binNumber = findEBin(tOrZDist_m.at(partIndex));
                        outputFile.width(17);
                        outputFile << binNumber;
                    }
                    outputFile << std::endl;
 
                }
            }
            outputFile.close();
        }
 
        // Wait for writing node before moving on.
        reduce(numberOfParticles, numberOfParticles, OpAddAssign());
    }
}
 
double Distribution::MDependentBehavior::get(double rand) {
    return 2.0 * std::sqrt(1.0 - std::pow(rand, ami_m));
}
 
double Distribution::GaussianLikeBehavior::get(double rand) {
    return std::sqrt(-2.0 * std::log(rand));
}
 
void Distribution::adjustPhaseSpace(double massIneV) {
    if (emitting_m || distrTypeT_m == DistributionType::FROMFILE || OpalData::getInstance()->isInOPALCyclMode())
        return;
 
    double deltaPx = Attributes::getReal(itsAttr[Attrib::Distribution::OFFSETPX]);
    double deltaPy = Attributes::getReal(itsAttr[Attrib::Distribution::OFFSETPY]);
    // Check input momentum units.
    if (inputMoUnits_m == InputMomentumUnits::EVOVERC) {
        deltaPx = Util::convertMomentumEVoverCToBetaGamma(deltaPx, massIneV);
        deltaPy = Util::convertMomentumEVoverCToBetaGamma(deltaPy, massIneV);
    }
 
    double avrg[6];
    avrg[0] = std::accumulate( xDist_m.begin(),      xDist_m.end(), 0.0) / totalNumberParticles_m;
    avrg[1] = std::accumulate(pxDist_m.begin(),     pxDist_m.end(), 0.0) / totalNumberParticles_m;
    avrg[2] = std::accumulate( yDist_m.begin(),      yDist_m.end(), 0.0) / totalNumberParticles_m;
    avrg[3] = std::accumulate(pyDist_m.begin(),     pyDist_m.end(), 0.0) / totalNumberParticles_m;
    avrg[4] = std::accumulate(tOrZDist_m.begin(), tOrZDist_m.end(), 0.0) / totalNumberParticles_m;
    avrg[5] = 0.0;
    for (unsigned int i = 0; i < pzDist_m.size(); ++ i) {
        // taylor series of sqrt(px*px + py*py + pz*pz) = pz * sqrt(1 + eps*eps) where eps << 1
        avrg[5] += (pzDist_m[i] +
                    (std::pow(pxDist_m[i] + deltaPx, 2) +
                     std::pow(pyDist_m[i] + deltaPy, 2)) / (2 * pzDist_m[i]));
    }
    allreduce(&(avrg[0]), 6, std::plus<double>());
    avrg[5] /= totalNumberParticles_m;
 
    // solve
    // \sum_{i = 0}^{N-1} \sqrt{(pz_i + \eps)^2 + px_i^2 + py_i^2} = N p
    double eps = avrgpz_m - avrg[5];
    for (unsigned int i = 0; i < pzDist_m.size(); ++ i) {
        xDist_m[i]    -= avrg[0];
        pxDist_m[i]   -= avrg[1];
        yDist_m[i]    -= avrg[2];
        pyDist_m[i]   -= avrg[3];
        tOrZDist_m[i] -= avrg[4];
        pzDist_m[i] += eps;
    }
}