Distribution.cpp

// ------------------------------------------------------------------------
// $RCSfile: Distribution.cpp,v $
// ------------------------------------------------------------------------
// $Revision: 1.3.4.1 $
// ------------------------------------------------------------------------
// Copyright: see Copyright.readme
// ------------------------------------------------------------------------
//
// Class: Distribution
//   The class for the OPAL Distribution command.
//
// ------------------------------------------------------------------------

#include "Distribution/Distribution.h"
#include "Distribution/SigmaGenerator.h"
#include "AbsBeamline/SpecificElementVisitor.h"

#include <cmath>
#include <cfloat>
#include <iomanip>
#include <iostream>
#include <string>
#include <vector>
#include <numeric>
#include <limits>

#include "AbstractObjects/Expressions.h"
#include "Utilities/Options.h"
#include "AbstractObjects/OpalData.h"
#include "Algorithms/PartBunch.h"
#include "Algorithms/PartBins.h"
#include "Algorithms/bet/EnvelopeBunch.h"
#include "Structure/Beam.h"
#include "Structure/BoundaryGeometry.h"
#include "Algorithms/PartBinsCyc.h"
#include "BasicActions/Option.h"
#include "Distribution/LaserProfile.h"
#include "Elements/OpalBeamline.h"
#include "AbstractObjects/BeamSequence.h"
#include "Structure/H5PartWrapper.h"
#include "Structure/H5PartWrapperForPC.h"
#include "Utilities/Util.h"

#include <gsl/gsl_cdf.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_sf_erf.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_blas.h>

#include <sys/time.h>

#include <boost/regex.hpp>

extern Inform *gmsg;

#define SMALLESTCUTOFF 1e-12

namespace {
    SymTenzor<double, 6> getUnit6x6() {
        SymTenzor<double, 6> unit6x6;
        for (unsigned int i = 0; i < 6u; ++ i) {
            unit6x6(i,i) = 1.0;
        }
        return unit6x6;
    }
}

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

Distribution::Distribution():
    Definition( Attrib::Legacy::Distribution::SIZE, "DISTRIBUTION",
                "The DISTRIBUTION statement defines data for the 6D particle distribution."),
    distrTypeT_m(DistrTypeT::NODIST),
    numberOfDistributions_m(1),
    emitting_m(false),
    scan_m(false),
    emissionModel_m(EmissionModelT::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(NULL),
    energyBinHist_m(NULL),
    randGen_m(NULL),
    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(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),
    I_m(0.0),
    E_m(0.0),
    M_m(0.0),
    referencePz_m(0.0),
    referenceZ_m(0.0),
    bega_m(0.0)
{
    setAttributes();

    Distribution *defaultDistribution = clone("UNNAMED_Distribution");
    defaultDistribution->builtin = true;

    try {
        OpalData::getInstance()->define(defaultDistribution);
    } catch(...) {
        delete defaultDistribution;
    }

    // setFieldEmissionParameters();

    gsl_rng_env_setup();
    randGen_m = gsl_rng_alloc(gsl_rng_default);
}
/**
 *
 *
 * @param name
 * @param parent
 */
Distribution::Distribution(const std::string &name, Distribution *parent):
    Definition(name, parent),
    distT_m(parent->distT_m),
    distrTypeT_m(DistrTypeT::NODIST),
    numberOfDistributions_m(parent->numberOfDistributions_m),
    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),
    tEmission_m(parent->tEmission_m),
    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),
    randGen_m(NULL),
    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),
    laserProfileFileName_m(parent->laserProfileFileName_m),
    laserImageName_m(parent->laserImageName_m),
    laserIntensityCut_m(parent->laserIntensityCut_m),
    laserProfile_m(NULL),
    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),
    secondaryFlag_m(parent->secondaryFlag_m),
    ppVw_m(parent->ppVw_m),
    vVThermal_m(parent->vVThermal_m),
    I_m(parent->I_m),
    E_m(parent->E_m),
    M_m(parent->M_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),
    bega_m(parent->bega_m)
{
    gsl_rng_env_setup();
    randGen_m = gsl_rng_alloc(gsl_rng_default);
}

Distribution::~Distribution() {

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

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

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

    if (randGen_m != NULL) {
        gsl_rng_free(randGen_m);
        randGen_m = NULL;
    }

    if (laserProfile_m) {
        delete laserProfile_m;
        laserProfile_m = NULL;
    }

}
/*
  void Distribution::printSigma(SigmaGenerator<double,unsigned int>::matrix_type& M, Inform& out) {
  for (int i=0; i<M.size1(); ++i) {
  for (int j=0; j<M.size2(); ++j) {
  *gmsg  << M(i,j) << " ";
  }
  *gmsg << endl;
  }
  }
*/

/**
 * Calculate the local number of particles evenly and adjust node 0
 * such that n is matched exactly.
 * @param n total number of particles
 * @return n / #cores
 * @param
 */

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;
}



/**
 * At the moment only write the header into the file dist.dat
 * PartBunch will then append (very ugly)
 * @param
 * @param
 * @param
 */
void Distribution::writeToFile() {
    /*
      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();
      }
      }
    */
}

/// Distribution can only be replaced by another distribution.
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) {

    /*
     * 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 != DistrTypeT::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);

    setFieldEmissionParameters();

    switch (distrTypeT_m) {

    case DistrTypeT::MATCHEDGAUSS:
        createMatchedGaussDistribution(numberOfLocalParticles, massIneV);
        break;
    case DistrTypeT::FROMFILE:
        createDistributionFromFile(numberOfParticles, massIneV);
        break;
    case DistrTypeT::GAUSS:
        createDistributionGauss(numberOfLocalParticles, massIneV);
        break;
    case DistrTypeT::BINOMIAL:
        createDistributionBinomial(numberOfLocalParticles, massIneV);
        break;
    case DistrTypeT::FLATTOP:
        createDistributionFlattop(numberOfLocalParticles, massIneV);
        break;
    case DistrTypeT::GUNGAUSSFLATTOPTH:
        createDistributionFlattop(numberOfLocalParticles, massIneV);
        break;
    case DistrTypeT::ASTRAFLATTOPTH:
        createDistributionFlattop(numberOfLocalParticles, massIneV);
        break;
    default:
        INFOMSG("Distribution unknown." << endl;);
        break;
    }

    if (emitting_m) {

        unsigned int numAdditionalRNsPerParticle = 0;
        if (emissionModel_m == EmissionModelT::ASTRA ||
            distrTypeT_m == DistrTypeT::ASTRAFLATTOPTH ||
            distrTypeT_m == DistrTypeT::GUNGAUSSFLATTOPTH) {

            numAdditionalRNsPerParticle = 2;
        } else if (emissionModel_m == EmissionModelT::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);

    if (Options::seed != -1)
        Options::seed = gsl_rng_uniform_int(randGen_m, gsl_rng_max(randGen_m));

    if (particlesPerDist_m.size() == 0) {
        particlesPerDist_m.push_back(tOrZDist_m.size());
    } else {
        particlesPerDist_m[0] = tOrZDist_m.size();
    }
}

void  Distribution::createPriPart(PartBunch *beam, BoundaryGeometry &bg) {

    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 = gsl_rng_uniform(randGen_m);
                            test_s *= f_max;
                            test_x = gsl_rng_uniform(randGen_m);
                            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;

                        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);
                        } else {
                            beam->R[lowMark + count] = bg.getCooridinate(count);
                            beam->P[lowMark + count] = betagamma * bg.getMomenta(count);
                        }
                        beam->Bin[lowMark + count] = 0;
                        beam->PType[lowMark + count] = ParticleType::REGULAR;
                        beam->TriID[lowMark + count] = 0;
                        beam->Q[lowMark + count] = beam->getChargePerParticle();
                        beam->Ef[lowMark + count] = Vector_t(0.0);
                        beam->Bf[lowMark + count] = Vector_t(0.0);
                        beam->dt[lowMark + count] = beam->getdT();
                        count ++;
                    }
                }
                pc++;
                if (pc == Ippl::getNodes())
                    pc = 0;
            }
            bg.clearCooridinateArray();
            bg.clearMomentaArray();
            beam->boundp();
        }
        *gmsg << *beam << endl;

    } else {// Normal procedure to create primary particles

        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());

        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) {
                        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] = ParticleType::REGULAR;
                        beam->TriID[lowMark + count] = 0;
                        beam->Q[lowMark + count] = beam->getChargePerParticle();
                        beam->Ef[lowMark + count] = Vector_t(0.0);
                        beam->Bf[lowMark + count] = Vector_t(0.0);
                        beam->dt[lowMark + count] = beam->getdT();
                        count++;

                    }

                }
                pc++;
                if (pc == Ippl::getNodes())
                    pc = 0;

            }

        }
        bg.clearCooridinateArray();
        beam->boundp();//fixme if bg.getN()==0?
    }
    *gmsg << *beam << endl;
}

void Distribution::doRestartOpalT(PartBunch &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;

    numParticles = lastParticle - firstParticle + 1;
    PAssert(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(PartBunch &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;

    numParticles = lastParticle - firstParticle + 1;
    PAssert(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()->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);

    double gamma = 1 + meanE / beam.getM() * 1.0e6;
    double beta = sqrt(1.0 - (1.0 / std::pow(gamma, 2.0)));

    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);
}

void Distribution::doRestartOpalE(EnvelopeBunch &beam, size_t Np, int restartStep,
                                  H5PartWrapper *dataSource) {
    IpplTimings::startTimer(beam.distrReload_m);
    int N = dataSource->getNumParticles();
    *gmsg << "total number of slices = " << N << endl;

    beam.distributeSlices(N);
    beam.createBunch();
    long long starti = beam.mySliceStartOffset();
    long long endi = beam.mySliceEndOffset();

    dataSource->readHeader();
    dataSource->readStep(beam, starti, endi);

    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;
    }

    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 = 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) {
    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;
        }
        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;
    }
    return tEmission_m;
}

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

    os << "* ************* 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.size() > 0)
            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);
            os << "* " << endl;
        } else
            os << "* Distribution is injected." << endl;
    }
    os << "* " << endl;
    os << "* **********************************************************************************" << endl;

    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.
     */

    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);
        }