Distribution.cpp 183 KB
Newer Older
gsell's avatar
gsell committed
1 2 3 4 5 6 7 8 9 10 11 12
// ------------------------------------------------------------------------
// $RCSfile: Distribution.cpp,v $
// ------------------------------------------------------------------------
// $Revision: 1.3.4.1 $
// ------------------------------------------------------------------------
// Copyright: see Copyright.readme
// ------------------------------------------------------------------------
//
// Class: Distribution
//   The class for the OPAL Distribution command.
//
// ------------------------------------------------------------------------
kraus's avatar
kraus committed
13 14 15

#include "Distribution/Distribution.h"

16 17 18 19 20 21
#include <cmath>
#include <cfloat>
#include <iomanip>
#include <iostream>
#include <string>
#include <vector>
22
#include <numeric>
23

24 25
#include "AbstractObjects/Expressions.h"
#include "Attributes/Attributes.h"
kraus's avatar
kraus committed
26
#include "Utilities/OpalOptions.h"
27 28 29 30 31 32
#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"
33
#include "Structure/Beam.h"
34
#include "Structure/BoundaryGeometry.h"
gsell's avatar
gsell committed
35 36 37
#include "Algorithms/PartBinsCyc.h"
#include "BasicActions/Option.h"
#include "Distribution/LaserProfile.h"
38 39 40 41

#include <gsl/gsl_cdf.h>
#include <gsl/gsl_randist.h>
#include <gsl/gsl_sf_erf.h>
42 43
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_blas.h>
gsell's avatar
gsell committed
44 45 46

extern Inform *gmsg;

kraus's avatar
kraus committed
47
#define DISTDBG1
adelmann's avatar
Cleanup  
adelmann committed
48
#define noDISTDBG2
49

gsell's avatar
gsell committed
50 51 52 53
//
// Class Distribution
// ------------------------------------------------------------------------

54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108
namespace AttributesT
{
    enum AttributesT {
                      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,
109
                      R,                          // the correlation matrix (a la transport)
110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148
                      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.
                      SIZE
gsell's avatar
gsell committed
149 150 151
    };
}

152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178
namespace LegacyAttributesT
{
    enum LegacyAttributesT {
    // DESCRIPTION OF THE DISTRIBUTION:
    DEBIN,
    SBIN,
    TEMISSION,
    SIGLASER,
    AG,
    SIGMAPT,
    TRANSVCUTOFF,
    CUTOFF,
    Z,
    T,
    PT,
    ALPHAX,
    ALPHAY,
    BETAX,
    BETAY,
    DX,
    DDX,
    DY,
    DDY,
    SIZE
};
}

gsell's avatar
gsell committed
179
Distribution::Distribution():
180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201
    Definition(AttributesT::SIZE + LegacyAttributesT::SIZE, "DISTRIBUTION",
               "The DISTRIBUTION statement defines data for the 6D particle distribution."),
    distrTypeT_m(DistrTypeT::NODIST),
    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),
    pTotThermal_m(0.0),
    cathodeWorkFunc_m(0.0),
    laserEnergy_m(0.0),
    cathodeFermiEnergy_m(0.0),
    cathodeTemp_m(0.0),
    emitEnergyUpperLimit_m(0.0),
202
    avrgpz_m(0.0),
203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224
    inputMoUnits_m(InputMomentumUnitsT::NONE),
    sigmaTRise_m(0.0),
    sigmaTFall_m(0.0),
    tPulseLengthFWHM_m(0.0),
    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),
225
    vVThermal_m(0.0) {
226 227 228 229 230

    SetAttributes();

    Distribution *defaultDistribution = clone("UNNAMED_Distribution");
    defaultDistribution->builtin = true;
gsell's avatar
gsell committed
231 232

    try {
233
        OpalData::getInstance()->define(defaultDistribution);
gsell's avatar
gsell committed
234
    } catch(...) {
235 236 237 238
        delete defaultDistribution;
    }

    SetFieldEmissionParameters();
gsell's avatar
gsell committed
239 240 241 242 243 244 245
}
/**
 *
 *
 * @param name
 * @param parent
 */
246
Distribution::Distribution(const std::string &name, Distribution *parent):
gsell's avatar
gsell committed
247
    Definition(name, parent),
248 249 250 251 252 253 254 255
    distT_m(parent->distT_m),
    distrTypeT_m(DistrTypeT::NODIST),
    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),
gsell's avatar
gsell committed
256
    tEmission_m(parent->tEmission_m),
257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283
    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),
    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),
284
    avrgpz_m(parent->avrgpz_m),
285 286 287 288 289 290 291 292 293 294 295 296 297
    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),
    distCorr_m(parent->distCorr_m),
    laserProfileFileName_m(parent->laserProfileFileName_m),
    laserImageName_m(parent->laserImageName_m),
    laserIntensityCut_m(parent->laserIntensityCut_m),
    laserProfile_m(NULL),
gsell's avatar
gsell committed
298 299 300 301 302 303 304 305 306 307 308 309
    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),
310 311 312 313 314 315 316
    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),
317
    cutoff_m(parent->cutoff_m){
gsell's avatar
gsell committed
318 319 320 321 322 323 324
}

Distribution::~Distribution() {

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

325 326 327
    if (energyBins_m != NULL) {
        delete energyBins_m;
        energyBins_m = NULL;
gsell's avatar
gsell committed
328 329
    }

330 331 332 333 334 335 336 337 338 339 340 341 342 343
    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;
    }
gsell's avatar
gsell committed
344 345 346 347

}

/**
348 349
 * At the moment only write the header into the file dist.dat
 * PartBunch will then append (very uggly)
350 351 352
 * @param
 * @param
 * @param
353
 */
354
void Distribution::WriteToFile() {
355
  /*
356
    if(Ippl::getNodes() == 1) {
357
        if(os_m.is_open()) {
358
            ;
359
        } else {
360
            *gmsg << " Write distribution to file data/dist.dat" << endl;
361
            std::string file("data/dist.dat");
362 363 364 365
            os_m.open(file.c_str());
            if(os_m.bad()) {
                *gmsg << "Unable to open output file " <<  file << endl;
            }
366
            os_m << "# x y ti px py pz "  << std::endl;
367 368 369
            os_m.close();
        }
    }
370
  */
371 372
}

373 374 375
/// Distribution can only be replaced by another distribution.
bool Distribution::canReplaceBy(Object *object) {
    return dynamic_cast<Distribution *>(object) != 0;
376 377
}

378 379 380
Distribution *Distribution::clone(const std::string &name) {
    return new Distribution(name, this);
}
381

382 383
void Distribution::execute() {
}
adelmann's avatar
adelmann committed
384

385 386
void Distribution::update() {
}
adelmann's avatar
adelmann committed
387

388
void Distribution::Create(size_t &numberOfParticles, double massIneV) {
adelmann's avatar
adelmann committed
389

390
    SetFieldEmissionParameters();
adelmann's avatar
adelmann committed
391

392
    switch (distrTypeT_m) {
adelmann's avatar
adelmann committed
393

394 395
    case DistrTypeT::FROMFILE:
        CreateDistributionFromFile(numberOfParticles, massIneV);
gsell's avatar
gsell committed
396
        break;
397 398
    case DistrTypeT::GAUSS:
        CreateDistributionGauss(numberOfParticles, massIneV);
gsell's avatar
gsell committed
399
        break;
400 401
    case DistrTypeT::BINOMIAL:
        CreateDistributionBinomial(numberOfParticles, massIneV);
gsell's avatar
gsell committed
402
        break;
403 404
    case DistrTypeT::FLATTOP:
        CreateDistributionFlattop(numberOfParticles, massIneV);
gsell's avatar
gsell committed
405
        break;
406 407
    case DistrTypeT::GUNGAUSSFLATTOPTH:
        CreateDistributionFlattop(numberOfParticles, massIneV);
gsell's avatar
gsell committed
408
        break;
409 410
    case DistrTypeT::ASTRAFLATTOPTH:
        CreateDistributionFlattop(numberOfParticles, massIneV);
gsell's avatar
gsell committed
411
        break;
412 413 414 415
    default:
        INFOMSG("Distribution unknown." << endl;);
        break;
    }
gsell's avatar
gsell committed
416

417
    // AAA Scale and shift coordinates according to distribution input.
418 419 420
    ScaleDistCoordinates();
    ShiftDistCoordinates(massIneV);
}
gsell's avatar
gsell committed
421

422
void  Distribution::CreatePriPart(PartBunch *beam, BoundaryGeometry &bg) {
gsell's avatar
gsell committed
423

424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452
    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;
gsell's avatar
gsell committed
453

454 455 456 457 458 459 460
                        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);
gsell's avatar
gsell committed
461
                        } else {
462 463
                            beam->R[lowMark + count] = bg.getCooridinate(count);
                            beam->P[lowMark + count] = betagamma * bg.getMomenta(count);
gsell's avatar
gsell committed
464
                        }
465 466 467 468 469 470 471 472 473
                        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 ++;
gsell's avatar
gsell committed
474 475
                    }
                }
476 477 478
                pc++;
                if(pc == Ippl::getNodes())
                    pc = 0;
gsell's avatar
gsell committed
479
            }
480 481 482
            bg.clearCooridinateArray();
            bg.clearMomentaArray();
            beam->boundp();
gsell's avatar
gsell committed
483
        }
484
        *gmsg << *beam << endl;
gsell's avatar
gsell committed
485

486
    } else {// Normal procedure to create primary particles
gsell's avatar
gsell committed
487

488 489 490 491 492
        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());
gsell's avatar
gsell committed
493

494 495 496 497
        if(Ippl::myNode() == 0)
            N_mean += N_extra;
        if(bg.getN() != 0) {
            for(size_t i = 0; i < bg.getN(); i++) {
gsell's avatar
gsell committed
498

499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515
                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++;
gsell's avatar
gsell committed
516 517

                    }
518

gsell's avatar
gsell committed
519
                }
520 521 522
                pc++;
                if(pc == Ippl::getNodes())
                    pc = 0;
523

524
            }
525

526 527 528 529 530 531
        }
        bg.clearCooridinateArray();
        beam->boundp();//fixme if bg.getN()==0?
    }
    *gmsg << *beam << endl;
}
532

533 534 535 536
void Distribution::DoRestartOpalT(PartBunch &beam, size_t Np, int restartStep) {
    h5_file_t *H5file;
    h5_int64_t rc;
    std::string fn;
537

538
    IpplTimings::startTimer(beam.distrReload_m);
539

540 541
    //        beam.setTEmission(Attributes::getReal(itsAttr[AttributesT::SIZE + LegacyAttributesT::TEMISSION]));
    fn = OpalData::getInstance()->getInputBasename() + std::string(".h5");
gsell's avatar
gsell committed
542 543 544 545

#ifdef PARALLEL_IO
    H5file = H5OpenFile(fn.c_str(), H5_O_RDONLY, Ippl::getComm());
#else
546
    H5file = H5OpenFile(fn.c_str(), H5_O_RDONLY, 0);
gsell's avatar
gsell committed
547 548
#endif

549
    if(H5file == (void*)H5_ERR) {
gsell's avatar
gsell committed
550 551 552 553 554
        ERRORMSG("could not open file '" << fn << "';  exiting!" << endl);
        exit(0);
    }

    if(restartStep == -1) {
555
        restartStep = H5GetNumSteps(H5file) - 1 ;
gsell's avatar
gsell committed
556 557 558 559 560 561 562 563 564 565 566 567 568
        OpalData::getInstance()->setRestartStep(restartStep);
    } else {
        if(restartStep != H5GetNumSteps(H5file) - 1 && !OpalData::getInstance()->hasRestartFile()) {
            ERRORMSG("can't append to the file '" << fn << "' exiting!" << endl);
            exit(0);
        }
    }

    rc = H5SetStep(H5file, restartStep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    int N = (int)H5PartGetNumParticles(H5file);

569 570 571 572 573 574 575 576 577
    int numberOfParticlesPerNode = (int) floor((double) N / Ippl::getNodes());
    long long starti = Ippl::myNode() * numberOfParticlesPerNode;
    long long endi = starti + numberOfParticlesPerNode - 1;

    // In case we miss some particles we add them at the end on the last core
    if(Ippl::myNode() == (Ippl::getNodes() - 1)) {
        if(Ippl::getNodes()*numberOfParticlesPerNode < N)
            endi += (N - (Ippl::getNodes() * numberOfParticlesPerNode));
    }
gsell's avatar
gsell committed
578 579 580 581 582

    rc = H5PartSetView(H5file, starti, endi);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    N = (int)H5PartGetNumParticles(H5file);
583
    assert(N >= 0);
gsell's avatar
gsell committed
584 585 586 587 588 589

    double actualT;
    rc = H5ReadStepAttribFloat64(H5file, "TIME", &actualT);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    beam.setT(actualT);
590

gsell's avatar
gsell committed
591 592 593 594 595 596
    double dPhiGlobal;
    rc = H5ReadFileAttribFloat64(H5file, "dPhiGlobal", &dPhiGlobal);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    OpalData::getInstance()->setGlobalPhaseShift(dPhiGlobal);

597 598 599 600 601 602 603 604 605 606 607
    h5_int64_t ltstep;
    rc = H5ReadStepAttribInt64(H5file, "LocalTrackStep", &ltstep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    beam.setLocalTrackStep((long long)ltstep);

    h5_int64_t gtstep;
    rc = H5ReadStepAttribInt64(H5file, "GlobalTrackStep", &gtstep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    beam.setGlobalTrackStep((long long)gtstep);
608

609
    std::unique_ptr<char[]> varray(new char[(N)*sizeof(double)]);
610
    h5_float64_t *farray = reinterpret_cast<h5_float64_t *>(varray.get());
611
    h5_int64_t *larray = reinterpret_cast<h5_int64_t *>(varray.get());
gsell's avatar
gsell committed
612

613 614
    beam.create(N);

gsell's avatar
gsell committed
615 616 617 618
    rc = H5PartReadDataFloat64(H5file, "x", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n) {
619 620
        beam.R[n](0) = farray[n];
        beam.Bin[n] = 0; // not initialized
gsell's avatar
gsell committed
621 622 623 624 625
    }
    rc = H5PartReadDataFloat64(H5file, "y", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
626
        beam.R[n](1) = farray[n];
gsell's avatar
gsell committed
627 628 629 630 631

    rc = H5PartReadDataFloat64(H5file, "z", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
632
        beam.R[n](2) = farray[n];
gsell's avatar
gsell committed
633 634 635 636 637

    rc = H5PartReadDataFloat64(H5file, "px", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
638
        beam.P[n](0) = farray[n];
gsell's avatar
gsell committed
639 640 641 642 643

    rc = H5PartReadDataFloat64(H5file, "py", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
644
        beam.P[n](1) = farray[n];
gsell's avatar
gsell committed
645

646
    rc = H5PartReadDataFloat64(H5file, "pz", farray);
gsell's avatar
gsell committed
647 648 649
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
650
        beam.P[n](2) = farray[n];
gsell's avatar
gsell committed
651

652
    rc = H5PartReadDataFloat64(H5file, "q", farray);
gsell's avatar
gsell committed
653 654 655
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
656
        beam.Q[n] = farray[n];
gsell's avatar
gsell committed
657 658 659 660 661 662 663 664 665 666 667

    rc = H5PartReadDataInt64(H5file, "lastsection", larray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.LastSection[n] = (short) larray[n];

    Ippl::Comm->barrier();
    rc = H5CloseFile(H5file);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
668 669 670

    beam.boundp();

gsell's avatar
gsell committed
671 672
    IpplTimings::stopTimer(beam.distrReload_m);

673 674 675 676
    *gmsg << "Total number of particles in the h5 file = " << N << " NPerBunch= " << beam.getTotalNum()
          << " Global step " << gtstep << " Local step " << ltstep << endl
          << " restart step= " << restartStep << " time of restart = " << actualT
          << " phishift= " << OpalData::getInstance()->getGlobalPhaseShift() << endl;
gsell's avatar
gsell committed
677 678
}

679
void Distribution::DoRestartOpalCycl(PartBunch &beam, size_t Np, int restartStep, const int specifiedNumBunch) {
adelmann's avatar
adelmann committed
680

681 682 683 684 685 686 687 688 689 690 691 692 693
    h5_int64_t rc;
    IpplTimings::startTimer(beam.distrReload_m);
    *gmsg << "---------------- Start reading hdf5 file----------------" << endl;
    h5_file_t *H5file;

    std::string fn = OpalData::getInstance()->getInputBasename() + std::string(".h5");

#ifdef PARALLEL_IO
    H5file = H5OpenFile(fn.c_str(), H5_O_RDONLY, Ippl::getComm());
#else
    H5file = H5OpenFile(fn.c_str(), H5_O_RDONLY, 0);
#endif

694
    if(H5file == (void*)H5_ERR) {
695 696 697 698 699 700 701 702 703 704 705 706 707 708
        ERRORMSG("File open failed:  exiting!" << endl);
        exit(0);
    }

    if(restartStep == -1) {
        restartStep = H5GetNumSteps(H5file) - 1;
        OpalData::getInstance()->setRestartStep(restartStep);
    } else {
        if(restartStep != H5GetNumSteps(H5file) - 1 && !OpalData::getInstance()->hasRestartFile()) {
            ERRORMSG("can't append to the file '" << fn << "' exiting!" << endl);
            exit(0);
        }
    }

kraus's avatar
kraus committed
709
    *gmsg << "Restart from hdf5 format file " << fn
710
          << ", read phase space data of DumpStep " << (int)restartStep << endl;
711 712 713 714 715 716 717 718 719 720 721 722 723 724 725

    rc = H5SetStep(H5file, restartStep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    const int globalN = (int)H5PartGetNumParticles(H5file);

    *gmsg << "total number of particles = " << globalN << endl;

    int numberOfParticlesPerNode = (int) floor((double) globalN / Ippl::getNodes());
    long long starti = Ippl::myNode() * numberOfParticlesPerNode;
    long long endi = 0;

    if(Ippl::myNode() == Ippl::getNodes() - 1)
        endi = -1;
    else
726
        endi = starti + numberOfParticlesPerNode - 1;
kraus's avatar
kraus committed
727

728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750
    rc = H5PartSetView(H5file, starti, endi);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    const int localN = (int)H5PartGetNumParticles(H5file);
    assert(localN >= 0);

    h5_int64_t ltstep;
    rc = H5ReadStepAttribInt64(H5file, "LocalTrackStep", &ltstep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    beam.setLocalTrackStep((long long)ltstep);

    h5_int64_t gtstep;
    rc = H5ReadStepAttribInt64(H5file, "GlobalTrackStep", &gtstep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    beam.setGlobalTrackStep((long long)gtstep);

    char opalFlavour[128];
    rc = H5ReadStepAttribString(H5file, "OPAL_flavour", opalFlavour);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

751 752 753 754
    rc = H5ReadStepAttribFloat64(H5file, "REFPR",&referencePr_m);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

755 756 757 758 759
    referencePt_m = 0.0;
    rc = H5ReadStepAttribFloat64(H5file, "REFPT",&referencePt_m);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

760 761 762 763 764
    referencePz_m = 0.0;
    rc = H5ReadStepAttribFloat64(H5file, "REFPZ",&referencePz_m);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

765 766 767 768 769 770 771 772
    rc = H5ReadStepAttribFloat64(H5file, "REFR",&referenceR_m);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

    rc = H5ReadStepAttribFloat64(H5file, "REFTHETA",&referenceTheta_m);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

773 774 775 776 777
    referenceZ_m = 0.0;
    rc = H5ReadStepAttribFloat64(H5file, "REFZ",&referenceZ_m);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

778 779 780 781 782
    double meanE;
    rc = H5ReadStepAttribFloat64(H5file, "ENERGY", &meanE);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

adelmann's avatar
adelmann committed
783 784 785 786 787 788 789
    double pathLength;;
    rc = H5ReadStepAttribFloat64(H5file, "SPOS", &pathLength);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

    beam.setLPath(pathLength);

790 791 792
    *gmsg << "* Restart Energy = " << meanE << " (MeV), Path lenght = " << pathLength << " (m)" <<  endl;

    // beam.getM() in eV, meanE in MeV had to change 1e3 to 1e6 -DW
793 794
    double ga = 1 + meanE / beam.getM() * 1.0e6;
    double be = sqrt(1.0 - (1.0 / (ga * ga)));
795

796
    bega_m = be * ga;
797

798
    *gmsg << "* Gamma = " << ga << ", Beta = " << be << endl;
799

800
    std::unique_ptr<char[]> varray(new char[(localN)*sizeof(double)]);
801

802
    double *farray = reinterpret_cast<double *>(varray.get());
803

804 805 806 807 808
    h5_int64_t *larray = reinterpret_cast<h5_int64_t *>(varray.get());

    beam.create(localN);

    if(strcmp(opalFlavour, "opal-t") == 0) {
809

810 811 812 813
        *gmsg << "Restart from hdf5 file generated by OPAL-t" << endl;

        // force the initial time to zero
        beam.setT(0.0);
adelmann's avatar
adelmann committed
814
	beam.setLocalTrackStep((long long) 0 );
815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857
        rc = H5PartReadDataFloat64(H5file, "x", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.R[n](0) = -farray[n];

        rc = H5PartReadDataFloat64(H5file, "y", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.R[n](2) = farray[n];

        rc = H5PartReadDataFloat64(H5file, "z", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.R[n](1) = farray[n];

        rc = H5PartReadDataFloat64(H5file, "px", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.P[n](0) = -farray[n];

        rc = H5PartReadDataFloat64(H5file, "py", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.P[n](2) = farray[n];

        rc = H5PartReadDataFloat64(H5file, "pz", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.P[n](1) = farray[n];

        rc = H5PartReadDataInt64(H5file, "id", larray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.ID[n] = larray[n];

    } else {
858

859 860
        *gmsg << "Restart from hdf5 file generated by OPAL-cycl" << endl;

861 862 863 864 865 866 867 868 869 870
        rc = H5ReadStepAttribFloat64(H5file, "AZIMUTH", &phi_m);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

        rc = H5ReadStepAttribFloat64(H5file, "ELEVATION", &psi_m);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

        h5_int64_t localDump = 0;
        previousH5Local_m = false;
871

872 873 874 875 876 877 878 879 880 881 882
        rc = H5ReadStepAttribInt64(H5file, "LOCAL", &localDump);
        if(rc != H5_SUCCESS) {

            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

            throw OpalException("Error during restart for Cyclotron Tracker:",
                                "You are trying to restart from a legacy file that doesn't contain\
  information on local/global frame. We are working on legacy support, but for now you have to use\
  OPAL 1.3.0!");

        } else {
883 884

            if (localDump == 1) previousH5Local_m = true;
885 886
        }

887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009
        double actualT;
        rc = H5ReadStepAttribFloat64(H5file, "TIME", &actualT);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        beam.setT(actualT);

        h5_int64_t SteptoLastInj;
        rc = H5ReadStepAttribInt64(H5file, "SteptoLastInj", &SteptoLastInj);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        beam.setSteptoLastInj((int)SteptoLastInj);
        *gmsg << "Tracking Step since last bunch injection is " << SteptoLastInj << endl;

        h5_int64_t numBunch;
        rc = H5ReadStepAttribInt64(H5file, "NumBunch", &numBunch);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        beam.setNumBunch((int)numBunch);
        *gmsg << numBunch << " Bunches(bins) exist in this file" << endl;

        rc = H5PartReadDataFloat64(H5file, "x", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.R[n](0) = farray[n];

        rc = H5PartReadDataFloat64(H5file, "y", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.R[n](1) = farray[n];

        rc = H5PartReadDataFloat64(H5file, "z", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.R[n](2) = farray[n];

        rc = H5PartReadDataFloat64(H5file, "px", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.P[n](0) = farray[n];

        rc = H5PartReadDataFloat64(H5file, "py", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.P[n](1) = farray[n];

        rc = H5PartReadDataFloat64(H5file, "pz", farray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.P[n](2) = farray[n];

        rc = H5PartReadDataInt64(H5file, "id", larray);
        if(rc != H5_SUCCESS)
            ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
        for(unsigned long int n = 0; n < (unsigned int) localN; ++n)
            beam.ID[n] = larray[n];

        // only for multi-bunch mode
        if(specifiedNumBunch > 1) {
            // the allowed maximal bin number is set to 1000
            beam.setPBins(new PartBinsCyc(1000, numBunch));
        }
    }

    Ippl::Comm->barrier();
    rc = H5CloseFile(H5file);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    beam.boundp();
    beam.Q = beam.getChargePerParticle();

    if(strcmp(opalFlavour, "opal-t") == 0) {
        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);
        *gmsg << "Rmean = " << meanR << "[m], Pmean=" << meanP << endl;

        for(unsigned int i = 0; i < newLocalN; ++i) {
            beam.R[i] -= meanR;
            beam.P[i] -= meanP;
        }
    }

    *gmsg << "----------------Finish reading hdf5 file----------------" << endl;
    IpplTimings::stopTimer(beam.distrReload_m);
}

void Distribution::DoRestartOpalE(EnvelopeBunch &beam, size_t Np, int restartStep) {
    h5_file_t *H5file;
    h5_int64_t rc;
    std::string fn;

    IpplTimings::startTimer(beam.distrReload_m);

    if(OpalData::getInstance()->hasRestartFile()) {
        fn = OpalData::getInstance()->getRestartFileName();
        *gmsg << "Restart from a specified file:" << fn << endl;

    } else {
        fn = OpalData::getInstance()->getInputBasename() + std::string(".h5");
    }

#ifdef PARALLEL_IO
    H5file = H5OpenFile(fn.c_str(), H5_O_RDONLY, Ippl::getComm());
#else
    H5file = H5PartOpenFile(fn.c_str(), H5_O_RDONLY, 0);
#endif

1010
    if(H5file == (void*)H5_ERR) {
1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244
        ERRORMSG("could not open file '" << fn << "';  exiting!" << endl);
        exit(0);
    }

    if(restartStep == -1) {
        restartStep = H5GetNumSteps(H5file) - 1;
        OpalData::getInstance()->setRestartStep(restartStep);
    } else {
        if(restartStep != H5GetNumSteps(H5file) - 1 && !OpalData::getInstance()->hasRestartFile()) {
            ERRORMSG("can't append to the file '" << fn << "' exiting!" << endl);
            exit(0);
        }
    }

    rc = H5SetStep(H5file, restartStep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    int N = (int)H5PartGetNumParticles(H5file);

    h5_int64_t totalSteps = H5GetNumSteps(H5file);
    *gmsg << "total number of slices = " << N << " total steps " << totalSteps << endl;

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

    rc = H5PartSetView(H5file, starti, endi);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    N = (int)H5PartGetNumParticles(H5file);
    assert(N >= 0 && (unsigned int) N != beam.numMySlices());

    double actualT;
    rc = H5ReadStepAttribFloat64(H5file, "TIME", &actualT);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);

    beam.setT(actualT);
    double dPhiGlobal;
    rc = H5ReadFileAttribFloat64(H5file, "dPhiGlobal", &dPhiGlobal);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    OpalData::getInstance()->setGlobalPhaseShift(dPhiGlobal);

    h5_int64_t ltstep;
    rc = H5ReadStepAttribInt64(H5file, "LocalTrackStep", &ltstep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    beam.setLocalTrackStep((long long)ltstep);

    h5_int64_t gtstep;
    rc = H5ReadStepAttribInt64(H5file, "GlobalTrackStep", &gtstep);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    beam.setGlobalTrackStep((long long)gtstep);

    std::unique_ptr<char[]> varray(new char[(N)*sizeof(double)]);
    double *farray = reinterpret_cast<double *>(varray.get());
    h5_int64_t *larray = reinterpret_cast<h5_int64_t *>(varray.get());

    rc = H5PartReadDataFloat64(H5file, "x", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n) {
        beam.setX(n, farray[n]);
    }
    rc = H5PartReadDataFloat64(H5file, "y", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setY(n, farray[n]);

    rc = H5PartReadDataFloat64(H5file, "z", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setZ(n, farray[n]);

    rc = H5PartReadDataFloat64(H5file, "px", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setPx(n, farray[n]);

    rc = H5PartReadDataFloat64(H5file, "py", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setPy(n, farray[n]);

    rc = H5PartReadDataFloat64(H5file, "beta", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setBeta(n, farray[n]);

    rc = H5PartReadDataFloat64(H5file, "X0", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setX0(n, farray[n]);

    rc = H5PartReadDataFloat64(H5file, "pX0", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setPx0(n, farray[n]);

    rc = H5PartReadDataFloat64(H5file, "Y0", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setY0(n, farray[n]);

    rc = H5PartReadDataFloat64(H5file, "pY0", farray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.setPy0(n, farray[n]);

    rc = H5PartReadDataInt64(H5file, "lastsection", larray);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    for(unsigned long int n = 0; n < (unsigned int) N; ++n)
        beam.LastSection[n] = (short) larray[n];

    Ippl::Comm->barrier();
    rc = H5CloseFile(H5file);
    if(rc != H5_SUCCESS)
        ERRORMSG("H5 rc= " << rc << " in " << __FILE__ << " @ line " << __LINE__ << endl);
    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]);
    cutoff_m = Attributes::getReal(itsAttr[AttributesT::SIZE + LegacyAttributesT::CUTOFF]);
    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) {
        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;
}

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 {

    os << "********************** DISTRIBUTION **********************" << endl;
    os << endl;
    if (OpalData::getInstance()->inRestartRun()) {
adelmann's avatar
adelmann committed
1245
        os << "* In restart. Distribution read in from .h5 file." << endl;
1246 1247
    } else {
        if (addedDistributions_m.size() > 0)
adelmann's avatar
adelmann committed
1248
            os << "* Main Distribution" << endl
1249 1250 1251 1252 1253 1254 1255 1256 1257 1258
            << "-----------------" << 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;
adelmann's avatar
adelmann committed
1259 1260
            os << "* Added Distribution #" << distCount << endl;
            os << "* ----------------------" << endl;
1261 1262 1263 1264 1265 1266
            addedDistributions_m.at(distIndex)->PrintDist(os, particlesPerDist_m.at(distCount));
            distCount++;
        }

        os << endl;
        if (numberOfEnergyBins_m > 0) {
adelmann's avatar
adelmann committed
1267
            os << "* Number of energy bins    = " << numberOfEnergyBins_m << endl;
1268

adelmann's avatar
adelmann committed
1269 1270
	    //            if (numberOfEnergyBins_m > 1)
            //    PrintEnergyBins(os);
1271 1272 1273
        }

        if (emitting_m) {
adelmann's avatar
adelmann committed
1274 1275 1276 1277
            os << "* Distribution is emitted. " << endl;
            os << "* Emission time            = " << tEmission_m << " [sec]" << endl;
	    os << "* Time per bin             = " << tEmission_m/numberOfEnergyBins_m << " [sec]" << endl;
            os << "* Bin delta t              = " << tBin_m << " [sec]" << endl;
1278 1279