ParallelCyclotronTracker.cpp 179 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
#include "AbsBeamline/Diagnostic.h"
#include "AbsBeamline/Drift.h"
#include "AbsBeamline/ElementBase.h"
#include "AbsBeamline/Lambertson.h"
33
#include "AbsBeamline/Offset.h"
gsell's avatar
gsell committed
34 35 36 37 38 39 40 41
#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"
42
#include "AbsBeamline/SBend3D.h"
gsell's avatar
gsell committed
43 44 45 46 47
#include "AbsBeamline/Separator.h"
#include "AbsBeamline/Septum.h"
#include "AbsBeamline/Solenoid.h"
#include "AbsBeamline/CyclotronValley.h"
#include "AbsBeamline/Stripper.h"
48
#include "AbsBeamline/VariableRFCavity.h"
49 50

#include "Elements/OpalBeamline.h"
51
#include "Elements/OpalRing.h"
gsell's avatar
gsell committed
52 53 54

#include "BeamlineGeometry/Euclid3D.h"
#include "BeamlineGeometry/PlanarArcGeometry.h"
Jianjun Yang's avatar
Jianjun Yang committed
55
#include "BeamlineGeometry/RBendGeometry.h"
gsell's avatar
gsell committed
56 57 58 59 60 61 62 63 64 65 66 67
#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"

68
#include "Structure/BoundaryGeometry.h"
gsell's avatar
gsell committed
69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87

#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
88 89 90
Vector_t const ParallelCyclotronTracker::xaxis = Vector_t(1.0, 0.0, 0.0);
Vector_t const ParallelCyclotronTracker::yaxis = Vector_t(0.0, 1.0, 0.0);
Vector_t const ParallelCyclotronTracker::zaxis = Vector_t(0.0, 0.0, 1.0);
gsell's avatar
gsell committed
91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109

#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),
110
    eta_m(0.01),
gsell's avatar
gsell committed
111 112
    myNode_m(Ippl::myNode()),
    initialLocalNum_m(0),
113 114
    initialTotalNum_m(0),
    opalRing_m(NULL) {
gsell's avatar
gsell committed
115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138
    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),
    maxSteps_m(maxSTEPS),
    timeIntegrator_m(timeIntegrator),
139
    eta_m(0.01),
gsell's avatar
gsell committed
140 141
    myNode_m(Ippl::myNode()),
    initialLocalNum_m(bunch.getLocalNum()),
142 143
    initialTotalNum_m(bunch.getTotalNum()),
    opalRing_m(NULL) {
gsell's avatar
gsell committed
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
    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;
169 170 171
    if (opalRing_m != NULL) {
        // delete opalRing_m;
    }
gsell's avatar
gsell committed
172 173
}

174 175 176 177 178 179 180 181 182 183 184 185 186
/**
 * AAA
 *
 * @param none
 */
void ParallelCyclotronTracker::initializeBoundaryGeometry() {
  for(list<Component *>::iterator compindex = myElements.begin(); compindex != myElements.end(); compindex++) {
    bgf_m = dynamic_cast<ElementBase *>(*compindex)->getBoundaryGeometry();
    if(!bgf_m) 
      continue;
    else
      break;
  }
adelmann's avatar
adelmann committed
187 188 189 190 191
  if (bgf_m) {
    itsDataSink->writeGeomToVtk(*bgf_m, string("data/testGeometry-00000.vtk"));
    OpalData::getInstance()->setGlobalGeometry(bgf_m);
    *gmsg << "* Boundary geometry initialized " << endl;
  }
192 193 194 195 196 197 198 199 200 201 202
}
/**
 *
 *
 * @param fn Base file name
 */
void ParallelCyclotronTracker::bgf_main_collision_test() {
  if(!bgf_m) return;

  Inform msg("bgf_main_collision_test ");
  
203 204 205 206
  /**                                                                                                      
   *Here we check if a particles is outside the domain, flag it for deletion
   */

gsell's avatar
gsell committed
207
  Vector_t intecoords = 0.0;
208 209 210 211 212

  // This has to match the dT in the rk4 pusher! -DW
  //double dtime = 0.5 * itsBunch->getdT();  // Old
  double dtime = itsBunch->getdT() * getHarmonicNumber();  // New

213 214 215
  int triId = 0;     
  size_t Nimpact = 0;
  for(size_t i = 0; i < itsBunch->getLocalNum(); i++) {
216
    int res = bgf_m->PartInside(itsBunch->R[i]*1.0e-3, itsBunch->P[i], dtime, itsBunch->PType[i], itsBunch->Q[i], intecoords, triId);
217 218 219 220 221 222 223 224
    if(res >= 0) { 
      itsBunch->Bin[i] = -1;
      Nimpact++;
    }               
  }
}


gsell's avatar
gsell committed
225 226 227 228 229 230 231 232 233 234 235 236
/**
 *
 *
 * @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
237
    outfTheta0_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma" << endl;
gsell's avatar
gsell committed
238 239 240 241 242

    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
243
    outfTheta1_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma"  << endl;
gsell's avatar
gsell committed
244 245 246 247 248

    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
249
    outfTheta2_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma"  << endl;
gsell's avatar
gsell committed
250 251 252 253 254 255 256 257 258

    // 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
259
    outfTheta2_m << "#  r [mm]      beta_r*gamma       theta [mm]      beta_theta*gamma        z [mm]          beta_z*gamma"  << endl;
gsell's avatar
gsell committed
260 261 262 263 264 265 266 267 268 269 270 271 272 273 274
}

/**
 * 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();
}

275 276 277 278 279
/** 
 *
 * @param ring
 */
void ParallelCyclotronTracker::visitOpalRing(const OpalRing &ring) {
Daniel Winklehner's avatar
Daniel Winklehner committed
280

281
    *gmsg << "Adding OpalRing" << endl;
Daniel Winklehner's avatar
Daniel Winklehner committed
282 283

    if (opalRing_m != NULL)
284
        delete opalRing_m;
Daniel Winklehner's avatar
Daniel Winklehner committed
285

286
    opalRing_m = dynamic_cast<OpalRing*>(ring.clone());
Daniel Winklehner's avatar
Daniel Winklehner committed
287

288
    myElements.push_back(opalRing_m);
Daniel Winklehner's avatar
Daniel Winklehner committed
289

290 291 292 293 294
    opalRing_m->initialise(itsBunch);

    referenceR = opalRing_m->getBeamRInit();
    referencePr = opalRing_m->getBeamPRInit();
    referenceTheta = opalRing_m->getBeamPhiInit();
Daniel Winklehner's avatar
Daniel Winklehner committed
295

296 297 298 299
    if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
        throw OpalException("Error in ParallelCyclotronTracker::visitOpalRing",
                            "PHIINIT is out of [-180, 180)!");
    }
Daniel Winklehner's avatar
Daniel Winklehner committed
300 301

    referenceZ = 0.0;
302
    referencePz = 0.0;
Daniel Winklehner's avatar
Daniel Winklehner committed
303 304 305 306

    referencePtot = itsReference.getGamma() * itsReference.getBeta();
    referencePt = sqrt(referencePtot * referencePtot - referencePr * referencePr);

307 308
    if(referencePtot < 0.0)
        referencePt *= -1.0;
Daniel Winklehner's avatar
Daniel Winklehner committed
309

310 311
    sinRefTheta_m = sin(referenceTheta / 180.0 * pi);
    cosRefTheta_m = cos(referenceTheta / 180.0 * pi);
gsell's avatar
gsell committed
312

313
    double BcParameter[8];
Daniel Winklehner's avatar
Daniel Winklehner committed
314 315 316 317

    for(int i = 0; i < 8; i++) 
        BcParameter[i] = 0.0;

318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334
    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
335 336 337 338 339 340 341 342 343 344

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

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

345 346
    Cyclotron *elptr = dynamic_cast<Cyclotron *>(cycl.clone());
    myElements.push_back(elptr);
347
     
348
    // Fresh run (no restart):
349
    if(!OpalData::getInstance()->inRestartRun()) {
350

351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382
        // Get reference values from cyclotron element
        referenceR     = elptr->getRinit();
        referenceTheta = elptr->getPHIinit();
        referenceZ     = elptr->getZinit();
        referencePr    = elptr->getPRinit();
        referencePz    = elptr->getPZinit();
         
        if(referenceTheta <= -180.0 || referenceTheta > 180.0) {
            throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron", "PHIINIT is out of [-180, 180)!");
        }

        referencePtot =  itsReference.getGamma() * itsReference.getBeta();

        // Calculate reference azimuthal (tangential) momentum from total-, z- and radial momentum:
        float insqrt = referencePtot * referencePtot - referencePr * referencePr - referencePz * referencePz;

        if(insqrt < 0) {

            if(insqrt > -1.0e-10) {

	        referencePt = 0.0;

            } else {

	        throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron", "Pt imaginary!");
            }

        } else {

            referencePt = sqrt(insqrt);
        }

Daniel Winklehner's avatar
Daniel Winklehner committed
383 384
        if(referencePtot < 0.0) 
            referencePt *= -1.0;
385 386 387 388 389 390 391 392 393 394 395 396 397
        // End calculate referencePt

    // Restart a run:
    } else {

        if(referenceTheta <= -180.0 || referenceTheta > 180.0) {

            throw OpalException("Error in ParallelCyclotronTracker::visitCyclotron", "PHIINIT is out of [-180, 180)!");

        }
      
        referencePtot =  bega;
        // Note: Nothing else has to be set, b/c everything comes from the h5 file -DW
398 399
    }

400
    /*
401 402 403 404 405 406 407 408 409 410 411
    // TEMP Debug Output -DW
    Vector_t const meanP = calcMeanP();
    *gmsg << endl;
    *gmsg << "** Reference P:"  << endl;
    *gmsg << "referencePtot = " << referencePtot << endl;
    *gmsg << "Ptot (from Bunch) = " << sqrt(dot(meanP, meanP)) << endl;
    *gmsg << "referencePr = "   << referencePr   << endl;
    *gmsg << "referencePz = "   << referencePz   << endl;
    *gmsg << "referencePt = "   << referencePt   << endl;
    *gmsg << endl;
    // ENDTEMP
412
    */
gsell's avatar
gsell committed
413

414
    sinRefTheta_m = sin(referenceTheta / 180.0 * pi);
415 416
    cosRefTheta_m = cos(referenceTheta / 180.0 * pi);   
   
417
    *gmsg << endl;
adelmann's avatar
adelmann committed
418
    *gmsg << "* Bunch global starting position:" << endl;
419 420
    *gmsg << "* RINIT = " << referenceR  << " [mm]" << endl;
    *gmsg << "* PHIINIT = " << referenceTheta << " [deg]" << endl;
421
    *gmsg << "* ZINIT = " << referenceZ << " [mm]" << endl;
422
    *gmsg << endl;
adelmann's avatar
adelmann committed
423
    *gmsg << "* Bunch global starting momenta:" << endl;
gsell's avatar
gsell committed
424 425
    *gmsg << "* Initial gamma = " << itsReference.getGamma() << endl;
    *gmsg << "* Initial beta = " << itsReference.getBeta() << endl;
426
    *gmsg << "* Reference total momentum (beta * gamma) = " << referencePtot * 1000.0 << " [MCU]" << endl;
427 428 429
    *gmsg << "* Reference azimuthal momentum (Pt) = " << referencePt * 1000.0 << " [MCU]" << endl;
    *gmsg << "* Reference radial momentum (Pr) = " << referencePr * 1000.0 << " [MCU]" << endl;
    *gmsg << "* Reference axial momentum (Pz) = " << referencePz * 1000.0 << " [MCU]" << endl;
430
    *gmsg << endl;
adelmann's avatar
adelmann committed
431

gsell's avatar
gsell committed
432
    double sym = elptr->getSymmetry();
433
    *gmsg << "* " << sym << "-fold field symmerty " << endl;
gsell's avatar
gsell committed
434

435 436 437
    // 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
438 439

    string fmfn = elptr->getFieldMapFN();
440
    *gmsg << "* Field map file name = " << fmfn << " " << endl;
gsell's avatar
gsell committed
441 442

    string type = elptr->getType();
443
    *gmsg << "* Type of cyclotron = " << type << " " << endl;
444 445 446
    
    double rmin = elptr->getMinR();
    double rmax = elptr->getMaxR();
447
    *gmsg << "* Radial aperture = " << rmin << " ... " << rmax<<" [mm] "<< endl;
448 449 450

    double zmin = elptr->getMinZ();
    double zmax = elptr->getMaxZ();
451
    *gmsg << "* Vertical aperture = " << zmin << " ... " << zmax<<" [mm]"<< endl;
gsell's avatar
gsell committed
452

453
    /**
454
    bool Sflag = elptr->getSuperpose();
455 456 457 458 459
    string flagsuperposed;
    if (Sflag)
      flagsuperposed="yes";
    else
      flagsuperposed="no";
460
    *gmsg << "* Electric field maps are superposed? " << flagsuperposed << " " << endl;
461
    */
462

gsell's avatar
gsell committed
463
    double h = elptr->getCyclHarm();
464
    *gmsg << "* Harmonic number h = " << h << " " << endl;
gsell's avatar
gsell committed
465

466
    /**
adelmann's avatar
adelmann committed
467
    if (elptr->getSuperpose())
468
        *gmsg << "* Fields are superposed " << endl;
469
    */
adelmann's avatar
adelmann committed
470

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
    /**
     * 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
500 501
    for(int i = 0; i < 8; i++) 
      BcParameter[i] = 0.0;
gsell's avatar
gsell committed
502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524
    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) {

525
    *gmsg << "* --------- Collimator -----------------------------" << endl;
gsell's avatar
gsell committed
526

527 528
    Collimator* elptr = dynamic_cast<Collimator *>(coll.clone());
    myElements.push_back(elptr);
gsell's avatar
gsell committed
529

530
    double xstart = elptr->getXStart();
adelmann's avatar
adelmann committed
531
    *gmsg << "* Xstart= " << xstart << " [mm]" << endl;
gsell's avatar
gsell committed
532

533
    double xend = elptr->getXEnd();
adelmann's avatar
adelmann committed
534
    *gmsg << "* Xend= " << xend << " [mm]" << endl;
gsell's avatar
gsell committed
535

536
    double ystart = elptr->getYStart();
adelmann's avatar
adelmann committed
537
    *gmsg << "* Ystart= " << ystart << " [mm]" << endl;
gsell's avatar
gsell committed
538

539
    double yend = elptr->getYEnd();
adelmann's avatar
adelmann committed
540
    *gmsg << "* Yend= " <<yend << " [mm]" << endl;
gsell's avatar
gsell committed
541

542
    double zstart = elptr->getZStart();
adelmann's avatar
adelmann committed
543
    *gmsg << "* Zstart= " << zstart << " [mm]" << endl;
544 545

    double zend = elptr->getZEnd();
adelmann's avatar
adelmann committed
546
    *gmsg << "* Zend= " <<zend << " [mm]" << endl;
547

548
    double width = elptr->getWidth();
adelmann's avatar
adelmann committed
549
    *gmsg << "* Width= " << width << " [mm]" << endl;
gsell's avatar
gsell committed
550 551 552 553 554 555 556

    elptr->initialise(itsBunch, 1.0);

    double BcParameter[8];
    for(int i = 0; i < 8; i++)
        BcParameter[i] = 0.0;
    string ElementType = "CCOLLIMATOR";
557 558 559 560
    BcParameter[0] = xstart ;
    BcParameter[1] = xend;
    BcParameter[2] = ystart ;
    BcParameter[3] = yend;
gsell's avatar
gsell committed
561 562 563 564 565 566 567 568 569 570 571 572 573 574
    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
575 576 577 578 579 580 581 582 583 584 585 586
/**
 *
 *
 * @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
587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616
/**
 *
 *
 * @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()));
}

617 618 619 620 621 622 623 624 625 626 627
void ParallelCyclotronTracker::visitOffset(const Offset & off) {
    if (opalRing_m == NULL)
        throw OpalException(
                        "ParallelCylcotronTracker::visitOffset",
                        "Attempt to place an offset when OpalRing not defined");
    Offset* offNonConst = const_cast<Offset*>(&off);
    offNonConst->updateGeometry(opalRing_m->getNextPosition(),
                       opalRing_m->getNextNormal());
    opalRing_m->appendElement(off);
}

gsell's avatar
gsell committed
628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649
/**
 *
 *
 * @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());
}

650

gsell's avatar
gsell committed
651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666
/**
 *
 *
 * @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) {
667
    *gmsg << "* -----------  Probe -------------------------------" << endl;
668 669
    Probe *elptr = dynamic_cast<Probe *>(prob.clone());
    myElements.push_back(elptr);
gsell's avatar
gsell committed
670

671
    double xstart = elptr->getXstart();
672
    *gmsg << "XStart= " << xstart << " [mm]" << endl;
gsell's avatar
gsell committed
673

674
    double xend = elptr->getXend();
675
    *gmsg << "XEnd= " << xend << " [mm]" << endl;
gsell's avatar
gsell committed
676

677
    double ystart = elptr->getYstart();
678
    *gmsg << "YStart= " << ystart << " [mm]" << endl;
gsell's avatar
gsell committed
679

680
    double yend = elptr->getYend();
681
    *gmsg << "YEnd= " << yend << " [mm]" << endl;
gsell's avatar
gsell committed
682

683
    double width = elptr->getWidth();
684
    *gmsg << "Width= " << width << " [mm]" << endl;
gsell's avatar
gsell committed
685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713


    // 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()));
}

714 715 716 717 718 719 720 721 722
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");
}

723 724 725 726 727 728 729 730 731
void ParallelCyclotronTracker::visitVariableRFCavity(const VariableRFCavity &cav) {
    *gmsg << "Adding Variable RF Cavity" << endl;
    if (opalRing_m != NULL)
        opalRing_m->appendElement(cav);
    else
        throw OpalException("ParallelCyclotronTracker::visitVariableRFCavity",
            "Need to define a RINGDEFINITION to use VariableRFCavity element");
}

gsell's avatar
gsell committed
732 733 734 735 736 737 738 739
/**
 *
 *
 * @param as
 */
void ParallelCyclotronTracker::visitRFCavity(const RFCavity &as) {

    *gmsg << "* --------- RFCavity ------------------------------" << endl;
740

741 742
    RFCavity *elptr = dynamic_cast<RFCavity *>(as.clone());
    myElements.push_back(elptr);
gsell's avatar
gsell committed
743 744 745 746 747 748 749

    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 ...");
    }

750
    double rmin = elptr->getRmin();
gsell's avatar
gsell committed
751 752
    *gmsg << "* Minimal radius of cavity= " << rmin << " [mm]" << endl;

753
    double rmax = elptr->getRmax();
gsell's avatar
gsell committed
754 755
    *gmsg << "* Maximal radius of cavity= " << rmax << " [mm]" << endl;

756
    double rff = elptr->getCycFrequency();
gsell's avatar
gsell committed
757 758
    *gmsg << "* RF frequency (2*pi*f)= " << rff << " [rad/s]" << endl;

759
    string fmfn = elptr->getFieldMapFN();
gsell's avatar
gsell committed
760 761
    *gmsg << "* RF Field map file name= " << fmfn << endl;

762
    double angle = elptr->getAzimuth();
gsell's avatar
gsell committed
763 764
    *gmsg << "* Cavity azimuth position= " << angle << " [deg] " << endl;

765
    double gap = elptr->getGapWidth();
gsell's avatar
gsell committed
766 767
    *gmsg << "* Cavity gap width= " << gap << " [mm] " << endl;

768
    double pdis = elptr->getPerpenDistance();
gsell's avatar
gsell committed
769 770 771
    *gmsg << "* Cavity Shift distance= " << pdis << " [mm] " << endl;


772
    double phi0 = elptr->getPhi0();
gsell's avatar
gsell committed
773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825
    *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) {
826 827

    *gmsg << "* -----------  Septum -------------------------------" << endl;
gsell's avatar
gsell committed
828

829 830
    Septum *elptr = dynamic_cast<Septum *>(sept.clone());
    myElements.push_back(elptr);
gsell's avatar
gsell committed
831

832
    double xstart = elptr->getXstart();
833
    *gmsg << "XStart= " << xstart << " [mm]" << endl;
gsell's avatar
gsell committed
834

835
    double xend = elptr->getXend();
836
    *gmsg << "XEnd= " << xend << " [mm]" << endl;
gsell's avatar
gsell committed
837

838
    double ystart = elptr->getYstart();
839
    *gmsg << "YStart= " << ystart << " [mm]" << endl;
gsell's avatar
gsell committed
840

841
    double yend = elptr->getYend();
842
    *gmsg << "YEnd= " << yend << " [mm]" << endl;
gsell's avatar
gsell committed
843

844
    double width = elptr->getWidth();
845
    *gmsg << "Width= " << width << " [mm]" << endl;
gsell's avatar
gsell committed
846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922


    // 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;

923 924 925 926
    Stripper *elptr = dynamic_cast<Stripper *>(stripper.clone());
    myElements.push_back(elptr);

    double xstart = elptr->getXstart();
gsell's avatar
gsell committed
927 928
    *gmsg << "XStart= " << xstart << " [mm]" << endl;

929
    double xend = elptr->getXend();
gsell's avatar
gsell committed
930 931
    *gmsg << "XEnd= " << xend << " [mm]" << endl;

932
    double ystart = elptr->getYstart();
gsell's avatar
gsell committed
933 934
    *gmsg << "YStart= " << ystart << " [mm]" << endl;

935
    double yend = elptr->getYend();
gsell's avatar
gsell committed
936 937
    *gmsg << "YEnd= " << yend << " [mm]" << endl;

938
    double width = elptr->getWidth();
gsell's avatar
gsell committed
939 940
    *gmsg << "Width= " << width << " [mm]" << endl;

941
    double opcharge = elptr->getOPCharge();
gsell's avatar
gsell committed
942 943
    *gmsg << "Charge of outcome particle = +e * " << opcharge << endl;

944
    double opmass = elptr->getOPMass();
adelmann's avatar
Cleanup  
adelmann committed
945
    *gmsg << "* Mass of the outcome particle = " << opmass << " [GeV/c^2]" << endl;
gsell's avatar
gsell committed
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

    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.
990
    if(ElementType == "OPALRING") {
gsell's avatar
gsell committed
991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007
        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
1008 1009 1010 1011
void ParallelCyclotronTracker::checkNumPart(std::string s) {
    int nlp = itsBunch->getLocalNum();
    int minnlp = 0;
    int maxnlp = 111111;
gsell's avatar
gsell committed
1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029
    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;
Daniel Winklehner's avatar
Daniel Winklehner committed
1030 1031

    // Record how many bunches have already been injected. ONLY FOR MPM
gsell's avatar
gsell committed
1032 1033 1034 1035 1036 1037
    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);
1038 1039
    if (opalRing_m != NULL)
        opalRing_m->lockRing();
gsell's avatar
gsell committed
1040

Daniel Winklehner's avatar
Daniel Winklehner committed
1041 1042
    // Display the selected elements
    *gmsg << "* -------------------------------------" << endl;
adelmann's avatar
Cleanup  
adelmann committed
1043
    *gmsg << "* The selected Beam line elements are :" << endl;
gsell's avatar
gsell committed
1044
    for(beamline_list::iterator sindex = FieldDimensions.begin(); sindex != FieldDimensions.end(); sindex++)
adelmann's avatar
Cleanup  
adelmann committed
1045
      *gmsg << "* -> " <<  ((*sindex)->first) << endl;
Daniel Winklehner's avatar
Daniel Winklehner committed
1046
    *gmsg << "* -------------------------------------" << endl;
1047

Daniel Winklehner's avatar
Daniel Winklehner committed
1048 1049
    // Don't initializeBoundaryGeometry()
    // Get BoundaryGeometry that is already initialized
1050
    bgf_m = OpalData::getInstance()->getGlobalGeometry(); 
1051

Daniel Winklehner's avatar
Daniel Winklehner committed
1052
    // External field arrays for dumping
gsell's avatar
gsell committed
1053 1054
    for(int k = 0; k < 2; k++)
        FDext_m[k] = Vector_t(0.0, 0.0, 0.0);
Daniel Winklehner's avatar
Daniel Winklehner committed
1055

gsell's avatar
gsell committed
1056 1057 1058
    extE_m = Vector_t(0.0, 0.0, 0.0);
    extB_m = Vector_t(0.0, 0.0, 0.0);

adelmann's avatar
adelmann committed
1059 1060
    *gmsg << *itsBunch << endl;

gsell's avatar
gsell committed
1061 1062 1063 1064 1065 1066
    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();
1067 1068 1069
    } else if(timeIntegrator_m == 2) {
        *gmsg << "* Multiple time stepping (MTS) integrator" << endl;
        Tracker_MTS();
gsell's avatar
gsell committed
1070 1071 1072 1073
    } else {
        *gmsg << "ERROR: Invalid name of TIMEINTEGRATOR in Track command" << endl;
        exit(1);
    }
Daniel Winklehner's avatar
Daniel Winklehner committed
1074
    *gmsg << "* -------------------------------------" << endl;
adelmann's avatar
Cleanup  
adelmann committed
1075
    *gmsg << "* Finalizing i.e. write data and close files :" << endl;
gsell's avatar
gsell committed
1076 1077 1078
    for(beamline_list::iterator sindex = FieldDimensions.begin(); sindex != FieldDimensions.end(); sindex++) {
        (((*sindex)->second).second)->finalise();
    }
Daniel Winklehner's avatar
Daniel Winklehner committed
1079
    *gmsg << "* -------------------------------------" << endl;
gsell's avatar
gsell committed
1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101
}

/**
   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() {

    BorisPusher pusher;

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

1102
    const double harm = getHarmonicNumber();
gsell's avatar
gsell committed
1103 1104 1105 1106 1107 1108 1109 1110 1111

    // 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;
    }

1112
    initTrackOrbitFile();
gsell's avatar
gsell committed
1113 1114 1115 1116

    int SteptoLastInj = itsBunch->getSteptoLastInj();

    // get data from h5 file for restart run
1117
    if(OpalData::getInstance()->inRestartRun()) {
1118
        restartStep0_m = itsBunch->getLocalTrackStep();
gsell's avatar
gsell committed
1119
        step_m = restartStep0_m;
1120
        if (numBunch_m > 1) itsBunch->resetPartBinID2(eta_m);
1121
        *gmsg << "* Restart at integration step " << restartStep0_m << endl;
gsell's avatar
gsell committed
1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133
    }

    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)
1134
        openFiles(OpalData::getInstance()->getInputBasename());
gsell's avatar
gsell committed
1135 1136

    double const initialReferenceTheta = referenceTheta / 180.0 * pi;
1137

1138
    initDistInGlobalFrame();
gsell's avatar
gsell committed
1139 1140 1141 1142 1143 1144 1145 1146

    //  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;


1147
    int boundpDestroyFreq = 10; // TODO: Should this be treated as a control parameter? 
gsell's avatar
gsell committed
1148 1149 1150 1151

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

adelmann's avatar
Cleanup  
adelmann committed
1152 1153
    *gmsg << "* Single particle trajectory dump frequency is set to " << SinglePartDumpFreq << endl;
    *gmsg << "* Repartition frequency is set to " << Options::repartFreq << endl;
gsell's avatar
gsell committed
1154 1155 1156 1157 1158 1159 1160 1161
    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;
1162
    turnnumber_m = 1;
gsell's avatar
gsell committed
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


    // 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!");
    }

1193
    // apply the plugin elements: probe, collimator, stripper, septum
1194 1195 1196
    // make sure that we apply elements even on first step
    applyPluginElements(dt);

gsell's avatar
gsell committed
1197 1198 1199
    // *****************II***************
    // main integration loop
    // *****************II***************
adelmann's avatar
Cleanup  
adelmann committed
1200
    *gmsg << "* ---------------------------- Start tracking ----------------------------" << endl;
gsell's avatar
gsell committed
1201 1202
    for(; step_m < maxSteps_m; step_m++) {
        bool dumpEachTurn = false;
1203 1204 1205
        if(step_m % SinglePartDumpFreq == 0) {
            singleParticleDump();
        }
gsell's avatar
gsell committed
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 1245 1246
        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;

1247
                        *gmsg << "*** Save beam distribution at turn #" << turnnumber_m << " ***" << endl;
1248
                        *gmsg << "*** After one revolution, Multi-Bunch Mode will be invoked ***" << endl;
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

                    }

                    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);
1276
                        itsBunch->resetPartBinID2(eta_m);
gsell's avatar
gsell committed
1277 1278 1279 1280 1281 1282 1283
                    } else if(multiBunchMode_m == 2) {

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