ParallelCyclotronTracker.cpp 151 KB
Newer Older
gsell's avatar
gsell committed
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
// ------------------------------------------------------------------------
// $RCSfile: ParallelCyclotronTracker.cpp,v $
// ------------------------------------------------------------------------
// $Revision: 1.1 $initialLocalNum_m
// ------------------------------------------------------------------------
// Copyright: see Copyright.readme
// ------------------------------------------------------------------------
//
// Class: ParallelCyclotronTracker
//   The class for tracking particles with 3D space charge in Cyclotrons and FFAG's
//
// ------------------------------------------------------------------------
//
// $Date: 2007/10/17 04:00:08 $
// $Author: adelmann, yang $
//
// ------------------------------------------------------------------------
#include <cfloat>
#include <iostream>
#include <fstream>
#include <vector>
22
#include "AbstractObjects/OpalData.h"
gsell's avatar
gsell committed
23 24 25 26 27
#include "Algorithms/ParallelCyclotronTracker.h"

#include "AbsBeamline/Collimator.h"
#include "AbsBeamline/Corrector.h"
#include "AbsBeamline/Cyclotron.h"
adelmann's avatar
adelmann committed
28
#include "AbsBeamline/Degrader.h"
gsell's avatar
gsell committed
29 30 31 32 33 34 35 36 37 38 39 40
#include "AbsBeamline/Diagnostic.h"
#include "AbsBeamline/Drift.h"
#include "AbsBeamline/ElementBase.h"
#include "AbsBeamline/Lambertson.h"
#include "AbsBeamline/Marker.h"
#include "AbsBeamline/Monitor.h"
#include "AbsBeamline/Multipole.h"
#include "AbsBeamline/Probe.h"
#include "AbsBeamline/RBend.h"
#include "AbsBeamline/RFCavity.h"
#include "AbsBeamline/RFQuadrupole.h"
#include "AbsBeamline/SBend.h"
41
#include "AbsBeamline/SBend3D.h"
gsell's avatar
gsell committed
42 43 44 45 46
#include "AbsBeamline/Separator.h"
#include "AbsBeamline/Septum.h"
#include "AbsBeamline/Solenoid.h"
#include "AbsBeamline/CyclotronValley.h"
#include "AbsBeamline/Stripper.h"
47
#include "Elements/OpalRing.h"
gsell's avatar
gsell committed
48 49 50

#include "BeamlineGeometry/Euclid3D.h"
#include "BeamlineGeometry/PlanarArcGeometry.h"
Jianjun Yang's avatar
Jianjun Yang committed
51
#include "BeamlineGeometry/RBendGeometry.h"
gsell's avatar
gsell committed
52 53 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
#include "Beamlines/Beamline.h"

#include "Fields/BMultipoleField.h"
#include "FixedAlgebra/FTps.h"
#include "FixedAlgebra/FTpsMath.h"
#include "FixedAlgebra/FVps.h"

#include "Physics/Physics.h"

#include "Utilities/NumToStr.h"
#include "Utilities/OpalException.h"


#include "Ctunes.h"
#include "Ctunes.cc"
#include <cassert>


#include <hdf5.h>
#include "H5hut.h"

class Beamline;
class PartData;
using Physics::c;
using Physics::m_p; // GeV
using Physics::PMASS;
using Physics::PCHARGE;
using Physics::pi;
using Physics::q_e;

const double c_mmtns = c * 1.0e-6; // m/s --> mm/ns
const double mass_coeff = 1.0e18 * q_e / c / c; // from GeV/c^2 to basic unit: GV*C*s^2/m^2

#define PSdim 6

extern Inform *gmsg;

// typedef FVector<double, PSdim> Vector;

/**
 * Constructor ParallelCyclotronTracker
 *
 * @param beamline
 * @param reference
 * @param revBeam
 * @param revTrack
 */
ParallelCyclotronTracker::ParallelCyclotronTracker(const Beamline &beamline,
        const PartData &reference,
        bool revBeam, bool revTrack):
    Tracker(beamline, reference, revBeam, revTrack),
    sphys(NULL),
104
    eta_m(0.01),
gsell's avatar
gsell committed
105 106
    myNode_m(Ippl::myNode()),
    initialLocalNum_m(0),
107 108
    initialTotalNum_m(0),
    opalRing_m(NULL) {
gsell's avatar
gsell committed
109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133
    itsBeamline = dynamic_cast<Beamline *>(beamline.clone());
}

/**
 * Constructor ParallelCyclotronTracker
 *
 * @param beamline
 * @param bunch
 * @param ds
 * @param reference
 * @param revBeam
 * @param revTrack
 * @param maxSTEPS
 * @param timeIntegrator
 */
ParallelCyclotronTracker::ParallelCyclotronTracker(const Beamline &beamline,
                                                   PartBunch &bunch,
                                                   DataSink &ds,
                                                   const PartData &reference,
                                                   bool revBeam, bool revTrack,
                                                   int maxSTEPS, int timeIntegrator):
    Tracker(beamline, reference, revBeam, revTrack),
    sphys(NULL),
    maxSteps_m(maxSTEPS),
    timeIntegrator_m(timeIntegrator),
134
    eta_m(0.01),
gsell's avatar
gsell committed
135 136
    myNode_m(Ippl::myNode()),
    initialLocalNum_m(bunch.getLocalNum()),
137 138
    initialTotalNum_m(bunch.getTotalNum()),
    opalRing_m(NULL) {
gsell's avatar
gsell committed
139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177
    itsBeamline = dynamic_cast<Beamline *>(beamline.clone());
    itsBunch = &bunch;
    itsDataSink = &ds;
    //  scaleFactor_m = itsBunch->getdT() * c;
    scaleFactor_m = 1;
    multiBunchMode_m = 0;

    IntegrationTimer_m = IpplTimings::getTimer("Integration");
    TransformTimer_m   = IpplTimings::getTimer("Frametransform");
    DumpTimer_m        = IpplTimings::getTimer("Dump");
    BinRepartTimer_m   = IpplTimings::getTimer("Binaryrepart");
}

/**
 * Destructor ParallelCyclotronTracker
 *
 */
ParallelCyclotronTracker::~ParallelCyclotronTracker() {
    for(list<Component *>::iterator compindex = myElements.begin(); compindex != myElements.end(); compindex++) {
        delete(*compindex);
    }
    for(beamline_list::iterator fdindex = FieldDimensions.begin(); fdindex != FieldDimensions.end(); fdindex++) {
        delete(*fdindex);
    }
    delete itsBeamline;
}

/**
 *
 *
 * @param fn Base file name
 */
void ParallelCyclotronTracker::openFiles(string SfileName) {

    string  SfileName2 = SfileName + string("-Angle0.dat");

    outfTheta0_m.precision(8);
    outfTheta0_m.setf(ios::scientific, ios::floatfield);
    outfTheta0_m.open(SfileName2.c_str());
Jianjun Yang's avatar
Jianjun Yang committed
178
    outfTheta0_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma" << endl;
gsell's avatar
gsell committed
179 180 181 182 183

    SfileName2 = SfileName + string("-Angle1.dat");
    outfTheta1_m.precision(8);
    outfTheta1_m.setf(ios::scientific, ios::floatfield);
    outfTheta1_m.open(SfileName2.c_str());
Jianjun Yang's avatar
Jianjun Yang committed
184
    outfTheta1_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma"  << endl;
gsell's avatar
gsell committed
185 186 187 188 189

    SfileName2 = SfileName + string("-Angle2.dat");
    outfTheta2_m.precision(8);
    outfTheta2_m.setf(ios::scientific, ios::floatfield);
    outfTheta2_m.open(SfileName2.c_str());
Jianjun Yang's avatar
Jianjun Yang committed
190
    outfTheta2_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma"  << endl;
gsell's avatar
gsell committed
191 192 193 194 195 196 197 198 199

    // for single Particle Mode, output after each turn, to define matched initial phase ellipse.

    SfileName2 = SfileName + string("-afterEachTurn.dat");

    outfThetaEachTurn_m.precision(8);
    outfThetaEachTurn_m.setf(ios::scientific, ios::floatfield);

    outfThetaEachTurn_m.open(SfileName2.c_str());
Jianjun Yang's avatar
Jianjun Yang committed
200
    outfTheta2_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma"  << endl;
gsell's avatar
gsell committed
201 202 203 204 205 206 207 208 209 210 211 212 213 214 215
}

/**
 * Close all files related to
 * special output in the Cyclotron
 * mode.
 */
void ParallelCyclotronTracker::closeFiles() {

    outfTheta0_m.close();
    outfTheta1_m.close();
    outfTheta2_m.close();
    outfThetaEachTurn_m.close();
}

216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243
/** 
 *
 * @param ring
 */
void ParallelCyclotronTracker::visitOpalRing(const OpalRing &ring) {
    *gmsg << "Adding OpalRing" << endl;
    if (opalRing_m != NULL) {
        delete opalRing_m;
    }
    opalRing_m = dynamic_cast<OpalRing*>(ring.clone());
    myElements.push_back(opalRing_m);
    opalRing_m->initialise(itsBunch);

    referenceR = opalRing_m->getBeamRInit();
    referencePr = opalRing_m->getBeamPRInit();
    referenceTheta = opalRing_m->getBeamPhiInit();
    if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
        throw OpalException("Error in ParallelCyclotronTracker::visitOpalRing",
                            "PHIINIT is out of [-180, 180)!");
    }
    referencePz = 0.0;
    referencePtot =  itsReference.getGamma() * itsReference.getBeta();
    referencePt = sqrt(referencePtot * referencePtot
                     - referencePr * referencePr);
    if(referencePtot < 0.0)
        referencePt *= -1.0;
    sinRefTheta_m = sin(referenceTheta / 180.0 * pi);
    cosRefTheta_m = cos(referenceTheta / 180.0 * pi);
gsell's avatar
gsell committed
244

245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263
    double BcParameter[8];
    for(int i = 0; i < 8; i++) BcParameter[i] = 0.0;
    buildupFieldList(BcParameter, "OPALRING", opalRing_m);

    // Finally print some diagnostic
    *gmsg << "* Initial beam radius = " << referenceR << " [mm] " << endl;
    *gmsg << "* Initial gamma = " << itsReference.getGamma() << endl;
    *gmsg << "* Initial beta = " << itsReference.getBeta() << endl;
    *gmsg << "* Total reference momentum   = " << referencePtot * 1000.0
          << " [MCU]" << endl;
    *gmsg << "* Reference azimuthal momentum  = " << referencePt * 1000.0
          << " [MCU]" << endl;
    *gmsg << "* Reference radial momentum     = " << referencePr * 1000.0
          << " [MCU]" << endl;
    *gmsg << "* " << opalRing_m->getSymmetry() << " fold field symmetry "
          << endl;
    *gmsg << "* Harmonic number h= " << opalRing_m->getHarmonicNumber() << " "
          << endl;
}
gsell's avatar
gsell committed
264 265 266 267 268 269 270 271 272 273

/**
 *
 *
 * @param cycl
 */
void ParallelCyclotronTracker::visitCyclotron(const Cyclotron &cycl) {

    *gmsg << "* --------- Cyclotron ------------------------------" << endl;

274 275
    Cyclotron *elptr = dynamic_cast<Cyclotron *>(cycl.clone());
    myElements.push_back(elptr);
276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292
    referencePz = 0.0;
    
    if(!OpalData::getInstance()->inRestartRun()) {
      // get values from cyclotron command
      referenceR     = elptr->getRinit();
      referencePr    = elptr->getPRinit();
      referenceTheta = elptr->getPHIinit();
      //msg << "PRINIT= " << pri << " [CU]" << endl;
      
      if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
        throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron", "PHIINIT is out of [-180, 180)!");
      }
      referencePtot =  itsReference.getGamma() * itsReference.getBeta();
    } 
    else {
      // in case of a restart the values from the h5 file are already within this class
      if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
gsell's avatar
gsell committed
293
        throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron", "PHIINIT is out of [-180, 180)!");
294 295
      }
      referencePtot =  bega;
gsell's avatar
gsell committed
296
    }
297
    
gsell's avatar
gsell committed
298 299 300
    referencePt = sqrt(referencePtot * referencePtot - referencePr * referencePr);
    if(referencePtot < 0.0) referencePt *= -1.0;

301 302 303 304 305 306
    sinRefTheta_m = sin(referenceTheta / 180.0 * pi);
    cosRefTheta_m = cos(referenceTheta / 180.0 * pi);      

    *gmsg << "* RINIT= " << referenceR  << " [mm]" << endl;

    *gmsg << "* PHIINIT= " << referenceTheta << " [deg]" << endl;
gsell's avatar
gsell committed
307 308 309 310 311 312 313 314 315 316 317 318 319 320

    *gmsg << "* Initial gamma = " << itsReference.getGamma() << endl;

    *gmsg << "* Initial beta = " << itsReference.getBeta() << endl;

    *gmsg << "* Total reference momentum   = " << referencePtot * 1000.0 << " [MCU]" << endl;

    *gmsg << "* Reference azimuthal momentum  = " << referencePt * 1000.0 << " [MCU]" << endl;

    *gmsg << "* Reference radial momentum     = " << referencePr * 1000.0 << " [MCU]" << endl;

    double sym = elptr->getSymmetry();
    *gmsg << "* " << sym << " fold field symmerty " << endl;

321 322 323
    // ckr: this just returned the default value as defined in Component.h
    // double rff = elptr->getRfFrequ();
    // *gmsg << "* Rf frequency= " << rff << " [MHz]" << endl;
gsell's avatar
gsell committed
324 325 326 327 328 329

    string fmfn = elptr->getFieldMapFN();
    *gmsg << "* Field map file name= " << fmfn << " " << endl;

    string type = elptr->getType();
    *gmsg << "* Type of cyclotron= " << type << " " << endl;
330 331 332 333 334 335 336 337
    
    double rmin = elptr->getMinR();
    double rmax = elptr->getMaxR();
    *gmsg << "* Radial aperture= " << rmin << " ... " << rmax<<" [mm] "<< endl;

    double zmin = elptr->getMinZ();
    double zmax = elptr->getMaxZ();
    *gmsg << "* Vertical aperture= " << zmin << " ... " << zmax<<" [mm]"<< endl;
gsell's avatar
gsell committed
338

339
    bool Sflag = elptr->getSuperpose();
340 341 342 343 344
    string flagsuperposed;
    if (Sflag)
      flagsuperposed="yes";
    else
      flagsuperposed="no";
adelmann's avatar
adelmann committed
345
    *gmsg << "* Electric field map are superposed ?  " << flagsuperposed << " " << endl;
346 347


gsell's avatar
gsell committed
348 349 350
    double h = elptr->getCyclHarm();
    *gmsg << "* Harmonic number h= " << h << " " << endl;

adelmann's avatar
adelmann committed
351 352 353
    if (elptr->getSuperpose())
        *gmsg << "* Fields are superimposed " << endl;

gsell's avatar
gsell committed
354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382
    /**
     * To ease the initialise() function, set a integral parameter fieldflag internally.
     * Its value is  by the option "TYPE" of the element  "CYCLOTRON"
     * fieldflag = 1, readin PSI format measured field file (default)
     * fieldflag = 2, readin carbon cyclotron field file created by Jianjun Yang, TYPE=CARBONCYCL
     * fieldflag = 3, readin ANSYS format file for CYCIAE-100 created by Jianjun Yang, TYPE=CYCIAE
     * fieldflag = 4, readin AVFEQ format file for Riken cyclotrons
     * fieldflag = 5, readin FFAG format file for MSU/FNAL FFAG
     * fieldflag = 6, readin both median plane B field map and 3D E field map of RF cavity for compact cyclotron
     */
    int  fieldflag;
    if(type == string("CARBONCYCL")) {
        fieldflag = 2;
    } else if(type == string("CYCIAE")) {
        fieldflag = 3;
    } else if(type == string("AVFEQ")) {
        fieldflag = 4;
    } else if(type == string("FFAG")) {
        fieldflag = 5;
    } else if(type == string("BANDRF")) {
        fieldflag = 6;
    } else
        fieldflag = 1;

    // read field map on the  middle plane of cyclotron.
    // currently scalefactor is set to 1.0
    elptr->initialise(itsBunch, fieldflag, 1.0);

    double BcParameter[8];
adelmann's avatar
adelmann committed
383 384
    for(int i = 0; i < 8; i++) 
      BcParameter[i] = 0.0;
gsell's avatar
gsell committed
385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408
    string ElementType = "CYCLOTRON";
    BcParameter[0] = elptr->getRmin();
    BcParameter[1] = elptr->getRmax();

    // store inner radius and outer radius of cyclotron field map in the list
    buildupFieldList(BcParameter, ElementType, elptr);

}

/**
 * Not implemented and most probable never used
 *
 */
void ParallelCyclotronTracker::visitBeamBeam(const BeamBeam &) {
    *gmsg << "In BeamBeam tracker is missing " << endl;
}

/**
 *
 *
 * @param coll
 */
void ParallelCyclotronTracker::visitCollimator(const Collimator &coll) {

409
    *gmsg << "* --------- Collimator -----------------------------" << endl;
gsell's avatar
gsell committed
410

411 412
    Collimator* elptr = dynamic_cast<Collimator *>(coll.clone());
    myElements.push_back(elptr);
gsell's avatar
gsell committed
413

414 415
    double xstart = elptr->getXStart();
    *gmsg << "Xstart= " << xstart << " [mm]" << endl;
gsell's avatar
gsell committed
416

417 418
    double xend = elptr->getXEnd();
    *gmsg << "Xend= " << xend << " [mm]" << endl;
gsell's avatar
gsell committed
419

420 421
    double ystart = elptr->getYStart();
    *gmsg << "Ystart= " << ystart << " [mm]" << endl;
gsell's avatar
gsell committed
422

423 424
    double yend = elptr->getYEnd();
    *gmsg << "Yend= " <<yend << " [mm]" << endl;
gsell's avatar
gsell committed
425

426 427 428 429 430 431
    double zstart = elptr->getZStart();
    *gmsg << "Zstart= " << zstart << " [mm]" << endl;

    double zend = elptr->getZEnd();
    *gmsg << "Zend= " <<zend << " [mm]" << endl;

432
    double width = elptr->getWidth();
433
    *gmsg << "Width= " << width << " [mm]" << endl;
gsell's avatar
gsell committed
434 435 436 437 438 439 440

    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "CCOLLIMATOR";
441 442 443 444
    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
gsell's avatar
gsell committed
445 446 447 448 449 450 451 452 453 454 455 456 457 458
    BcParameter[4] = width ;
    buildupFieldList(BcParameter, ElementType, elptr);
}

/**
 *
 *
 * @param corr
 */
void ParallelCyclotronTracker::visitCorrector(const Corrector &corr) {
    *gmsg << "In Corrector; L= " << corr.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Corrector *>(corr.clone()));
}

adelmann's avatar
adelmann committed
459 460 461 462 463 464 465 466 467 468 469 470
/**
 *
 *
 * @param degrader
 */
void ParallelCyclotronTracker::visitDegrader(const Degrader &deg) {
    *gmsg << "In Degrader; L= " << deg.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Degrader *>(deg.clone()));

}


gsell's avatar
gsell committed
471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522
/**
 *
 *
 * @param diag
 */
void ParallelCyclotronTracker::visitDiagnostic(const Diagnostic &diag) {
    *gmsg << "In Diagnostic; L= " << diag.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Diagnostic *>(diag.clone()));
}

/**
 *
 *
 * @param drift
 */
void ParallelCyclotronTracker::visitDrift(const Drift &drift) {
    *gmsg << "In drift L= " << drift.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Drift *>(drift.clone()));
}

/**
 *
 *
 * @param lamb
 */
void ParallelCyclotronTracker::visitLambertson(const Lambertson &lamb) {
    *gmsg << "In Lambertson; L= " << lamb.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Lambertson *>(lamb.clone()));
}

/**
 *
 *
 * @param marker
 */
void ParallelCyclotronTracker::visitMarker(const Marker &marker) {
    //   *gmsg << "In Marker; L= " << marker.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Marker *>(marker.clone()));
    // Do nothing.
}

/**
 *
 *
 * @param corr
 */
void ParallelCyclotronTracker::visitMonitor(const Monitor &corr) {
    //   *gmsg << "In Monitor; L= " << corr.getElementLength() << endl;
    myElements.push_back(dynamic_cast<Monitor *>(corr.clone()));
    //   applyDrift(flip_s * corr.getElementLength());
}

523

gsell's avatar
gsell committed
524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539
/**
 *
 *
 * @param mult
 */
void ParallelCyclotronTracker::visitMultipole(const Multipole &mult) {
    *gmsg << "In Multipole; L= " << mult.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<Multipole *>(mult.clone()));
}

/**
 *
 *
 * @param prob
 */
void ParallelCyclotronTracker::visitProbe(const Probe &prob) {
540
    *gmsg << "* -----------  Probe -------------------------------" << endl;
541 542
    Probe *elptr = dynamic_cast<Probe *>(prob.clone());
    myElements.push_back(elptr);
gsell's avatar
gsell committed
543

544
    double xstart = elptr->getXstart();
545
    *gmsg << "XStart= " << xstart << " [mm]" << endl;
gsell's avatar
gsell committed
546

547
    double xend = elptr->getXend();
548
    *gmsg << "XEnd= " << xend << " [mm]" << endl;
gsell's avatar
gsell committed
549

550
    double ystart = elptr->getYstart();
551
    *gmsg << "YStart= " << ystart << " [mm]" << endl;
gsell's avatar
gsell committed
552

553
    double yend = elptr->getYend();
554
    *gmsg << "YEnd= " << yend << " [mm]" << endl;
gsell's avatar
gsell committed
555

556
    double width = elptr->getWidth();
557
    *gmsg << "Width= " << width << " [mm]" << endl;
gsell's avatar
gsell committed
558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586


    // initialise, do nothing
    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "PROBE";
    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
    BcParameter[4] = width ;

    // store probe parameters in the list
    buildupFieldList(BcParameter, ElementType, elptr);
}

/**
 *
 *
 * @param bend
 */
void ParallelCyclotronTracker::visitRBend(const RBend &bend) {
    *gmsg << "In RBend; L= " << bend.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<RBend *>(bend.clone()));
}

587 588 589 590 591 592 593 594 595
void ParallelCyclotronTracker::visitSBend3D(const SBend3D &bend) {
    *gmsg << "Adding SBend3D" << endl;
    if (opalRing_m != NULL)
        opalRing_m->appendElement(bend);
    else
        throw OpalException("ParallelCyclotronTracker::visitSBend3D",
                      "Need to define a RINGDEFINITION to use SBend3D element");
}

gsell's avatar
gsell committed
596 597 598 599 600 601 602 603
/**
 *
 *
 * @param as
 */
void ParallelCyclotronTracker::visitRFCavity(const RFCavity &as) {

    *gmsg << "* --------- RFCavity ------------------------------" << endl;
604

605 606
    RFCavity *elptr = dynamic_cast<RFCavity *>(as.clone());
    myElements.push_back(elptr);
gsell's avatar
gsell committed
607 608 609 610 611 612 613

    if((elptr->getComponentType() != "SINGLEGAP") && (elptr->getComponentType() != "DOUBLEGAP")) {
        *gmsg << (elptr->getComponentType()) << endl;
        throw OpalException("ParallelCyclotronTracker::visitRFCavity",
                            "The ParallelCyclotronTracker can only play with cyclotron type RF system currently ...");
    }

614
    double rmin = elptr->getRmin();
gsell's avatar
gsell committed
615 616
    *gmsg << "* Minimal radius of cavity= " << rmin << " [mm]" << endl;

617
    double rmax = elptr->getRmax();
gsell's avatar
gsell committed
618 619
    *gmsg << "* Maximal radius of cavity= " << rmax << " [mm]" << endl;

620
    double rff = elptr->getCycFrequency();
gsell's avatar
gsell committed
621 622
    *gmsg << "* RF frequency (2*pi*f)= " << rff << " [rad/s]" << endl;

623
    string fmfn = elptr->getFieldMapFN();
gsell's avatar
gsell committed
624 625
    *gmsg << "* RF Field map file name= " << fmfn << endl;

626
    double angle = elptr->getAzimuth();
gsell's avatar
gsell committed
627 628
    *gmsg << "* Cavity azimuth position= " << angle << " [deg] " << endl;

629
    double gap = elptr->getGapWidth();
gsell's avatar
gsell committed
630 631
    *gmsg << "* Cavity gap width= " << gap << " [mm] " << endl;

632
    double pdis = elptr->getPerpenDistance();
gsell's avatar
gsell committed
633 634 635
    *gmsg << "* Cavity Shift distance= " << pdis << " [mm] " << endl;


636
    double phi0 = elptr->getPhi0();
gsell's avatar
gsell committed
637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689
    *gmsg << "* Initial RF phase (t=0)= " << phi0 << " [deg] " << endl;

    // read cavity voltage profile data from file.
    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "CAVITY";
    BcParameter[0] = rmin;
    BcParameter[1] = rmax;
    BcParameter[2] = pdis;
    BcParameter[3] = angle;

    buildupFieldList(BcParameter, ElementType, elptr);
}

/**
 *
 *
 * @param rfq
 */
void ParallelCyclotronTracker::visitRFQuadrupole(const RFQuadrupole &rfq) {
    *gmsg << "In RFQuadrupole; L= " << rfq.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<RFQuadrupole *>(rfq.clone()));
}

/**
 *
 *
 * @param bend
 */
void ParallelCyclotronTracker::visitSBend(const SBend &bend) {
    *gmsg << "In SBend; L= " << bend.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<SBend *>(bend.clone()));
}

/**
 *
 *
 * @param sep
 */
void ParallelCyclotronTracker::visitSeparator(const Separator &sep) {
    *gmsg << "In Seapator L= " << sep.getElementLength() << " however the element is missing " << endl;
    myElements.push_back(dynamic_cast<Separator *>(sep.clone()));
}

/**
 *
 *
 * @param sept
 */
void ParallelCyclotronTracker::visitSeptum(const Septum &sept) {
690 691

    *gmsg << "* -----------  Septum -------------------------------" << endl;
gsell's avatar
gsell committed
692

693 694
    Septum *elptr = dynamic_cast<Septum *>(sept.clone());
    myElements.push_back(elptr);
gsell's avatar
gsell committed
695

696
    double xstart = elptr->getXstart();
697
    *gmsg << "XStart= " << xstart << " [mm]" << endl;
gsell's avatar
gsell committed
698

699
    double xend = elptr->getXend();
700
    *gmsg << "XEnd= " << xend << " [mm]" << endl;
gsell's avatar
gsell committed
701

702
    double ystart = elptr->getYstart();
703
    *gmsg << "YStart= " << ystart << " [mm]" << endl;
gsell's avatar
gsell committed
704

705
    double yend = elptr->getYend();
706
    *gmsg << "YEnd= " << yend << " [mm]" << endl;
gsell's avatar
gsell committed
707

708
    double width = elptr->getWidth();
709
    *gmsg << "Width= " << width << " [mm]" << endl;
gsell's avatar
gsell committed
710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786


    // initialise, do nothing
    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "SEPTUM";
    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
    BcParameter[4] = width ;

    // store septum parameters in the list
    buildupFieldList(BcParameter, ElementType, elptr);
}

/**
 *
 *
 * @param solenoid
 */
void ParallelCyclotronTracker::visitSolenoid(const Solenoid &solenoid) {
    myElements.push_back(dynamic_cast<Solenoid *>(solenoid.clone()));
    Component *elptr = *(--myElements.end());
    if(!elptr->hasAttribute("ELEMEDGE")) {
        *gmsg << "Solenoid: no position of the element given!" << endl;
        return;
    }
}

/**
 *
 *
 * @param pplate
 */
void ParallelCyclotronTracker::visitParallelPlate(const ParallelPlate &pplate) {//do nothing

    //*gmsg << "ParallelPlate: not in use in ParallelCyclotronTracker!" << endl;

    //buildupFieldList(startField, endField, elptr);

}

/**
 *
 *
 * @param cv
 */
void ParallelCyclotronTracker::visitCyclotronValley(const CyclotronValley &cv) {
    // Do nothing here.
}
/**
 * not used
 *
 * @param angle
 * @param curve
 * @param field
 * @param scale
 */
void ParallelCyclotronTracker::applyEntranceFringe(double angle, double curve,
        const BMultipoleField &field, double scale) {

}

/**
 *
 *
 * @param stripper
 */

void ParallelCyclotronTracker::visitStripper(const Stripper &stripper) {

    *gmsg << "* ---------Stripper------------------------------" << endl;

787 788 789 790
    Stripper *elptr = dynamic_cast<Stripper *>(stripper.clone());
    myElements.push_back(elptr);

    double xstart = elptr->getXstart();
gsell's avatar
gsell committed
791 792
    *gmsg << "XStart= " << xstart << " [mm]" << endl;

793
    double xend = elptr->getXend();
gsell's avatar
gsell committed
794 795
    *gmsg << "XEnd= " << xend << " [mm]" << endl;

796
    double ystart = elptr->getYstart();
gsell's avatar
gsell committed
797 798
    *gmsg << "YStart= " << ystart << " [mm]" << endl;

799
    double yend = elptr->getYend();
gsell's avatar
gsell committed
800 801
    *gmsg << "YEnd= " << yend << " [mm]" << endl;

802
    double width = elptr->getWidth();
gsell's avatar
gsell committed
803 804
    *gmsg << "Width= " << width << " [mm]" << endl;

805
    double opcharge = elptr->getOPCharge();
gsell's avatar
gsell committed
806 807
    *gmsg << "Charge of outcome particle = +e * " << opcharge << endl;

808
    double opmass = elptr->getOPMass();
gsell's avatar
gsell committed
809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853
    *gmsg << "Mass of the outcome particle = " << opmass << " [GeV/c^2]" << endl;

    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "STRIPPER";
    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
    BcParameter[4] = width ;
    BcParameter[5] = opcharge;
    BcParameter[6] = opmass;

    buildupFieldList(BcParameter, ElementType, elptr);
}


void ParallelCyclotronTracker::applyExitFringe(double angle, double curve,
        const BMultipoleField &field, double scale) {

}


/**
 *
 *
 * @param BcParameter
 * @param ElementType
 * @param elptr
 */
void ParallelCyclotronTracker::buildupFieldList(double BcParameter[], string ElementType, Component *elptr) {
    beamline_list::iterator sindex;

    type_pair *localpair = new type_pair();
    localpair->first = ElementType;

    for(int i = 0; i < 8; i++)
        *(((localpair->second).first) + i) = *(BcParameter + i);

    (localpair->second).second = elptr;

    // always put cyclotron as the first element in the list.
854
    if(ElementType == "OPALRING") {
gsell's avatar
gsell committed
855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871
        sindex = FieldDimensions.begin();
    } else {
        sindex = FieldDimensions.end();
    }
    FieldDimensions.insert(sindex, localpair);

}

/**
 *
 *
 * @param bl
 */
void ParallelCyclotronTracker::visitBeamline(const Beamline &bl) {
    itsBeamline->iterate(*dynamic_cast<BeamlineVisitor *>(this), false);
}

Matthias Toggweiler's avatar
Matthias Toggweiler committed
872 873 874 875
void ParallelCyclotronTracker::checkNumPart(std::string s) {
    int nlp = itsBunch->getLocalNum();
    int minnlp = 0;
    int maxnlp = 111111;
gsell's avatar
gsell committed
876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900
    reduce(nlp, minnlp, OpMinAssign());
    reduce(nlp, maxnlp, OpMaxAssign());
    *gmsg << s << " min local particle number " << minnlp << " max local particle number: " << maxnlp << endl;
}

/**
 *
 *
 */
void ParallelCyclotronTracker::execute() {

    /*
      Initialize common variables and structures
      for the integrators
    */

    step_m = 0;
    restartStep0_m = 0;
    // record how many bunches has already been injected. ONLY FOR MPM
    BunchCount_m = itsBunch->getNumBunch();

    // For the time being, we set bin number equal to bunch number. FixMe: not used
    BinCount_m = BunchCount_m;

    itsBeamline->accept(*this);
901 902
    if (opalRing_m != NULL)
        opalRing_m->lockRing();
gsell's avatar
gsell committed
903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922

    // display the selected elements
    *gmsg << "-----------------------------" << endl;
    *gmsg << "The selected Beam line elements are :" << endl;
    for(beamline_list::iterator sindex = FieldDimensions.begin(); sindex != FieldDimensions.end(); sindex++)
        *gmsg << ((*sindex)->first) << endl;
    *gmsg << "-----------------------------" << endl;

    // external field arrays for dumping
    for(int k = 0; k < 2; k++)
        FDext_m[k] = Vector_t(0.0, 0.0, 0.0);
    extE_m = Vector_t(0.0, 0.0, 0.0);
    extB_m = Vector_t(0.0, 0.0, 0.0);

    if(timeIntegrator_m == 0) {
        *gmsg << "* 4th order Runge-Kutta integrator" << endl;
        Tracker_RK4();
    } else if(timeIntegrator_m == 1) {
        *gmsg << "* 2nd order Leap-Frog integrator" << endl;
        Tracker_LF();
923 924 925
    } else if(timeIntegrator_m == 2) {
        *gmsg << "* Multiple time stepping (MTS) integrator" << endl;
        Tracker_MTS();
gsell's avatar
gsell committed
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
    } else {
        *gmsg << "ERROR: Invalid name of TIMEINTEGRATOR in Track command" << endl;
        exit(1);
    }

    *gmsg << "-----------------------------" << endl;
    *gmsg << "Finalize i.e. write data and close files :" << endl;
    for(beamline_list::iterator sindex = FieldDimensions.begin(); sindex != FieldDimensions.end(); sindex++) {
        (((*sindex)->second).second)->finalise();
    }
    *gmsg << "-----------------------------" << endl;
}

/**
   In general the two tracker have much code in common.
   This is a great source of errors.
   Need to avoid this

*/



/**
 *
 *
 */
void ParallelCyclotronTracker::Tracker_LF() {

    Inform *gmsgAll;
    gmsgAll = new  Inform("CycTracker LF", INFORM_ALL_NODES);

    BorisPusher pusher;

    // time steps interval between bunches for multi-bunch simulation.
    const int stepsPerTurn = itsBunch->getStepsPerTurn();

962
    const double harm = getHarmonicNumber();
gsell's avatar
gsell committed
963 964 965 966 967 968 969 970 971

    // load time
    const double dt = itsBunch->getdT() * 1.0e9 * harm; //[s]-->[ns]

    // find the injection time interval
    if(numBunch_m > 1) {
        *gmsg << "Time interval between neighbour bunches is set to " << stepsPerTurn *dt << "[ns]" << endl;
    }

972
    initTrackOrbitFile();
gsell's avatar
gsell committed
973 974 975 976

    int SteptoLastInj = itsBunch->getSteptoLastInj();

    // get data from h5 file for restart run
977
    if(OpalData::getInstance()->inRestartRun()) {
978
        restartStep0_m = itsBunch->getLocalTrackStep();
gsell's avatar
gsell committed
979
        step_m = restartStep0_m;
980
        if (numBunch_m > 1) itsBunch->resetPartBinID2(eta_m);
981
        *gmsg << "* Restart at integration step " << restartStep0_m << endl;
gsell's avatar
gsell committed
982 983 984 985 986 987 988 989 990 991 992 993
    }

    if(OpalData::getInstance()->hasBunchAllocated() && Options::scan) {
        lastDumpedStep_m = 0;
        itsBunch->setT(0.0);
    }

    *gmsg << "* Beginning of this run is at t= " << itsBunch->getT() * 1e9 << " [ns]" << endl;
    *gmsg << "* The time step is set to dt= " << dt << " [ns]" << endl;

    // for single Particle Mode, output at zero degree.
    if(initialTotalNum_m == 1)
994
        openFiles(OpalData::getInstance()->getInputBasename());
gsell's avatar
gsell committed
995 996

    double const initialReferenceTheta = referenceTheta / 180.0 * pi;
997

998
    initDistInGlobalFrame();
gsell's avatar
gsell committed
999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021

    //  read in some control parameters
    const int SinglePartDumpFreq = Options::sptDumpFreq;
    const int resetBinFreq = Options::rebinFreq;
    const int scSolveFreq = Options::scSolveFreq;
    const bool doDumpAfterEachTurn = Options::psDumpEachTurn;


    int boundpDestroyFreq = 10; // todo: is it better treat as a control parameter

    // prepare for dump after each turn
    double oldReferenceTheta = initialReferenceTheta;

    *gmsg << "single particle trajectory dump frequency is set to " << SinglePartDumpFreq << endl;
    *gmsg << "particles repartition frequency is set to " << Options::repartFreq << endl;
    if(numBunch_m > 1)
        *gmsg << "particles energy bin ID reset frequency is set to " << resetBinFreq << endl;

    // if initialTotalNum_m = 2, trigger SEO mode
    // prepare for transverse tuning calculation
    vector<double> Ttime, Tdeltr, Tdeltz;
    // prepare for transverse tuning calculation
    vector<int> TturnNumber;
1022
    turnnumber_m = 1;
gsell's avatar
gsell committed
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


    // flag to determine when to transit from single-bunch to multi-bunches mode
    bool flagTransition = false;
    // step point determining the next time point of check for transition
    int stepsNextCheck = step_m + itsBunch->getStepsPerTurn();

    const  double deltaTheta = pi / (stepsPerTurn);
    // record at which angle the space charge are solved
    double angleSpaceChargeSolve = 0.0;

    if(initialTotalNum_m == 1) {
        *gmsg << "* *---------------------------- SINGLE PARTICLE MODE------ ----------------------------*** " << endl;
        *gmsg << "* Instruction: when the total particle number equal to 1, single particle mode is triggered automatically," << endl
              << "* The initial distribution file must be specified which should contain only one line for the single particle " << endl
              << "* *------------NOTE: SINGLE PARTICLE MODE ONLY WORKS SERIALLY ON SINGLE NODE ------------------*** " << endl;
        if(Ippl::getNodes() != 1)
            throw OpalException("Error in ParallelCyclotronTracker::execute", "SINGLE PARTICLE MODE ONLY WORKS SERIALLY ON SINGLE NODE!");

    } else if(initialTotalNum_m == 2) {
        *gmsg << "* *------------------------ STATIC EQUILIBRIUM ORBIT MODE ----------------------------*** " << endl;
        *gmsg << "* Instruction: when the total particle number equal to 2, SEO mode is triggered automatically." << endl
              << "* This mode does NOT include any RF cavities. The initial distribution file must be specified" << endl
              << "* In the file the first line is for reference particle and the second line is for offcenter particle." << endl
              << "* The tunes are calculated by FFT routines based on these two particles. " << endl
              << "* *------------NOTE: SEO MODE ONLY WORKS SERIALLY ON SINGLE NODE ------------------*** " << endl;
        if(Ippl::getNodes() != 1)
            throw OpalException("Error in ParallelCyclotronTracker::execute", "SEO MODE ONLY WORKS SERIALLY ON SINGLE NODE!");
    }

1053 1054 1055 1056
    // apply the plugin elements: probe, colilmator, stripper, septum
    // make sure that we apply elements even on first step
    applyPluginElements(dt);

gsell's avatar
gsell committed
1057 1058 1059 1060 1061 1062
    // *****************II***************
    // main integration loop
    // *****************II***************
    *gmsg << "---------------------------- Start tracking ----------------------------" << endl;
    for(; step_m < maxSteps_m; step_m++) {
        bool dumpEachTurn = false;
1063 1064 1065
        if(step_m % SinglePartDumpFreq == 0) {
            singleParticleDump();
        }
gsell's avatar
gsell committed
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
        Ippl::Comm->barrier();

        // Push for first half step
        itsBunch->R *= Vector_t(0.001);
        push(0.5 * dt * 1e-9);
        itsBunch->R *= Vector_t(1000.0);

        // bunch injection
        if(numBunch_m > 1) {

            if((BunchCount_m == 1) && (multiBunchMode_m == 2) && (!flagTransition)) {
                if(step_m == stepsNextCheck) {
                    // under 3 conditions, following code will be execute
                    // to check the distance between two neighborring bunches
                    // 1.multi-bunch mode, AUTO sub-mode
                    // 2.After each revolution
                    // 3.only one bunch exists

                    *gmsg << "checking for automatically injecting new bunch ..." << endl;

                    itsBunch->R /= Vector_t(1000.0); // mm --> m
                    itsBunch->calcBeamParameters_cycl();
                    itsBunch->R *= Vector_t(1000.0); // m --> mm

                    Vector_t Rmean = itsBunch->get_centroid() * 1000.0; // m --> mm

                    RThisTurn_m = sqrt(pow(Rmean[0], 2.0) + pow(Rmean[1], 2.0));

                    Vector_t Rrms = itsBunch->get_rrms() * 1000.0; // m --> mm

                    double XYrms =  sqrt(pow(Rrms[0], 2.0) + pow(Rrms[1], 2.0));


                    // if the distance between two neighbour bunch is less than CoeffDBunches_m times of its 2D rms size
                    // start multi-bunch simulation, fill current phase space to initialR and initialP arrays

                    if((RThisTurn_m - RLastTurn_m) < CoeffDBunches_m * XYrms) {
                        // since next turn, start multi-bunches
                        saveOneBunch();
                        flagTransition = true;

1107
                        *gmsg << "*** Save beam distribution at turn #" << turnnumber_m << " ***" << endl;
gsell's avatar
gsell committed
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
                        *gmsg << "*** After one revolution, Multi-Bunch Mode will be invorked ***" << endl;

                    }

                    stepsNextCheck += stepsPerTurn;

                    *gmsg << "RLastTurn = " << RLastTurn_m << " [mm]" << endl;
                    *gmsg << "RThisTurn = " << RThisTurn_m << " [mm]" << endl;
                    *gmsg << "    XYrms = " << XYrms    << " [mm]" << endl;

                    RLastTurn_m = RThisTurn_m;
                }
            } else if(SteptoLastInj == stepsPerTurn - 1) {
                if(BunchCount_m < numBunch_m) {

                    // under 4 conditions, following code will be execute
                    // to read new bunch from hdf5 format file for FORCE or AUTO mode
                    // 1.multi-bunch mode
                    // 2.after each revolution
                    // 3.existing bunches is less than the specified bunches
                    // 4.FORCE mode, or AUTO mode with flagTransition = true
                    // Note: restart from 1 < BunchCount < numBunch_m must be avoided.
                    *gmsg << "step " << step_m << ", inject a new bunch... ... ..." << endl;
                    BunchCount_m++;

                    // read initial distribution from h5 file
                    if(multiBunchMode_m == 1) {
                        readOneBunch(BunchCount_m - 1);
1136
                        itsBunch->resetPartBinID2(eta_m);
gsell's avatar
gsell committed
1137 1138 1139 1140 1141 1142 1143
                    } else if(multiBunchMode_m == 2) {

                        if(OpalData::getInstance()->inRestartRun())
                            readOneBunchFromFile(BunchCount_m - 1);
                        else
                            readOneBunch(BunchCount_m - 1);

1144
                        itsBunch->resetPartBinID2(eta_m);
gsell's avatar
gsell committed
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
                    }

                    SteptoLastInj = 0;

                    itsBunch->setNumBunch(BunchCount_m);

                    stepsNextCheck += stepsPerTurn;

                    // update  after injection
                    itsBunch->boundp();

                    Ippl::Comm->barrier();
                    *gmsg << BunchCount_m << "'th bunch injected, total particle number = " << itsBunch->getTotalNum() << endl;
                }
            } else if(BunchCount_m == numBunch_m) {
                // After this, numBunch_m is wrong but useless
                numBunch_m--;

            } else {
                SteptoLastInj++;
            }
        }

        // calculate self fields Space Charge effects are included only when total macropaticles number is NOT LESS THAN 1000.
        if(itsBunch->hasFieldSolver() && initialTotalNum_m >= 1000) {
            if(step_m % scSolveFreq == 0) {
                //    *gmsg << "Calculate space charge at step " << step_m<<endl;
                // Firstly reset E and B to zero before fill new space charge field data for each track step
                itsBunch->Bf = Vector_t(0.0);
                itsBunch->Ef = Vector_t(0.0);

                Vector_t const meanR = calcMeanR();
                if((itsBunch->weHaveBins()) && BunchCount_m > 1) {
                    IpplTimings::startTimer(TransformTimer_m);
                    double const binsPhi = itsBunch->calcMeanPhi() - 0.5 * pi;
                    angleSpaceChargeSolve = binsPhi;
                    globalToLocal(itsBunch->R, binsPhi, meanR);

                    //scale coordinates
                    itsBunch->R /= Vector_t(1000.0); // mm --> m

                    if((step_m + 1) % boundpDestroyFreq == 0)
                        itsBunch->boundp_destroy();
                    else
                        itsBunch->boundp();

                    IpplTimings::stopTimer(TransformTimer_m);

                    // calcualte gamma for each energy bin
                    itsBunch->calcGammas_cycl();

                    repartition();
1197

gsell's avatar
gsell committed
1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218
                    // calculate space charge field for each energy bin
                    for(int b = 0; b < itsBunch->getLastemittedBin() ; b++) {

                        if(itsBunch->pbin_m->getTotalNumPerBin(b) >= 1000) {
                            //if(itsBunch->getNumPartInBin(b) >= 1000) {
                            itsBunch->setBinCharge(b, itsBunch->getChargePerParticle());
                            //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%//
                            itsBunch->computeSelfFields_cycl(b);
                            //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%//
                            INFOMSG("Bin:" << b << ", charge per particle " <<  itsBunch->getChargePerParticle() << endl);
                        } else {
                            INFOMSG("Note: Bin " << b << ": less than 1000 particles, omit space charge fields" << endl);
                        }
                    }

                    itsBunch->Q = itsBunch->getChargePerParticle();

                    IpplTimings::startTimer(TransformTimer_m);

                    //scale coordinates back
                    itsBunch->R *= Vector_t(1000.0); // m --> mm
1219

gsell's avatar
gsell committed
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 1245 1246 1247
                    localToGlobal(itsBunch->R, binsPhi, meanR);
                    localToGlobal(itsBunch->Ef, binsPhi);
                    localToGlobal(itsBunch->Bf, binsPhi);
                } else {
                    Vector_t const meanP = calcMeanP();
                    double const phi = calculateAngle(meanP(0), meanP(1)) - 0.5 * pi;
                    angleSpaceChargeSolve = phi;
                    globalToLocal(itsBunch->R, phi, meanR);

                    //scale coordinates
                    itsBunch->R /= Vector_t(1000.0); // mm --> m

                    if((step_m + 1) % boundpDestroyFreq == 0)
                        itsBunch->boundp_destroy();
                    else
                        itsBunch->boundp();

                    IpplTimings::stopTimer(TransformTimer_m);
                    repartition();
                    //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%//
                    double const meanGamma = sqrt(1.0 + pow(meanP(0), 2.0) + pow(meanP(1), 2.0));
                    itsBunch->computeSelfFields_cycl(meanGamma);
                    //%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%//

                    IpplTimings::startTimer(TransformTimer_m);

                    //scale coordinates back
                    itsBunch->R *= Vector_t(1000.0); // m --> mm
1248

gsell's avatar
gsell committed
1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297
                    localToGlobal(itsBunch->R, phi, meanR);
                    localToGlobal(itsBunch->Ef, phi);
                    localToGlobal(itsBunch->Bf, phi);
                }

                IpplTimings::stopTimer(TransformTimer_m);
            } else {
                Vector_t const meanP = calcMeanP();
                double const phi = calculateAngle(meanP(0), meanP(1)) - 0.5 * pi;
                double const deltaPhi = phi - angleSpaceChargeSolve;
                localToGlobal(itsBunch->Ef, deltaPhi);
                localToGlobal(itsBunch->Bf, deltaPhi);
            }
        } else {
            // if field solver is not available , only update bunch, to transfer particles between nodes if needed,
            // reset parameters such as LocalNum, initialTotalNum_m.
            // INFOMSG("No space charge Effects are included!"<<endl;);
            if((step_m % Options::repartFreq * 100) == 0 && initialTotalNum_m >= 1000) {
                Vector_t const meanR = calcMeanR();
                Vector_t const meanP = calcMeanP();
                double const phi = calculateAngle(meanP(0), meanP(1)) - 0.5 * pi;
                angleSpaceChargeSolve = phi; // we do not solve anything why set this?
                globalToLocal(itsBunch->R, phi, meanR);

                //scale coordinates
                itsBunch->R /= Vector_t(1000.0); // mm --> m

                if((step_m + 1) % boundpDestroyFreq == 0)
                    itsBunch->boundp_destroy();
                else
                    itsBunch->boundp();
                repartition();

                //scale coordinates back
                itsBunch->R *= Vector_t(1000.0); // m --> mm

                localToGlobal(itsBunch->R, phi, meanR);
            }
        }

        //  kick particles for one step
        IpplTimings::startTimer(IntegrationTimer_m);
        for(unsigned int i = 0; i < itsBunch->getLocalNum(); ++i) {
            Vector_t externalE, externalB;

            externalB = Vector_t(0.0, 0.0, 0.0);
            externalE = Vector_t(0.0, 0.0, 0.0);

            beamline_list::iterator sindex = FieldDimensions.begin();
1298 1299
            (((*sindex)->second).second)->apply(i, itsBunch->getT() * 1e9, externalE, externalB);
            externalB = externalB / 10.0; // kgauss -> T
gsell's avatar
gsell committed
1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312

            if(itsBunch->hasFieldSolver()) {
                externalE += itsBunch->Ef[i];
                externalB += itsBunch->Bf[i];
            }
            pusher.kick(itsBunch->R[i], itsBunch->P[i], externalE , externalB, dt * 1.0e-9, itsBunch->M[i] * 1.0e9, itsBunch->Q[i] / q_e);
        }
        IpplTimings::stopTimer(IntegrationTimer_m);

        // Push for second half step
        itsBunch->R *= Vector_t(0.001);
        push(0.5 * dt * 1e-9);
        itsBunch->R *= Vector_t(1000.0);
1313

1314 1315 1316 1317 1318 1319
        // apply the plugin elements: probe, colilmator, stripper, septum
        applyPluginElements(dt);
        // destroy particles if they are marked as Bin=-1 in the plugin elements or out of global apeture
        bool flagNeedUpdate = deleteParticle(); 
        if(itsBunch->weHaveBins() && flagNeedUpdate)
          itsBunch->resetPartBinID2(eta_m);
1320

1321 1322
        // recalculate bingamma and reset the BinID for each particles according to its current gamma
        if((itsBunch->weHaveBins()) && BunchCount_m > 1 && step_m % resetBinFreq == 0)
1323
            itsBunch->resetPartBinID2(eta_m);
gsell's avatar
gsell committed
1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337

        // dump  data after one push in single particle tracking
        if(initialTotalNum_m == 1) {
            int i = 0;

            // change phase space parameters from local reference frame of bunch (dr,dtheta,dz) to global Cartesian frame (X,Y,Z)
            for(int j = 0; j < 3; j++) {
                variable_m[j]   = itsBunch->R[i](j);  //[x,y,z]  units: [mm]
                variable_m[j+3] = itsBunch->P[i](j);  //[px,py,pz]  units: dimensionless
            }

            double temp_meanTheta = calculateAngle2(variable_m[0], variable_m[1]);//[ -pi ~ pi ]
            if((oldReferenceTheta < initialReferenceTheta - deltaTheta) &&
               (temp_meanTheta >= initialReferenceTheta - deltaTheta)) {
1338 1339
                ++turnnumber_m;
                *gmsg << "Turn " << turnnumber_m << endl;
gsell's avatar
gsell committed
1340
                dumpEachTurn = true;
1341
                outfThetaEachTurn_m << "#Turn number = " << turnnumber_m << ", Time = " << itsBunch->getT() * 1e9 << " [ns]" << endl;
gsell's avatar
gsell committed
1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354
                outfThetaEachTurn_m << " " << sqrt(variable_m[0]*variable_m[0] + variable_m[1]*variable_m[1])
                                    << " " << variable_m[3]*cos(temp_meanTheta) + variable_m[4]*sin(temp_meanTheta)
                                    << " " << temp_meanTheta / pi * 180
                                    << " " << -variable_m[3]*sin(temp_meanTheta) + variable_m[4]*cos(temp_meanTheta)
                                    << " " << variable_m[2]
                                    << " " << variable_m[5] << endl;
            }
            // FixMe: should be defined elesewhere !
            // define 3 special azimuthal angles where dump particle's six parameters  at each turn into 3 ASCII files.
            const double azimuth_angle0 = 0.0;
            const double azimuth_angle1 = 22.5 / 180.0 * pi;
            const double azimuth_angle2 = 45.0 / 180.0 * pi;
            if((oldReferenceTheta < azimuth_angle0 - deltaTheta) && (temp_meanTheta >= azimuth_angle0 - deltaTheta)) {
1355
                outfTheta0_m << "#Turn number = " << turnnumber_m << ", Time = " << itsBunch->getT() * 1e9 << " [ns]" << endl;
gsell's avatar
gsell committed
1356 1357 1358 1359 1360 1361 1362 1363 1364
                outfTheta0_m << " " << sqrt(variable_m[0]*variable_m[0] + variable_m[1]*variable_m[1])
                             << " " << variable_m[3]*cos(temp_meanTheta) + variable_m[4]*sin(temp_meanTheta)
                             << " " << temp_meanTheta / pi * 180
                             << " " << -variable_m[3]*sin(temp_meanTheta) + variable_m[4]*cos(temp_meanTheta)
                             << " " << variable_m[2]
                             << " " << variable_m[5] << endl;
            }

            if((oldReferenceTheta < azimuth_angle1 - deltaTheta) && (temp_meanTheta >= azimuth_angle1 - deltaTheta)) {
1365
                outfTheta1_m << "#Turn number = " << turnnumber_m << ", Time = " << itsBunch->getT() * 1e9 << " [ns]" << endl;
gsell's avatar
gsell committed
1366 1367 1368 1369 1370 1371 1372 1373 1374
                outfTheta1_m << " " << sqrt(variable_m[0]*variable_m[0] + variable_m[1]*variable_m[1])
                             << " " << variable_m[3]*cos(temp_meanTheta) + variable_m[4]*sin(temp_meanTheta)
                             << " " << temp_meanTheta / pi * 180
                             << " " << -variable_m[3]*sin(temp_meanTheta) + variable_m[4]*cos(temp_meanTheta)
                             << " " << variable_m[2]
                             << " " << variable_m[5] << endl;
            }

            if((oldReferenceTheta < azimuth_angle2 - deltaTheta) && (temp_meanTheta >= azimuth_angle2 - deltaTheta)) {
1375
                outfTheta2_m << "#Turn number = " << turnnumber_m << ", Time = " << itsBunch->getT() * 1e9 << " [ns]" << endl;
gsell's avatar
gsell committed
1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397
                outfTheta2_m << " " << sqrt(variable_m[0]*variable_m[0] + variable_m[1]*variable_m[1])
                             << " " << variable_m[3]*cos(temp_meanTheta) + variable_m[4]*sin(temp_meanTheta)
                             << " " << temp_meanTheta / pi * 180
                             << " " << -variable_m[3]*sin(temp_meanTheta) + variable_m[4]*cos(temp_meanTheta)
                             << " " << variable_m[2]
                             << " " << variable_m[5] << endl;
            }
            oldReferenceTheta = temp_meanTheta;
        }


        // check whether one turn over for multi-bunch tracking.
        if(doDumpAfterEachTurn && initialTotalNum_m > 2) {
            Vector_t const meanR = calcMeanR();

            // in global Cartesian frame, calculate the location in global frame of bunch
            oldReferenceTheta = calculateAngle2(meanR(0), meanR(1));

            // both for single bunch and multi-bunch
            // avoid dump at the first step
            // dumpEachTurn has not been changed in first push
            if((step_m > 10) && ((step_m + 1) % stepsPerTurn) == 0) {
1398
                ++turnnumber_m;
gsell's avatar
gsell committed
1399
                dumpEachTurn = true;
1400
                *gmsg << "Turn " << turnnumber_m << " total particles " << itsBunch->getTotalNum() << endl;
gsell's avatar
gsell committed
1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411
            }
        }

        // dump phase space distribution of bunch
        if((((step_m + 1) % Options::psDumpFreq == 0) && initialTotalNum_m != 2) ||
           (doDumpAfterEachTurn && dumpEachTurn && initialTotalNum_m != 2)) {

            IpplTimings::startTimer(DumpTimer_m);

            itsBunch->setSteptoLastInj(SteptoLastInj);

1412
            itsBunch->setLocalTrackStep((step_m + 1));
gsell's avatar
gsell committed
1413 1414 1415 1416 1417 1418 1419

            extE_m = Vector_t(0.0, 0.0, 0.0);
            extB_m = Vector_t(0.0, 0.0, 0.0);

            //--------------------- calculate mean coordinates  of bunch -------------------------------//
            //------------  and calculate the external field at the mass of bunch-----------------------//

1420
            Vector_t const meanR = calcMeanR();
gsell's avatar
gsell committed
1421 1422 1423
            *gmsg << "meanR=( " << meanR(0) << " " << meanR(1) << " " << meanR(2) << " ) [mm] " << endl;

            beamline_list::iterator DumpSindex = FieldDimensions.begin();
1424
            (((*DumpSindex)->second).second)->apply(meanR, Vector_t(0.0), itsBunch->getT() * 1e9, extE_m, extB_m);
gsell's avatar
gsell committed
1425 1426 1427 1428 1429 1430 1431 1432 1433
            FDext_m[0] = extB_m / 10.0; // kgauss -> T
            FDext_m[1] = extE_m;

            //----------------------------dump in global frame-------------------------------------//
            // Note: Don't dump when
            // 1. after one turn
            // in order to sychronize the dump step for multi-bunch and single bunch for compare
            // with each other during post-process phase.
            if(!(Options::psDumpLocalFrame)) {
1434
   	        double E = itsBunch->get_meanEnergy(); 
gsell's avatar
gsell committed
1435
                itsBunch->R /= Vector_t(1000.0); // mm --> m
1436 1437 1438


                lastDumpedStep_m = itsDataSink->writePhaseSpace_cycl(*itsBunch, FDext_m, E, referencePr, referenceR, referenceTheta);
1439
                itsDataSink->writeStatData(*itsBunch, FDext_m ,0.0,0.0,0.0);
gsell's avatar
gsell committed
1440 1441
                itsBunch->R *= Vector_t(1000.0); // m --> mm
                *gmsg << "* Phase space dump " << lastDumpedStep_m << " (global frame) at integration step "
1442
                      << step_m + 1 << " T= " << itsBunch->getT() * 1e9 << " [ns]" 	    << " E= " << itsBunch->get_meanEnergy()  << endl;
gsell's avatar
gsell committed
1443 1444 1445

                //----------------------------dump in local frame-------------------------------------//
            } else {
1446 1447 1448 1449 1450 1451
	      Vector_t const meanP = calcMeanP();
	      double const phi = calculateAngle(meanP(0), meanP(1)) - 0.5 * pi;
	      double E = itsBunch->get_meanEnergy();
	      globalToLocal(itsBunch->R, phi, meanR);
	      globalToLocal(itsBunch->P, phi, meanP);
	      itsBunch->R /= Vector_t(1000.0); // mm --> m
1452
	      lastDumpedStep_m = itsDataSink->writePhaseSpace_cycl(*itsBunch, FDext_m, E, referencePr, referenceR, referenceTheta);