Distribution.cpp 174 KB
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// ------------------------------------------------------------------------
// $RCSfile: Distribution.cpp,v $
// ------------------------------------------------------------------------
// $Revision: 1.3.4.1 $
// ------------------------------------------------------------------------
// Copyright: see Copyright.readme
// ------------------------------------------------------------------------
//
// Class: Distribution
//   The class for the OPAL Distribution command.
//
// ------------------------------------------------------------------------
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#include "Distribution/Distribution.h"
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#include "Distribution/SigmaGenerator.h"
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#include "AbsBeamline/SpecificElementVisitor.h"
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#include <cmath>
#include <cfloat>
#include <iomanip>
#include <iostream>
#include <string>
#include <vector>
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#include <numeric>
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#include "AbstractObjects/Expressions.h"
#include "Attributes/Attributes.h"
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#include "Utilities/OpalOptions.h"
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#include "Utilities/Options.h"
#include "halton1d_sequence.hh"
#include "AbstractObjects/OpalData.h"
#include "Algorithms/PartBunch.h"
#include "Algorithms/PartBins.h"
#include "Algorithms/bet/EnvelopeBunch.h"
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#include "Structure/Beam.h"
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#include "Structure/BoundaryGeometry.h"
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#include "Algorithms/PartBinsCyc.h"
#include "BasicActions/Option.h"
#include "Distribution/LaserProfile.h"
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#include "Elements/OpalBeamline.h"
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#include "AbstractObjects/BeamSequence.h"
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#include "Structure/H5PartWrapper.h"
#include "Structure/H5PartWrapperForPC.h"
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#include <gsl/gsl_cdf.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_sf_erf.h>
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#include <gsl/gsl_linalg.h>
#include <gsl/gsl_blas.h>
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#include "MagneticField.h"

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extern Inform *gmsg;

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#define DISTDBG1
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#define noDISTDBG2
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#define COMPLAINONFAILURE(rc)     complainOnFailure(rc, __FILE__, __LINE__);
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inline
void complainOnFailure(int rc, const std::string &file, int line) {
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << file << " @ line " << line << endl);
}
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SymTenzor<double, 6> getUnit6x6() {
    SymTenzor<double, 6> unit6x6;
    for (unsigned int i = 0; i < 6u; ++ i) {
        unit6x6(i,i) = 1.0;
    }
    return unit6x6;
}

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//
// Class Distribution
// ------------------------------------------------------------------------

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namespace AttributesT
{
    enum AttributesT {
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        DISTRIBUTION,
        FNAME,
        WRITETOFILE,
        WEIGHT,
        INPUTMOUNITS,
        EMITTED,
        EMISSIONSTEPS,
        EMISSIONMODEL,
        EKIN,
        ELASER,
        W,
        FE,
        CATHTEMP,
        NBIN,
        XMULT,
        YMULT,
        ZMULT,
        TMULT,
        PXMULT,
        PYMULT,
        PZMULT,
        OFFSETX,
        OFFSETY,
        OFFSETZ,
        OFFSETT,
        OFFSETPX,
        OFFSETPY,
        OFFSETPZ,
        SIGMAX,
        SIGMAY,
        SIGMAR,
        SIGMAZ,
        SIGMAT,
        TPULSEFWHM,
        TRISE,
        TFALL,
        SIGMAPX,
        SIGMAPY,
        SIGMAPZ,
        MX,
        MY,
        MZ,
        MT,
        CUTOFFX,
        CUTOFFY,
        CUTOFFR,
        CUTOFFLONG,
        CUTOFFPX,
        CUTOFFPY,
        CUTOFFPZ,
        FTOSCAMPLITUDE,
        FTOSCPERIODS,
        R,                          // the correlation matrix (a la transport)
        CORRX,
        CORRY,
        CORRZ,
        CORRT,
        R51,
        R52,
        R61,
        R62,
        LASERPROFFN,
        IMAGENAME,
        INTENSITYCUT,
        NPDARKCUR,
        INWARDMARGIN,
        EINITHR,
        FNA,
        FNB,
        FNY,
        FNVYZERO,
        FNVYSECOND,
        FNPHIW,
        FNBETA,
        FNFIELDTHR,
        FNMAXEMI,
        SECONDARYFLAG,
        NEMISSIONMODE,
        VSEYZERO,                   // sey_0 in Vaughn's model.
        VEZERO,                     // Energy related to sey_0 in Vaughan's model.
        VSEYMAX,                    // sey max in Vaughan's model.
        VEMAX,                      // Emax in Vaughan's model.
        VKENERGY,                   // Fitting parameter denotes the roughness of
        // surface for impact energy in Vaughn's model.
        VKTHETA,                    // Fitting parameter denotes the roughness of
        // surface for impact angle in Vaughn's model.
        VVTHERMAL,                  // Thermal velocity of Maxwellian distribution
        // of secondaries in Vaughan's model.
        VW,
        SURFMATERIAL,               // Add material type, currently 0 for copper
        // and 1 for stainless steel.
        EX,                         // below is for the matched distribution
        EY,
        ET,
        MAGSYM,                     // number of sector magnets
        LINE,
        FMAPFN,
        RESIDUUM,
        MAXSTEPSCO,
        MAXSTEPSSI,
        ORDERMAPS,
        E2,
        SIZE
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    };
}

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namespace LegacyAttributesT
{
    enum LegacyAttributesT {
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        // DESCRIPTION OF THE DISTRIBUTION:
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        DEBIN = AttributesT::SIZE,
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        SBIN,
        TEMISSION,
        SIGLASER,
        AG,
        SIGMAPT,
        TRANSVCUTOFF,
        CUTOFF,
        Z,
        T,
        PT,
        ALPHAX,
        ALPHAY,
        BETAX,
        BETAY,
        DX,
        DDX,
        DY,
        DDY,
        SIZE
    };
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}

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Distribution::Distribution():
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    Definition( LegacyAttributesT::SIZE, "DISTRIBUTION",
                "The DISTRIBUTION statement defines data for the 6D particle distribution."),
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    distrTypeT_m(DistrTypeT::NODIST),
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    numberOfDistributions_m(1),
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    emitting_m(false),
    scan_m(false),
    emissionModel_m(EmissionModelT::NONE),
    tEmission_m(0.0),
    tBin_m(0.0),
    currentEmissionTime_m(0.0),
    currentEnergyBin_m(0.0),
    currentSampleBin_m(0.0),
    numberOfEnergyBins_m(0),
    numberOfSampleBins_m(0),
    energyBins_m(NULL),
    energyBinHist_m(NULL),
    randGenEmit_m(NULL),
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    pTotThermal_m(0.0),
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    pmean_m(0.0),
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    cathodeWorkFunc_m(0.0),
    laserEnergy_m(0.0),
    cathodeFermiEnergy_m(0.0),
    cathodeTemp_m(0.0),
    emitEnergyUpperLimit_m(0.0),
    inputMoUnits_m(InputMomentumUnitsT::NONE),
    sigmaTRise_m(0.0),
    sigmaTFall_m(0.0),
    tPulseLengthFWHM_m(0.0),
    correlationMatrix_m(getUnit6x6()),
    laserProfileFileName_m(""),
    laserImageName_m(""),
    laserIntensityCut_m(0.0),
    laserProfile_m(NULL),
    darkCurrentParts_m(0),
    darkInwardMargin_m(0.0),
    eInitThreshold_m(0.0),
    workFunction_m(0.0),
    fieldEnhancement_m(0.0),
    fieldThrFN_m(0.0),
    maxFN_m(0),
    paraFNA_m(0.0),
    paraFNB_m(0.0),
    paraFNY_m(0.0),
    paraFNVYSe_m(0.0),
    paraFNVYZe_m(0.0),
    secondaryFlag_m(0),
    ppVw_m(0.0),
    vVThermal_m(0.0),
    referencePz_m(0.0),
    referenceZ_m(0.0),
    avrgpz_m(0.0),
    I_m(0.0),
    E_m(0.0),
    bega_m(0.0),
    M_m(0.0)
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{
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    SetAttributes();

    Distribution *defaultDistribution = clone("UNNAMED_Distribution");
    defaultDistribution->builtin = true;
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    try {
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        OpalData::getInstance()->define(defaultDistribution);
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    } catch(...) {
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        delete defaultDistribution;
    }

    SetFieldEmissionParameters();
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}
/**
 *
 *
 * @param name
 * @param parent
 */
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Distribution::Distribution(const std::string &name, Distribution *parent):
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    Definition(name, parent),
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    distT_m(parent->distT_m),
    distrTypeT_m(DistrTypeT::NODIST),
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    numberOfDistributions_m(parent->numberOfDistributions_m),
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    emitting_m(parent->emitting_m),
    scan_m(parent->scan_m),
    particleRefData_m(parent->particleRefData_m),
    addedDistributions_m(parent->addedDistributions_m),
    particlesPerDist_m(parent->particlesPerDist_m),
    emissionModel_m(parent->emissionModel_m),
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    tEmission_m(parent->tEmission_m),
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    tBin_m(parent->tBin_m),
    currentEmissionTime_m(parent->currentEmissionTime_m),
    currentEnergyBin_m(parent->currentEmissionTime_m),
    currentSampleBin_m(parent->currentSampleBin_m),
    numberOfEnergyBins_m(parent->numberOfEnergyBins_m),
    numberOfSampleBins_m(parent->numberOfSampleBins_m),
    energyBins_m(NULL),
    energyBinHist_m(NULL),
    randGenEmit_m(parent->randGenEmit_m),
    pTotThermal_m(parent->pTotThermal_m),
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    pmean_m(parent->pmean_m),
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    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),
    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),
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    avrgpz_m(parent->avrgpz_m),
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    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),
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    correlationMatrix_m(parent->correlationMatrix_m),
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    laserProfileFileName_m(parent->laserProfileFileName_m),
    laserImageName_m(parent->laserImageName_m),
    laserIntensityCut_m(parent->laserIntensityCut_m),
    laserProfile_m(NULL),
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    darkCurrentParts_m(parent->darkCurrentParts_m),
    darkInwardMargin_m(parent->darkInwardMargin_m),
    eInitThreshold_m(parent->eInitThreshold_m),
    workFunction_m(parent->workFunction_m),
    fieldEnhancement_m(parent->fieldEnhancement_m),
    fieldThrFN_m(parent->fieldThrFN_m),
    maxFN_m(parent->maxFN_m),
    paraFNA_m(parent-> paraFNA_m),
    paraFNB_m(parent-> paraFNB_m),
    paraFNY_m(parent-> paraFNY_m),
    paraFNVYSe_m(parent-> paraFNVYSe_m),
    paraFNVYZe_m(parent-> paraFNVYZe_m),
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    secondaryFlag_m(parent->secondaryFlag_m),
    ppVw_m(parent->ppVw_m),
    vVThermal_m(parent->vVThermal_m),
    tRise_m(parent->tRise_m),
    tFall_m(parent->tFall_m),
    sigmaRise_m(parent->sigmaRise_m),
    sigmaFall_m(parent->sigmaFall_m),
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    cutoff_m(parent->cutoff_m),
    I_m(parent->I_m),
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    E_m(parent->E_m),
    bega_m(parent->bega_m),
    M_m(parent->M_m)
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{
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}

Distribution::~Distribution() {

    if((Ippl::getNodes() == 1) && (os_m.is_open()))
        os_m.close();

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    if (energyBins_m != NULL) {
        delete energyBins_m;
        energyBins_m = NULL;
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    }

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    if (energyBinHist_m != NULL) {
        gsl_histogram_free(energyBinHist_m);
        energyBinHist_m = NULL;
    }

    if (randGenEmit_m != NULL) {
        delete randGenEmit_m;
        randGenEmit_m = NULL;
    }

    if(laserProfile_m) {
        delete laserProfile_m;
        laserProfile_m = NULL;
    }
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}
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/*
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  void Distribution::printSigma(SigmaGenerator<double,unsigned int>::matrix_type& M, Inform& out) {
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  for(int i=0; i<M.size1(); ++i) {
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  for(int j=0; j<M.size2(); ++j) {
  *gmsg  << M(i,j) << " ";
  }
  *gmsg << endl;
  }
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  }
*/
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/**
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 * At the moment only write the header into the file dist.dat
 * PartBunch will then append (very uggly)
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 * @param
 * @param
 * @param
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 */
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void Distribution::WriteToFile() {
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    /*
      if(Ippl::getNodes() == 1) {
      if(os_m.is_open()) {
      ;
      } else {
      *gmsg << " Write distribution to file data/dist.dat" << endl;
      std::string file("data/dist.dat");
      os_m.open(file.c_str());
      if(os_m.bad()) {
      *gmsg << "Unable to open output file " <<  file << endl;
      }
      os_m << "# x y ti px py pz "  << std::endl;
      os_m.close();
      }
      }
    */
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}

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/// Distribution can only be replaced by another distribution.
bool Distribution::canReplaceBy(Object *object) {
    return dynamic_cast<Distribution *>(object) != 0;
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}

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Distribution *Distribution::clone(const std::string &name) {
    return new Distribution(name, this);
}
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void Distribution::execute() {
}
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void Distribution::update() {
}
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void Distribution::Create(size_t &numberOfParticles, double massIneV) {
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    SetFieldEmissionParameters();
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    switch (distrTypeT_m) {
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    case DistrTypeT::MATCHEDGAUSS:
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        CreateMatchedGaussDistribution(numberOfParticles, massIneV);
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        break;
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    case DistrTypeT::FROMFILE:
        CreateDistributionFromFile(numberOfParticles, massIneV);
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        break;
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    case DistrTypeT::GAUSS:
        CreateDistributionGauss(numberOfParticles, massIneV);
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        break;
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    case DistrTypeT::BINOMIAL:
        CreateDistributionBinomial(numberOfParticles, massIneV);
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        break;
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    case DistrTypeT::FLATTOP:
        CreateDistributionFlattop(numberOfParticles, massIneV);
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        break;
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    case DistrTypeT::GUNGAUSSFLATTOPTH:
        CreateDistributionFlattop(numberOfParticles, massIneV);
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        break;
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    case DistrTypeT::ASTRAFLATTOPTH:
        CreateDistributionFlattop(numberOfParticles, massIneV);
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        break;
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    default:
        INFOMSG("Distribution unknown." << endl;);
        break;
    }
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    // AAA Scale and shift coordinates according to distribution input.
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    ScaleDistCoordinates();
    ShiftDistCoordinates(massIneV);
}
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void  Distribution::CreatePriPart(PartBunch *beam, BoundaryGeometry &bg) {
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    if(Options::ppdebug) {  // This is Parallel Plate Benchmark.
        int pc = 0;
        size_t lowMark = beam->getLocalNum();
        double vw = this->GetVw();
        double vt = this->GetvVThermal();
        double f_max = vw / vt * exp(-0.5);
        double test_a = vt / vw;
        double test_asq = test_a * test_a;
        size_t count = 0;
        size_t N_mean = static_cast<size_t>(floor(bg.getN() / Ippl::getNodes()));
        size_t N_extra = static_cast<size_t>(bg.getN() - N_mean * Ippl::getNodes());
        if(Ippl::myNode() == 0)
            N_mean += N_extra;
        if(bg.getN() != 0) {
            for(size_t i = 0; i < bg.getN(); i++) {
                if(pc == Ippl::myNode()) {
                    if(count < N_mean) {
                        /*==============Parallel Plate Benchmark=====================================*/
                        double test_s = 1;
                        double f_x = 0;
                        double test_x = 0;
                        while(test_s > f_x) {
                            test_s = IpplRandom();
                            test_s *= f_max;
                            test_x = IpplRandom();
                            test_x *= 10 * test_a; //range for normalized emission speed(0,10*test_a);
                            f_x = test_x / test_asq * exp(-test_x * test_x / 2 / test_asq);
                        }
                        double v_emi = test_x * vw;
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                        double betaemit = v_emi / Physics::c;
                        double betagamma = betaemit / sqrt(1 - betaemit * betaemit);
                        /*============================================================================ */
                        beam->create(1);
                        if(pc != 0) {
                            beam->R[lowMark + count] = bg.getCooridinate(Ippl::myNode() * N_mean + count + N_extra);
                            beam->P[lowMark + count] = betagamma * bg.getMomenta(Ippl::myNode() * N_mean + count);
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                        } else {
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                            beam->R[lowMark + count] = bg.getCooridinate(count);
                            beam->P[lowMark + count] = betagamma * bg.getMomenta(count);
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                        }
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                        beam->Bin[lowMark + count] = 0;
                        beam->PType[lowMark + count] = 0; // create primary particle bunch;
                        beam->TriID[lowMark + count] = 0;
                        beam->Q[lowMark + count] = beam->getChargePerParticle();
                        beam->LastSection[lowMark + count] = 0;
                        beam->Ef[lowMark + count] = Vector_t(0.0);
                        beam->Bf[lowMark + count] = Vector_t(0.0);
                        beam->dt[lowMark + count] = beam->getdT();
                        count ++;
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                    }
                }
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                pc++;
                if(pc == Ippl::getNodes())
                    pc = 0;
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            }
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            bg.clearCooridinateArray();
            bg.clearMomentaArray();
            beam->boundp();
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        }
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        *gmsg << *beam << endl;
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    } else {// Normal procedure to create primary particles
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        int pc = 0;
        size_t lowMark = beam->getLocalNum();
        size_t count = 0;
        size_t N_mean = static_cast<size_t>(floor(bg.getN() / Ippl::getNodes()));
        size_t N_extra = static_cast<size_t>(bg.getN() - N_mean * Ippl::getNodes());
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        if(Ippl::myNode() == 0)
            N_mean += N_extra;
        if(bg.getN() != 0) {
            for(size_t i = 0; i < bg.getN(); i++) {
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                if(pc == Ippl::myNode()) {
                    if(count < N_mean) {
                        beam->create(1);
                        if(pc != 0)
                            beam->R[lowMark + count] = bg.getCooridinate(Ippl::myNode() * N_mean + count + N_extra); // node 0 will emit the particle with coordinate ID from 0 to N_mean+N_extra, so other nodes should shift to node_number*N_mean+N_extra
                        else
                            beam->R[lowMark + count] = bg.getCooridinate(count); // for node0 the particle number N_mean =  N_mean + N_extra
                        beam->P[lowMark + count] = Vector_t(0.0);
                        beam->Bin[lowMark + count] = 0;
                        beam->PType[lowMark + count] = 0; // create primary particle bunch.
                        beam->TriID[lowMark + count] = 0;
                        beam->Q[lowMark + count] = beam->getChargePerParticle();
                        beam->LastSection[lowMark + count] = 0;
                        beam->Ef[lowMark + count] = Vector_t(0.0);
                        beam->Bf[lowMark + count] = Vector_t(0.0);
                        beam->dt[lowMark + count] = beam->getdT();
                        count++;
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                    }
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                }
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                pc++;
                if(pc == Ippl::getNodes())
                    pc = 0;
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            }
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        }
        bg.clearCooridinateArray();
        beam->boundp();//fixme if bg.getN()==0?
    }
    *gmsg << *beam << endl;
}
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void Distribution::DoRestartOpalT(PartBunch &beam, size_t Np, int restartStep, H5PartWrapper *dataSource) {
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    IpplTimings::startTimer(beam.distrReload_m);
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    long numParticles = dataSource->getNumParticles();
    size_t numParticlesPerNode = numParticles / Ippl::getNodes();
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    size_t firstParticle = numParticlesPerNode * Ippl::myNode();
    size_t lastParticle = firstParticle + numParticlesPerNode - 1;
    if (Ippl::myNode() == Ippl::getNodes() - 1)
        lastParticle = numParticles - 1;
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    numParticles = lastParticle - firstParticle + 1;
    PAssert(numParticles >= 0);
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    beam.create(numParticles);
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    dataSource->readHeader();
    dataSource->readStep(beam, firstParticle, lastParticle);
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    beam.boundp();

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    double actualT = beam.getT();
    long long ltstep = beam.getLocalTrackStep();
    long long gtstep = beam.getGlobalTrackStep();

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    IpplTimings::stopTimer(beam.distrReload_m);

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    *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;
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}

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void Distribution::DoRestartOpalCycl(PartBunch &beam,
                                     size_t Np,
                                     int restartStep,
                                     const int specifiedNumBunch,
                                     H5PartWrapper *dataSource) {
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    // h5_int64_t rc;
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    IpplTimings::startTimer(beam.distrReload_m);
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    INFOMSG("---------------- Start reading hdf5 file----------------" << endl);
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    long numParticles = dataSource->getNumParticles();
    size_t numParticlesPerNode = numParticles / Ippl::getNodes();
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    size_t firstParticle = numParticlesPerNode * Ippl::myNode();
    size_t lastParticle = firstParticle + numParticlesPerNode - 1;
    if (Ippl::myNode() == Ippl::getNodes() - 1)
        lastParticle = numParticles - 1;
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    numParticles = lastParticle - firstParticle + 1;
    PAssert(numParticles >= 0);
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    beam.create(numParticles);
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    dataSource->readHeader();
    dataSource->readStep(beam, firstParticle, lastParticle);
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    beam.Q = beam.getChargePerParticle();
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    beam.boundp();
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    double meanE = static_cast<H5PartWrapperForPC*>(dataSource)->getMeanKineticEnergy();
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    const int globalN = beam.getTotalNum();
    INFOMSG("Restart from hdf5 format file " << OpalData::getInstance()->getInputBasename() << ".h5" << endl);
    INFOMSG("total number of particles = " << globalN << endl);
    INFOMSG("* Restart Energy = " << meanE << " (MeV), Path lenght = " << beam.getLPath() << " (m)" <<  endl);
    INFOMSG("Tracking Step since last bunch injection is " << beam.getSteptoLastInj() << endl);
    INFOMSG(beam.getNumBunch() << " Bunches(bins) exist in this file" << endl);
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    double gamma = 1 + meanE / beam.getM() * 1.0e6;
    double beta = sqrt(1.0 - (1.0 / std::pow(gamma, 2.0)));
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    INFOMSG("* Gamma = " << gamma << ", Beta = " << beta << endl);
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    if(dataSource->predecessorIsSameFlavour()) {
        INFOMSG("Restart from hdf5 file generated by OPAL-cycl" << endl);
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        if(specifiedNumBunch > 1) {
            // the allowed maximal bin number is set to 1000
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            beam.setPBins(new PartBinsCyc(1000, beam.getNumBunch()));
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        }

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    } else {
        INFOMSG("Restart from hdf5 file generated by OPAL-t" << endl);
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        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);
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        INFOMSG("Rmean = " << meanR << "[m], Pmean=" << meanP << endl);
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        for(unsigned int i = 0; i < newLocalN; ++i) {
            beam.R[i] -= meanR;
            beam.P[i] -= meanP;
        }
    }

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    INFOMSG("---------------Finished reading hdf5 file---------------" << endl);
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    IpplTimings::stopTimer(beam.distrReload_m);
}

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void Distribution::DoRestartOpalE(EnvelopeBunch &beam, size_t Np, int restartStep,
                                  H5PartWrapper *dataSource) {
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    IpplTimings::startTimer(beam.distrReload_m);
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    int N = dataSource->getNumParticles();
    *gmsg << "total number of slices = " << N << endl;
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    beam.distributeSlices(N);
    beam.createBunch();
    long long starti = beam.mySliceStartOffset();
    long long endi = beam.mySliceEndOffset();

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    dataSource->readHeader();
    dataSource->readStep(beam, starti, endi);
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    beam.setCharge(beam.getChargePerParticle());
    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;
    }

    distT_m = Attributes::getString(itsAttr[AttributesT::DISTRIBUTION]);
    if(distT_m == "GAUSS")
        distrTypeT_m = DistrTypeT::GAUSS;
    else if(distT_m == "GUNGAUSSFLATTOPTH")
        distrTypeT_m = DistrTypeT::GUNGAUSSFLATTOPTH;
    else if(distT_m == "FROMFILE")
        distrTypeT_m = DistrTypeT::FROMFILE;
    else if(distT_m == "BINOMIAL")
        distrTypeT_m = DistrTypeT::BINOMIAL;

    tPulseLengthFWHM_m = Attributes::getReal(itsAttr[AttributesT::TPULSEFWHM]);
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    cutoff_m = Attributes::getReal(itsAttr[ LegacyAttributesT::CUTOFF]);
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    tRise_m = Attributes::getReal(itsAttr[AttributesT::TRISE]);
    tFall_m = Attributes::getReal(itsAttr[AttributesT::TFALL]);
    double tratio = sqrt(2.0 * log(10.0)) - sqrt(2.0 * log(10.0 / 9.0));
    sigmaRise_m = tRise_m / tratio;
    sigmaFall_m = tFall_m / tratio;

    switch(distrTypeT_m) {
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    case DistrTypeT::ASTRAFLATTOPTH: {
        double a = tPulseLengthFWHM_m / 2;
        double sig = tRise_m / 2;
        double inv_erf08 = 0.906193802436823; // erfinv(0.8)
        double sqr2 = 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;
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        }
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        tEmission_m = tPulseLengthFWHM_m + 10 * sig;
        break;
    }
    case DistrTypeT::GUNGAUSSFLATTOPTH: {
        tEmission_m = tPulseLengthFWHM_m + (cutoff_m - sqrt(2.0 * log(2.0))) * (sigmaRise_m + sigmaFall_m);
        break;
    }
    default:
        tEmission_m = 0.0;
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    }
    return tEmission_m;
}

double Distribution::GetEkin() const {return Attributes::getReal(itsAttr[AttributesT::EKIN]);}
double Distribution::GetLaserEnergy() const {return Attributes::getReal(itsAttr[AttributesT::ELASER]);}
double Distribution::GetWorkFunctionRf() const {return Attributes::getReal(itsAttr[AttributesT::W]);}

size_t Distribution::GetNumberOfDarkCurrentParticles() { return (size_t) Attributes::getReal(itsAttr[AttributesT::NPDARKCUR]);}
double Distribution::GetDarkCurrentParticlesInwardMargin() { return Attributes::getReal(itsAttr[AttributesT::INWARDMARGIN]);}
double Distribution::GetEInitThreshold() { return Attributes::getReal(itsAttr[AttributesT::EINITHR]);}
double Distribution::GetWorkFunction() { return Attributes::getReal(itsAttr[AttributesT::FNPHIW]); }
double Distribution::GetFieldEnhancement() { return Attributes::getReal(itsAttr[AttributesT::FNBETA]); }
size_t Distribution::GetMaxFNemissionPartPerTri() { return (size_t) Attributes::getReal(itsAttr[AttributesT::FNMAXEMI]);}
double Distribution::GetFieldFNThreshold() { return Attributes::getReal(itsAttr[AttributesT::FNFIELDTHR]);}
double Distribution::GetFNParameterA() { return Attributes::getReal(itsAttr[AttributesT::FNA]);}
double Distribution::GetFNParameterB() { return Attributes::getReal(itsAttr[AttributesT::FNB]);}
double Distribution::GetFNParameterY() { return Attributes::getReal(itsAttr[AttributesT::FNY]);}
double Distribution::GetFNParameterVYZero() { return Attributes::getReal(itsAttr[AttributesT::FNVYZERO]);}
double Distribution::GetFNParameterVYSecond() { return Attributes::getReal(itsAttr[AttributesT::FNVYSECOND]);}
int    Distribution::GetSecondaryEmissionFlag() { return Attributes::getReal(itsAttr[AttributesT::SECONDARYFLAG]);}
bool   Distribution::GetEmissionMode() { return Attributes::getBool(itsAttr[AttributesT::NEMISSIONMODE]);}

std::string Distribution::GetTypeofDistribution() { return (std::string) Attributes::getString(itsAttr[AttributesT::DISTRIBUTION]);}

double Distribution::GetvSeyZero() {return Attributes::getReal(itsAttr[AttributesT::VSEYZERO]);}// return sey_0 in Vaughan's model
double Distribution::GetvEZero() {return Attributes::getReal(itsAttr[AttributesT::VEZERO]);}// return the energy related to sey_0 in Vaughan's model
double Distribution::GetvSeyMax() {return Attributes::getReal(itsAttr[AttributesT::VSEYMAX]);}// return sey max in Vaughan's model
double Distribution::GetvEmax() {return Attributes::getReal(itsAttr[AttributesT::VEMAX]);}// return Emax in Vaughan's model
double Distribution::GetvKenergy() {return Attributes::getReal(itsAttr[AttributesT::VKENERGY]);}// return fitting parameter denotes the roughness of surface for impact energy in Vaughan's model
double Distribution::GetvKtheta() {return Attributes::getReal(itsAttr[AttributesT::VKTHETA]);}// return fitting parameter denotes the roughness of surface for impact angle in Vaughan's model
double Distribution::GetvVThermal() {return Attributes::getReal(itsAttr[AttributesT::VVTHERMAL]);}// thermal velocity of Maxwellian distribution of secondaries in Vaughan's model
double Distribution::GetVw() {return Attributes::getReal(itsAttr[AttributesT::VW]);}// velocity scalar for parallel plate benchmark;

int Distribution::GetSurfMaterial() {return (int)Attributes::getReal(itsAttr[AttributesT::SURFMATERIAL]);}// Surface material number for Furman-Pivi's Model;

Inform &Distribution::printInfo(Inform &os) const {

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    os << "* ************* D I S T R I B U T I O N ********************************************" << endl;
    os << "* " << endl;
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    if (OpalData::getInstance()->inRestartRun()) {
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        os << "* In restart. Distribution read in from .h5 file." << endl;
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    } else {
        if (addedDistributions_m.size() > 0)
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            os << "* Main Distribution" << endl
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               << "-----------------" << endl;
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        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++) {
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            os << "* " << endl;
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            os << "* Added Distribution #" << distCount << endl;
            os << "* ----------------------" << endl;
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            addedDistributions_m.at(distIndex)->PrintDist(os, particlesPerDist_m.at(distCount));
            distCount++;
        }

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        os << "* " << endl;
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        if (numberOfEnergyBins_m > 0) {
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            os << "* Number of energy bins    = " << numberOfEnergyBins_m << endl;
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            //            if (numberOfEnergyBins_m > 1)
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            //    PrintEnergyBins(os);
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        }

        if (emitting_m) {
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            os << "* Distribution is emitted. " << endl;
            os << "* Emission time            = " << tEmission_m << " [sec]" << endl;
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            os << "* Time per bin             = " << tEmission_m/numberOfEnergyBins_m << " [sec]" << endl;
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            os << "* Bin delta t              = " << tBin_m << " [sec]" << endl;
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            os << "* " << endl;
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            PrintEmissionModel(os);
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            os << "* " << endl;
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        } else
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            os << "* Distribution is injected." << endl;
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    }
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    os << "* " << endl;
    os << "* **********************************************************************************" << endl;
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    return os;
}

const PartData &Distribution::GetReference() const {
    // Cast away const, to allow logically constant Distribution to update.
    const_cast<Distribution *>(this)->update();
    return particleRefData_m;
}

void Distribution::AddDistributions() {
    /*
     * Move particle coordinates from added distributions to main distribution.
     */
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    std::vector<Distribution *>::iterator addedDistIt;
    for (addedDistIt = addedDistributions_m.begin();
         addedDistIt != addedDistributions_m.end(); addedDistIt++) {

        std::vector<double>::iterator distIt;
        for (distIt = (*addedDistIt)->GetXDist().begin();
             distIt != (*addedDistIt)->GetXDist().end();
             distIt++) {
            xDist_m.push_back(*distIt);
        }
        (*addedDistIt)->EraseXDist();

        for (distIt = (*addedDistIt)->GetBGxDist().begin();
             distIt != (*addedDistIt)->GetBGxDist().end();
             distIt++) {
            pxDist_m.push_back(*distIt);
        }
        (*addedDistIt)->EraseBGxDist();

        for (distIt = (*addedDistIt)->GetYDist().begin();
             distIt != (*addedDistIt)->GetYDist().end();
             distIt++) {
            yDist_m.push_back(*distIt);
        }
        (*addedDistIt)->EraseYDist();

        for (distIt = (*addedDistIt)->GetBGyDist().begin();
             distIt != (*addedDistIt)->GetBGyDist().end();
             distIt++) {
            pyDist_m.push_back(*distIt);
        }
        (*addedDistIt)->EraseBGyDist();

        for (distIt = (*addedDistIt)->GetTOrZDist().begin();
             distIt != (*addedDistIt)->GetTOrZDist().end();
             distIt++) {
            tOrZDist_m.push_back(*distIt);
        }
        (*addedDistIt)->EraseTOrZDist();

        for (distIt = (*addedDistIt)->GetBGzDist().begin();
             distIt != (*addedDistIt)->GetBGzDist().end();
             distIt++) {
            pzDist_m.push_back(*distIt);
        }
        (*addedDistIt)->EraseBGzDist();
    }
}

void Distribution::ApplyEmissionModel(double eZ, double &px, double &py, double &pz) {

    switch (emissionModel_m) {

    case EmissionModelT::NONE:
        ApplyEmissModelNone(pz);
        break;
    case EmissionModelT::ASTRA:
        ApplyEmissModelAstra(px, py, pz);
        break;
    case EmissionModelT::NONEQUIL:
        ApplyEmissModelNonEquil(eZ, px, py, pz);
        break;
    default:
        break;
    }
}

void Distribution::ApplyEmissModelAstra(double &px, double &py, double &pz) {

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    double phi = 2.0 * acos(sqrt(gsl_rng_uniform(randGenEmit_m)));
    double theta = 2.0 * Physics::pi * gsl_rng_uniform(randGenEmit_m);
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    px = pTotThermal_m * sin(phi) * cos(theta);
    py = pTotThermal_m * sin(phi) * sin(theta);
    pz = pTotThermal_m * std::abs(cos(phi));

}

void Distribution::ApplyEmissModelNone(double &pz) {
    pz += pTotThermal_m;
}

void Distribution::ApplyEmissModelNonEquil(double eZ,
                                           double &bgx,
                                           double &bgy,
                                           double &bgz) {

    double phiEffective = cathodeWorkFunc_m
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        - sqrt(Physics::q_e * eZ /
               (4.0 * Physics::pi * Physics::epsilon_0));
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    double lowEnergyLimit = cathodeFermiEnergy_m + phiEffective - laserEnergy_m;

    // Generate emission energy.
    double energy = 0.0;
    bool allow = false;
    while (!allow) {
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        energy = lowEnergyLimit + (gsl_rng_uniform(randGenEmit_m)*emitEnergyUpperLimit_m);
        double randFuncValue = gsl_rng_uniform(randGenEmit_m);
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        double funcValue = (1.0
                            - 1.0
                            / (1.0
                               + exp((energy + laserEnergy_m - cathodeFermiEnergy_m)
                                     / (Physics::kB * cathodeTemp_m))))
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            / (1.0
               + exp((energy - cathodeFermiEnergy_m)
                     / (Physics::kB * cathodeTemp_m)));
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        if (randFuncValue <= funcValue)
            allow = true;
    }

    // Compute emission angles.
    double energyInternal = energy + laserEnergy_m;
    double energyExternal = energy + laserEnergy_m
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        - cathodeFermiEnergy_m - phiEffective;
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    double thetaInMax = acos(sqrt((cathodeFermiEnergy_m + phiEffective)
                                  / (energy + laserEnergy_m)));
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    double thetaIn = gsl_rng_uniform(randGenEmit_m)*thetaInMax;
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    double sinThetaOut = sin(thetaIn) * sqrt(energyInternal / energyExternal);
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    double phi = Physics::two_pi * gsl_rng_uniform(randGenEmit_m);
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    // Compute emission momenta.
    double betaGammaExternal
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        = sqrt(pow(energyExternal / (Physics::m_e * 1.0e9) + 1.0, 2.0) - 1.0);
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    bgx = betaGammaExternal * sinThetaOut * cos(phi);
    bgy = betaGammaExternal * sinThetaOut * sin(phi);
    bgz = betaGammaExternal * sqrt(1.0 - pow(sinThetaOut, 2.0));

}

void Distribution::CalcPartPerDist(size_t numberOfParticles) {

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    typedef std::vector<Distribution *>::iterator iterator;
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    if (numberOfDistributions_m == 1)
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        particlesPerDist_m.push_back(numberOfParticles);
    else {
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        double totalWeight = GetWeight();
        for (iterator it = addedDistributions_m.begin(); it != addedDistributions_m.end(); it++) {
            totalWeight += (*it)->GetWeight();
        }
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        particlesPerDist_m.push_back(0);
        size_t numberOfCommittedPart = 0;
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        for (iterator it = addedDistributions_m.begin(); it != addedDistributions_m.end(); it++) {
            size_t particlesCurrentDist = numberOfParticles * (*it)->GetWeight() / totalWeight;
            particlesPerDist_m.push_back(particlesCurrentDist);
            numberOfCommittedPart += particlesCurrentDist;
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        }

        // Remaining particles go into main distribution.
        particlesPerDist_m.at(0) = numberOfParticles - numberOfCommittedPart;

    }

}

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[AttributesT::NBIN])));
    if (numberOfEnergyBins_m == 0)
        numberOfEnergyBins_m = 1;

    int emissionSteps = std::abs(static_cast<int> (Attributes::getReal(itsAttr[AttributesT::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[AttributesT::EMITTED]);

    switch (distrTypeT_m) {

    case DistrTypeT::ASTRAFLATTOPTH:
        emitting_m = true;
        break;
    case DistrTypeT::GUNGAUSSFLATTOPTH:
        emitting_m = true;
        break;
    default:
        break;
    }
}

void Distribution::CheckParticleNumber(size_t &numberOfParticles) {

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    size_t numberOfDistParticles = tOrZDist_m.size();
    reduce(numberOfDistParticles, numberOfDistParticles, OpAddAssign());
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    if (numberOfDistParticles != numberOfParticles) {
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        *gmsg << "\n--------------------------------------------------" << endl
              << "Warning!! The number of particles in the initial" << endl
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              << "distribution is " << numberOfDistParticles << "." << endl << endl
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              << "This is different from the number of particles" << endl
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              << "defined by the BEAM command: " << numberOfParticles << endl << endl
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              << "This is often happens when using a FROMFILE type" << endl
              << "distribution and not matching the number of" << endl
              << "particles in the particles file(s) with the number" << endl
              << "given in the BEAM command." << endl << endl
              << "The number of particles in the initial distribution" << endl
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              << "(" << numberOfDistParticles << ") "
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              << "will take precedence." << endl
              << "---------------------------------------------------\n" << endl;
    }
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    numberOfParticles = numberOfDistParticles;
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}

void Distribution::ChooseInputMomentumUnits(InputMomentumUnitsT::InputMomentumUnitsT inputMoUnits) {

    /*
     * Toggle what units to use for inputing momentum.
     */
    std::string inputUnits = Attributes::getString(itsAttr[AttributesT::INPUTMOUNITS]);
    if (inputUnits == "NONE")
        inputMoUnits_m = InputMomentumUnitsT::NONE;
    else if (inputUnits == "EV")
        inputMoUnits_m = InputMomentumUnitsT::EV;
    else
        inputMoUnits_m = inputMoUnits;

}

double Distribution::ConvertBetaGammaToeV(double valueInBetaGamma, double massIneV) {
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    if (valueInBetaGamma < 0)
        return -1.0 * (sqrt(pow(valueInBetaGamma, 2.0) + 1.0) - 1.0) * massIneV;
    else
        return (sqrt(pow(valueInBetaGamma, 2.0) + 1.0) - 1.0) * massIneV;
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}

double Distribution::ConverteVToBetaGamma(double valueIneV, double massIneV) {
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    if (valueIneV < 0)
        return -1.0 * sqrt( pow( -1.0 * valueIneV / massIneV + 1.0, 2.0) - 1.0);
    else
        return sqrt( pow( valueIneV / massIneV + 1.0, 2.0) - 1.0);
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}

double Distribution::ConvertMeVPerCToBetaGamma(double valueInMeVPerC, double massIneV) {
    return sqrt(pow(valueInMeVPerC * 1.0e6 * Physics::c / massIneV + 1.0, 2.0) - 1.0);
}

void Distribution::CreateDistributionBinomial(size_t numberOfParticles, double massIneV) {

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    SetDistParametersBinomial(massIneV);
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    GenerateBinomial(numberOfParticles);
}

void Distribution::CreateDistributionFlattop(size_t numberOfParticles, double massIneV) {

    SetDistParametersFlattop(massIneV);

    if (emitting_m) {
        if (laserProfile_m == NULL)
            GenerateFlattopT(numberOfParticles);
        else
            GenerateFlattopLaserProfile(numberOfParticles);
    } else
        GenerateFlattopZ(numberOfParticles);
}

void Distribution::CreateDistributionFromFile(size_t numberOfParticles, double massIneV) {

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    *gmsg << level3 << "\n"
          << "------------------------------------------------------------------------------------\n";
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