~ubuntu-branches/ubuntu/trusty/travis/trusty-proposed

tf = sqrt(pow((random->RandomUniform()*2000.0)-1000.0,2) + pow((random->RandomUniform()*2000.0)-1000.0,2) + pow((random->RandomUniform()*2000.0)-1000.0,2) );

206

tedf->AddToBin(tf);

207

tedf->m_pSDEngine->FinishStep();

208

}

209

mprintf("]\n\n");

210

211

mprintf(GREEN,"\n>>> SD Engine >>>\n\n");

212

tedf->m_pSDEngine->FinishAnalysis();

213

tedf->m_pSDEngine->DumpData(tedf);

214

mprintf(GREEN,"\n<<< SD Engine <<<\n\n");

215

tedf->Write("","testrdf.csv","",false);

216

217

return 0;*/

218

219

220

/* // Exp Spectrum Test 2

221

g_pLogFile = OpenFileWrite("travis.log",true);

222

223

CDF *tedf;

224

CRandom *random;

225

226

tedf = new CDF();

227

random = new CRandom();

228

229

tedf->m_fMinVal = 0;

230

tedf->m_fMaxVal = 200.0;

231

tedf->m_iResolution = 200;

232

tedf->Create();

233

234

for (z=0;z<10000;z++)

235

{

236

tf = (random->RandomNormal()*50.0)+60.0;

237

if (tf < 0)

238

continue;

239

240

for (z2=0;z2<200;z2++)

241

{

242

tf2 = 1.0 - (z2/tf);

243

if (tf2 < 0)

244

break;

245

tedf->m_pBin[z2] += tf2;

246

}

247

}

248

249

tf2 = tedf->m_pBin[0];

250

for (z2=0;z2<200;z2++)

251

tedf->m_pBin[z2] /= tf2;

252

253

tedf->Fit_ExpSpectrum(50,0.01,1.0);

254

255

tedf->Write("","exp.csv","",false);

256

257

return 0;*/

258

259

260

/* // Exp Spectrum Test

261

g_pLogFile = OpenFileWrite("travis.log",true);

262

263

CDF *tedf;

264

265

tedf = new CDF();

266

267

tedf->m_fMinVal = 0;

268

tedf->m_fMaxVal = 200.0;

269

tedf->m_iResolution = 200;

270

tedf->Create();

271

272

for (z=0;z<200;z++)

273

{

274

tedf->m_pBin[z] = exp(-0.1*z) + exp(-0.05*z);

275

// tedf->m_pBin[z] = (z<100)?1.0-(z/100.0):0;

276

}

277

278

tedf->Fit_ExpSpectrum(30,0.01,1.0);

279

280

tedf->Write("","exp.csv","",false);

281

282

return 0;*/

283

284

285

/* // Random Test

286

287

CRandom *random;

288

CDF *dfu, *dfn, *dfe;

289

290

random = new CRandom();

291

292

dfu = new CDF();

293

dfu->m_iResolution = 100;

294

dfu->m_fMinVal = 0;

295

dfu->m_fMaxVal = 1;

296

dfu->Create();

297

298

dfn = new CDF();

299

dfn->m_iResolution = 800;

300

dfn->m_fMinVal = -4;

301

dfn->m_fMaxVal = 4;

302

dfn->Create();

303

304

dfe = new CDF();

305

dfe->m_iResolution = 400;

306

dfe->m_fMinVal = 0;

307

dfe->m_fMaxVal = 4;

308

dfe->Create();

309

310

for (z=0;z<1000000;z++)

311

{

312

dfu->AddToBin(random->RandomUniform());

313

dfn->AddToBin(random->RandomNormal());

314

dfe->AddToBin

315

(random->RandomExp());

316

// if ((z%50000) == 0)

317

// mprintf("#");

318

if ((z%10000) == 0)

319

mprintf("%f\n",random->RandomNormal());

320

}

321

mprintf("\n");

322

323

dfu->Write("","uniform.csv","",false);

324

dfn->Write("","normal.csv","",false);

325

dfe->Write("","exp.csv","",false);

326

327

return 0;*/

328

329

/* a = fopen("E:\\tmptraj.xyz","wt");

330

331

for (z=0;z<20000;z++)

332

{

333

mfprintf(a,"2\n\n");

334

mfprintf(a,"C %f %f %f\n",sin(pow(z/50.0,1.0))*(1.2+sin(z/30.0)*0.4),cos(pow(z/50.0,1.0))*(1.2+sin(z/30.0)*0.4),0);

335

mfprintf(a,"Si %f %f %f\n",-sin(pow(z/50.0,1.0))*0.0,-cos(pow(z/50.0,1.0))*0.0,0);

336

}

337

338

fclose(a);

339

return 0;*/

340

341

InitGlobalVars();

342

343

/**** Initialize Local Variables ***/

344

tdmat2.Unity();

345

tq2.Unity();

346

multicounter = 0;

347

pSwapMatrix = NULL;

348

apfa = NULL;

349

tda = NULL;

350

ReactSecondRun = false;

351

/***********************************/

352

353

354

AddElementData();

355

356

try { g_sExeName = new char[strlen(argv[0])+1]; } catch(...) { g_sExeName = NULL; }

357

if (g_sExeName == NULL) NewException((double)(strlen(argv[0])+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

358

359

strcpy(g_sExeName,argv[0]);

360

361

GetTravisPath();

362

363

InstallSignalHandler();

364

365

InitColor();

366

367

g_pLogFile = OpenFileWrite("travis.log",true);

368

369

fprintf(g_pLogFile,"Command line:\n\"");

370

for (z=0;z<argc;z++)

371

{

372

fprintf(g_pLogFile,"%s",argv[z]);

373

if (z < argc-1)

374

fprintf(g_pLogFile," ");

375

}

376

fprintf(g_pLogFile,"\"\n\n");

377

fflush(g_pLogFile);

378

379

showinterval = 1;

380

381

srand(time(NULL));

382

383

#ifdef TARGET_WINDOWS

384

tul = 256;

385

g_sHomeDir = getenv("APPDATA");

386

if (GetComputerName(buf,&tul))

387

{

388

try { g_sHostName = new char[strlen(buf)+1]; } catch(...) { g_sHostName = NULL; }

389

if (g_sHostName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

390

391

strcpy(g_sHostName,buf);

392

} else g_sHostName = NULL;

393

394

g_sWorkingDir = _getcwd(NULL,1024);

395

#elif defined(TARGET_LINUX)

396

g_sHomeDir = getenv("HOME");

397

buf[0] = 0;

398

if (gethostname(buf,256)==0)

399

{

400

try { g_sHostName = new char[strlen(buf)+1]; } catch(...) { g_sHostName = NULL; }

401

if (g_sHostName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

402

403

strcpy(g_sHostName,buf);

404

} else g_sHostName = NULL;

405

406

g_sWorkingDir = getcwd(NULL,1024);

407

#else

408

g_sHomeDir = NULL;

409

g_sHostName = NULL;

410

g_sWorkingDir = NULL;

411

#endif

412

413

ParsePassiveArgs(argc,argv);

414

415

InitAnalyses();

416

417

WriteHeader();

418

419

InitDatabase();

420

421

/* C2DF *t2df;

422

int N;

423

424

t2df = new C2DF();

425

t2df->m_iRes[0] = 150;

426

t2df->m_iRes[1] = 150;

427

t2df->m_fMinVal[0] = 0;

428

t2df->m_fMaxVal[0] = 1.0;

429

t2df->m_fMinVal[1] = 0;

430

t2df->m_fMaxVal[1] = 0.5;

431

t2df->SetLabelX("Relative Cube Edge Length");

432

t2df->SetLabelY("Total mass [g/mol]");

433

t2df->Create();

434

t2df->m_iPlotType = 2;

435

t2df->m_iSmoothGrade = 0;

436

t2df->m_fPlotExp = 0.15;

437

t2df->m_iInterpolationOrder = 1;

438

t2df->m_iPlotPixel = 2000;

439

t2df->m_bContourLines = false;

440

t2df->m_iGPInterpolation = 5;

441

442

N = 1024;

443

444

for (z=0;z<150;z++)

445

{

446

tf = pow((double)(z+1)/150.0,3); // Percentage of total volume

447

448

for (z2=0;z2<=N;z2++)

449

{

450

tf2 = pow(tf,z2) * pow(1.0-tf,N-z2) * BinomialCoeff(N,z2); // Probability for z2 Ar in Cube

451

452

t2df->AddToBin_IntX(z,z2*10.0 / tf / 5600.0 / 5600.0 / 5600.0 * 1.0e9 * 0.0016605,tf2);

453

}

454

}

455

456

457

458

t2df->NormalizeBinIntegral(1000000.0);

459

460

t2df->WriteGnuplotInput("","2df","",false);

461

462

return 0;*/

463

464

/********************************************************************/

465

466

/* CDF *tedf;

467

FILE *tfil;

468

469

g_fTimestepLength = 1.0;

470

g_iTrajSteps = 1000000;

471

472

tedf = new CDF();

473

474

tedf->m_fMinVal = 0;

475

tedf->m_fMaxVal = 40.0;

476

tedf->m_iResolution = 40000;

477

tedf->Create();

478

479

tfil = fopen("D:\\Software\\WaterClassic300Eval\\4b\\rdyn_H2O_[O_H]_P2.csv","rt");

480

fgets(buf,256,tfil);

481

482

for (z=0;z<40000;z++)

483

{

484

fgets(buf,256,tfil);

485

buf[strlen(buf)-1] = 0;

486

p = strchr(buf,';');

487

p++;

488

tf = atof(p);

489

mprintf("%f\n",tf);

490

tedf->m_pBin[z] = tf;

491

}

492

493

fclose(tfil);

494

495

496

try { tedf->m_pParameters = new double*[4+1]; } catch(...) { tedf->m_pParameters = NULL; }

497

if (tedf->m_pParameters == NULL) NewException((double)(4+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

498

499

try { tedf->m_pFitIntegral = new double[4+1]; } catch(...) { tedf->m_pFitIntegral = NULL; }

500

if (tedf->m_pFitIntegral == NULL) NewException((double)(4+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

501

502

try { tedf->m_pCorrCoeff = new double[4+1]; } catch(...) { tedf->m_pCorrCoeff = NULL; }

503

if (tedf->m_pCorrCoeff == NULL) NewException((double)(4+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

504

505

try { tedf->m_pAdditionalSets = new double*[4+1]; } catch(...) { tedf->m_pAdditionalSets = NULL; }

506

if (tedf->m_pAdditionalSets == NULL) NewException((double)(4+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

507

508

try { tedf->m_pAdditionalSetLabels = new char*[4+1]; } catch(...) { tedf->m_pAdditionalSetLabels = NULL; }

509

if (tedf->m_pAdditionalSetLabels == NULL) NewException((double)(4+1)*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

510

511

tedf->m_iAdditionalSets = 4+1;

512

513

for (z2=0;z2<=4;z2++)

514

{

515

tedf->m_pAdditionalSets[z2] = NULL;

516

tedf->m_pAdditionalSetLabels[z2] = NULL;

517

}

518

519

mprintf(YELLOW," Please note: ");

520

mprintf("The lifetime is two times the integral value!\n\n");

521

522

for (z2=1;z2<=4;z2++)

523

tedf->Fit_PolyExp(z2,5000);

524

525

// if (o->m_pDACF->m_iFitDegreeMin != o->m_pDACF->m_iFitDegreeMax)

526

{

527

mprintf(YELLOW," DACF fit integral overview:\n");

528

mprintf(" (use the row with the highest R value)\n\n");

529

mprintf(WHITE," Degree R Integral [ps] Lifetime [ps]\n");

530

for (z2=1;z2<=4;z2++)

531

{

532

if (tedf->m_pFitIntegral[z2] >= 0)

533

mprintf(" %d %10.8f %-10G %-10G\n",z2,tedf->m_pCorrCoeff[z2],tedf->m_pFitIntegral[z2],tedf->m_pFitIntegral[z2]*2.0);

534

else mprintf(" %d %10.8f - -\n",z2,tedf->m_pCorrCoeff[z2]);

535

}

536

mprintf("\n");

537

}

538

539

sprintf(buf,"dacf_D.csv");

540

mprintf(" Saving DACF File as \"%s\"...\n",buf);

541

tedf->Write("",buf,"",false);

542

543

return 0;*/

544

545

546

/********************************************************************/

547

548

549

if (g_bDipolGrimme)

550

{

551

if (argc < 3)

552

DipolGrimme(NULL);

553

else DipolGrimme(argv[2]);

554

return 0;

555

}

556

557

if (!ParseArgs(argc,argv))

558

goto _ende;

559

560

if (g_sInputTraj == NULL)

561

{

562

eprintf(" No trajectory file specified.\n");

563

mprintf(" Please use the -p flag to specify an input trajectory in the command line.\n\n");

564

mprintf(" Enter the file name of the trajectory file to open: [Quit] ");

565

myget(buf);

566

mprintf("\n");

567

if (strlen(buf)==0)

568

{

569

CommandLineHelp();

570

goto _ende;

571

}

572

573

try { g_sInputTraj = new char[strlen(buf)+1]; } catch(...) { g_sInputTraj = NULL; }

574

if (g_sInputTraj == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

575

576

strcpy(g_sInputTraj,buf);

577

}

578

579

if (!DetermineTrajFormat())

580

goto _ende;

581

582

g_bInputRedirected = false;

583

if (g_sInputFile != NULL)

584

{

585

g_fInputFile = fopen(g_sInputFile,"rt");

586

if (g_fInputFile == NULL)

587

{

588

eprintf("Could not open input file \"%s\".\n",g_sInputFile);

589

goto _ende;

590

}

591

g_bInputRedirected = true;

592

}

593

594

if (IsTTY(stdin) && (!g_bInputRedirected))

595

{

596

g_fInput = OpenFileWrite("input.txt",true);

597

g_bInputRedirected = false;

598

inpprintf("! TRAVIS input file\n! Created with TRAVIS version compiled at %s %s\n",__DATE__,__TIME__);

599

600

time(&ltime);

601

today = localtime(&ltime);

602

strcpy(buf,asctime(today));

603

buf[strlen(buf)-1] = 0;

604

inpprintf("! Input file written at %s.\n",buf);

605

} else g_bInputRedirected = true;

606

607

if (g_sInputTraj[0] != 0)

608

{

609

mprintf(" Opening position trajectory %s ...",g_sInputTraj);

610

if (!FileExist(g_sInputTraj))

611

{

612

eprintf("\nError. File does not exist or cannot be read.\n");

613

goto _ende;

614

}

615

}

616

if (g_sInputVel[0] != 0)

617

{

618

mprintf(" Opening velocity trajectory %s ...",g_sInputVel);

619

if (!FileExist(g_sInputVel))

620

{

621

eprintf("\nError. File does not exist or cannot be read.\n");

622

goto _ende;

623

}

624

}

625

if (g_sInputForce[0] != 0)

626

{

627

mprintf(" Opening Force Trajectory %s ...",g_sInputForce);

628

if (!FileExist(g_sInputForce))

629

{

630

eprintf("\nError. File does not exist or cannot be read.\n");

631

goto _ende;

632

}

633

}

634

mprintf("\n");

635

if (g_sInputTraj[0] == 0)

636

{

637

eprintf("Error: No trajectory file specified.\n");

638

goto _ende;

639

}

640

g_fPos = fopen(g_sInputTraj,"rt");

641

if (g_fPos == NULL)

642

{

643

eprintf("Error. Could not open \"%s\".\n",g_sInputTraj);

644

goto _ende;

645

}

646

647

if (!g_TimeStep.ReadTimestep(g_fPos,true))

648

{

649

eprintf("\nError reading first time step from trajectory. Leaving.\n");

650

goto _ende;

651

}

652

653

if (g_bXYZ4thCol)

654

mprintf("\n Found 4th column of numbers in XYZ file.\n");

655

656

g_TimeStep.CalcMinMax();

657

658

if (!g_bStreamInput)

659

{

660

// fgetpos(g_fPos,&fpos);

661

fpos = ftell(g_fPos);

662

fseek(g_fPos,0,SEEK_END);

663

fpos2 = ftell(g_fPos);

664

// fgetpos(g_fPos,&fpos2);

665

fclose(g_fPos);

666

} else fpos2 = -1;

667

668

if (fpos2 < 0)

669

{

670

mprintf("\n Could not determine trajectory file size.\n\n");

671

g_iTrajSteps = -1;

672

} else

673

{

674

g_iTrajSteps = fpos2/fpos;

675

mprintf("\n Trajectory contains approximately %d time steps (file size %s).\n\n",g_iTrajSteps,FormatBytes(fpos2));

676

}

677

678

g_iGesAtomCount = g_TimeStep.m_iGesAtomCount;

679

680

if (g_iGesAtomCount == 0)

681

{

682

eprintf("\n\nNo atoms found. This is probably not what you want. Leaving.\n");

683

goto _ende;

684

}

685

686

g_iGesVirtAtomCount = g_iGesAtomCount;

687

g_TimeStep.AddAtoms();

688

if (g_bUnknownElements)

689

mprintf("\n");

690

691

SortAtoms();

692

mprintf(WHITE," %d atoms in the system: ",g_iGesAtomCount);

693

for (z=0;z<g_oaAtoms.GetSize();z++)

694

{

695

mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);

696

if (z < (int)g_oaAtoms.GetSize()-1)

697

mprintf(", ");

698

}

699

mprintf("\n\n");

700

mprintf(" System extent: X = { %+5.0f .. %+5.0f pm }, dX = %.0f pm\n",g_TimeStep.m_vMin[0],g_TimeStep.m_vMax[0],g_TimeStep.m_vMax[0]-g_TimeStep.m_vMin[0]);

701

mprintf(" (in step 1) Y = { %+5.0f .. %+5.0f pm }, dY = %.0f pm\n",g_TimeStep.m_vMin[1],g_TimeStep.m_vMax[1],g_TimeStep.m_vMax[1]-g_TimeStep.m_vMin[1]);

702

mprintf(" Z = { %+5.0f .. %+5.0f pm }, dZ = %.0f pm\n",g_TimeStep.m_vMin[2],g_TimeStep.m_vMax[2],g_TimeStep.m_vMax[2]-g_TimeStep.m_vMin[2]);

703

704

g_iVirtAtomType = (unsigned char)g_oaAtoms.GetSize();

705

706

xAddAtom("#");

707

708

/****************************/

709

710

if (!GatherInfos())

711

goto _ende;

712

713

/************** Beginn Analyse **************/

714

715

if (g_bStreamInput)

716

{

717

if (g_bScanVelocities)

718

{

719

eprintf("\nError: Velocity pre-analysis not compatible with stream input.\n\n");

720

goto _ende;

721

}

722

723

if ((g_bSaveRefEnv) && (g_iNbhMode == 3))

724

{

725

eprintf("\nError: Neighborhood pre-analysis not compatible with stream input.\n\n");

726

goto _ende;

727

}

728

}

729

730

g_iStartTime = time(NULL);

731

732

if (g_iMaxStep != -1)

733

{

734

g_iTrajSteps = g_iMaxStep;

735

} else

736

{

737

if (g_iTrajSteps != -1)

738

{

739

g_iTrajSteps -= g_iBeginStep;

740

if (g_iTrajSteps < 1)

741

g_iTrajSteps = 1;

742

}

743

}

744

745

if (g_bResp || g_bFFGen)

746

goto _ende;

747

748

g_iStepHistory = 3;

749

multicounter = 0;

750

751

_multiintervalstart:

752

if (g_bMultiInterval)

753

{

754

g_iBeginStep = g_laMultiIntervalStart[multicounter];

755

g_iScanNbhStart = g_iBeginStep;

756

g_iMaxStep = g_laMultiIntervalEnd[multicounter] - g_laMultiIntervalStart[multicounter] + 1;

757

g_iScanNbhSteps = g_iMaxStep;

758

mprintf(YELLOW,"***********************************************\n");

759

mprintf(YELLOW,"*** Interval %2d (%6d - %6d) starting. ***\n",multicounter+1,g_laMultiIntervalStart[multicounter]+1,g_laMultiIntervalEnd[multicounter]+1);

760

mprintf(YELLOW,"***********************************************\n\n");

761

sprintf(multibuf,"_I%d_%d-%d",multicounter+1,g_laMultiIntervalStart[multicounter],g_laMultiIntervalEnd[multicounter]);

762

} else multibuf[0] = 0;

763

764

mprintf(WHITE,">>> Initialization >>>\n\n");

765

766

g_bAbortAnalysis = false;

767

768

if (!g_bStreamInput)

769

{

770

g_fPos = fopen(g_sInputTraj,"rb"); // Eingabedatei erneut oeffnen

771

if (g_fPos == NULL)

772

{

773

eprintf("\nError. Input Trajectory suddenly vanished ^^\n");

774

goto _ende;

775

}

776

if ((g_bNPT) && (g_sNPTFile[0] != 0))

777

{

778

g_fNPTFile = fopen(g_sNPTFile,"rt");

779

if (g_fNPTFile == NULL)

780

{

781

eprintf("\nCould not open cell vector file.\n");

782

goto _ende;

783

}

784

}

785

}

786

787

if (g_iBeginStep != 0)

788

{

789

mprintf("Fast-forwarding to step %d...\n",g_iBeginStep+1);

790

if (g_iBeginStep != g_iScanMolStep)

791

{

792

mprintf(WHITE," [");

793

for (z=0;z<g_iBeginStep;z++)

794

{

795

if (fmod(z,g_iBeginStep/50.0) < 1.0)

796

mprintf(WHITE,"#");

797

if (!g_TimeStep.SkipTimestep(g_fPos))

798

{

799

eprintf("\nError: Unexpected end of position trajectory.\n");

800

goto _ende;

801

}

802

if ((g_bNPT) && (g_sNPTFile[0] != 0))

803

fgets(buf,256,g_fNPTFile);

804

}

805

mprintf(WHITE,"]\n");

806

if (!g_bStreamInput)

807

g_iFastForwardPos = ftell(g_fPos);

808

else g_iFastForwardPos = 0;

809

} else

810

{

811

mprintf(" Position already known from molecule recognition, directly seeking.\n");

812

fseek(g_fPos,g_iFastForwardPos,SEEK_SET);

813

}

814

if (!g_bStreamInput)

815

mprintf(" Step %d begins at offset %lu (%.1f MB).\n\n",g_iBeginStep+1,g_iFastForwardPos,g_iFastForwardPos/1024.0/1024.0);

816

}

817

// fclose(g_fPos);

818

// g_fPos = fopen(g_sInputTraj,"rb");

819

// mprintf("Seek: %d.\n",g_iFastForwardPos);

820

// fseek(g_fPos,g_iFastForwardPos,SEEK_SET);

821

822

if (!g_bStreamInput)

823

{

824

g_TimeStep.ReadTimestep(g_fPos,true);

825

if ((g_bNPT) && (g_sNPTFile[0] != 0))

826

{

827

g_TimeStep.ReadCellVector(g_fNPTFile);

828

fclose(g_fNPTFile);

829

}

830

fclose(g_fPos);

831

}

832

833

g_TimeStep.CalcCenters();

834

835

if (g_bPeriodic)

836

g_TimeStep.UniteMolecules(false);

837

838

if (g_bScanVelocities && (!g_bStreamInput))

839

{

840

mprintf(WHITE,"\n>>> Pre-Analysis for velocity distribution >>>\n\n");

841

842

g_fPos = fopen(g_sInputTraj,"rt"); // Eingabedatei erneut Oeffnen

843

if (g_fPos == NULL)

844

{

845

eprintf("Error. Input Trajectory suddenly vanished ^^\n");

846

return 0;

847

}

848

g_iSteps = 0; // Der Zaehler der Zeitschritte

849

if (g_iScanVelStart != 0)

850

{

851

mprintf("Fast-forwarding to step %d...\n",g_iScanVelStart+1);

852

mprintf(WHITE," [");

853

for (z=0;z<g_iScanVelStart;z++)

854

{

855

if (fmod(z,g_iScanVelStart/60.0) < 1.0)

856

mprintf(WHITE,"#");

857

if (!g_TimeStep.SkipTimestep(g_fPos))

858

break;

859

}

860

mprintf(WHITE,"]\n");

861

}

862

863

while (!feof(g_fPos)) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

864

{

865

if (!g_TimeStep.ReadTimestep(g_fPos,false))

866

goto _endvel;

867

if (g_TimeStep.m_iGesAtomCount == 0)

868

goto _endvel;

869

870

g_TimeStep.CalcCenters();

871

872

if ((g_iSteps % 4) == 0)

873

{

874

if ((g_iSteps % 200) == 0)

875

mprintf("\nStep %6d...",g_iSteps);

876

else mprintf(".");

877

}

878

879

g_iSteps++;

880

881

if ((g_iScanVelSteps > 0) && ((int)g_iSteps >= g_iScanVelSteps))

882

break;

883

}

884

_endvel:

885

886

fclose(g_fPos);

887

888

mprintf(WHITE,"\n<<< End of Pre-Analysis for velocity distribution <<<\n\n");

889

} // END IF g_bScanVelocities

890

891

892

if (g_bSaveRefEnv && (g_iNbhMode == 1))

893

{

894

mprintf("Creating statical neighborhood...\n");

895

g_pNbSet->Scan((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[g_iSaveRefMol]],&g_TimeStep);

896

if (g_bSaveRefWithEnv)

897

{

898

mprintf("Adding reference molecule to neighborhood...\n");

899

g_pNbSet->AddMolecule(g_iFixMol,g_iSaveRefMol);

900

}

901

mprintf("\n");

902

g_pNbSet->Dump();

903

mprintf("\n");

904

}

905

906

if (g_bVACF && g_bGlobalVACF)

907

{

908

mprintf("Initializing Global Velocity Autocorrelation Function...\n");

909

g_pGlobalVACF->Create();

910

911

if (!g_bVACFCacheMode)

912

{

913

if (g_pGlobalVACF->m_iSize > g_iStepHistory)

914

g_iStepHistory = g_pGlobalVACF->m_iSize;

915

} else

916

{

917

mprintf(" VACF Cache: Trying to allocate %s of memory...\n",FormatBytes((double)g_iGesAtomCount*g_iTrajSteps*3.1*sizeof(float)));

918

for (z=0;z<g_iGesAtomCount;z++)

919

{

920

// mprintf("%d: %s: %f\n",z,((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_sLabel,((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_fRadius);

921

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z] > 1000))

922

continue;

923

// mprintf(" --> Ok\n");

924

925

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

926

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

927

928

if (g_iTrajSteps != -1)

929

{

930

ptfa->SetMaxSize((long)(g_iTrajSteps*3.1));

931

ptfa->SetGrow((long)(g_iTrajSteps*0.1));

932

} else ptfa->SetGrow(1000);

933

g_pGlobalVACF->m_oaCache.Add(ptfa);

934

}

935

}

936

}

937

938

if (g_bIRSpec && g_bGlobalIR)

939

{

940

mprintf(" Creating global IR Spectrum...\n");

941

g_pGlobalIR->m_pRDyn->m_fMinVal = 0;

942

g_pGlobalIR->m_pRDyn->m_fMaxVal = g_pGlobalIR->m_iDepth * g_fTimestepLength / 1000.0f;

943

g_pGlobalIR->m_pRDyn->m_iResolution = g_pGlobalIR->m_iDepth/g_pGlobalIR->m_iStride;

944

g_pGlobalIR->m_pRDyn->SetLabelX("Tau [ps]");

945

g_pGlobalIR->m_pRDyn->SetLabelY("Dipole autocorrelation");

946

g_pGlobalIR->m_pRDyn->Create();

947

if (g_bRDynCacheMode)

948

{

949

if (g_iTrajSteps != -1)

950

mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)g_oaSingleMolecules.GetSize()*g_iTrajSteps/g_iStride*3.1*sizeof(float)));

951

else mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)g_oaSingleMolecules.GetSize()*10000/g_iStride*3.1*sizeof(float)));

952

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

953

{

954

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

955

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

956

957

if (g_iTrajSteps != -1)

958

{

959

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.3));

960

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.3));

961

} else ptfa->SetGrow(10000);

962

g_pGlobalIR->m_oaCache.Add(ptfa);

963

}

964

} else

965

{

966

try { g_pGlobalIR->m_pCount = new double[g_pGlobalIR->m_pRDyn->m_iResolution]; } catch(...) { g_pGlobalIR->m_pCount = NULL; }

967

if (g_pGlobalIR->m_pCount == NULL) NewException((double)g_pGlobalIR->m_pRDyn->m_iResolution*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

968

969

for (z2=0;z2<g_pGlobalIR->m_pRDyn->m_iResolution;z2++)

970

g_pGlobalIR->m_pCount[z2] = 0;

971

if (!g_bRDynCacheMode)

972

{

973

if (g_pGlobalIR->m_iDepth > g_iStepHistory)

974

g_iStepHistory = g_pGlobalIR->m_iDepth;

975

}

976

}

977

}

978

979

/* if (g_bSFac)

980

{

981

mprintf(" Creating Structure Factor Analysis...\n");

982

g_pSFac->Create();

983

}*/

984

985

if (g_bSaveCondSnapshot)

986

g_fSaveCondFile = OpenFileWrite("savecondition.xyz",true);

987

988

for (z=0;z<g_oaObserv.GetSize();z++)

989

{

990

mprintf("Initializing Observation %d...\n",z+1);

991

o = (CObservation*)g_oaObserv[z];

992

993

if (g_bAggregation)

994

{

995

mprintf(" Creating Aggregation Functions (%d value sets)...\n",o->m_pDACF->m_oaSubDACFs.GetSize());

996

for (z2=0;z2<o->m_pDACF->m_oaSubDACFs.GetSize();z2++)

997

{

998

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[z2];

999

if (g_bDLDisp)

1000

{

1001

try { dacfsub->m_pDLDisp = new C2DF(); } catch(...) { dacfsub->m_pDLDisp = NULL; }

1002

if (dacfsub->m_pDLDisp == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1003

1004

dacfsub->m_pDLDisp->m_iRes[0] = o->m_pDACF->m_iLifetimeRes;

1005

dacfsub->m_pDLDisp->m_fMinVal[0] = 0.0f;

1006

dacfsub->m_pDLDisp->m_fMaxVal[0] = o->m_pDACF->m_fLargestLifetime;

1007

dacfsub->m_pDLDisp->m_iRes[1] = o->m_pDACF->m_iDisplacementRes;

1008

dacfsub->m_pDLDisp->m_fMinVal[1] = 0.0f;

1009

dacfsub->m_pDLDisp->m_fMaxVal[1] = o->m_pDACF->m_fLargestDisplacement;

1010

dacfsub->m_pDLDisp->Create();

1011

dacfsub->m_pDLDisp->SetLabelX("Lifetime [ps]");

1012

dacfsub->m_pDLDisp->SetLabelY("Displacement [pm]");

1013

}

1014

1015

if (g_bPairMSD)

1016

{

1017

try { dacfsub->m_pPairMSD = new CAF(); } catch(...) { dacfsub->m_pPairMSD = NULL; }

1018

if (dacfsub->m_pPairMSD == NULL) NewException((double)sizeof(CAF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1019

1020

dacfsub->m_pPairMSD->m_iResolution = o->m_pDACF->m_iDACFRes;

1021

dacfsub->m_pPairMSD->m_fMinVal = 0.0f;

1022

dacfsub->m_pPairMSD->m_fMaxVal = o->m_pDACF->m_fLargestLifetime;

1023

dacfsub->m_pPairMSD->Create();

1024

}

1025

1026

if (g_bDDisp)

1027

{

1028

try { dacfsub->m_pDDisp = new CDF(); } catch(...) { dacfsub->m_pDDisp = NULL; }

1029

if (dacfsub->m_pDDisp == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1030

1031

dacfsub->m_pDDisp->m_iResolution = o->m_pDACF->m_iDisplacementRes;

1032

dacfsub->m_pDDisp->m_fMinVal = 0.0f;

1033

dacfsub->m_pDDisp->m_fMaxVal = o->m_pDACF->m_fLargestDisplacement;

1034

dacfsub->m_pDDisp->SetLabelX("Dimer displacement [pm]");

1035

dacfsub->m_pDDisp->SetLabelY("Occurrence");

1036

dacfsub->m_pDDisp->Create();

1037

}

1038

1039

if (g_bDLDF)

1040

{

1041

try { dacfsub->m_pDLDF = new CDF(); } catch(...) { dacfsub->m_pDLDF = NULL; }

1042

if (dacfsub->m_pDLDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1043

1044

dacfsub->m_pDLDF->m_bLeft = true;

1045

dacfsub->m_pDLDF->m_iResolution = o->m_pDACF->m_iLifetimeRes;

1046

dacfsub->m_pDLDF->m_fMinVal = 0.0f;

1047

dacfsub->m_pDLDF->m_fMaxVal = o->m_pDACF->m_fLargestLifetime;

1048

dacfsub->m_pDLDF->SetLabelX("Tau [ps]");

1049

dacfsub->m_pDLDF->SetLabelY("Occurrence");

1050

dacfsub->m_pDLDF->Create();

1051

}

1052

1053

if (g_bDACF)

1054

{

1055

try { dacfsub->m_pDACF = new CDF(); } catch(...) { dacfsub->m_pDACF = NULL; }

1056

if (dacfsub->m_pDACF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1057

1058

dacfsub->m_pDACF->m_bLeft = true;

1059

dacfsub->m_pDACF->m_iResolution = o->m_pDACF->m_iDACFRes;

1060

dacfsub->m_pDACF->m_fMinVal = 0;

1061

dacfsub->m_pDACF->m_fMaxVal = o->m_pDACF->m_iDACFRes * g_fTimestepLength / 1000.0;

1062

dacfsub->m_pDACF->SetLabelX("Tau [ps]");

1063

dacfsub->m_pDACF->SetLabelY("Occurrence");

1064

dacfsub->m_pDACF->Create();

1065

1066

if (dacfsub->m_bNewMode)

1067

{

1068

// mprintf("Create: %d*%d=%d\n",((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize(),((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize(),((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()*((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize());

1069

try { dacfsub->m_piaIntervals = new CxIntArray[((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()*((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize()]; } catch(...) { dacfsub->m_piaIntervals = NULL; }

1070

if (dacfsub->m_piaIntervals == NULL) NewException((double)((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()*((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize()*sizeof(CxIntArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1071

}

1072

}

1073

1074

try { dacfsub->m_pNDF = new CDF(); } catch(...) { dacfsub->m_pNDF = NULL; }

1075

if (dacfsub->m_pNDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1076

1077

dacfsub->m_pNDF->m_iResolution = ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+1;

1078

dacfsub->m_pNDF->m_fMinVal = 0.0f;

1079

dacfsub->m_pNDF->m_fMaxVal = ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+1;

1080

dacfsub->m_pNDF->Create();

1081

}

1082

}

1083

1084

if (g_bSDF)

1085

{

1086

mprintf(" Creating SDF...\n");

1087

o->m_pSDF->m_pSDF->m_fMinVal[0] = -o->m_pSDF->m_fRadius;

1088

o->m_pSDF->m_pSDF->m_fMaxVal[0] = o->m_pSDF->m_fRadius;

1089

o->m_pSDF->m_pSDF->m_fMinVal[1] = -o->m_pSDF->m_fRadius;

1090

o->m_pSDF->m_pSDF->m_fMaxVal[1] = o->m_pSDF->m_fRadius;

1091

o->m_pSDF->m_pSDF->m_fMinVal[2] = -o->m_pSDF->m_fRadius;

1092

o->m_pSDF->m_pSDF->m_fMaxVal[2] = o->m_pSDF->m_fRadius;

1093

o->m_pSDF->m_pSDF->m_iRes[0] = o->m_pSDF->m_iResolution;

1094

o->m_pSDF->m_pSDF->m_iRes[1] = o->m_pSDF->m_iResolution;

1095

o->m_pSDF->m_pSDF->m_iRes[2] = o->m_pSDF->m_iResolution;

1096

o->m_pSDF->m_pSDF->m_iHistogramRes = o->m_pSDF->m_iHistogramRes;

1097

o->m_pSDF->m_pSDF->Create();

/*****************************************************************************

TRAVIS - Trajectory Analyzer and Visualizer

http://www.travis-analyzer.de/

2012-2014 Martin Thomas

This file written by Martin Brehm.

This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the

GNU General Public License for more details.

You should have received a copy of the GNU General Public License

along with this program. If not, see <http://www.gnu.org/licenses/>.

*****************************************************************************/

#include "travis.h"

#include "tools.h"

#include "database.h"

#include "statistics.h"

#include "maintools.h"

#include <float.h>

#include "dacf.h"

#include "lmwrapper.h"

#include "cluster.h"

#include "xdvector3.h"

#include "xdmatrix3.h"

#include "xquaternion.h"

#include "interface.h"

#include "random.h"

#include "ltspec.h"

//#include "structurefactor.h"

#include "plproj.h"

#ifdef TARGET_WINDOWS

#include <windows.h>

#include <direct.h>

#endif

#ifdef TARGET_LINUX

#include <unistd.h>

#endif

/***************************************************************************************************************

********************** Beginn Quellcode ***********************************************************************

***************************************************************************************************************/

int main(int argc, const char *argv[])

{

BTIN;

// FILE *fff;

FILE *a, *tfi;

char buf[256], buf2[64], buf3[256], *p, *q;

int ti=-1, ti2=-1, ti3, cc, cc2, ticomb, tic_r=-1, tic_o=-1;

int z0, z, z2, z3, z4, z5, z6, z7, z8, zr, zs, zi, z2b, z3b;

int z1a, z1t, z2a, z2t;

CxIntArray *a1, *a2;

CAtomGroup *g1, *g2;

int tia[3];

CxVector3 vec0, vec1, vec2, vec3, vec4, vec5, vecv, vecc;

CxMatrix3 mat;

double tf, tf2, /*tfr,*/ tf3, tf4, tfs;

double c0, c1, r;

double *pd;

float *pf;

CMolecule *m, *tm, *m2;

CSingleMolecule *sm, *smfix, *sm2, *tsm;

char tc;

unsigned long t0, t1, eta;

int showinterval;

CObservation *o;

CTimeStep rot_ts;

C3DF *tempSDF;

C3DF *temp3DF;

CDF *tdf;

int sic;

// CxIntArray tempwa, *twa; // "Temporaeres "W"ord-"A"rray

CxIntArray templa, *tla;

CxDoubleArray **apfa; // "A"rray von "P"ointern auf "F"loat-"A"rrays

double *tda; // "T"emporaeres "D"ouble-"Array"

CxByteArray **apba;

CxVec3Array tempvel;

CAtomGroup *atgr, *ag;

struct tm *today;

time_t ltime;

bool secondmolrun, tb, tbs;

int multicounter;

char multibuf[64];

long fpos, fpos2;

CMolBondGroup *bg;

CMolBond *bond;

CxFloatArray tempfa, tempfa2, *ptfa, *ptfab;

100

CxFloatArray *ptfa2, *ptfa3, *ptfa2b;

101

CGrace *gc, *gc2;

102

CFFT *fft/*, *fft2*/;

103

C2DF *temp2df, *tempc2df, **temp2dfa;

104

// CNbSet *nbset;

105

CConditionGroup *cg;

106

// CNbSearch *nbs;

107

int *tpi;

108

bool ReactSecondRun;

109

CAutoCorrelation *ac;

110

CCrossCorrelation *ccr;

111

CDACFSub *dacfsub;

112

CMicroHetObservation *mho;

113

unsigned int *pSwapMatrix;

114

CxDMatrix3 tdmat, tdmat2;

115

CxDVector3 dvec0, dvec1, dvec2, dvec3, dvec4;

116

CxQuaternion tq, tq2;

117

CReorDyn *trdyn;

118

119

#ifdef TARGET_WINDOWS

120

unsigned long tul;

121

#endif

122

123

/* CxVector3 va, vb, vc;

124

125

for (z=0;z<100;z++)

126

{

127

va[0] = ((rand()%20001)-10000)/10000.0;

128

va[1] = ((rand()%20001)-10000)/10000.0;

129

va[2] = ((rand()%20001)-10000)/10000.0;

130

vb[0] = ((rand()%20001)-10000)/10000.0;

131

vb[1] = ((rand()%20001)-10000)/10000.0;

132

vb[2] = ((rand()%20001)-10000)/10000.0;

133

vc[0] = ((rand()%20001)-10000)/10000.0;

134

vc[1] = ((rand()%20001)-10000)/10000.0;

135

vc[2] = ((rand()%20001)-10000)/10000.0;

136

137

tf = Dihedral(va,vb,vc,true);

138

tf2 = Dihedral2(va,vb,vc,true);

139

140

mprintf("%G, %G, %G\n",tf,tf2,tf-tf2);

141

}

142

143

return 0;*/

144

145

/* int maj, min;

146

for (tf=10;tf<=100;tf+=1.0)

147

{

148

CreateTicks(0,tf,maj,min);

149

printf("*******************************\n");

150

}

151

return 0;*/

152

153

154

/* a = fopen("test.xyz","wt");

155

156

for (z=0;z<1000;z++)

157

fprintf(a,"2\n\nNe %f 0.0 0.0\nNe 0.0 0.0 5.0\n",(float)(z%50));

158

159

fclose(a);

160

return 0;*/

161

162

163

/* // RDF Error 2 Particle test

164

g_pLogFile = OpenFileWrite("travis.log",true);

165

166

CDF *tedf;

167

CRandom *random;

168

int bc, bma, bmi;

169

long N;

170

171

tedf = new CDF();

172

random = new CRandom();

173

174

tedf->m_fMinVal = 0;

175

tedf->m_fMaxVal = 1000.0;

176

tedf->m_iResolution = 100;

177

tedf->Create();

178

179

bc = 100;

180

bma = 1000;

181

bmi = 1;

182

183

mprintf(" Initializing SD Engine...\n");

184

tedf->m_pSDEngine = new CSDEngine();

185

tedf->m_pSDEngine->m_iaBlockSizes.SetSize(bc);

186

mprintf(" Using the following %d block sizes:\n",bc);

187

tf2 = 0;

188

for (z4=0;z4<bc;z4++)

189

{

190

tf = 3.0;

191

tedf->m_pSDEngine->m_iaBlockSizes[z4] = (int)((exp(z4*tf/bc)-1.0) / (exp((bc-1.0)*tf/bc)-1.0) * (bma - bmi)) + bmi;

192

mprintf(" %3d: %6d\n",z4+1,tedf->m_pSDEngine->m_iaBlockSizes[z4]);

193

tf2 += (g_iTrajSteps/tedf->m_pSDEngine->m_iaBlockSizes[z4]) + 1;

194

}

195

tf2 *= tedf->m_iResolution * sizeof(double);

196

mprintf("\n This requires %s of memory.\n",FormatBytes(tf2));

197

tedf->m_pSDEngine->Init(tedf->m_iResolution);

198

199

N = 100000;

200

201

mprintf("[");

202

for (z=0;z<N;z++)

203

{

204

if ((z%(N/100))==0)

205

mprintf("#");

206

tf = sqrt(pow((random->RandomUniform()*2000.0)-1000.0,2) + pow((random->RandomUniform()*2000.0)-1000.0,2) + pow((random->RandomUniform()*2000.0)-1000.0,2) );

207

tedf->AddToBin(tf);

208

tedf->m_pSDEngine->FinishStep();

209

}

210

mprintf("]\n\n");

211

212

mprintf(GREEN,"\n>>> SD Engine >>>\n\n");

213

tedf->m_pSDEngine->FinishAnalysis();

214

tedf->m_pSDEngine->DumpData(tedf);

215

mprintf(GREEN,"\n<<< SD Engine <<<\n\n");

216

tedf->Write("","testrdf.csv","",false);

217

218

return 0;*/

219

220

221

/* // Exp Spectrum Test 2

222

g_pLogFile = OpenFileWrite("travis.log",true);

223

224

CDF *tedf;

225

CRandom *random;

226

227

tedf = new CDF();

228

random = new CRandom();

229

230

tedf->m_fMinVal = 0;

231

tedf->m_fMaxVal = 200.0;

232

tedf->m_iResolution = 200;

233

tedf->Create();

234

235

for (z=0;z<10000;z++)

236

{

237

tf = (random->RandomNormal()*50.0)+60.0;

238

if (tf < 0)

239

continue;

240

241

for (z2=0;z2<200;z2++)

242

{

243

tf2 = 1.0 - (z2/tf);

244

if (tf2 < 0)

245

break;

246

tedf->m_pBin[z2] += tf2;

247

}

248

}

249

250

tf2 = tedf->m_pBin[0];

251

for (z2=0;z2<200;z2++)

252

tedf->m_pBin[z2] /= tf2;

253

254

tedf->Fit_ExpSpectrum(50,0.01,1.0);

255

256

tedf->Write("","exp.csv","",false);

257

258

return 0;*/

259

260

261

/* // Exp Spectrum Test

262

g_pLogFile = OpenFileWrite("travis.log",true);

263

264

CDF *tedf;

265

266

tedf = new CDF();

267

268

tedf->m_fMinVal = 0;

269

tedf->m_fMaxVal = 200.0;

270

tedf->m_iResolution = 200;

271

tedf->Create();

272

273

for (z=0;z<200;z++)

274

{

275

tedf->m_pBin[z] = exp(-0.1*z) + exp(-0.05*z);

276

// tedf->m_pBin[z] = (z<100)?1.0-(z/100.0):0;

277

}

278

279

tedf->Fit_ExpSpectrum(30,0.01,1.0);

280

281

tedf->Write("","exp.csv","",false);

282

283

return 0;*/

284

285

286

/* // Random Test

287

288

CRandom *random;

289

CDF *dfu, *dfn, *dfe;

290

291

random = new CRandom();

292

293

dfu = new CDF();

294

dfu->m_iResolution = 100;

295

dfu->m_fMinVal = 0;

296

dfu->m_fMaxVal = 1;

297

dfu->Create();

298

299

dfn = new CDF();

300

dfn->m_iResolution = 800;

301

dfn->m_fMinVal = -4;

302

dfn->m_fMaxVal = 4;

303

dfn->Create();

304

305

dfe = new CDF();

306

dfe->m_iResolution = 400;

307

dfe->m_fMinVal = 0;

308

dfe->m_fMaxVal = 4;

309

dfe->Create();

310

311

for (z=0;z<1000000;z++)

312

{

313

dfu->AddToBin(random->RandomUniform());

314

dfn->AddToBin(random->RandomNormal());

315

dfe->AddToBin

316

(random->RandomExp());

317

// if ((z%50000) == 0)

318

// mprintf("#");

319

if ((z%10000) == 0)

320

mprintf("%f\n",random->RandomNormal());

321

}

322

mprintf("\n");

323

324

dfu->Write("","uniform.csv","",false);

325

dfn->Write("","normal.csv","",false);

326

dfe->Write("","exp.csv","",false);

327

328

return 0;*/

329

330

/* a = fopen("E:\\tmptraj.xyz","wt");

331

332

for (z=0;z<20000;z++)

333

{

334

mfprintf(a,"2\n\n");

335

mfprintf(a,"C %f %f %f\n",sin(pow(z/50.0,1.0))*(1.2+sin(z/30.0)*0.4),cos(pow(z/50.0,1.0))*(1.2+sin(z/30.0)*0.4),0);

336

mfprintf(a,"Si %f %f %f\n",-sin(pow(z/50.0,1.0))*0.0,-cos(pow(z/50.0,1.0))*0.0,0);

337

}

338

339

fclose(a);

340

return 0;*/

341

342

InitGlobalVars();

343

344

/**** Initialize Local Variables ***/

345

tdmat2.Unity();

346

tq2.Unity();

347

multicounter = 0;

348

pSwapMatrix = NULL;

349

apfa = NULL;

350

tda = NULL;

351

ReactSecondRun = false;

352

/***********************************/

353

354

355

AddElementData();

356

357

try { g_sExeName = new char[strlen(argv[0])+1]; } catch(...) { g_sExeName = NULL; }

358

if (g_sExeName == NULL) NewException((double)(strlen(argv[0])+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

359

360

strcpy(g_sExeName,argv[0]);

361

362

GetTravisPath();

363

364

InstallSignalHandler();

365

366

InitColor();

367

368

g_pLogFile = OpenFileWrite("travis.log",true);

369

370

fprintf(g_pLogFile,"Command line:\n\"");

371

for (z=0;z<argc;z++)

372

{

373

fprintf(g_pLogFile,"%s",argv[z]);

374

if (z < argc-1)

375

fprintf(g_pLogFile," ");

376

}

377

fprintf(g_pLogFile,"\"\n\n");

378

fflush(g_pLogFile);

379

380

showinterval = 1;

381

382

srand(time(NULL));

383

384

#ifdef TARGET_WINDOWS

385

tul = 256;

386

g_sHomeDir = getenv("APPDATA");

387

if (GetComputerName(buf,&tul))

388

{

389

try { g_sHostName = new char[strlen(buf)+1]; } catch(...) { g_sHostName = NULL; }

390

if (g_sHostName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

391

392

strcpy(g_sHostName,buf);

393

} else g_sHostName = NULL;

394

395

g_sWorkingDir = _getcwd(NULL,1024);

396

#elif defined(TARGET_LINUX)

397

g_sHomeDir = getenv("HOME");

398

buf[0] = 0;

399

if (gethostname(buf,256)==0)

400

{

401

try { g_sHostName = new char[strlen(buf)+1]; } catch(...) { g_sHostName = NULL; }

402

if (g_sHostName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

403

404

strcpy(g_sHostName,buf);

405

} else g_sHostName = NULL;

406

407

g_sWorkingDir = getcwd(NULL,1024);

408

#else

409

g_sHomeDir = NULL;

410

g_sHostName = NULL;

411

g_sWorkingDir = NULL;

412

#endif

413

414

ParsePassiveArgs(argc,argv);

415

416

InitAnalyses();

417

418

WriteHeader();

419

420

InitDatabase();

421

422

/* C2DF *t2df;

423

int N;

424

425

t2df = new C2DF();

426

t2df->m_iRes[0] = 150;

427

t2df->m_iRes[1] = 150;

428

t2df->m_fMinVal[0] = 0;

429

t2df->m_fMaxVal[0] = 1.0;

430

t2df->m_fMinVal[1] = 0;

431

t2df->m_fMaxVal[1] = 0.5;

432

t2df->SetLabelX("Relative Cube Edge Length");

433

t2df->SetLabelY("Total mass [g/mol]");

434

t2df->Create();

435

t2df->m_iPlotType = 2;

436

t2df->m_iSmoothGrade = 0;

437

t2df->m_fPlotExp = 0.15;

438

t2df->m_iInterpolationOrder = 1;

439

t2df->m_iPlotPixel = 2000;

440

t2df->m_bContourLines = false;

441

t2df->m_iGPInterpolation = 5;

442

443

N = 1024;

444

445

for (z=0;z<150;z++)

446

{

447

tf = pow((double)(z+1)/150.0,3); // Percentage of total volume

448

449

for (z2=0;z2<=N;z2++)

450

{

451

tf2 = pow(tf,z2) * pow(1.0-tf,N-z2) * BinomialCoeff(N,z2); // Probability for z2 Ar in Cube

452

453

t2df->AddToBin_IntX(z,z2*10.0 / tf / 5600.0 / 5600.0 / 5600.0 * 1.0e9 * 0.0016605,tf2);

454

}

455

}

456

457

458

459

t2df->NormalizeBinIntegral(1000000.0);

460

461

t2df->WriteGnuplotInput("","2df","",false);

462

463

return 0;*/

464

465

/********************************************************************/

466

467

/* CDF *tedf;

468

FILE *tfil;

469

470

g_fTimestepLength = 1.0;

471

g_iTrajSteps = 1000000;

472

473

tedf = new CDF();

474

475

tedf->m_fMinVal = 0;

476

tedf->m_fMaxVal = 40.0;

477

tedf->m_iResolution = 40000;

478

tedf->Create();

479

480

tfil = fopen("D:\\Software\\WaterClassic300Eval\\4b\\rdyn_H2O_[O_H]_P2.csv","rt");

481

fgets(buf,256,tfil);

482

483

for (z=0;z<40000;z++)

484

{

485

fgets(buf,256,tfil);

486

buf[strlen(buf)-1] = 0;

487

p = strchr(buf,';');

488

p++;

489

tf = atof(p);

490

mprintf("%f\n",tf);

491

tedf->m_pBin[z] = tf;

492

}

493

494

fclose(tfil);

495

496

497

try { tedf->m_pParameters = new double*[4+1]; } catch(...) { tedf->m_pParameters = NULL; }

498

if (tedf->m_pParameters == NULL) NewException((double)(4+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

499

500

try { tedf->m_pFitIntegral = new double[4+1]; } catch(...) { tedf->m_pFitIntegral = NULL; }

501

if (tedf->m_pFitIntegral == NULL) NewException((double)(4+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

502

503

try { tedf->m_pCorrCoeff = new double[4+1]; } catch(...) { tedf->m_pCorrCoeff = NULL; }

504

if (tedf->m_pCorrCoeff == NULL) NewException((double)(4+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

505

506

try { tedf->m_pAdditionalSets = new double*[4+1]; } catch(...) { tedf->m_pAdditionalSets = NULL; }

507

if (tedf->m_pAdditionalSets == NULL) NewException((double)(4+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

508

509

try { tedf->m_pAdditionalSetLabels = new char*[4+1]; } catch(...) { tedf->m_pAdditionalSetLabels = NULL; }

510

if (tedf->m_pAdditionalSetLabels == NULL) NewException((double)(4+1)*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

511

512

tedf->m_iAdditionalSets = 4+1;

513

514

for (z2=0;z2<=4;z2++)

515

{

516

tedf->m_pAdditionalSets[z2] = NULL;

517

tedf->m_pAdditionalSetLabels[z2] = NULL;

518

}

519

520

mprintf(YELLOW," Please note: ");

521

mprintf("The lifetime is two times the integral value!\n\n");

522

523

for (z2=1;z2<=4;z2++)

524

tedf->Fit_PolyExp(z2,5000);

525

526

// if (o->m_pDACF->m_iFitDegreeMin != o->m_pDACF->m_iFitDegreeMax)

527

{

528

mprintf(YELLOW," DACF fit integral overview:\n");

529

mprintf(" (use the row with the highest R value)\n\n");

530

mprintf(WHITE," Degree R Integral [ps] Lifetime [ps]\n");

531

for (z2=1;z2<=4;z2++)

532

{

533

if (tedf->m_pFitIntegral[z2] >= 0)

534

mprintf(" %d %10.8f %-10G %-10G\n",z2,tedf->m_pCorrCoeff[z2],tedf->m_pFitIntegral[z2],tedf->m_pFitIntegral[z2]*2.0);

535

else mprintf(" %d %10.8f - -\n",z2,tedf->m_pCorrCoeff[z2]);

536

}

537

mprintf("\n");

538

}

539

540

sprintf(buf,"dacf_D.csv");

541

mprintf(" Saving DACF File as \"%s\"...\n",buf);

542

tedf->Write("",buf,"",false);

543

544

return 0;*/

545

546

547

/********************************************************************/

548

549

550

if (g_bDipolGrimme)

551

{

552

if (argc < 3)

553

DipolGrimme(NULL);

554

else DipolGrimme(argv[2]);

555

return 0;

556

}

557

558

if (!ParseArgs(argc,argv))

559

goto _ende;

560

561

if (g_sInputTraj == NULL)

562

{

563

eprintf(" No trajectory file specified.\n");

564

mprintf(" Please use the -p flag to specify an input trajectory in the command line.\n\n");

565

566

if (argc == 1)

567

{

568

mprintf(" Enter the file name of the trajectory file to open: [Quit] ");

569

myget(buf);

570

mprintf("\n");

571

if (strlen(buf)==0)

572

{

573

CommandLineHelp();

574

goto _ende;

575

}

576

577

try { g_sInputTraj = new char[strlen(buf)+1]; } catch(...) { g_sInputTraj = NULL; }

578

if (g_sInputTraj == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

579

580

strcpy(g_sInputTraj,buf);

581

} else

582

{

583

CommandLineHelp();

584

goto _ende;

585

}

586

}

587

588

if (!DetermineTrajFormat())

589

goto _ende;

590

591

g_bInputRedirected = false;

592

if (g_sInputFile != NULL)

593

{

594

g_fInputFile = fopen(g_sInputFile,"rt");

595

if (g_fInputFile == NULL)

596

{

597

eprintf("Could not open input file \"%s\".\n",g_sInputFile);

598

goto _ende;

599

}

600

g_bInputRedirected = true;

601

}

602

603

if (IsTTY(stdin) && (!g_bInputRedirected))

604

{

605

g_fInput = OpenFileWrite("input.txt",true);

606

g_bInputRedirected = false;

607

inpprintf("! TRAVIS input file\n! Created with TRAVIS version compiled at %s %s\n",__DATE__,__TIME__);

608

609

time(&ltime);

610

today = localtime(&ltime);

611

strcpy(buf,asctime(today));

612

buf[strlen(buf)-1] = 0;

613

inpprintf("! Input file written at %s.\n",buf);

614

} else g_bInputRedirected = true;

615

616

if (g_sInputTraj[0] != 0)

617

{

618

mprintf(" Opening position trajectory %s ...",g_sInputTraj);

619

if (!FileExist(g_sInputTraj))

620

{

621

eprintf("\nError. File does not exist or cannot be read.\n");

622

goto _ende;

623

}

624

}

625

if (g_sInputVel[0] != 0)

626

{

627

mprintf(" Opening velocity trajectory %s ...",g_sInputVel);

628

if (!FileExist(g_sInputVel))

629

{

630

eprintf("\nError. File does not exist or cannot be read.\n");

631

goto _ende;

632

}

633

}

634

if (g_sInputForce[0] != 0)

635

{

636

mprintf(" Opening Force Trajectory %s ...",g_sInputForce);

637

if (!FileExist(g_sInputForce))

638

{

639

eprintf("\nError. File does not exist or cannot be read.\n");

640

goto _ende;

641

}

642

}

643

mprintf("\n");

644

if (g_sInputTraj[0] == 0)

645

{

646

eprintf("Error: No trajectory file specified.\n");

647

goto _ende;

648

}

649

g_fPos = fopen(g_sInputTraj,"rt");

650

if (g_fPos == NULL)

651

{

652

eprintf("Error. Could not open \"%s\".\n",g_sInputTraj);

653

goto _ende;

654

}

655

656

if (!g_TimeStep.ReadTimestep(g_fPos,true))

657

{

658

eprintf("\nError reading first time step from trajectory. Leaving.\n");

659

goto _ende;

660

}

661

662

if (g_bXYZ4thCol)

663

mprintf("\n Found 4th column of numbers in XYZ file.\n");

664

665

g_TimeStep.CalcMinMax();

666

667

if (!g_bStreamInput)

668

{

669

// fgetpos(g_fPos,&fpos);

670

fpos = ftell(g_fPos);

671

fseek(g_fPos,0,SEEK_END);

672

fpos2 = ftell(g_fPos);

673

// fgetpos(g_fPos,&fpos2);

674

fclose(g_fPos);

675

} else fpos2 = -1;

676

677

if (fpos2 < 0)

678

{

679

mprintf("\n Could not determine trajectory file size.\n\n");

680

g_iTrajSteps = -1;

681

} else

682

{

683

g_iTrajSteps = fpos2/fpos;

684

mprintf("\n Trajectory contains approximately %d time steps (file size %s).\n\n",g_iTrajSteps,FormatBytes(fpos2));

685

}

686

687

g_iGesAtomCount = g_TimeStep.m_iGesAtomCount;

688

689

if (g_iGesAtomCount == 0)

690

{

691

eprintf("\n\nNo atoms found. This is probably not what you want. Leaving.\n");

692

goto _ende;

693

}

694

695

g_iGesVirtAtomCount = g_iGesAtomCount;

696

g_TimeStep.AddAtoms();

697

if (g_bUnknownElements)

698

mprintf("\n");

699

700

SortAtoms();

701

mprintf(WHITE," %d atoms in the system: ",g_iGesAtomCount);

702

for (z=0;z<g_oaAtoms.GetSize();z++)

703

{

704

mprintf("%dx %s",((CAtom*)g_oaAtoms[z])->m_iCount,((CAtom*)g_oaAtoms[z])->m_sName);

705

if (z < (int)g_oaAtoms.GetSize()-1)

706

mprintf(", ");

707

}

708

mprintf("\n\n");

709

mprintf(" System extent: X = { %+5.0f .. %+5.0f pm }, dX = %.0f pm\n",g_TimeStep.m_vMin[0],g_TimeStep.m_vMax[0],g_TimeStep.m_vMax[0]-g_TimeStep.m_vMin[0]);

710

mprintf(" (in step 1) Y = { %+5.0f .. %+5.0f pm }, dY = %.0f pm\n",g_TimeStep.m_vMin[1],g_TimeStep.m_vMax[1],g_TimeStep.m_vMax[1]-g_TimeStep.m_vMin[1]);

711

mprintf(" Z = { %+5.0f .. %+5.0f pm }, dZ = %.0f pm\n",g_TimeStep.m_vMin[2],g_TimeStep.m_vMax[2],g_TimeStep.m_vMax[2]-g_TimeStep.m_vMin[2]);

712

713

g_iVirtAtomType = (unsigned char)g_oaAtoms.GetSize();

714

715

xAddAtom("#");

716

717

/****************************/

718

719

if (!GatherInfos())

720

goto _ende;

721

722

/************** Beginn Analyse **************/

723

724

if (g_bStreamInput)

725

{

726

if (g_bScanVelocities)

727

{

728

eprintf("\nError: Velocity pre-analysis not compatible with stream input.\n\n");

729

goto _ende;

730

}

731

732

if ((g_bSaveRefEnv) && (g_iNbhMode == 3))

733

{

734

eprintf("\nError: Neighborhood pre-analysis not compatible with stream input.\n\n");

735

goto _ende;

736

}

737

}

738

739

g_iStartTime = time(NULL);

740

741

if (g_iMaxStep != -1)

742

{

743

g_iTrajSteps = g_iMaxStep;

744

} else

745

{

746

if (g_iTrajSteps != -1)

747

{

748

g_iTrajSteps -= g_iBeginStep;

749

if (g_iTrajSteps < 1)

750

g_iTrajSteps = 1;

751

}

752

}

753

754

if (g_bResp || g_bFFGen)

755

goto _ende;

756

757

g_iStepHistory = 3;

758

multicounter = 0;

759

760

_multiintervalstart:

761

if (g_bMultiInterval)

762

{

763

g_iBeginStep = g_laMultiIntervalStart[multicounter];

764

g_iScanNbhStart = g_iBeginStep;

765

g_iMaxStep = g_laMultiIntervalEnd[multicounter] - g_laMultiIntervalStart[multicounter] + 1;

766

g_iScanNbhSteps = g_iMaxStep;

767

mprintf(YELLOW,"***********************************************\n");

768

mprintf(YELLOW,"*** Interval %2d (%6d - %6d) starting. ***\n",multicounter+1,g_laMultiIntervalStart[multicounter]+1,g_laMultiIntervalEnd[multicounter]+1);

769

mprintf(YELLOW,"***********************************************\n\n");

770

sprintf(multibuf,"_I%d_%d-%d",multicounter+1,g_laMultiIntervalStart[multicounter],g_laMultiIntervalEnd[multicounter]);

771

} else multibuf[0] = 0;

772

773

mprintf(WHITE,">>> Initialization >>>\n\n");

774

775

g_bAbortAnalysis = false;

776

777

if (!g_bStreamInput)

778

{

779

g_fPos = fopen(g_sInputTraj,"rb"); // Eingabedatei erneut oeffnen

780

if (g_fPos == NULL)

781

{

782

eprintf("\nError. Input Trajectory suddenly vanished ^^\n");

783

goto _ende;

784

}

785

if ((g_bNPT) && (g_sNPTFile[0] != 0))

786

{

787

g_fNPTFile = fopen(g_sNPTFile,"rt");

788

if (g_fNPTFile == NULL)

789

{

790

eprintf("\nCould not open cell vector file.\n");

791

goto _ende;

792

}

793

}

794

}

795

796

if (g_iBeginStep != 0)

797

{

798

mprintf("Fast-forwarding to step %d...\n",g_iBeginStep+1);

799

if (g_iBeginStep != g_iScanMolStep)

800

{

801

mprintf(WHITE," [");

802

for (z=0;z<g_iBeginStep;z++)

803

{

804

if (fmod(z,g_iBeginStep/50.0) < 1.0)

805

mprintf(WHITE,"#");

806

if (!g_TimeStep.SkipTimestep(g_fPos))

807

{

808

eprintf("\nError: Unexpected end of position trajectory.\n");

809

goto _ende;

810

}

811

if ((g_bNPT) && (g_sNPTFile[0] != 0))

812

fgets(buf,256,g_fNPTFile);

813

}

814

mprintf(WHITE,"]\n");

815

if (!g_bStreamInput)

816

g_iFastForwardPos = ftell(g_fPos);

817

else g_iFastForwardPos = 0;

818

} else

819

{

820

mprintf(" Position already known from molecule recognition, directly seeking.\n");

821

fseek(g_fPos,g_iFastForwardPos,SEEK_SET);

822

}

823

if (!g_bStreamInput)

824

mprintf(" Step %d begins at offset %lu (%.1f MB).\n\n",g_iBeginStep+1,g_iFastForwardPos,g_iFastForwardPos/1024.0/1024.0);

825

}

826

// fclose(g_fPos);

827

// g_fPos = fopen(g_sInputTraj,"rb");

828

// mprintf("Seek: %d.\n",g_iFastForwardPos);

829

// fseek(g_fPos,g_iFastForwardPos,SEEK_SET);

830

831

if (!g_bStreamInput)

832

{

833

g_TimeStep.ReadTimestep(g_fPos,true);

834

if ((g_bNPT) && (g_sNPTFile[0] != 0))

835

{

836

g_TimeStep.ReadCellVector(g_fNPTFile);

837

fclose(g_fNPTFile);

838

}

839

fclose(g_fPos);

840

}

841

842

g_TimeStep.CalcCenters();

843

844

if (g_bPeriodic)

845

g_TimeStep.UniteMolecules(false);

846

847

if (g_bScanVelocities && (!g_bStreamInput))

848

{

849

mprintf(WHITE,"\n>>> Pre-Analysis for velocity distribution >>>\n\n");

850

851

g_fPos = fopen(g_sInputTraj,"rt"); // Eingabedatei erneut Oeffnen

852

if (g_fPos == NULL)

853

{

854

eprintf("Error. Input Trajectory suddenly vanished ^^\n");

855

return 0;

856

}

857

g_iSteps = 0; // Der Zaehler der Zeitschritte

858

if (g_iScanVelStart != 0)

859

{

860

mprintf("Fast-forwarding to step %d...\n",g_iScanVelStart+1);

861

mprintf(WHITE," [");

862

for (z=0;z<g_iScanVelStart;z++)

863

{

864

if (fmod(z,g_iScanVelStart/60.0) < 1.0)

865

mprintf(WHITE,"#");

866

if (!g_TimeStep.SkipTimestep(g_fPos))

867

break;

868

}

869

mprintf(WHITE,"]\n");

870

}

871

872

while (!feof(g_fPos)) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

873

{

874

if (!g_TimeStep.ReadTimestep(g_fPos,false))

875

goto _endvel;

876

if (g_TimeStep.m_iGesAtomCount == 0)

877

goto _endvel;

878

879

g_TimeStep.CalcCenters();

880

881

if ((g_iSteps % 4) == 0)

882

{

883

if ((g_iSteps % 200) == 0)

884

mprintf("\nStep %6d...",g_iSteps);

885

else mprintf(".");

886

}

887

888

g_iSteps++;

889

890

if ((g_iScanVelSteps > 0) && ((int)g_iSteps >= g_iScanVelSteps))

891

break;

892

}

893

_endvel:

894

895

fclose(g_fPos);

896

897

mprintf(WHITE,"\n<<< End of Pre-Analysis for velocity distribution <<<\n\n");

898

} // END IF g_bScanVelocities

899

900

901

if (g_bSaveRefEnv && (g_iNbhMode == 1))

902

{

903

mprintf("Creating statical neighborhood...\n");

904

g_pNbSet->Scan((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[g_iSaveRefMol]],&g_TimeStep);

905

if (g_bSaveRefWithEnv)

906

{

907

mprintf("Adding reference molecule to neighborhood...\n");

908

g_pNbSet->AddMolecule(g_iFixMol,g_iSaveRefMol);

909

}

910

mprintf("\n");

911

g_pNbSet->Dump();

912

mprintf("\n");

913

}

914

915

if (g_bVACF && g_bGlobalVACF)

916

{

917

mprintf("Initializing Global Velocity Autocorrelation Function...\n");

918

g_pGlobalVACF->Create();

919

920

if (!g_bVACFCacheMode)

921

{

922

if (g_pGlobalVACF->m_iSize > g_iStepHistory)

923

g_iStepHistory = g_pGlobalVACF->m_iSize;

924

} else

925

{

926

mprintf(" VACF Cache: Trying to allocate %s of memory...\n",FormatBytes((double)g_iGesAtomCount*g_iTrajSteps*3.1*sizeof(float)));

927

for (z=0;z<g_iGesAtomCount;z++)

928

{

929

// mprintf("%d: %s: %f\n",z,((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_sLabel,((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_fRadius);

930

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z] > 1000))

931

continue;

932

// mprintf(" --> Ok\n");

933

934

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

935

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

936

937

if (g_iTrajSteps != -1)

938

{

939

ptfa->SetMaxSize((long)(g_iTrajSteps*3.1));

940

ptfa->SetGrow((long)(g_iTrajSteps*0.1));

941

} else ptfa->SetGrow(1000);

942

g_pGlobalVACF->m_oaCache.Add(ptfa);

943

}

944

}

945

}

946

947

if (g_bIRSpec && g_bGlobalIR)

948

{

949

mprintf(" Creating global IR Spectrum...\n");

950

g_pGlobalIR->m_pRDyn->m_fMinVal = 0;

951

g_pGlobalIR->m_pRDyn->m_fMaxVal = g_pGlobalIR->m_iDepth * g_fTimestepLength / 1000.0f;

952

g_pGlobalIR->m_pRDyn->m_iResolution = g_pGlobalIR->m_iDepth/g_pGlobalIR->m_iStride;

953

g_pGlobalIR->m_pRDyn->SetLabelX("Tau [ps]");

954

g_pGlobalIR->m_pRDyn->SetLabelY("Dipole autocorrelation");

955

g_pGlobalIR->m_pRDyn->Create();

956

if (g_bRDynCacheMode)

957

{

958

if (g_iTrajSteps != -1)

959

mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)g_oaSingleMolecules.GetSize()*g_iTrajSteps/g_iStride*3.1*sizeof(float)));

960

else mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)g_oaSingleMolecules.GetSize()*10000/g_iStride*3.1*sizeof(float)));

961

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

962

{

963

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

964

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

965

966

if (g_iTrajSteps != -1)

967

{

968

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.3));

969

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.3));

970

} else ptfa->SetGrow(10000);

971

g_pGlobalIR->m_oaCache.Add(ptfa);

972

}

973

} else

974

{

975

try { g_pGlobalIR->m_pCount = new double[g_pGlobalIR->m_pRDyn->m_iResolution]; } catch(...) { g_pGlobalIR->m_pCount = NULL; }

976

if (g_pGlobalIR->m_pCount == NULL) NewException((double)g_pGlobalIR->m_pRDyn->m_iResolution*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

977

978

for (z2=0;z2<g_pGlobalIR->m_pRDyn->m_iResolution;z2++)

979

g_pGlobalIR->m_pCount[z2] = 0;

980

if (!g_bRDynCacheMode)

981

{

982

if (g_pGlobalIR->m_iDepth > g_iStepHistory)

983

g_iStepHistory = g_pGlobalIR->m_iDepth;

984

}

985

}

986

}

987

988

/* if (g_bSFac)

989

{

990

mprintf(" Creating Structure Factor Analysis...\n");

991

g_pSFac->Create();

992

}*/

993

994

if (g_bSaveCondSnapshot)

995

g_fSaveCondFile = OpenFileWrite("savecondition.xyz",true);

996

997

for (z=0;z<g_oaObserv.GetSize();z++)

998

{

999

mprintf("Initializing Observation %d...\n",z+1);

1000

o = (CObservation*)g_oaObserv[z];

1001

1002

if (g_bAggregation)

1003

{

1004

mprintf(" Creating Aggregation Functions (%d value sets)...\n",o->m_pDACF->m_oaSubDACFs.GetSize());

1005

for (z2=0;z2<o->m_pDACF->m_oaSubDACFs.GetSize();z2++)

1006

{

1007

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[z2];

1008

if (g_bDLDisp)

1009

{

1010

try { dacfsub->m_pDLDisp = new C2DF(); } catch(...) { dacfsub->m_pDLDisp = NULL; }

1011

if (dacfsub->m_pDLDisp == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1012

1013

dacfsub->m_pDLDisp->m_iRes[0] = o->m_pDACF->m_iLifetimeRes;

1014

dacfsub->m_pDLDisp->m_fMinVal[0] = 0.0f;

1015

dacfsub->m_pDLDisp->m_fMaxVal[0] = o->m_pDACF->m_fLargestLifetime;

1016

dacfsub->m_pDLDisp->m_iRes[1] = o->m_pDACF->m_iDisplacementRes;

1017

dacfsub->m_pDLDisp->m_fMinVal[1] = 0.0f;

1018

dacfsub->m_pDLDisp->m_fMaxVal[1] = o->m_pDACF->m_fLargestDisplacement;

1019

dacfsub->m_pDLDisp->Create();

1020

dacfsub->m_pDLDisp->SetLabelX("Lifetime [ps]");

1021

dacfsub->m_pDLDisp->SetLabelY("Displacement [pm]");

1022

}

1023

1024

if (g_bPairMSD)

1025

{

1026

try { dacfsub->m_pPairMSD = new CAF(); } catch(...) { dacfsub->m_pPairMSD = NULL; }

1027

if (dacfsub->m_pPairMSD == NULL) NewException((double)sizeof(CAF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1028

1029

dacfsub->m_pPairMSD->m_iResolution = o->m_pDACF->m_iDACFRes;

1030

dacfsub->m_pPairMSD->m_fMinVal = 0.0f;

1031

dacfsub->m_pPairMSD->m_fMaxVal = o->m_pDACF->m_fLargestLifetime;

1032

dacfsub->m_pPairMSD->Create();

1033

}

1034

1035

if (g_bDDisp)

1036

{

1037

try { dacfsub->m_pDDisp = new CDF(); } catch(...) { dacfsub->m_pDDisp = NULL; }

1038

if (dacfsub->m_pDDisp == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1039

1040

dacfsub->m_pDDisp->m_iResolution = o->m_pDACF->m_iDisplacementRes;

1041

dacfsub->m_pDDisp->m_fMinVal = 0.0f;

1042

dacfsub->m_pDDisp->m_fMaxVal = o->m_pDACF->m_fLargestDisplacement;

1043

dacfsub->m_pDDisp->SetLabelX("Dimer displacement [pm]");

1044

dacfsub->m_pDDisp->SetLabelY("Occurrence");

1045

dacfsub->m_pDDisp->Create();

1046

}

1047

1048

if (g_bDLDF)

1049

{

1050

try { dacfsub->m_pDLDF = new CDF(); } catch(...) { dacfsub->m_pDLDF = NULL; }

1051

if (dacfsub->m_pDLDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1052

1053

dacfsub->m_pDLDF->m_bLeft = true;

1054

dacfsub->m_pDLDF->m_iResolution = o->m_pDACF->m_iLifetimeRes;

1055

dacfsub->m_pDLDF->m_fMinVal = 0.0f;

1056

dacfsub->m_pDLDF->m_fMaxVal = o->m_pDACF->m_fLargestLifetime;

1057

dacfsub->m_pDLDF->SetLabelX("Tau [ps]");

1058

dacfsub->m_pDLDF->SetLabelY("Occurrence");

1059

dacfsub->m_pDLDF->Create();

1060

}

1061

1062

if (g_bDACF)

1063

{

1064

try { dacfsub->m_pDACF = new CDF(); } catch(...) { dacfsub->m_pDACF = NULL; }

1065

if (dacfsub->m_pDACF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1066

1067

dacfsub->m_pDACF->m_bLeft = true;

1068

dacfsub->m_pDACF->m_iResolution = o->m_pDACF->m_iDACFRes;

1069

dacfsub->m_pDACF->m_fMinVal = 0;

1070

dacfsub->m_pDACF->m_fMaxVal = o->m_pDACF->m_iDACFRes * g_fTimestepLength / 1000.0;

1071

dacfsub->m_pDACF->SetLabelX("Tau [ps]");

1072

dacfsub->m_pDACF->SetLabelY("Occurrence");

1073

dacfsub->m_pDACF->Create();

1074

1075

if (dacfsub->m_bNewMode)

1076

{

1077

1078

1079

1080

}

1081

}

1082

1083

try { dacfsub->m_pNDF = new CDF(); } catch(...) { dacfsub->m_pNDF = NULL; }

1084

if (dacfsub->m_pNDF == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1085

1086

dacfsub->m_pNDF->m_iResolution = ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+1;

1087

dacfsub->m_pNDF->m_fMinVal = 0.0f;

1088

dacfsub->m_pNDF->m_fMaxVal = ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+1;

1089

dacfsub->m_pNDF->Create();

1090

}

1091

}

1092

1093

if (g_bSDF)

1094

{

1095

mprintf(" Creating SDF...\n");

1096

o->m_pSDF->m_pSDF->m_fMinVal[0] = -o->m_pSDF->m_fRadius;

1097

o->m_pSDF->m_pSDF->m_fMaxVal[0] = o->m_pSDF->m_fRadius;

1098

o->m_pSDF->m_pSDF->m_fMinVal[1] = -o->m_pSDF->m_fRadius;

1099

o->m_pSDF->m_pSDF->m_fMaxVal[1] = o->m_pSDF->m_fRadius;

1100

o->m_pSDF->m_pSDF->m_fMinVal[2] = -o->m_pSDF->m_fRadius;

1101

o->m_pSDF->m_pSDF->m_fMaxVal[2] = o->m_pSDF->m_fRadius;

1102

o->m_pSDF->m_pSDF->m_iRes[0] = o->m_pSDF->m_iResolution;

1103

o->m_pSDF->m_pSDF->m_iRes[1] = o->m_pSDF->m_iResolution;

1104

o->m_pSDF->m_pSDF->m_iRes[2] = o->m_pSDF->m_iResolution;

1105

o->m_pSDF->m_pSDF->m_iHistogramRes = o->m_pSDF->m_iHistogramRes;

1106

o->m_pSDF->m_pSDF->Create();

1107

// mprintf("Observation %d: Creating %d VecArrays.\n",z+1,o->m_iShowMolCount);

1108

1109

try { o->m_pSDF->m_vaData = new CxVec3Array[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_vaData = NULL; }

1110

if (o->m_pSDF->m_vaData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxVec3Array),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1111

1112

if (o->m_pSDF->m_bVdWSpheres)

1113

{

1114

try { o->m_pSDF->m_faRadius = new CxFloatArray[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_faRadius = NULL; }

1115

if (o->m_pSDF->m_faRadius == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1116

}

1117

1118

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1119

{

1120

try { o->m_pSDF->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_baDataEnabled = NULL; }

1121

if (o->m_pSDF->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1122

}

1123

}

1124

1125

if (g_bPlProj)

1126

{

1127

mprintf(" Creating Plane Projection DF...\n");

1128

o->m_pPlProj->m_p2DF->m_fMinVal[0] = o->m_pPlProj->m_fMinVal[0];

1129

o->m_pPlProj->m_p2DF->m_fMaxVal[0] = o->m_pPlProj->m_fMaxVal[0];

1130

o->m_pPlProj->m_p2DF->m_fMinVal[1] = o->m_pPlProj->m_fMinVal[1];

1131

o->m_pPlProj->m_p2DF->m_fMaxVal[1] = o->m_pPlProj->m_fMaxVal[1];

1132

o->m_pPlProj->m_p2DF->m_iRes[0] = o->m_pPlProj->m_iResolution[0];

1133

o->m_pPlProj->m_p2DF->m_iRes[1] = o->m_pPlProj->m_iResolution[1];

1134

o->m_pPlProj->m_p2DF->m_iHistogramRes = o->m_pPlProj->m_iHistogramRes;

1135

o->m_pPlProj->m_p2DF->SetLabelX("X [pm]");

1136

o->m_pPlProj->m_p2DF->SetLabelY("Y [pm]");

1137

o->m_pPlProj->m_p2DF->Create();

1098

1138

// mprintf("Observation %d: Creating %d VecArrays.\n",z+1,o->m_iShowMolCount);

1099

1139

1100

try { o->m_pSDF->m_vaData = new CxVec3Array[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_vaData = NULL; }

1101

if (o->m_pSDF->m_vaData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxVec3Array),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1140

try { o->m_pPlProj->m_vaData = new CxVec3Array[o->m_iShowMolCount]; } catch(...) { o->m_pPlProj->m_vaData = NULL; }

1141

if (o->m_pPlProj->m_vaData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxVec3Array),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1102

1142

1103

if (o->m_pSDF->m_bVdWSpheres)

1104

{

1105

try { o->m_pSDF->m_faRadius = new CxFloatArray[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_faRadius = NULL; }

1106

if (o->m_pSDF->m_faRadius == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1107

}

1108

1109

1143

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1110

1144

{

1111

try { o->m_pSDF->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pSDF->m_baDataEnabled = NULL; }

1112

if (o->m_pSDF->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1113

}

1114

}

1115

1116

if (g_bRDyn)

1117

{

1118

mprintf(" Creating Reorientation Dynamics...\n");

1119

o->m_pRDyn->m_pRDyn->m_fMinVal = 0;

1120

o->m_pRDyn->m_pRDyn->m_fMaxVal = o->m_pRDyn->m_iDepth * g_fTimestepLength / 1000.0f;

1121

o->m_pRDyn->m_pRDyn->m_iResolution = o->m_pRDyn->m_iDepth/o->m_pRDyn->m_iStride;

1122

o->m_pRDyn->m_pRDyn->SetLabelX("Tau [ps]");

1123

o->m_pRDyn->m_pRDyn->SetLabelY("Vector autocorrelation");

1124

o->m_pRDyn->m_pRDyn->Create();

1125

if (g_bRDynCacheMode)

1126

{

1127

if (g_iTrajSteps != -1)

1128

mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations*g_iTrajSteps/g_iStride*3.1*sizeof(float)));

1129

else mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations*10000/g_iStride*3.1*sizeof(float)));

1130

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations;z2++)

1131

{

1132

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

1133

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1134

1135

if (g_iTrajSteps != -1)

1136

{

1137

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.3));

1138

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.3));

1139

} else ptfa->SetGrow(10000);

1140

o->m_pRDyn->m_oaCache.Add(ptfa);

1141

}

1142

} else

1143

{

1144

try { o->m_pRDyn->m_pCount = new double[o->m_pRDyn->m_pRDyn->m_iResolution]; } catch(...) { o->m_pRDyn->m_pCount = NULL; }

1145

if (o->m_pRDyn->m_pCount == NULL) NewException((double)o->m_pRDyn->m_pRDyn->m_iResolution*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1146

1147

for (z2=0;z2<o->m_pRDyn->m_pRDyn->m_iResolution;z2++)

1148

o->m_pRDyn->m_pCount[z2] = 0;

1149

if (!g_bRDynCacheMode)

1150

{

1151

if (o->m_pRDyn->m_iDepth > g_iStepHistory)

1152

g_iStepHistory = o->m_pRDyn->m_iDepth;

1153

}

1154

}

1155

}

1156

1157

if (g_bIRSpec)

1158

{

1159

mprintf(" Creating IR Spectrum...\n");

1160

o->m_pIRSpec->m_pRDyn->m_fMinVal = 0;

1161

o->m_pIRSpec->m_pRDyn->m_fMaxVal = o->m_pIRSpec->m_iDepth * g_fTimestepLength / 1000.0f;

1162

o->m_pIRSpec->m_pRDyn->m_iResolution = o->m_pIRSpec->m_iDepth/o->m_pIRSpec->m_iStride;

1163

o->m_pIRSpec->m_pRDyn->SetLabelX("Tau [ps]");

1164

o->m_pIRSpec->m_pRDyn->SetLabelY("Dipole autocorrelation");

1165

o->m_pIRSpec->m_pRDyn->Create();

1166

if (g_bRDynCacheMode)

1167

{

1168

if (g_iTrajSteps != -1)

1169

mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pIRSpec->m_iCombinations*g_iTrajSteps/g_iStride*3.1*sizeof(float)));

1170

else mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pIRSpec->m_iCombinations*10000/g_iStride*3.1*sizeof(float)));

1171

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pIRSpec->m_iCombinations;z2++)

1172

{

1173

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

1174

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1175

1176

if (g_iTrajSteps != -1)

1177

{

1178

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.3));

1179

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.3));

1180

} else ptfa->SetGrow(10000);

1181

o->m_pIRSpec->m_oaCache.Add(ptfa);

1182

}

1183

} else

1184

{

1185

try { o->m_pIRSpec->m_pCount = new double[o->m_pIRSpec->m_pRDyn->m_iResolution]; } catch(...) { o->m_pIRSpec->m_pCount = NULL; }

1186

if (o->m_pIRSpec->m_pCount == NULL) NewException((double)o->m_pIRSpec->m_pRDyn->m_iResolution*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1187

1188

for (z2=0;z2<o->m_pIRSpec->m_pRDyn->m_iResolution;z2++)

1189

o->m_pIRSpec->m_pCount[z2] = 0;

1190

if (!g_bRDynCacheMode)

1191

{

1192

if (o->m_pIRSpec->m_iDepth > g_iStepHistory)

1193

g_iStepHistory = o->m_pIRSpec->m_iDepth;

1194

}

1195

}

1196

}

1197

1198

if (g_bDens)

1199

{

1200

mprintf(" Creating Density Distribution Function...\n");

1201

o->m_pDensityDF->m_pDensDF->m_fMinVal = o->m_pDensityDF->m_fMinDist;

1202

o->m_pDensityDF->m_pDensDF->m_fMaxVal = o->m_pDensityDF->m_fMaxDist;

1203

o->m_pDensityDF->m_pDensDF->m_iResolution = o->m_pDensityDF->m_iResolution;

1204

o->m_pDensityDF->m_pDensDF->m_iHistogramRes = o->m_pDensityDF->m_iHistogramRes;

1205

o->m_pDensityDF->m_pDensDF->SetLabelX("Distance [pm]");

1206

if (o->m_pDensityDF->m_bDensityMass)

1207

o->m_pDensityDF->m_pDensDF->SetLabelY("Mass Density [g/cm^3]");

1208

else o->m_pDensityDF->m_pDensDF->SetLabelY("Particle Density [1/nm^3]");

1209

o->m_pDensityDF->m_pDensDF->Create();

1210

}

1211

1212

if (g_bVHDF)

1213

{

1214

mprintf(" Creating VHCF...\n");

1215

o->m_pVHDF->m_pVHDF->m_fMinVal[1] = o->m_pVHDF->m_fMinDist;

1216

o->m_pVHDF->m_pVHDF->m_fMaxVal[1] = o->m_pVHDF->m_fMaxDist;

1217

o->m_pVHDF->m_pVHDF->m_iRes[1] = o->m_pVHDF->m_iResolution;

1218

o->m_pVHDF->m_pVHDF->m_fMinVal[0] = 0.0;

1219

o->m_pVHDF->m_pVHDF->m_fMaxVal[0] = o->m_pVHDF->m_iDepth * g_fTimestepLength / 1000.0f;

1220

o->m_pVHDF->m_pVHDF->m_iRes[0] = o->m_pVHDF->m_iDepth / o->m_pVHDF->m_iStride;

1221

o->m_pVHDF->m_pVHDF->Create();

1222

1223

try { o->m_pVHDF->m_pCount = new double[o->m_pVHDF->m_pVHDF->m_iRes[0]]; } catch(...) { o->m_pVHDF->m_pCount = NULL; }

1224

if (o->m_pVHDF->m_pCount == NULL) NewException((double)o->m_pVHDF->m_pVHDF->m_iRes[0]*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1225

1226

for (z0=0;z0<o->m_pVHDF->m_pVHDF->m_iRes[0];z0++)

1227

o->m_pVHDF->m_pCount[z0] = 0;

1228

o->m_pVHDF->m_pVHDF->SetLabelY("Distance [pm]");

1229

o->m_pVHDF->m_pVHDF->SetLabelX("Tau [ps]");

1230

// o->m_pVHDF->m_pVHDF->m_fPlotExp = 1.0;

1231

if (o->m_pVHDF->m_iDepth > g_iStepHistory)

1232

g_iStepHistory = o->m_pVHDF->m_iDepth;

1233

mprintf(" Setting trajectory ring buffer to %s...\n",FormatBytes(g_iStepHistory*g_iGesVirtAtomCount*sizeof(float)*3));

1234

}

1235

1236

if (g_bNbAnalysis)

1237

{

1238

mprintf(" Creating Neighborhood Analysis...\n");

1239

1240

try { o->m_pNbAnalysis->m_pNPFCount = new CDF(); } catch(...) { o->m_pNbAnalysis->m_pNPFCount = NULL; }

1241

if (o->m_pNbAnalysis->m_pNPFCount == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1242

1243

o->m_pNbAnalysis->m_pNPFCount->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1244

o->m_pNbAnalysis->m_pNPFCount->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1245

o->m_pNbAnalysis->m_pNPFCount->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1246

1247

o->m_pNbAnalysis->m_pNPFCount->Create();

1248

1249

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1250

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1251

1252

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1253

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1254

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1255

tdf->SetLabelX("Distance [pm]");

1256

tdf->SetLabelY("Occurrence");

1257

tdf->Create();

1258

o->m_pNbAnalysis->m_oaNPF.Add(tdf);

1259

1260

for (z2=0;z2<=o->m_pNbAnalysis->m_iNbCount;z2++)

1261

{

1262

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1263

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1264

1265

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1266

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1267

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1268

tdf->SetLabelX("Distance [pm]");

1269

tdf->SetLabelY("Occurrence");

1270

tdf->Create();

1271

o->m_pNbAnalysis->m_oaDF.Add(tdf);

1272

1273

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1274

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1275

1276

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1277

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1278

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1279

tdf->SetLabelX("Distance [pm]");

1280

tdf->SetLabelY("Occurrence");

1281

tdf->Create();

1282

o->m_pNbAnalysis->m_oaNPF.Add(tdf);

1283

}

1284

}

1285

1286

for (z0=0;z0<g_iCDFChannels;z0++)

1287

{

1288

if (g_bRDF && (o->m_pRDF[z0] != NULL))

1289

{

1290

mprintf(" Creating RDF...\n");

1291

o->m_pRDF[z0]->m_pRDF->m_fMinVal = o->m_pRDF[z0]->m_fMinDist;

1292

o->m_pRDF[z0]->m_pRDF->m_fMaxVal = o->m_pRDF[z0]->m_fMaxDist;

1293

o->m_pRDF[z0]->m_pRDF->m_iResolution = o->m_pRDF[z0]->m_iResolution;

1294

o->m_pRDF[z0]->m_pRDF->m_iHistogramRes = o->m_pRDF[z0]->m_iHistogramRes;

1295

o->m_pRDF[z0]->m_pRDF->SetLabelX("Distance [pm]");

1296

if (o->m_pRDF[z0]->m_bProbDens)

1297

o->m_pRDF[z0]->m_pRDF->SetLabelY("g(r) [nm^(-3)]");

1298

else o->m_pRDF[z0]->m_pRDF->SetLabelY("g(r)");

1299

1300

if (o->m_bObsCertain && o->m_bDecompDist)

1301

{

1302

o->m_pRDF[z0]->m_pRDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1303

1304

/* try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = new char*[o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = NULL; }

1305

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti == NULL) NewException((double)o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize()*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1306

1307

for (z=0;z<o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize();z++)

1308

{

1309

try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = new char[128]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = NULL; }

1310

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] == NULL) NewException((double)128*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1311

}

1312

1313

for (z3=0;z3<o->m_waObsRefList.GetSize();z3++)

1314

{

1315

for (z2=0;z2<o->m_waObsShowList.GetSize();z2++)

1316

{

1317

if ((o->m_waObsRefList.GetSize() > 1) && (o->m_waObsShowList.GetSize() > 1))

1318

sprintf(buf,"RM%d-OM%d",o->m_waObsRefList[z3]+1,o->m_waObsShowList[z2]+1);

1319

else if (o->m_waObsRefList.GetSize() > 1)

1320

sprintf(buf,"RM%d",o->m_waObsRefList[z3]+1);

1321

else

1322

sprintf(buf,"OM%d",o->m_waObsShowList[z2]+1);

1323

1324

o->m_pRDF[z0]->m_pRDF->SetLabelMulti(z3*o->m_waObsShowList.GetSize()+z2,buf);

1325

}

1326

}

1327

} else if (o->m_bDecompType)

1328

{

1329

m = (CMolecule*)g_oaMolecules[g_iFixMol];

1330

o->m_waDecompTypeRefOffs.SetSize(g_iGesVirtAtomCount);

1331

for (z3=0;z3<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z3++)

1332

{

1333

ag = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z3*2];

1334

for (z2=0;z2<ag->m_baRealAtomType.GetSize();z2++)

1335

{

1336

for (z3=0;z3<o->m_waDecompTypeRefList.GetSize();z3++)

1337

if (o->m_waDecompTypeRefList[z3] == ag->m_baRealAtomType[z2])

1338

goto _decomptype1;

1339

z3 = o->m_waDecompTypeRefList.GetSize();

1340

o->m_waDecompTypeRefList.Add(ag->m_baRealAtomType[z2]);

1341

_decomptype1:

1342

for (z4=0;z4<m->m_laSingleMolIndex.GetSize();z4++)

1343

{

1344

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z4]];

1345

for (z5=0;z5<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z5++)

1346

o->m_waDecompTypeRefOffs[((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z5))] = z3;

1347

}

1348

}

1349

}

1350

1351

if (o->m_bOthers)

1352

m = (CMolecule*)g_oaMolecules[o->m_iShowMol];

1353

else m = (CMolecule*)g_oaMolecules[g_iFixMol];

1354

o->m_waDecompTypeObsOffs.SetSize(g_iGesVirtAtomCount);

1355

for (z6=0;z6<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z6++)

1356

{

1357

ag = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z6*2+1];

1358

for (z2=0;z2<ag->m_baRealAtomType.GetSize();z2++)

1359

{

1360

for (z3=0;z3<o->m_waDecompTypeObsList.GetSize();z3++)

1361

if (o->m_waDecompTypeObsList[z3] == ag->m_baRealAtomType[z2])

1362

goto _decomptype2;

1363

z3 = o->m_waDecompTypeObsList.GetSize();

1364

o->m_waDecompTypeObsList.Add(ag->m_baRealAtomType[z2]);

1365

_decomptype2:

1366

for (z4=0;z4<m->m_laSingleMolIndex.GetSize();z4++)

1367

{

1368

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z4]];

1369

for (z5=0;z5<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z5++)

1370

o->m_waDecompTypeObsOffs[((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z5))] = z3;

1371

}

1372

}

1373

}

1374

1375

o->m_pRDF[z0]->m_pRDF->CreateMulti(o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize());

1376

1377

/* try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = new char*[o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = NULL; }

1378

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti == NULL) NewException((double)o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize()*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1379

1380

for (z=0;z<o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize();z++)

1381

{

1382

try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = new char[128]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = NULL; }

1383

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] == NULL) NewException((double)128*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1384

}*/

1385

1386

for (z3=0;z3<o->m_waDecompTypeRefList.GetSize();z3++)

1387

{

1388

for (z2=0;z2<o->m_waDecompTypeObsList.GetSize();z2++)

1389

{

1390

sprintf(buf,"%s-%s",((CAtom*)g_oaAtoms[o->m_waDecompTypeRefList[z3]])->m_sName,((CAtom*)g_oaAtoms[o->m_waDecompTypeObsList[z2]])->m_sName);

1391

o->m_pRDF[z0]->m_pRDF->SetLabelMulti(z*o->m_waDecompTypeObsList.GetSize()+z2,buf);

1392

}

1393

}

1394

} else o->m_pRDF[z0]->m_pRDF->Create();

1395

1396

if (o->m_bSecondShowMol && (z0 == 1))

1397

{

1398

try { o->m_pRDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pRDF[z0]->m_faData = NULL; }

1399

if (o->m_pRDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1400

1401

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1402

{

1403

try { o->m_pRDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pRDF[z0]->m_baDataEnabled = NULL; }

1404

if (o->m_pRDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1405

}

1406

} else

1407

{

1408

try { o->m_pRDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pRDF[z0]->m_faData = NULL; }

1409

if (o->m_pRDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1410

1411

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1412

{

1413

try { o->m_pRDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pRDF[z0]->m_baDataEnabled = NULL; }

1414

if (o->m_pRDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1415

}

1416

}

1417

if (o->m_bTimeDev)

1418

{

1419

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1420

{

1421

try { o->m_pRDF[z0]->m_fDist = new FILE*[1]; } catch(...) { o->m_pRDF[z0]->m_fDist = NULL; }

1422

if (o->m_pRDF[z0]->m_fDist == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1423

1424

sprintf(buf,"rdf_timedev_%s%s.csv",o->m_pRDF[z0]->m_sName,multibuf);

1425

o->m_pRDF[z0]->m_fDist[0] = OpenFileWrite(buf,true);

1426

} else

1427

{

1428

try { o->m_pRDF[z0]->m_fDist = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_fDist = NULL; }

1429

if (o->m_pRDF[z0]->m_fDist == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1430

1431

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1432

{

1433

sprintf(buf,"rdf_timedev_%s_ref%d%s.csv",o->m_pRDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1434

o->m_pRDF[z0]->m_fDist[z2] = OpenFileWrite(buf,true);

1435

}

1436

}

1437

if (o->m_bCombinedPlot)

1438

{

1439

// mprintf("Combined: Reflist %d, Showlist %d, Combinations %d, Steps %d.\n",o->m_waSaveRefList.GetSize(),o->m_waSaveShowList.GetSize(),o->m_pRDF[z0]->m_iCombinations,g_iTrajSteps);

1440

1441

try { o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot = NULL; }

1442

if (o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1443

1444

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetTitle("Combined distance time development/histogram");

1445

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetSubTitle(o->m_pRDF[z0]->m_sShortName);

1446

// smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]];

1447

// sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[0]];

1448

// o->m_pRDF[z0]->BuildAtomList(smfix,sm,sm,&templa);

1449

mprintf(" Trying to reserve %s of memory for combined plot...\n",FormatBytes((double)sizeof(double)*o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pRDF[z0]->m_iCombinations*g_iTrajSteps/g_iStride));

1450

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1451

{

1452

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1453

{

1454

/* for (z4=0;z4<templa.GetSize()/2;z4++)

1455

{

1456

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->AddDataset();

1457

sprintf(buf,"%s[%d] %s%d - %s[%d] %s%d",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,o->m_waSaveRefList[z2]+1,((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[g_waAtomElement[templa[z4*2]]]])->m_sName,g_waAtomMolNumber[templa[z4*2]]+1,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,o->m_waSaveShowList[z3]+1,((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[g_waAtomElement[templa[z4*2+1]]]])->m_sName,g_waAtomMolNumber[templa[z4*2+1]]+1);

1458

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetDatasetName(buf);

1459

if (g_iTrajSteps != -1)

1460

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize() *g_iTrajSteps);

1461

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize() *100);

1462

if (o->m_bCombinedGreyMode)

1463

{

1464

ti = o->m_iCombinedGreyMin + ((z4+z3*o->m_pRDF[z0]->m_iCombinations+z2*o->m_pRDF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1465

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_iLineColor = ti*0x10000 + ti*0x100 + ti;

1466

}

1467

}*/

1468

1469

ti2 = 0;

1470

for (z4=0;z4<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z4++)

1471

{

1472

g1 = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z4*2];

1473

for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)

1474

{

1475

a1 = (CxIntArray*)g1->m_oaAtoms[z1t];

1476

for (z1a=0;z1a<a1->GetSize();z1a++)

1477

{

1478

g2 = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z4*2+1];

1479

for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)

1480

{

1481

a2 = (CxIntArray*)g2->m_oaAtoms[z2t];

1482

for (z2a=0;z2a<a2->GetSize();z2a++)

1483

{

1484

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->AddDataset();

1485

if (o->m_bOthers)

1486

sprintf(buf,"%s[%d] %s%d - %s[%d] %s%d",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,o->m_waSaveRefList[z2]+1,((CAtom*)g_oaAtoms[g1->m_baRealAtomType[z1t]])->m_sName,a1->GetAt(z1a)+1,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_sName,o->m_waSaveShowList[z3]+1,((CAtom*)g_oaAtoms[g2->m_baRealAtomType[z2t]])->m_sName,a2->GetAt(z2a)+1);

1487

else sprintf(buf,"%s[%d] %s%d - %s%d",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,o->m_waSaveRefList[z2]+1,((CAtom*)g_oaAtoms[g1->m_baRealAtomType[z1t]])->m_sName,a1->GetAt(z1a)+1,((CAtom*)g_oaAtoms[g2->m_baRealAtomType[z2t]])->m_sName,a2->GetAt(z2a)+1);

1488

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetDatasetName(buf);

1489

if (g_iTrajSteps != -1)

1490

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()/**o->m_pRDF[z0]->m_iCombinations*/ *g_iTrajSteps/g_iStride);

1491

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()/**o->m_pRDF[z0]->m_iCombinations*/ *100);

1492

if (o->m_bCombinedGreyMode)

1493

{

1494

ti = o->m_iCombinedGreyMin + ((ti2+z3*o->m_pRDF[z0]->m_iCombinations+z2*o->m_pRDF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1495

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1496

}

1497

ti2++;

1498

/* if (o->m_pRDF[z0]->m_iRefOrSec[0])

1499

vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));

1500

else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));

1501

if (o->m_pRDF[z0]->m_iRefOrSec[1])

1502

vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));

1503

else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));

1504

*/ // mprintf("Vector z=%d, z1t=%d, z1a=%d, z2t=%d, z2a=%d.\n",z,z1t,z1a,z2t,z2a);

1505

}

1506

}

1507

}

1508

}

1509

}

1510

1511

}

1512

}

1513

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetLabelX("Time [ps] / g(r)");

1514

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetLabelY("Distance [pm]");

1515

}

1516

} // END IF TIMEDEV

1517

1518

if (o->m_bTimeDiff)

1519

o->CreateTimeDiff(o->m_pRDF[z0]->m_pRDF,o->m_pRDF[z0]->m_iCombinations);

1520

1521

if (g_bDeriv)

1522

o->m_pRDF[z0]->InitDeriv();

1523

1524

if (o->m_pRDF[z0]->m_bCalcSD)

1525

{

1526

mprintf(" Initializing Standard Deviation Engine...\n");

1527

o->m_pRDF[z0]->m_pRDF->m_pSDEngine = new CSDEngine();

1528

o->m_pRDF[z0]->m_pRDF->m_pSDEngine->m_iaBlockSizes.SetSize(o->m_pRDF[z0]->m_iSDBlocks);

1529

mprintf(" Using the following %d trajectory block sizes:",o->m_pRDF[z0]->m_iSDBlocks);

1530

tf2 = 0;

1531

tf = 3.0;

1532

for (z4=0;z4<o->m_pRDF[z0]->m_iSDBlocks;z4++)

1533

{

1534

if ((z4 % 10) == 0)

1535

mprintf("\n ");

1536

o->m_pRDF[z0]->m_pRDF->m_pSDEngine->m_iaBlockSizes[z4] = (int)((exp(z4*tf/o->m_pRDF[z0]->m_iSDBlocks)-1.0) / (exp((o->m_pRDF[z0]->m_iSDBlocks-1.0)*tf/o->m_pRDF[z0]->m_iSDBlocks)-1.0) * (o->m_pRDF[z0]->m_iSDBlockMax - o->m_pRDF[z0]->m_iSDBlockMin)) + o->m_pRDF[z0]->m_iSDBlockMin;

1537

mprintf("%5d",o->m_pRDF[z0]->m_pRDF->m_pSDEngine->m_iaBlockSizes[z4]);

1538

if (z4 < o->m_pRDF[z0]->m_iSDBlocks-1)

1539

mprintf(", ");

1540

else mprintf(".");

1541

tf2 += (g_iTrajSteps/o->m_pRDF[z0]->m_pRDF->m_pSDEngine->m_iaBlockSizes[z4]) + 1;

1542

}

1543

tf2 *= o->m_pRDF[z0]->m_pRDF->m_iResolution * sizeof(double);

1544

mprintf("\n This requires %s of memory.\n\n",FormatBytes(tf2));

1545

o->m_pRDF[z0]->m_pRDF->m_pSDEngine->Init(o->m_pRDF[z0]->m_pRDF->m_iResolution);

1546

}

1547

} // END IF RDF

1548

1549

if (g_bADF && (o->m_pADF[z0] != NULL))

1550

{

1551

mprintf(" Creating ADF...\n");

1552

o->m_pADF[z0]->m_pADF->m_fMinVal = o->m_pADF[z0]->m_fMinAngle;

1553

o->m_pADF[z0]->m_pADF->m_fMaxVal = o->m_pADF[z0]->m_fMaxAngle;

1554

o->m_pADF[z0]->m_pADF->m_iResolution = o->m_pADF[z0]->m_iResolution;

1555

o->m_pADF[z0]->m_pADF->m_iHistogramRes = o->m_pADF[z0]->m_iHistogramRes;

1556

if (o->m_pADF[z0]->m_bCosine)

1557

o->m_pADF[z0]->m_pADF->SetLabelX("Cos(angle)");

1558

else o->m_pADF[z0]->m_pADF->SetLabelX("Angle (degree)");

1559

o->m_pADF[z0]->m_pADF->SetLabelY("Occurrence");

1560

if (o->m_bObsCertain && o->m_bDecompDist)

1561

o->m_pADF[z0]->m_pADF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1562

else o->m_pADF[z0]->m_pADF->Create();

1563

if (o->m_bSecondShowMol && (z0 == 1))

1564

{

1565

try { o->m_pADF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pADF[z0]->m_faData = NULL; }

1566

if (o->m_pADF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1567

1568

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1569

{

1570

try { o->m_pADF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pADF[z0]->m_baDataEnabled = NULL; }

1571

if (o->m_pADF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1572

}

1573

} else

1574

{

1575

try { o->m_pADF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pADF[z0]->m_faData = NULL; }

1576

if (o->m_pADF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1577

1578

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1579

{

1580

try { o->m_pADF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pADF[z0]->m_baDataEnabled = NULL; }

1581

if (o->m_pADF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1582

}

1583

}

1584

if (o->m_bTimeDev)

1585

{

1586

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1587

{

1588

try { o->m_pADF[z0]->m_fAngle = new FILE*[1]; } catch(...) { o->m_pADF[z0]->m_fAngle = NULL; }

1589

if (o->m_pADF[z0]->m_fAngle == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1590

1591

sprintf(buf,"adf_timedev_%s%s.csv",o->m_pADF[z0]->m_sName,multibuf);

1592

o->m_pADF[z0]->m_fAngle[0] = OpenFileWrite(buf,true);

1593

} else

1594

{

1595

try { o->m_pADF[z0]->m_fAngle = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pADF[z0]->m_fAngle = NULL; }

1596

if (o->m_pADF[z0]->m_fAngle == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1597

1598

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1599

{

1600

sprintf(buf,"adf_timedev_%s_ref%d%s.csv",o->m_pADF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1601

o->m_pADF[z0]->m_fAngle[z2] = OpenFileWrite(buf,true);

1602

}

1603

}

1604

if (o->m_bCombinedPlot)

1605

{

1606

try { o->m_pADF[z0]->m_pADF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pADF[z0]->m_pADF->m_pCombinedPlot = NULL; }

1607

if (o->m_pADF[z0]->m_pADF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1608

1609

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetTitle("Combined angle time development/histogram");

1610

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSubTitle(o->m_pADF[z0]->m_sShortName);

1611

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1612

{

1613

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1614

{

1615

for (z4=0;z4<o->m_pADF[z0]->m_iCombinations;z4++)

1616

{

1617

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->AddDataset();

1618

if (g_iTrajSteps != -1)

1619

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pADF[z0]->m_iCombinations*g_iTrajSteps);

1620

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pADF[z0]->m_iCombinations*100);

1621

if (o->m_bCombinedGreyMode)

1622

{

1623

ti = o->m_iCombinedGreyMin + ((z4+z3*o->m_pADF[z0]->m_iCombinations+z2*o->m_pADF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1624

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1625

}

1626

// o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSetLineWidth((z2*o->m_waSaveRefList.GetSize()+z3)*o->m_pADF[z0]->m_iCombinations+z4,2.0f);

1627

}

1628

}

1629

}

1630

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetLabelX("Time [ps] / ADF(r)");

1631

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetLabelY("Angle [Degree]");

1632

}

1633

} // END IF TIMEDEV

1634

1635

if (o->m_bTimeDiff)

1636

o->CreateTimeDiff(o->m_pADF[z0]->m_pADF,o->m_pADF[z0]->m_iCombinations);

1637

1638

if (g_bDeriv)

1639

o->m_pADF[z0]->InitDeriv();

1640

} // END IF ADF

1641

1642

if (g_bDipDF && (o->m_pDipDF[z0] != NULL))

1643

{

1644

mprintf(" Creating DipDF...\n");

1645

o->m_pDipDF[z0]->m_pDipoleDF->m_fMinVal = o->m_pDipDF[z0]->m_fDipoleMin;

1646

o->m_pDipDF[z0]->m_pDipoleDF->m_fMaxVal = o->m_pDipDF[z0]->m_fDipoleMax;

1647

o->m_pDipDF[z0]->m_pDipoleDF->m_iResolution = o->m_pDipDF[z0]->m_iResolution;

1648

o->m_pDipDF[z0]->m_pDipoleDF->m_iHistogramRes = o->m_pDipDF[z0]->m_iHistogramRes;

1649

o->m_pDipDF[z0]->m_pDipoleDF->SetLabelX("Dipole moment (Debye)");

1650

o->m_pDipDF[z0]->m_pDipoleDF->SetLabelY("Occurrence");

1651

if (o->m_bObsCertain && o->m_bDecompDist)

1652

o->m_pDipDF[z0]->m_pDipoleDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1653

else o->m_pDipDF[z0]->m_pDipoleDF->Create();

1654

if (o->m_bSecondShowMol && (z0 == 1))

1655

{

1656

try { o->m_pDipDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDipDF[z0]->m_faData = NULL; }

1657

if (o->m_pDipDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1658

1659

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1660

{

1661

try { o->m_pDipDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDipDF[z0]->m_baDataEnabled = NULL; }

1662

if (o->m_pDipDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1663

}

1664

} else

1665

{

1666

try { o->m_pDipDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pDipDF[z0]->m_faData = NULL; }

1667

if (o->m_pDipDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1668

1669

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1670

{

1671

try { o->m_pDipDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pDipDF[z0]->m_baDataEnabled = NULL; }

1672

if (o->m_pDipDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1673

}

1674

}

1675

if (o->m_bTimeDev)

1676

{

1677

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1678

{

1679

try { o->m_pDipDF[z0]->m_fDipole = new FILE*[1]; } catch(...) { o->m_pDipDF[z0]->m_fDipole = NULL; }

1680

if (o->m_pDipDF[z0]->m_fDipole == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1681

1682

sprintf(buf,"dipole_timedev_%s%s.csv",o->m_pDipDF[z0]->m_sName,multibuf);

1683

o->m_pDipDF[z0]->m_fDipole[0] = OpenFileWrite(buf,true);

1684

} else

1685

{

1686

try { o->m_pDipDF[z0]->m_fDipole = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pDipDF[z0]->m_fDipole = NULL; }

1687

if (o->m_pDipDF[z0]->m_fDipole == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1688

1689

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1690

{

1691

sprintf(buf,"dipole_timedev_%s_ref%d%s.csv",o->m_pDipDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1692

o->m_pDipDF[z0]->m_fDipole[z2] = OpenFileWrite(buf,true);

1693

}

1694

}

1695

if (o->m_bCombinedPlot)

1696

{

1697

try { o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot = NULL; }

1698

if (o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1699

1700

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetTitle("Combined dipole moment time development/histogram");

1701

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetSubTitle(o->m_pDipDF[z0]->m_sShortName);

1702

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1703

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1704

{

1705

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->AddDataset();

1706

if (g_iTrajSteps != -1)

1707

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*g_iTrajSteps);

1708

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*100);

1709

if (o->m_bCombinedGreyMode)

1710

{

1711

ti = o->m_iCombinedGreyMin + ((z3+z2*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1712

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1713

}

1714

}

1715

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetLabelX("Time [ps] / DipDF(r)");

1716

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetLabelY("Dipole moment [Debye]");

1717

}

1718

} // END IF TIMEDEV

1719

1720

if (o->m_bTimeDiff)

1721

o->CreateTimeDiff(o->m_pDipDF[z0]->m_pDipoleDF,1);

1722

1723

if (g_bDeriv)

1724

o->m_pDipDF[z0]->InitDeriv();

1725

} // END IF DIPOLE

1726

1727

if (g_bVDF && (o->m_pVDF[z0] != NULL))

1728

{

1729

mprintf(" Creating VDF...\n");

1730

o->m_pVDF[z0]->m_pVDF->m_fMinVal = o->m_pVDF[z0]->m_fMinSpeed;

1731

o->m_pVDF[z0]->m_pVDF->m_fMaxVal = o->m_pVDF[z0]->m_fMaxSpeed;

1732

o->m_pVDF[z0]->m_pVDF->m_iResolution = o->m_pVDF[z0]->m_iResolution;

1733

o->m_pVDF[z0]->m_pVDF->m_iHistogramRes = o->m_pVDF[z0]->m_iHistogramRes;

1734

o->m_pVDF[z0]->m_pVDF->SetLabelX("Velocity [pm/ps]");

1735

o->m_pVDF[z0]->m_pVDF->SetLabelY("Occurrence");

1736

if (o->m_bObsCertain && o->m_bDecompDist)

1737

o->m_pVDF[z0]->m_pVDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1738

else o->m_pVDF[z0]->m_pVDF->Create();

1739

if (o->m_bSecondShowMol && (z0 == 1))

1740

{

1741

try { o->m_pVDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pVDF[z0]->m_faData = NULL; }

1742

if (o->m_pVDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1743

1744

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1745

{

1746

try { o->m_pVDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pVDF[z0]->m_baDataEnabled = NULL; }

1747

if (o->m_pVDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1748

}

1749

} else

1750

{

1751

try { o->m_pVDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pVDF[z0]->m_faData = NULL; }

1752

if (o->m_pVDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1753

1754

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1755

{

1756

try { o->m_pVDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pVDF[z0]->m_baDataEnabled = NULL; }

1757

if (o->m_pVDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1758

}

1759

}

1760

if (o->m_bTimeDev)

1761

{

1762

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1763

{

1764

try { o->m_pVDF[z0]->m_fSpeed = new FILE*[1]; } catch(...) { o->m_pVDF[z0]->m_fSpeed = NULL; }

1765

if (o->m_pVDF[z0]->m_fSpeed == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1766

1767

sprintf(buf,"vdf_timedev_%s%s.csv",o->m_pVDF[z0]->m_sName,multibuf);

1768

o->m_pVDF[z0]->m_fSpeed[0] = OpenFileWrite(buf,true);

1769

} else

1770

{

1771

try { o->m_pVDF[z0]->m_fSpeed = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pVDF[z0]->m_fSpeed = NULL; }

1772

if (o->m_pVDF[z0]->m_fSpeed == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1773

1774

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1775

{

1776

sprintf(buf,"vdf_timedev_%s_ref%d%s.csv",o->m_pVDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1777

o->m_pVDF[z0]->m_fSpeed[z2] = OpenFileWrite(buf,true);

1778

}

1779

}

1780

if (o->m_bCombinedPlot)

1781

{

1782

try { o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot = NULL; }

1783

if (o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1784

1785

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetTitle("Combined velocity time development/histogram");

1786

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSubTitle(o->m_pVDF[z0]->m_sShortName);

1787

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1788

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1789

for (z4=0;z4<o->m_pVDF[z0]->m_iCombinations;z4++)

1790

{

1791

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->AddDataset();

1792

if (g_iTrajSteps != -1)

1793

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pVDF[z0]->m_iCombinations*g_iTrajSteps);

1794

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pVDF[z0]->m_iCombinations*100);

1795

if (o->m_bCombinedGreyMode)

1796

{

1797

ti = o->m_iCombinedGreyMin + ((z4+z3*o->m_pVDF[z0]->m_iCombinations+z2*o->m_pVDF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1798

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1799

}

1800

// o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSetLineWidth(z2*o->m_waSaveRefList.GetSize()+z3,3.0f);

1801

}

1802

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetLabelX("Time [ps] / VDF(r)");

1803

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetLabelY("Velocity [pm/ps]");

1804

}

1805

} // END IF TIMEDEV

1806

1807

if (o->m_bTimeDiff)

1808

o->CreateTimeDiff(o->m_pVDF[z0]->m_pVDF,o->m_pVDF[z0]->m_iCombinations);

1809

1810

if (g_bDeriv)

1811

o->m_pVDF[z0]->InitDeriv();

1812

} // END IF VDF

1813

1814

if (g_bDDF && (o->m_pDDF[z0] != NULL))

1815

{

1816

mprintf(" Creating DDF...\n");

1817

o->m_pDDF[z0]->m_pDDF->m_fMinVal = o->m_pDDF[z0]->m_fMinAngle;

1818

o->m_pDDF[z0]->m_pDDF->m_fMaxVal = o->m_pDDF[z0]->m_fMaxAngle;

1819

o->m_pDDF[z0]->m_pDDF->m_iResolution = o->m_pDDF[z0]->m_iResolution;

1820

o->m_pDDF[z0]->m_pDDF->m_iHistogramRes = o->m_pDDF[z0]->m_iHistogramRes;

1821

if (o->m_pDDF[z0]->m_bCosine)

1822

o->m_pDDF[z0]->m_pDDF->SetLabelX("Cos(Dihedral Angle)");

1823

else o->m_pDDF[z0]->m_pDDF->SetLabelX("Dihedral Angle (Degree)");

1824

o->m_pDDF[z0]->m_pDDF->SetLabelY("Occurrence");

1825

if (o->m_bObsCertain && o->m_bDecompDist)

1826

o->m_pDDF[z0]->m_pDDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1827

else o->m_pDDF[z0]->m_pDDF->Create();

1828

if (o->m_bSecondShowMol && (z0 == 1))

1829

{

1830

try { o->m_pDDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDDF[z0]->m_faData = NULL; }

1831

if (o->m_pDDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1832

1833

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1834

{

1835

try { o->m_pDDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDDF[z0]->m_baDataEnabled = NULL; }

1836

if (o->m_pDDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1837

}

1838

} else

1839

{

1840

try { o->m_pDDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pDDF[z0]->m_faData = NULL; }

1841

if (o->m_pDDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1842

1843

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1844

{

1845

try { o->m_pDDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pDDF[z0]->m_baDataEnabled = NULL; }

1846

if (o->m_pDDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1847

}

1848

1849

if (o->m_pDDF[z0]->m_bRotate)

1850

{

1851

for (z2=0;z2<o->m_iShowMolCount * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() * o->m_pDDF[z0]->m_iCombinations;z2++)

1852

{

1853

o->m_pDDF[z0]->m_faLastData.Add(0);

1854

o->m_pDDF[z0]->m_laRotation.Add(0);

1855

}

1856

}

1857

}

1858

if (o->m_bTimeDev)

1859

{

1860

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1861

{

1862

try { o->m_pDDF[z0]->m_fAngle = new FILE*[1]; } catch(...) { o->m_pDDF[z0]->m_fAngle = NULL; }

1863

if (o->m_pDDF[z0]->m_fAngle == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1864

1865

sprintf(buf,"ddf_timedev_%s%s.csv",o->m_pDDF[z0]->m_sName,multibuf);

1866

o->m_pDDF[z0]->m_fAngle[0] = OpenFileWrite(buf,true);

1867

} else

1868

{

1869

try { o->m_pDDF[z0]->m_fAngle = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pDDF[z0]->m_fAngle = NULL; }

1870

if (o->m_pDDF[z0]->m_fAngle == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1871

1872

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1873

{

1874

sprintf(buf,"ddf_timedev_%s_ref%d%s.csv",o->m_pDDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1875

o->m_pDDF[z0]->m_fAngle[z2] = OpenFileWrite(buf,true);

1876

}

1877

}

1878

if (o->m_bCombinedPlot)

1879

{

1880

try { o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot = NULL; }

1881

if (o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1882

1883

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetTitle("Combined dihedral time development/histogram");

1884

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSubTitle(o->m_pDDF[z0]->m_sShortName);

1885

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1886

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1887

for (z4=0;z4<o->m_pDDF[z0]->m_iCombinations;z4++)

1888

{

1889

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->AddDataset();

1890

if (g_iTrajSteps != -1)

1891

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pDDF[z0]->m_iCombinations*g_iTrajSteps);

1892

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pDDF[z0]->m_iCombinations*100);

1893

if (o->m_bCombinedGreyMode)

1894

{

1895

ti = o->m_iCombinedGreyMin + ((z4+z3*o->m_pDDF[z0]->m_iCombinations+z2*o->m_pDDF[z0]->m_iCombinations*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1896

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1897

}

1898

// o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSetLineWidth((z2*o->m_waSaveRefList.GetSize()+z3)*o->m_pDDF[z0]->m_iCombinations+z4,2.0f);

1899

}

1900

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetLabelX("Time [ps] / DDF(r)");

1901

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetLabelY("Dihedral [Degree]");

1902

}

1903

} // END IF TIMEDEV

1904

1905

if (o->m_bTimeDiff)

1906

o->CreateTimeDiff(o->m_pDDF[z0]->m_pDDF,o->m_pDDF[z0]->m_iCombinations);

1907

1908

if (g_bDeriv)

1909

o->m_pDDF[z0]->InitDeriv();

1910

} // END IF DDF

1911

1912

if (g_bPlDF && (o->m_pPlDF[z0] != NULL))

1913

{

1914

mprintf(" Creating PlDF...\n");

1915

o->m_pPlDF[z0]->m_pPlDF->m_fMinVal = o->m_pPlDF[z0]->m_fMinDist;

1916

o->m_pPlDF[z0]->m_pPlDF->m_fMaxVal = o->m_pPlDF[z0]->m_fMaxDist;

1917

o->m_pPlDF[z0]->m_pPlDF->m_iResolution = o->m_pPlDF[z0]->m_iResolution;

1918

o->m_pPlDF[z0]->m_pPlDF->m_iHistogramRes = o->m_pPlDF[z0]->m_iHistogramRes;

1919

o->m_pPlDF[z0]->m_pPlDF->SetLabelX("Distance from plane [pm]");

1920

o->m_pPlDF[z0]->m_pPlDF->SetLabelY("Occurrence");

1921

o->m_pPlDF[z0]->m_pPlDF->Create();

1922

if (o->m_bSecondShowMol && (z0 == 1))

1923

{

1924

try { o->m_pPlDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pPlDF[z0]->m_faData = NULL; }

1925

if (o->m_pPlDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1926

1927

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1928

{

1929

try { o->m_pPlDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pPlDF[z0]->m_baDataEnabled = NULL; }

1930

if (o->m_pPlDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1931

}

1932

} else

1933

{

1934

try { o->m_pPlDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pPlDF[z0]->m_faData = NULL; }

1935

if (o->m_pPlDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1936

1937

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1938

{

1939

try { o->m_pPlDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pPlDF[z0]->m_baDataEnabled = NULL; }

1940

if (o->m_pPlDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1941

}

1942

}

1943

} // END IF PlDF

1944

1945

if (g_bLiDF && (o->m_pLiDF[z0] != NULL))

1946

{

1947

mprintf(" Creating LiDF...\n");

1948

o->m_pLiDF[z0]->m_pLiDF->m_fMinVal = o->m_pLiDF[z0]->m_fMinDist;

1949

o->m_pLiDF[z0]->m_pLiDF->m_fMaxVal = o->m_pLiDF[z0]->m_fMaxDist;

1950

o->m_pLiDF[z0]->m_pLiDF->m_iResolution = o->m_pLiDF[z0]->m_iResolution;

1951

o->m_pLiDF[z0]->m_pLiDF->m_iHistogramRes = o->m_pLiDF[z0]->m_iHistogramRes;

1952

o->m_pLiDF[z0]->m_pLiDF->SetLabelX("Distance from line [pm]");

1953

o->m_pLiDF[z0]->m_pLiDF->SetLabelY("Occurrence");

1954

o->m_pLiDF[z0]->m_pLiDF->Create();

1955

if (o->m_bSecondShowMol && (z0 == 1))

1956

{

1957

try { o->m_pLiDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pLiDF[z0]->m_faData = NULL; }

1958

if (o->m_pLiDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1959

1960

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1961

{

1962

try { o->m_pLiDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pLiDF[z0]->m_baDataEnabled = NULL; }

1963

if (o->m_pLiDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1964

}

1965

} else

1966

{

1967

try { o->m_pLiDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pLiDF[z0]->m_faData = NULL; }

1968

if (o->m_pLiDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1969

1970

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1971

{

1972

try { o->m_pLiDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pLiDF[z0]->m_baDataEnabled = NULL; }

1973

if (o->m_pLiDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1974

}

1975

}

1976

} // END IF LiDF

1977

1978

} // END FOR z0

1979

1980

if (g_bCDF)

1981

{

1982

mprintf(" Creating CDF...\n");

1983

if (g_iCDFChannels == 2)

1984

{

1985

try { o->m_pCDF->m_p2DF = new C2DF(); } catch(...) { o->m_pCDF->m_p2DF = NULL; }

1986

if (o->m_pCDF->m_p2DF == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1987

1988

buf[0] = 0;

1989

for (z2=0;z2<2;z2++)

1990

{

1991

o->m_pCDF->m_p2DF->m_iRes[z2] = o->m_pCDF->m_iResolution[z2];

1992

switch(g_iObsChannel[z2])

1993

{

1994

case 0:

1995

strcat(buf,"_rdf");

1996

strcat(buf,o->m_pRDF[z2]->m_sShortName);

1997

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pRDF[z2]->m_fMinDist;

1998

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pRDF[z2]->m_fMaxDist;

1999

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pRDF[z2]->m_pRDF;

2000

break;

2001

2002

case 1:

2003

strcat(buf,"_adf");

2004

strcat(buf,o->m_pADF[z2]->m_sShortName);

2005

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pADF[z2]->m_fMinAngle;

2006

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pADF[z2]->m_fMaxAngle;

2007

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pADF[z2]->m_pADF;

2008

break;

2009

2010

case 2:

2011

strcat(buf,"_ddf");

2012

strcat(buf,o->m_pDDF[z2]->m_sShortName);

2013

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pDDF[z2]->m_fMinAngle;

2014

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pDDF[z2]->m_fMaxAngle;

2015

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pDDF[z2]->m_pDDF;

2016

break;

2017

2018

case 3:

2019

strcat(buf,"_dipole");

2020

strcat(buf,o->m_pDipDF[z2]->m_sShortName);

2021

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pDipDF[z2]->m_fDipoleMin;

2022

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pDipDF[z2]->m_fDipoleMax;

2023

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pDipDF[z2]->m_pDipoleDF;

2024

break;

2025

2026

case 4:

2027

strcat(buf,"_vdf");

2028

strcat(buf,o->m_pVDF[z2]->m_sShortName);

2029

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pVDF[z2]->m_fMinSpeed;

2030

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pVDF[z2]->m_fMaxSpeed;

2031

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pVDF[z2]->m_pVDF;

2032

break;

2033

2034

case 5:

2035

strcat(buf,"_pldf");

2036

strcat(buf,o->m_pPlDF[z2]->m_sShortName);

2037

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pPlDF[z2]->m_fMinDist;

2038

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pPlDF[z2]->m_fMaxDist;

2039

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pPlDF[z2]->m_pPlDF;

2040

break;

2041

2042

case 6:

2043

strcat(buf,"_lidf");

2044

strcat(buf,o->m_pLiDF[z2]->m_sShortName);

2045

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pLiDF[z2]->m_fMinDist;

2046

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pLiDF[z2]->m_fMaxDist;

2047

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pLiDF[z2]->m_pLiDF;

2048

break;

2049

}

2050

}

2051

o->m_pCDF->m_p2DF->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

2052

o->m_pCDF->m_p2DF->Create();

2053

switch(g_iObsChannel[0])

2054

{

2055

case 0:

2056

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[0]->m_sShortName);

2057

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2058

break;

2059

case 1:

2060

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[0]->m_sShortName);

2061

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2062

break;

2063

case 2:

2064

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[0]->m_sShortName);

2065

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2066

break;

2067

case 3:

2068

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[0]->m_sShortName);

2069

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2070

break;

2071

case 4:

2072

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[0]->m_sShortName);

2073

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2074

break;

2075

case 5:

2076

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[0]->m_sShortName);

2077

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2078

break;

2079

case 6:

2080

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[0]->m_sShortName);

2081

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2082

break;

2083

}

2084

switch(g_iObsChannel[1])

2085

{

2086

case 0:

2087

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[1]->m_sShortName);

2088

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2089

break;

2090

case 1:

2091

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[1]->m_sShortName);

2092

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2093

break;

2094

case 2:

2095

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[1]->m_sShortName);

2096

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2097

break;

2098

case 3:

2099

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[1]->m_sShortName);

2100

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2101

break;

2102

case 4:

2103

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[1]->m_sShortName);

2104

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2105

break;

2106

case 5:

2107

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[1]->m_sShortName);

2108

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2109

break;

2110

case 6:

2111

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[1]->m_sShortName);

2112

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2113

break;

2114

}

2115

} // END IF CHANNELS == 2

2116

2117

if (g_iCDFChannels == 3)

2118

{

2119

try { o->m_pCDF->m_p3DF = new C3DF(); } catch(...) { o->m_pCDF->m_p3DF = NULL; }

2120

if (o->m_pCDF->m_p3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2121

2122

buf[0] = 0;

2123

for (z2=0;z2<g_iCDFChannels;z2++)

2124

{

2125

o->m_pCDF->m_p3DF->m_iRes[z2] = o->m_pCDF->m_iResolution[z2];

2126

switch(g_iObsChannel[z2])

2127

{

2128

case 0:

2129

strcat(buf,"_rdf");

2130

strcat(buf,o->m_pRDF[z2]->m_sShortName);

2131

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pRDF[z2]->m_fMinDist;

2132

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pRDF[z2]->m_fMaxDist;

2133

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pRDF[z2]->m_pRDF;

2134

break;

2135

case 1:

2136

strcat(buf,"_adf");

2137

strcat(buf,o->m_pADF[z2]->m_sShortName);

2138

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pADF[z2]->m_fMinAngle;

2139

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pADF[z2]->m_fMaxAngle;

2140

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pADF[z2]->m_pADF;

2141

break;

2142

case 2:

2143

strcat(buf,"_ddf");

2144

strcat(buf,o->m_pDDF[z2]->m_sShortName);

2145

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pDDF[z2]->m_fMinAngle;

2146

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pDDF[z2]->m_fMaxAngle;

2147

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pDDF[z2]->m_pDDF;

2148

break;

2149

case 3:

2150

strcat(buf,"_dipole");

2151

strcat(buf,o->m_pDipDF[z2]->m_sShortName);

2152

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pDipDF[z2]->m_fDipoleMin;

2153

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pDipDF[z2]->m_fDipoleMax;

2154

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pDipDF[z2]->m_pDipoleDF;

2155

break;

2156

case 4:

2157

strcat(buf,"_vdf");

2158

strcat(buf,o->m_pVDF[z2]->m_sShortName);

2159

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pVDF[z2]->m_fMinSpeed;

2160

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pVDF[z2]->m_fMaxSpeed;

2161

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pVDF[z2]->m_pVDF;

2162

break;

2163

case 5:

2164

strcat(buf,"_pldf");

2165

strcat(buf,o->m_pPlDF[z2]->m_sShortName);

2166

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pPlDF[z2]->m_fMinDist;

2167

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pPlDF[z2]->m_fMaxDist;

2168

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pPlDF[z2]->m_pPlDF;

2169

break;

2170

case 6:

2171

strcat(buf,"_lidf");

2172

strcat(buf,o->m_pLiDF[z2]->m_sShortName);

2173

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pLiDF[z2]->m_fMinDist;

2174

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pLiDF[z2]->m_fMaxDist;

2175

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pLiDF[z2]->m_pLiDF;

2176

break;

2177

}

2178

}

2179

o->m_pCDF->m_p3DF->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

2180

o->m_pCDF->m_p3DF->Create();

2181

switch(g_iObsChannel[0])

2182

{

2183

case 0:

2184

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[0]->m_sShortName);

2185

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2186

break;

2187

case 1:

2188

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[0]->m_sShortName);

2189

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2190

break;

2191

case 2:

2192

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[0]->m_sShortName);

2193

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2194

break;

2195

case 3:

2196

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[0]->m_sShortName);

2197

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2198

break;

2199

case 4:

2200

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[0]->m_sShortName);

2201

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2202

break;

2203

case 5:

2204

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[0]->m_sShortName);

2205

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2206

break;

2207

case 6:

2208

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[0]->m_sShortName);

2209

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2210

break;

2211

}

2212

switch(g_iObsChannel[1])

2213

{

2214

case 0:

2215

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[1]->m_sShortName);

2216

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2217

break;

2218

case 1:

2219

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[1]->m_sShortName);

2220

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2221

break;

2222

case 2:

2223

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[1]->m_sShortName);

2224

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2225

break;

2226

case 3:

2227

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[1]->m_sShortName);

2228

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2229

break;

2230

case 4:

2231

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[1]->m_sShortName);

2232

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2233

break;

2234

case 5:

2235

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[1]->m_sShortName);

2236

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2237

break;

2238

case 6:

2239

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[1]->m_sShortName);

2240

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2241

break;

2242

}

2243

switch(g_iObsChannel[2])

2244

{

2245

case 0:

2246

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[2]->m_sShortName);

2247

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2248

break;

2249

case 1:

2250

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[2]->m_sShortName);

2251

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2252

break;

2253

case 2:

2254

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[2]->m_sShortName);

2255

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2256

break;

2257

case 3:

2258

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[2]->m_sShortName);

2259

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2260

break;

2261

case 4:

2262

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[2]->m_sShortName);

2263

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2264

break;

2265

case 5:

2266

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[2]->m_sShortName);

2267

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2268

break;

2269

case 6:

2270

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[2]->m_sShortName);

2271

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2272

break;

2273

}

2274

2275

// Fuer jede C3DF noch die 3 C2DFs erzeugen

2276

for (z3=0;z3<3;z3++)

2277

{

2278

try { o->m_pCDF->m_p3DF->m_p2DF[z3] = new C2DF(); } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3] = NULL; }

2279

if (o->m_pCDF->m_p3DF->m_p2DF[z3] == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2280

2281

buf3[0] = 0;

2282

switch(z3)

2283

{

2284

case 0:

2285

tia[0] = 0;

2286

tia[1] = 1;

2287

break;

2288

case 1:

2289

tia[0] = 0;

2290

tia[1] = 2;

2291

break;

2292

case 2:

2293

tia[0] = 1;

2294

tia[1] = 2;

2295

break;

2296

}

2297

for (z2=0;z2<2;z2++)

2298

{

2299

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_iRes[z2] = o->m_pCDF->m_iResolution[tia[z2]];

2300

switch(g_iObsChannel[tia[z2]])

2301

{

2302

case 0:

2303

strcat(buf3,"_rdf");

2304

strcat(buf3,o->m_pRDF[tia[z2]]->m_sShortName);

2305

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pRDF[tia[z2]]->m_fMinDist;

2306

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pRDF[tia[z2]]->m_fMaxDist;

2307

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pRDF[tia[z2]]->m_pRDF;

2308

break;

2309

case 1:

2310

strcat(buf3,"_adf");

2311

strcat(buf3,o->m_pADF[tia[z2]]->m_sShortName);

2312

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pADF[tia[z2]]->m_fMinAngle;

2313

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pADF[tia[z2]]->m_fMaxAngle;

2314

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pADF[tia[z2]]->m_pADF;

2315

break;

2316

case 2:

2317

strcat(buf3,"_ddf");

2318

strcat(buf3,o->m_pDDF[tia[z2]]->m_sShortName);

2319

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pDDF[tia[z2]]->m_fMinAngle;

2320

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pDDF[tia[z2]]->m_fMaxAngle;

2321

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pDDF[tia[z2]]->m_pDDF;

2322

break;

2323

case 3:

2324

strcat(buf3,"_dipole");

2325

strcat(buf3,o->m_pDipDF[tia[z2]]->m_sShortName);

2326

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pDipDF[tia[z2]]->m_fDipoleMin;

2327

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pDipDF[tia[z2]]->m_fDipoleMax;

2328

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pDipDF[tia[z2]]->m_pDipoleDF;

2329

break;

2330

case 4:

2331

strcat(buf3,"_vdf");

2332

strcat(buf3,o->m_pVDF[tia[z2]]->m_sShortName);

2333

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pVDF[tia[z2]]->m_fMinSpeed;

2334

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pVDF[tia[z2]]->m_fMaxSpeed;

2335

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pVDF[tia[z2]]->m_pVDF;

2336

break;

2337

case 5:

2338

strcat(buf3,"_pldf");

2339

strcat(buf3,o->m_pPlDF[tia[z2]]->m_sShortName);

2340

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pPlDF[tia[z2]]->m_fMinDist;

2341

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pPlDF[tia[z2]]->m_fMaxDist;

2342

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pPlDF[tia[z2]]->m_pPlDF;

2343

break;

2344

case 6:

2345

strcat(buf3,"_lidf");

2346

strcat(buf3,o->m_pLiDF[tia[z2]]->m_sShortName);

2347

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pLiDF[tia[z2]]->m_fMinDist;

2348

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pLiDF[tia[z2]]->m_fMaxDist;

2349

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pLiDF[tia[z2]]->m_pLiDF;

2350

break;

2351

}

2352

}

2353

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

2354

o->m_pCDF->m_p3DF->m_p2DF[z3]->Create();

2355

switch(g_iObsChannel[tia[0]])

2356

{

2357

case 0:

2358

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[tia[0]]->m_sShortName);

2359

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2360

break;

2361

case 1:

2362

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[tia[0]]->m_sShortName);

2363

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2364

break;

2365

case 2:

2366

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[tia[0]]->m_sShortName);

2367

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2368

break;

2369

case 3:

2370

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[tia[0]]->m_sShortName);

2371

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2372

break;

2373

case 4:

2374

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[tia[0]]->m_sShortName);

2375

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2376

break;

2377

case 5:

2378

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[tia[0]]->m_sShortName);

2379

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2380

break;

2381

case 6:

2382

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[tia[0]]->m_sShortName);

2383

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2384

break;

2385

}

2386

switch(g_iObsChannel[tia[1]])

2387

{

2388

case 0:

2389

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[tia[1]]->m_sShortName);

2390

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2391

break;

2392

case 1:

2393

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[tia[1]]->m_sShortName);

2394

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2395

break;

2396

case 2:

2397

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[tia[1]]->m_sShortName);

2398

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2399

break;

2400

case 3:

2401

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[tia[1]]->m_sShortName);

2402

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2403

break;

2404

case 4:

2405

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[tia[1]]->m_sShortName);

2406

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2407

break;

2408

case 5:

2409

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[tia[1]]->m_sShortName);

2410

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2411

break;

2412

case 6:

2413

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[tia[1]]->m_sShortName);

2414

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2415

break;

2416

}

2417

try { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName = new char[strlen(buf3)+1]; } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName = NULL; }

2418

if (o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName == NULL) NewException((double)(strlen(buf3)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2419

2420

strcpy(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName,buf3);

2421

sprintf(buf3,"cdf_2");

2422

strcat(buf3,o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName);

2423

2424

try { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName = new char[strlen(buf3)+1]; } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName = NULL; }

2425

if (o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName == NULL) NewException((double)(strlen(buf3)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2426

2427

strcpy(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,buf3);

2428

} // END FOR z3

2429

} // END IF CHANNELS == 3

2430

2431

try { o->m_pCDF->m_sShortName = new char[strlen(buf)+1]; } catch(...) { o->m_pCDF->m_sShortName = NULL; }

2432

if (o->m_pCDF->m_sShortName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2433

2434

strcpy(o->m_pCDF->m_sShortName,buf);

2435

sprintf(buf,"cdf_%d",g_iCDFChannels);

2436

strcat(buf,o->m_pCDF->m_sShortName);

2437

2438

try { o->m_pCDF->m_sName = new char[strlen(buf)+1]; } catch(...) { o->m_pCDF->m_sName = NULL; }

2439

if (o->m_pCDF->m_sName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2440

2441

strcpy(o->m_pCDF->m_sName,buf);

2442

if (o->m_pCDF->m_bDumpDat)

2443

{

2444

sprintf(buf,"cdfdump_%dd%s%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

2445

o->m_pCDF->m_fDump = OpenFileWrite(buf,true);

2446

mfprintf(o->m_pCDF->m_fDump,"# step; RM; OM1; OM2; channels\n");

2447

}

2448

if (o->m_bTimeDev)

2449

{

2450

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

2451

{

2452

try { o->m_pCDF->m_fTimeDev = new FILE*[1]; } catch(...) { o->m_pCDF->m_fTimeDev = NULL; }

2453

if (o->m_pCDF->m_fTimeDev == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2454

2455

sprintf(buf,"cdf_timedev_%dd%s%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

2456

o->m_pCDF->m_fTimeDev[0] = OpenFileWrite(buf,true);

2457

} else

2458

{

2459

try { o->m_pCDF->m_fTimeDev = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pCDF->m_fTimeDev = NULL; }

2460

if (o->m_pCDF->m_fTimeDev == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2461

2462

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

2463

{

2464

sprintf(buf,"cdf_timedev_%dd%s_ref%d%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

2465

o->m_pCDF->m_fTimeDev[z2] = OpenFileWrite(buf,true);

2466

}

2467

}

2468

if (o->m_pCDF->m_bTDAnimation)

2469

{

2470

try { o->m_pCDF->m_pTDAPlot = new CGrace(); } catch(...) { o->m_pCDF->m_pTDAPlot = NULL; }

2471

if (o->m_pCDF->m_pTDAPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2472

2473

o->m_pCDF->m_pTDAPlot->SetTitle("CDF Time Development");

2474

o->m_pCDF->m_pTDAPlot->SetSubTitle(&o->m_pCDF->m_sShortName[1]);

2475

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

2476

{

2477

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

2478

{

2479

for (z4=0;z4<o->m_pCDF->m_iCombinationsEnabled;z4++)

2480

{

2481

o->m_pCDF->m_pTDAPlot->AddDataset();

2482

if (g_iTrajSteps != -1)

2483

o->m_pCDF->m_pTDAPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled*g_iTrajSteps);

2484

o->m_pCDF->m_pTDAPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled*100);

2485

}

2486

}

2487

}

2488

o->m_pCDF->m_pTDAPlot->SetRangeX(o->m_pCDF->m_p2DF->m_fMinVal[0],o->m_pCDF->m_p2DF->m_fMaxVal[0]);

2489

o->m_pCDF->m_pTDAPlot->SetRangeY(o->m_pCDF->m_p2DF->m_fMinVal[1],o->m_pCDF->m_p2DF->m_fMaxVal[1]);

2490

o->m_pCDF->m_pTDAPlot->MakeTicks();

2491

o->m_pCDF->m_pTDAPlot->SetLabelX(o->m_pCDF->m_p2DF->m_sLabelX);

2492

o->m_pCDF->m_pTDAPlot->SetLabelY(o->m_pCDF->m_p2DF->m_sLabelY);

2493

}

2494

}

2495

} // END IF CDF

2496

2497

if (g_bVACF)

2498

{

2499

mprintf(" Creating VACF...\n");

2500

o->m_pVACF->Create();

2501

if (g_bVACFCacheMode)

2502

{

2503

mprintf(" VACF Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes*g_iTrajSteps*3.1*sizeof(float)));

2504

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

2505

{

2506

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

2507

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2508

2509

if (g_iTrajSteps != -1)

2510

{

2511

ptfa->SetMaxSize((long)(g_iTrajSteps*3.1));

2512

ptfa->SetGrow((long)(g_iTrajSteps*0.1));

2513

} else ptfa->SetGrow(1000);

2514

o->m_pVACF->m_oaCache.Add(ptfa);

2515

}

2516

} else

2517

{

2518

if (o->m_pVACF->m_iSize > g_iStepHistory)

2519

g_iStepHistory = o->m_pVACF->m_iSize;

2520

}

2521

}

2522

2523

/* if (g_bDipACF)

2524

{

2525

mprintf(" Creating DipACF...\n");

2526

o->m_pDipACF->Create();

2527

}*/

2528

2529

if (g_bMSD)

2530

{

2531

mprintf(" Creating MSD...\n");

2532

o->m_pMSD->m_pMSD->m_fMinVal = 0.0f;

2533

o->m_pMSD->m_pMSD->m_fMaxVal = o->m_pMSD->m_iResolution*g_fTimestepLength*g_iStride/1000.0;

2534

o->m_pMSD->m_pMSD->m_iResolution = o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;

2535

o->m_pMSD->m_pMSD->Create();

2536

if (g_bMSDCacheMode)

2537

{

2538

mprintf(" MSD Cache: Trying to reserve %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms*g_iTrajSteps/g_iStride*3.1*sizeof(float)));

2539

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

2540

{

2541

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

2542

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2543

2544

if (g_iTrajSteps != -1)

2545

{

2546

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.1));

2547

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.1));

2548

} else ptfa->SetGrow(1000);

2549

o->m_pMSD->m_oaCache.Add(ptfa);

2550

}

2551

if (o->m_pMSD->m_bSplit)

2552

{

2553

mprintf(" MSD Split: Trying to reserve %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms*o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride*sizeof(double)));

2554

try { o->m_pMSD->m_pSplitMSD = new CAF*[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms]; } catch(...) { o->m_pMSD->m_pSplitMSD = NULL; }

2555

if (o->m_pMSD->m_pSplitMSD == NULL) NewException((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms*sizeof(CAF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2556

2557

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

2558

{

2559

try { o->m_pMSD->m_pSplitMSD[z2] = new CAF(); } catch(...) { o->m_pMSD->m_pSplitMSD[z2] = NULL; }

2560

if (o->m_pMSD->m_pSplitMSD[z2] == NULL) NewException((double)sizeof(CAF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2561

2562

o->m_pMSD->m_pSplitMSD[z2]->m_fMinVal = 0.0f;

2563

o->m_pMSD->m_pSplitMSD[z2]->m_fMaxVal = o->m_pMSD->m_iResolution*g_fTimestepLength/1000.0;

2564

o->m_pMSD->m_pSplitMSD[z2]->m_iResolution = o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;

2565

o->m_pMSD->m_pSplitMSD[z2]->Create();

2566

}

2567

}

2568

} else

2569

{

2570

if (!g_bMSDCacheMode)

2571

{

2572

if (o->m_pMSD->m_iResolution > g_iStepHistory)

2573

g_iStepHistory = o->m_pMSD->m_iResolution;

2574

}

2575

}

2576

}

2577

2578

if (g_bRevSDF)

2579

{

2580

mprintf(" Creating Pseudo SDF...\n");

2581

o->m_pRevSDF->m_p2DF->m_fMinVal[0] = -o->m_pRevSDF->m_fRadius;

2582

o->m_pRevSDF->m_p2DF->m_fMaxVal[0] = o->m_pRevSDF->m_fRadius;

2583

o->m_pRevSDF->m_p2DF->m_fMinVal[1] = -o->m_pRevSDF->m_fRadius;

2584

o->m_pRevSDF->m_p2DF->m_fMaxVal[1] = o->m_pRevSDF->m_fRadius;

2585

o->m_pRevSDF->m_p2DF->m_iRes[0] = o->m_pRevSDF->m_iResolution;

2586

o->m_pRevSDF->m_p2DF->m_iRes[1] = o->m_pRevSDF->m_iResolution;

2587

o->m_pRevSDF->m_p2DF->SetLabelX("X [pm]");

2588

o->m_pRevSDF->m_p2DF->SetLabelY("Y [pm]");

2589

o->m_pRevSDF->m_p2DF->m_iHistogramRes = o->m_pRevSDF->m_iHistogramRes;

2590

o->m_pRevSDF->m_p2DF->Create();

2591

2592

try { o->m_pRevSDF->m_vaData = new CxVec3Array[o->m_iShowMolCount]; } catch(...) { o->m_pRevSDF->m_vaData = NULL; }

2593

if (o->m_pRevSDF->m_vaData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxVec3Array),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2594

}

2595

}

2596

2597

if (g_bBondACF)

2598

{

2599

mprintf(" Creating BondACF...\n");

2600

for (z=0;z<g_oaSingleMolecules.GetSize();z++)

2601

{

2602

sm = (CSingleMolecule*)g_oaSingleMolecules[z];

2603

for (z2=0;z2<sm->m_oaBondGroups.GetSize();z2++)

2604

{

2605

bg = (CMolBondGroup*)sm->m_oaBondGroups[z2];

2606

for (z3=0;z3<bg->m_oaBonds.GetSize();z3++)

2607

{

2608

if (g_iTrajSteps != -1)

2609

{

2610

((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetMaxSize(g_iTrajSteps);

2611

((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetGrow(g_iTrajSteps/10);

2612

} else ((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetGrow(10000);

2613

}

2614

}

2615

}

2616

}

2617

2618

if (g_bClusterAnalysis)

2619

{

2620

mprintf(" Creating Cluster Analysis...\n");

2621

g_pClusterAnalysis->Create();

2622

}

2623

2624

if (g_bFESA)

2625

{

2626

mprintf(" Creating FES Analysis...\n");

2627

g_pFESA->Create();

2628

}

2629

2630

if (g_bMicroHet)

2631

{

2632

mprintf(" Creating Microheterogeneity Analysis...\n");

2633

g_pMicroHet->Create();

2634

}

2635

2636

if (g_bThermo)

2637

{

2638

mprintf(" Creating Thermodynamic Analysis...\n");

2639

g_pThermoAnalysis->Create();

2640

}

2641

2642

if (g_iRefSystemDim == 3)

2643

g_pRefMol.SetSize(((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes);

2644

if ((g_iRefSystemDim == 3) && !g_bMiddleAvg) // Einfach das erstbeste Molekuel als Referenz nehmen

2645

{

2646

mprintf("Creating reference molecule from first time step...");

2647

g_TimeStep.CalcCenters();

2648

vec1 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]])->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

2649

vec2 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]])->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

2650

vec3 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]])->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

2651

vec2 -= vec1;

2652

vec3 -= vec1;

2653

mat.MatUltra(vec2,vec3);

2654

cc = 0;

2655

// Jeden Atomtyp des Zielmolekuels durchgehen

2656

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z3++)

2657

{

2658

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z4++)

2659

{

2660

vec2 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]])->m_oaAtomOffset[z3])->GetAt(z4)];

2661

vec2 -= vec1;

2662

g_pRefMol[cc] = mat * vec2;

2663

cc++;

2664

}

2665

}

2666

mprintf("Done.\n");

2667

} // Ende Referenzbestimmung

2668

2669

if (g_iSwapAtoms)

2670

{

2671

mprintf("Creating Reference Molecule Swap Matrix...\n");

2672

2673

try { pSwapMatrix = new unsigned int[((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes]; } catch(...) { pSwapMatrix = NULL; }

2674

if (pSwapMatrix == NULL) NewException((double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*sizeof(unsigned int),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2675

2676

for (z=0;z<((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes;z++)

2677

pSwapMatrix[z] = 0;

2678

}

2679

2680

g_iCurrentTimeStep = -1;

2681

g_iNextTimeStep = -1;

2682

g_iLastTimeStep = -1;

2683

2684

try { g_pTempTimestep = new CTimeStep(); } catch(...) { g_pTempTimestep = NULL; }

2685

if (g_pTempTimestep == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2686

2687

if ((g_bSaveRefEnv) && (g_iNbhMode == 3) && (!g_bStreamInput))

2688

{

2689

mprintf(WHITE,"\n>>> Pre-analysis for neighborhood search >>>\n");

2690

2691

g_fPos = fopen(g_sInputTraj,"rt"); // Eingabedatei erneut Oeffnen

2692

if (g_fPos == NULL)

2693

{

2694

eprintf("\nError. Input Trajectory suddenly vanished ^^\n");

2695

return 0;

2696

}

2697

g_iSteps = 0; // Der Zaehler der Zeitschritte

2698

if (g_iScanNbhStart != 0)

2699

{

2700

mprintf("\nFast-forwarding to step %d...\n",g_iScanNbhStart+1);

2701

mprintf(WHITE," [");

2702

for (z=0;z<g_iScanNbhStart;z++)

2703

{

2704

if (fmod(z,g_iScanNbhStart/60.0) < 1.0)

2705

mprintf(WHITE,"#");

2706

if (!g_TimeStep.SkipTimestep(g_fPos))

2707

break;

2708

}

2709

mprintf(WHITE,"]\n");

2710

}

2711

while (!feof(g_fPos)) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

2712

{

2713

for (z=0;z<(g_iScanNbhStride-1);z++)

2714

if (!g_TimeStep.SkipTimestep(g_fPos))

2715

goto _endnbs;

2716

if (!g_TimeStep.ReadTimestep(g_fPos,false))

2717

goto _endnbs;

2718

if (g_TimeStep.m_iGesAtomCount == 0)

2719

goto _endnbs;

2720

// g_TimeStep.m_vaCoords.SetSize(g_iGesVirtAtomCount);

2721

// g_TimeStep.UniteMolecules();

2722

// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

2723

g_TimeStep.CalcCenters();

2724

2725

if ((g_iSteps % (4*g_iScanNbhStride)) == 0)

2726

{

2727

if ((g_iSteps % (200*g_iScanNbhStride)) == 0)

2728

mprintf("\nStep %6d...",g_iSteps);

2729

else mprintf(".");

2730

}

2731

2732

g_iSteps+=g_iScanNbhStride;

2733

2734

// vec1 = g_TimeStep.m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[g_iSaveRefMol]])->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

2735

2736

// g_TimeStep.CenterPos(vec1);

2737

2738

// if (g_bFold)

2739

// g_TimeStep.FoldMolecules();

2740

2741

// for (z=0;z<g_oaNbSearches.GetSize();z++)

2742

g_pNbSet->Scan((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[g_iSaveRefMol]],&g_TimeStep);

2743

2744

if ((g_iScanNbhSteps > 0) && ((int)g_iSteps >= g_iScanNbhSteps))

2745

break;

2746

}

2747

_endnbs:

2748

2749

fclose(g_fPos);

2750

mprintf(WHITE,"\n\n<<< Neighborhood search done <<<\n");

2751

// for (z0=0;z0<g_oaNbSearches.GetSize();z0++)

2752

{

2753

mprintf(YELLOW,"\n*** Choose Neighbors\n");

2754

// nbset = (CNbSet*)g_oaNbSearches[z0];

2755

// Sort Neighbors after time they have been neighbors

2756

for (z=0;z<g_pNbSet->m_oaConditionGroups.GetSize();z++)

2757

{

2758

if (g_pNbSet->m_oaConditionGroups[z] == NULL)

2759

continue;

2760

cg = (CConditionGroup*)g_pNbSet->m_oaConditionGroups[z];

2761

2762

try { tpi = new int[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize()]; } catch(...) { tpi = NULL; }

2763

if (tpi == NULL) NewException((double)((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize()*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2764

2765

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)

2766

{

2767

cg->m_bAlwaysTrue[z2] = false;

2768

tpi[z2] = -1;

2769

}

2770

ti3 = 0;

2771

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)

2772

{

2773

ti = 0;

2774

for (z3=z2;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)

2775

{

2776

for (z4=0;z4<z2;z4++)

2777

if (tpi[z4] == z3)

2778

goto _nbhave;

2779

if (cg->m_iPassCounter[z3] > ti)

2780

{

2781

ti = cg->m_iPassCounter[z3];

2782

ti2 = z3;

2783

}

2784

_nbhave:;

2785

}

2786

if (ti == 0)

2787

break;

2788

ti3++;

2789

tpi[z2] = ti2;

2790

}

2791

mprintf(WHITE,"\n Molecule type %s. %d neighbors found in total:\n",((CMolecule*)g_oaMolecules[z])->m_sName,ti3);

2792

for (z2=0;z2<ti3;z2++)

2793

mprintf(" %2d.) Molecule %3d (%8.4f percent of the time, %d hits)\n",z2+1,tpi[z2]+1,((double)cg->m_iPassCounter[tpi[z2]])*g_iScanNbhStride/g_iSteps*100.0,cg->m_iPassCounter[tpi[z2]]);

2794

2795

if (ti3 != 0)

2796

{

2797

z3 = AskUnsignedInteger("\nUse how many of the frequentiest neighbors for molecule %s? [%d] ",ti3,((CMolecule*)g_oaMolecules[z])->m_sName,ti3);

2798

for (z2=0;z2<z3;z2++)

2799

cg->m_bAlwaysTrue[tpi[z2]] = true;

2800

}

2801

2802

delete[] tpi;

2803

cg->m_bInactive = true;

2804

}

2805

}

2806

mprintf("\n");

2807

// for (z0=0;z0<g_oaNbSearches.GetSize();z0++)

2808

if (g_bSaveRefWithEnv)

2809

{

2810

mprintf("Adding reference molecule to neighborhood...\n");

2811

g_pNbSet->AddMolecule(g_iFixMol,g_iSaveRefMol);

2812

}

2813

2814

g_pNbSet->Reset();

2815

g_pNbSet->Dump();

2816

}

2817

2818

if (g_bVFDF)

2819

{

2820

g_iVFCorrCount = 0;

2821

for (z=0;z<g_oaMolecules.GetSize();z++)

2822

{

2823

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_baAtomIndex.GetSize();z2++)

2824

{

2825

sprintf(buf,"vfcorr_%s_%s%s.dat",((CMolecule*)g_oaMolecules[z])->m_sName,((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[z2]])->m_sName,multibuf);

2826

// FreeFileName(buf);

2827

g_fVFCorr[g_iVFCorrCount] = OpenFileWrite(buf,true);

2828

g_iVFCorrCount++;

2829

}

2830

}

2831

}

2832

2833

if (g_bReact)

2834

{

2835

g_pReact->Create();

2836

g_pReact->InitMolecules(&g_TimeStep);

2837

}

2838

2839

if (g_bSaveRefEnv)

2840

{

2841

mprintf("\n");

2842

sprintf(g_sRefEnv,"refenv_%s.%d.",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1);

2843

/* for (z=0;z<g_oaMolecules.GetSize();z++)

2844

if (g_pNbAll->m_waMolCount[z] != 0)

2845

{

2846

sprintf(buf2,"%dx%s.",g_pNbAll->m_waMolCount[z],((CMolecule*)g_oaMolecules[z])->m_sName);

2847

strcat(g_sRefEnv,buf2);

2848

}*/

2849

/* if (!g_bDynamicNeighbor)

2850

strcat(g_sRefEnv,"static.");

2851

if (g_bRefEnvCenter)

2852

strcat(g_sRefEnv,"center.");

2853

if (g_bRefEnvFix)

2854

strcat(g_sRefEnv,"fix.");

2855

if (g_bScanNeighbors)

2856

strcat(g_sRefEnv,"scannb.");*/

2857

strcat(g_sRefEnv,multibuf);

2858

strcat(g_sRefEnv,"xyz");

2859

mprintf(">>> Saving reference environment as %s\n",g_sRefEnv);

2860

// FreeFileName(g_sRefEnv);

2861

g_fRefEnv = OpenFileWrite(g_sRefEnv,true);

2862

mprintf("\n");

2863

}

2864

2865

if (g_bCutCluster)

2866

{

2867

mprintf("\n");

2868

sprintf(g_sRefEnv,"cluster_%s.",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);

2869

/* for (z=0;z<g_oaMolecules.GetSize();z++)

2870

if (g_pNbAll->m_waMolCount[z] != 0)

2871

{

2872

sprintf(buf2,"%dx%s.",g_pNbAll->m_waMolCount[z],((CMolecule*)g_oaMolecules[z])->m_sName);

2873

strcat(g_sRefEnv,buf2);

2874

}*/

2875

/* if (g_bRefEnvCenter)

2876

strcat(g_sRefEnv,"center.");

2877

if (g_bRefEnvFix)

2878

strcat(g_sRefEnv,"fix.");*/

2879

strcat(g_sRefEnv,multibuf);

2880

strcat(g_sRefEnv,"xyz");

2881

mprintf(">>> Saving cluster list as %s\n",g_sRefEnv);

2882

// FreeFileName(g_sRefEnv);

2883

g_fRefEnv = OpenFileWrite(g_sRefEnv,true);

2884

mprintf("\n");

2885

}

2886

2887

if (g_bSaveJustTraj)

2888

{

2889

strcpy(buf,g_sInputTraj);

2890

p = strrchr(buf,'/');

2891

q = strrchr(buf,'\\');

2892

if (q > p)

2893

p = q;

2894

if (p == NULL)

2895

p = buf;

2896

else p++;

2897

strcpy(buf2,p);

2898

p = strrchr(buf2,'.');

2899

if (p != NULL)

2900

*p = 0;

2901

strcat(buf2,multibuf);

2902

strcat(buf2,"_out.xyz");

2903

// FreeFileName(buf);

2904

// sprintf(buf,"traj_out.xyz");

2905

mprintf("Saving processed trajectory as %s ...\n",buf2);

2906

g_fSaveJustTraj = OpenFileWrite(buf2,true);

2907

}

2908

2909

2910

/******* Interface *******************/

2911

if (!Interface_Initialization())

2912

goto _ende;

2913

2914

2915

mprintf(WHITE,"\n<<< End of Initialization <<<\n\n");

2916

2917

_beginmain:

2918

if (ReactSecondRun)

2919

{

2920

mprintf(WHITE,"\n### Starting Second Pass ###\n");

2921

} else

2922

{

2923

mprintf(WHITE,"\n### Starting Main Analysis ###\n");

2924

if (g_bVHDF)

2925

mprintf("\n Please note: The VHCF analysis will become slower while it proceeds.\n");

2926

}

2927

2928

#ifdef TARGET_LINUX

2929

if (!g_bMultiInterval || (multicounter == 0))

2930

{

2931

mprintf(WHITE,"\nHint: ");

2932

mprintf("Press CTRL+C once to softly interrupt analysis and still write the results.\n");

2933

mprintf(" Creating an empty file named EXIT (\"touch EXIT\") has the same effect.\n");

2934

}

2935

#endif

2936

2937

if (!g_bStreamInput)

2938

{

2939

g_fPos = fopen(g_sInputTraj,"rb");

2940

if (g_fPos == NULL)

2941

{

2942

eprintf("\nCould not open position trajectory.\n");

2943

goto _ende;

2944

}

2945

}

2946

2947

if ((g_bNPT) && (g_sNPTFile[0] != 0))

2948

{

2949

g_fNPTFile = fopen(g_sNPTFile,"rt");

2950

if (g_fNPTFile == NULL)

2951

{

2952

eprintf("\nCould not open cell vector file.\n");

2953

goto _ende;

2954

}

2955

}

2956

2957

if (g_bUseVelocities && (g_sInputVel[0] != 0))

2958

{

2959

g_fVel = fopen(g_sInputVel,"rt");

2960

if (g_fVel == NULL)

2961

{

2962

eprintf("\nCould not open velocity trajectory.\n");

2963

goto _ende;

2964

}

2965

}

2966

if (g_bUseForces && (g_sInputForce[0] != 0))

2967

{

2968

g_fForce = fopen(g_sInputForce,"rt");

2969

if (g_fForce == NULL)

2970

{

2971

eprintf("\nCould not open force trajectory.\n");

2972

goto _ende;

2973

}

2974

}

2975

2976

// fff = fopen("dipole.txt","wt");

2977

2978

if (g_iBeginStep != 0)

2979

{

2980

mprintf("\nFast-forwarding to step %d...\n",g_iBeginStep+1);

2981

// mprintf("Seek: %d.\n",g_iFastForwardPos);

2982

fseek(g_fPos,g_iFastForwardPos,SEEK_SET);

2983

if ((g_fVel != NULL) || (g_fForce != NULL) || ((g_bNPT) && (g_sNPTFile[0] != 0)))

2984

{

2985

mprintf(WHITE," [");

2986

for (z=0;z<g_iBeginStep;z++)

2987

{

2988

/* if (!g_TimeStep.SkipTimestep(g_fPos))

2989

{

2990

eprintf("Error. Unexpected end of position trajectory.\n");

2991

goto _endmainloop;

2992

}*/

2993

if (fmod(z,g_iBeginStep/60.0) < 1.0)

2994

mprintf(WHITE,"#");

2995

if (g_fVel != NULL)

2996

{

2997

if (!g_TimeStep.SkipTimestep(g_fVel))

2998

{

2999

eprintf("Error. Unexpected end of velocity trajectory.\n");

3000

goto _endmainloop;

3001

}

3002

}

3003

if (g_fForce != NULL)

3004

{

3005

if (!g_TimeStep.SkipTimestep(g_fForce))

3006

{

3007

eprintf("Error. Unexpected end of force trajectory.\n");

3008

goto _endmainloop;

3009

}

3010

}

3011

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

3012

fgets(buf,256,g_fNPTFile);

3013

}

3014

mprintf(WHITE,"]\n");

3015

}

3016

}

3017

3018

g_oaTimeSteps.SetSize(g_iStepHistory);

3019

for (z=0;z<g_iStepHistory;z++)

3020

g_oaTimeSteps[z] = NULL;

3021

3022

g_iSteps = 0; // Der Zaehler der Zeitschritte

3023

g_iCurrentTimeStep = 0;

3024

t0 = time(NULL);

3025

g_iClusterPos = 0;

3026

sic = 0;

3027

g_iSaveCondCount = 0;

3028

3029

try { apfa = new CxDoubleArray*[g_iCDFChannels]; } catch(...) { apfa = NULL; }

3030

if (apfa == NULL) NewException((double)g_iCDFChannels*sizeof(CxDoubleArray*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3031

3032

try { apba = new CxByteArray*[g_iCDFChannels]; } catch(...) { apba = NULL; }

3033

if (apba == NULL) NewException((double)g_iCDFChannels*sizeof(CxByteArray*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3034

3035

try { tda = new double[g_iCDFChannels]; } catch(...) { tda = NULL; }

3036

if (tda == NULL) NewException((double)g_iCDFChannels*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3037

3038

if (g_bDeriv)

3039

{

3040

g_iDerivNext = 2;

3041

g_iDerivCurr = 1;

3042

g_iDerivLast = 0;

3043

}

3044

3045

if (g_bDipole && g_bDumpDipoleVector)

3046

{

3047

g_fDumpDipole = OpenFileWrite("dipole_vectors.csv",true);

3048

fprintf(g_fDumpDipole,"#Step");

3049

for (z=0;z<g_oaMolecules.GetSize();z++)

3050

{

3051

if (g_oaDumpDipoleVector[z] == NULL)

3052

continue;

3053

for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)

3054

{

3055

fprintf(g_fDumpDipole,"; %s[%d]_X; Y; Z",((CMolecule*)g_oaMolecules[z])->m_sName,((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)+1);

3056

if (g_bDumpDipoleAbs)

3057

fprintf(g_fDumpDipole,"; Abs");

3058

}

3059

}

3060

fprintf(g_fDumpDipole,"\n");

3061

3062

if (g_bDumpDipoleXYZ)

3063

{

3064

g_fDumpDipoleXYZ = OpenFileWrite("dipole_vectors.xyz",true);

3065

3066

fprintf(g_fDumpDipoleXYZ,"%d\n\n",g_iDumpDipoleXYZAtoms);

3067

3068

for (z=0;z<g_oaMolecules.GetSize();z++)

3069

{

3070

if (g_oaDumpDipoleVector[z] == NULL)

3071

continue;

3072

m = (CMolecule*)g_oaMolecules[z];

3073

for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)

3074

{

3075

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)]];

3076

3077

for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)

3078

{

3079

if (m->m_baAtomIndex[z3] == g_iVirtAtomType)

3080

continue;

3081

for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)

3082

{

3083

ti = ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4);

3084

fprintf(g_fDumpDipoleXYZ,"%s %12f %12f %12f\n",((CAtom*)g_oaAtoms[m->m_baAtomIndex[z3]])->m_sName,g_TimeStep.m_vaCoords[ti][0]/100.0,g_TimeStep.m_vaCoords[ti][1]/100.0,g_TimeStep.m_vaCoords[ti][2]/100.0);

3085

}

3086

}

3087

}

3088

}

3089

3090

ti2 = 0;

3091

for (z=0;z<g_oaMolecules.GetSize();z++)

3092

{

3093

if (g_oaDumpDipoleVector[z] == NULL)

3094

continue;

3095

m = (CMolecule*)g_oaMolecules[z];

3096

for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)

3097

{

3098

fprintf(g_fDumpDipoleXYZ,"B %12f 0 0\n",100.0+ti2*3.0);

3099

fprintf(g_fDumpDipoleXYZ,"B %12f 0.5 0\n",100.0+ti2*3.0);

3100

ti2++;

3101

}

3102

}

3103

}

3104

}

3105

3106

3107

/*****************************************************************************

3108

*************** Beginn Hauptschleife *****************************************

3109

*****************************************************************************/

3110

3111

g_iLastTimeStep = -1;

3112

g_iDotCounter = 0;

3113

g_bStepSkipped = false;

3114

g_iFirstStepSkipped = -1;

3115

tbs = false;

3116

3117

while (true) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

3118

{

3119

if (feof(g_fPos))

3120

{

3121

mprintf("\nEnd of trajectory file reached.\n");

3122

break;

3123

}

3124

if (g_bAbortAnalysis)

3125

{

3126

mprintf("\nAnalysis aborted by user.\n");

3127

break;

3128

}

3129

g_iCurrentTimeStep++;

3130

if (g_iCurrentTimeStep >= g_iStepHistory)

3131

g_iCurrentTimeStep = 0;

3132

3133

if (g_bDeriv)

3134

{

3135

g_iDerivNext++;

3136

if (g_iDerivNext > 2)

3137

g_iDerivNext = 0;

3138

g_iDerivCurr++;

3139

if (g_iDerivCurr > 2)

3140

g_iDerivCurr = 0;

3141

g_iDerivLast++;

3142

if (g_iDerivLast > 2)

3143

g_iDerivLast = 0;

3144

}

3145

3146

for (z=0;z<(g_iStride-1);z++)

3147

{

3148

if (!g_TimeStep.SkipTimestep(g_fPos))

3149

{

3150

if (!feof(g_fPos))

3151

eprintf("\nError while skipping time step %d.\n",g_iSteps+z+1);

3152

goto _endmainloop;

3153

}

3154

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

3155

fgets(buf,256,g_fNPTFile);

3156

if (g_fVel != NULL)

3157

{

3158

if (!g_TimeStep.SkipTimestep(g_fVel))

3159

{

3160

eprintf("\nError while skipping velocity time step %d.\n",g_iSteps+z+1);

3161

goto _endmainloop;

3162

}

3163

}

3164

if (g_fForce != NULL)

3165

{

3166

if (!g_TimeStep.SkipTimestep(g_fForce))

3167

{

3168

eprintf("\nError while skipping force time step %d.\n",g_iSteps+z+1);

3169

goto _endmainloop;

3170

}

3171

}

3172

}

3173

_readagain:

3174

if (g_bUseVelocities || g_bUseForces)

3175

{

3176

if (GetTimeStep(-1) == NULL)

3177

{

3178

try { *GetTimeStepAddress(-1) = new CTimeStep(); } catch(...) { *GetTimeStepAddress(-1) = NULL; }

3179

if (*GetTimeStepAddress(-1) == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3180

}

3181

if (!GetTimeStep(-1)->ReadTimestep(g_fPos,false))

3182

{

3183

if (feof(g_fPos))

3184

{

3185

mprintf("\nEnd of Trajectory File reached.\n");

3186

break;

3187

}

3188

eprintf("\nError while reading time step %d.\n",g_iSteps+1);

3189

goto _endmainloop;

3190

}

3191

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

3192

GetTimeStep(-1)->ReadCellVector(g_fNPTFile);

3193

if (g_bSkipDoubleSteps)

3194

{

3195

if (GetTimeStep(-1)->ExtractNumber(g_iNumberPos) <= g_iLastTimeStep)

3196

{

3197

if (!g_bStepSkipped)

3198

{

3199

g_bStepSkipped = true;

3200

g_iFirstStepSkipped = GetTimeStep(-1)->ExtractNumber(g_iNumberPos);

3201

mprintf("\nSkipping:");

3202

}

3203

mprintf("*");

3204

goto _readagain;

3205

} else if (g_iFirstStepSkipped != -1)

3206

{

3207

if (g_iFirstStepSkipped == GetTimeStep(-1)->ExtractNumber(g_iNumberPos))

3208

mprintf("\nRepeated step %d skipped.",g_iFirstStepSkipped);

3209

else mprintf("\nRepeated steps %d-%d skipped.",g_iFirstStepSkipped,GetTimeStep(-1)->ExtractNumber(g_iNumberPos));

3210

g_iDotCounter = 0;

3211

g_iFirstStepSkipped = -1;

3212

}

3213

3214

if (g_iLastTimeStep != -1)

3215

{

3216

if (g_iStrideDetect == -1)

3217

{

3218

g_iStrideDetect = GetTimeStep(-1)->ExtractNumber(g_iNumberPos) - g_iLastTimeStep;

3219

} else

3220

{

3221

if (g_iStrideDetect != (GetTimeStep(-1)->ExtractNumber(g_iNumberPos) - g_iLastTimeStep))

3222

{

3223

if (!tbs)

3224

eprintf("\n");

3225

eprintf("Warning: Two successive steps %d (%d) and %d (%d) have different distance than seen before: %d.\n",g_iSteps-1,g_iLastTimeStep,g_iSteps,GetTimeStep(-1)->ExtractNumber(g_iNumberPos),g_iStrideDetect);

3226

tbs = true;

3227

} else tbs = false;

3228

}

3229

}

3230

3231

if (GetTimeStep(-1)->ExtractNumber(g_iNumberPos) > g_iLastTimeStep)

3232

g_iLastTimeStep = GetTimeStep(-1)->ExtractNumber(g_iNumberPos);

3233

}

3234

if (GetTimeStep(-1)->m_iGesAtomCount == 0)

3235

{

3236

eprintf("\nError: Atom count = 0 at time step %d.\n",g_iSteps+1);

3237

goto _endmainloop;

3238

}

3239

GetTimeStep(-1)->UniteMolecules(false);

3240

if (g_bRemoveCOM)

3241

GetTimeStep(-1)->CenterCOM();

3242

GetTimeStep(-1)->CalcCenters();

3243

if (g_bDipole)

3244

{

3245

if (g_bWannier)

3246

GetTimeStep(-1)->ScanWannier(false);

3247

GetTimeStep(-1)->CalcDipoles();

3248

if (g_bDumpDipoleVector)

3249

GetTimeStep(-1)->DumpDipoles();

3250

}

3251

} else

3252

{

3253

if (GetTimeStep(0) == NULL)

3254

{

3255

try { *GetTimeStepAddress(0) = new CTimeStep(); } catch(...) { *GetTimeStepAddress(0) = NULL; }

3256

if (*GetTimeStepAddress(0) == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3257

}

3258

if (!GetTimeStep(0)->ReadTimestep(g_fPos,false))

3259

{

3260

if (feof(g_fPos))

3261

{

3262

mprintf("\nEnd of trajectory file reached.\n");

3263

break;

3264

}

3265

eprintf("\nError while reading time step %d.\n",g_iSteps+1);

3266

goto _endmainloop;

3267

}

3268

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

3269

GetTimeStep(0)->ReadCellVector(g_fNPTFile);

3270

if (g_bSkipDoubleSteps)

3271

{

3272

if (GetTimeStep(0)->ExtractNumber(g_iNumberPos) <= g_iLastTimeStep)

3273

{

3274

// mprintf("\n[Skip %d/%d]",GetTimeStep(0)->ExtractNumber(),g_iLastTimeStep);

3275

if (!g_bStepSkipped)

3276

{

3277

g_bStepSkipped = true;

3278

g_iFirstStepSkipped = GetTimeStep(0)->ExtractNumber(g_iNumberPos);

3279

mprintf("\nSkipping:");

3280

}

3281

mprintf("*");

3282

goto _readagain;

3283

} else if (g_iFirstStepSkipped != -1)

3284

{

3285

if (g_iFirstStepSkipped == GetTimeStep(0)->ExtractNumber(g_iNumberPos))

3286

mprintf("\nRepeated step %d skipped.",g_iFirstStepSkipped);

3287

else mprintf("\nRepeated steps %d-%d skipped.",g_iFirstStepSkipped,GetTimeStep(0)->ExtractNumber(g_iNumberPos));

3288

g_iDotCounter = 0;

3289

g_iFirstStepSkipped = -1;

3290

}

3291

// mprintf("\nNumber %d.",GetTimeStep(0)->ExtractNumber());

3292

3293

if (g_iLastTimeStep != -1)

3294

{

3295

if (g_iStrideDetect == -1)

3296

{

3297

g_iStrideDetect = GetTimeStep(0)->ExtractNumber(g_iNumberPos) - g_iLastTimeStep;

3298

} else

3299

{

3300

if (g_iStrideDetect != (GetTimeStep(0)->ExtractNumber(g_iNumberPos) - g_iLastTimeStep))

3301

{

3302

if (!tbs)

3303

eprintf("\n");

3304

eprintf("Warning: Successive steps %d (%d) and %d (%d) have different distance than seen before: %d.\n",g_iSteps-1,g_iLastTimeStep,g_iSteps,GetTimeStep(0)->ExtractNumber(g_iNumberPos),g_iStrideDetect);

3305

tbs = true;

3306

} else tbs = false;

3307

}

3308

}

3309

3310

if (GetTimeStep(0)->ExtractNumber(g_iNumberPos) > g_iLastTimeStep)

3311

g_iLastTimeStep = GetTimeStep(0)->ExtractNumber(g_iNumberPos);

3312

}

3313

if (GetTimeStep(0)->m_iGesAtomCount == 0)

3314

{

3315

eprintf("\nError: Atom count = 0 at time step %d.\n",g_iSteps+1);

3316

goto _endmainloop;

3317

}

3318

if (!g_bSaveCoordsUnchanged)

3319

{

3320

GetTimeStep(0)->UniteMolecules(false);

3321

if (g_bRemoveCOM)

3322

GetTimeStep(0)->CenterCOM();

3323

}

3324

GetTimeStep(0)->CalcCenters();

3325

if (g_bDipole)

3326

{

3327

if (g_bWannier)

3328

GetTimeStep(0)->ScanWannier(false);

3329

GetTimeStep(0)->CalcDipoles();

3330

if (g_bDumpDipoleVector)

3331

GetTimeStep(0)->DumpDipoles();

3332

}

3333

}

3334

g_bWarnUnsteady = false;

3335

3336

if (((g_iSteps-(sic*g_iStride*50)) % (showinterval*g_iStride)) == 0)

3337

{

3338

if ((g_iSteps == 0) || g_bStepSkipped)

3339

{

3340

g_bStepSkipped = false;

3341

if (!g_bSilentProgress)

3342

mprintf("\nStep %6d ",g_iSteps);

3343

}

3344

if (g_bAsciiArt && (!g_bSilentProgress))

3345

{

3346

tc = g_oAsciiArt.GetChar();

3347

if (tc == 0)

3348

{

3349

if ((g_iSteps != 0) && (g_iTrajSteps != -1))

3350

{

3351

if ((time(NULL) - t0) > 5)

3352

{

3353

eta = (unsigned long)(((double)time(NULL) - t0) / g_iSteps * ((double)max(long(0),(((g_iMaxStep > 0)?g_iMaxStep:g_iTrajSteps) - ((long)g_iSteps)))));

3354

FormatTime(eta,buf);

3355

mprintf(" ETA %s",buf);

3356

}

3357

}

3358

mprintf("\nStep %6d ",g_iSteps);

3359

if (g_iSteps != 0)

3360

g_oAsciiArt.NewLine();

3361

} else mprintf("%c",tc);

3362

} else

3363

{

3364

if (g_iDotCounter >= 50)

3365

{

3366

g_iDotCounter = 0;

3367

if (!g_bSilentProgress)

3368

{

3369

if ((g_iSteps != 0) && (g_iTrajSteps != -1))

3370

{

3371

if ((time(NULL) - t0) > 5)

3372

{

3373

eta = (unsigned long)(((double)time(NULL) - t0) / g_iSteps * ((double)max(long(0),g_iTrajSteps - ((long)g_iSteps))));

3374

FormatTime(eta,buf);

3375

mprintf(" ETA %s",buf);

3376

}

3377

}

3378

mprintf("\nStep %6d ",g_iSteps);

3379

}

3380

}

3381

g_iDotCounter++;

3382

if (!g_bSilentProgress)

3383

mprintf(".");

3384

}

3385

if (FileExist("EXIT"))

3386

{

3387

mprintf("\n\n*** File \"EXIT\" detected. Aborting analysis. ***\n\n");

3388

remove("EXIT");

3389

break;

3390

}

3391

}

3392

3393

if ((int)g_iSteps == /*showinterval**/g_iStride*50)

3394

{

3395

t1 = time(NULL);

3396

if (t1 == t0)

3397

showinterval = 20;

3398

else showinterval = (int)(20.0f/(t1-t0));

3399

if (showinterval == 0)

3400

showinterval = 1;

3401

sic = 1;

3402

}

3403

3404

g_iSteps += g_iStride;

3405

3406

if (GetTimeStep(0)==NULL)

3407

continue;

3408

3409

if ((g_bUseVelocities || g_bUseForces) && (GetTimeStep(1)==NULL))

3410

continue;

3411

3412

if (g_bUseVelocities)

3413

{

3414

if (g_fVel == NULL)

3415

{

3416

CalcVelocities();

3417

} else if (!GetTimeStep(-1)->ReadTimestepVel(g_fVel))

3418

{

3419

eprintf("\nError reading velocity time step %d.\n",g_iSteps+1);

3420

goto _endmainloop;

3421

}

3422

}

3423

if (g_bUseForces)

3424

{

3425

if (g_fForce == NULL)

3426

{

3427

CalcForces();

3428

} else if (!GetTimeStep(-1)->ReadTimestepForce(g_fForce))

3429

{

3430

eprintf("\nError reading force time step %d.\n",g_iSteps+1);

3431

goto _endmainloop;

3432

}

3433

}

3434

3435

if (g_bCutCluster)

3436

{

3437

if (((int)g_iSteps/g_iStride) >= g_iClusterSteps)

3438

break;

3439

3440

if (g_iClusterPos >= g_iClusterCount)

3441

break;

3442

3443

if (g_iaClusterSteps[g_iClusterPos] != ((int)g_iSteps/g_iStride))

3444

continue;

3445

}

3446

// mprintf("\nStep %d for clusters.",((int)g_iSteps/g_iStride));

3447

3448

if (g_bUnwrap && ((int)g_iSteps > g_iStride))

3449

// Nicht im ersten Schritt

3450

{

3451

for (z=0;z<g_oaMolecules.GetSize();z++)

3452

{

3453

m = (CMolecule*)g_oaMolecules[z];

3454

for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)

3455

{

3456

if (m->m_baAtomIndex[z3] != g_iVirtAtomType)

3457

continue;

3458

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

3459

{

3460

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];

3461

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] > g_fBoxX/2.0f)

3462

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][0] -= g_fBoxX;

3463

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] < -g_fBoxX/2.0f)

3464

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][0] += g_fBoxX;

3465

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] > g_fBoxY/2.0f)

3466

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][1] -= g_fBoxY;

3467

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] < -g_fBoxY/2.0f)

3468

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][1] += g_fBoxY;

3469

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] > g_fBoxZ/2.0f)

3470

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][2] -= g_fBoxZ;

3471

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] < -g_fBoxZ/2.0f)

3472

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][2] += g_fBoxZ;

3473

// mprintf("\n%2d.%2d: %f, %f, %f",z,z2,g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][0],g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][1],g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][2]);

3474

}

3475

}

3476

}

3477

}

3478

3479

if (g_bKeepUnfoldedCoords)

3480

GetTimeStep(0)->m_vaCoords_Unfolded.CopyFrom(&GetTimeStep(0)->m_vaCoords);

3481

3482

/******* Interface *********/

3483

Interface_ProcessStep(GetTimeStep(0));

3484

3485

if (g_bMSD)

3486

{

3487

g_pT2Timestep = GetTimeStep(0);

3488

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3489

{

3490

ti2 = 0;

3491

o = (CObservation*)g_oaObserv[z0];

3492

if (g_bMSDCacheMode)

3493

{

3494

for (z2=0;z2<o->m_pMSD->m_pAtomGroup->m_oaAtoms.GetSize();z2++)

3495

{

3496

for (z3=0;z3<((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetSize();z3++)

3497

{

3498

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z4++)

3499

{

3500

ti = ((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z4]])->m_oaAtomOffset[o->m_pMSD->m_pAtomGroup->m_baAtomType[z2]])->GetAt(((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetAt(z3));

3501

ptfa = (CxFloatArray*)o->m_pMSD->m_oaCache[ti2];

3502

3503

if (g_bPeriodic && (ptfa->GetSize() > 0))

3504

{

3505

ti3 = ptfa->GetSize()-3;

3506

vec1[0] = ptfa->GetAt(ti3++);

3507

vec1[1] = ptfa->GetAt(ti3++);

3508

vec1[2] = ptfa->GetAt(ti3);

3509

tf = (g_pT2Timestep->m_vaCoords[ti]-vec1).GetLength();

3510

if (tf > g_fMinPeriodic/2.0)

3511

eprintf("\nDiscontinuity in step %d: %s[%d] %s%d moved %.2f pm. Can't compute MSD from wrapped trajectory - unwrap first.",g_iSteps,((CMolecule*)g_oaMolecules[g_waAtomMolIndex[ti]])->m_sName,g_laAtomSMLocalIndex[ti]+1,((CAtom*)g_oaAtoms[g_waAtomRealElement[ti]])->m_sName,g_waAtomMolNumber[ti]+1,tf);

3512

}

3513

3514

ptfa->Add(g_pT2Timestep->m_vaCoords[ti][0]);

3515

ptfa->Add(g_pT2Timestep->m_vaCoords[ti][1]);

3516

ptfa->Add(g_pT2Timestep->m_vaCoords[ti][2]);

3517

3518

ti2++;

3519

}

3520

}

3521

}

3522

} else

3523

{

3524

for (z=0;z<o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;z++)

3525

{

3526

g_pTempTimestep = GetTimeStep(z*o->m_pMSD->m_iStride);

3527

if (g_pTempTimestep == NULL)

3528

continue;

3529

for (z2=0;z2<o->m_pMSD->m_pAtomGroup->m_oaAtoms.GetSize();z2++)

3530

{

3531

for (z3=0;z3<((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetSize();z3++)

3532

{

3533

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z4++)

3534

{

3535

3536

o->m_pMSD->m_pMSD->AddToBin_Index(z,(double)(pow(g_pTempTimestep->m_vaCoords[ti][0]-g_pT2Timestep->m_vaCoords[ti][0],2)+pow(g_pTempTimestep->m_vaCoords[ti][1]-g_pT2Timestep->m_vaCoords[ti][1],2)+pow(g_pTempTimestep->m_vaCoords[ti][2]-g_pT2Timestep->m_vaCoords[ti][2],2)));

3537

}

3538

}

3539

}

3540

}

3541

}

3542

}

3543

} // END IF MSD

3544

3545

if (g_bSaveJustTraj)

3546

{

3547

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3548

3549

if (g_bSaveJustCenter && (!g_bSaveCoordsUnchanged))

3550

{

3551

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iSaveJustMol])->m_laSingleMolIndex[g_iSaveJustSM]])->m_oaAtomOffset[g_iSaveJustAtomType])->GetAt(g_iSaveJustAtom)];

3552

g_pTempTimestep->CenterPos(vec0);

3553

}

3554

3555

if (g_bSaveTrajNoRot)

3556

{

3557

g_pTempTimestep->CenterCOM();

3558

3559

// mfprintf(g_fSaveJustTraj," %d\n\n",(int)g_iSaveGesAtoms*3);

3560

3561

// for (z=0;z<g_iGesAtomCount;z++)

3562

// mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_pTempTimestep->m_vaCoords[z][0]/100.0,g_pTempTimestep->m_vaCoords[z][1]/100.0,g_pTempTimestep->m_vaCoords[z][2]/100.0);

3563

3564

// g_pTempTimestep->Transform(tdmat2);

3565

g_pTempTimestep->Transform(tq2);

3566

3567

// for (z=0;z<g_iGesAtomCount;z++)

3568

// mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_pTempTimestep->m_vaCoords[z][0]/100.0+10.0,g_pTempTimestep->m_vaCoords[z][1]/100.0,g_pTempTimestep->m_vaCoords[z][2]/100.0);

3569

3570

if ((int)g_iSteps > g_iStride)

3571

{

3572

dvec1 = 0;

3573

for (z=0;z<g_iGesAtomCount;z++)

3574

{

3575

dvec2 = (g_pTempTimestep->m_vaCoords[z] - rot_ts.m_vaCoords[z]);

3576

dvec4 = (g_pTempTimestep->m_vaCoords[z] + rot_ts.m_vaCoords[z]) / 2.0;

3577

3578

// tf3 = dvec4.GetLength();

3579

// tf2 = dvec2.GetLength();

3580

// if (4*tf3*tf3 > 0.25*tf2*tf2)

3581

// {

3582

// dvec4 *= (1.0 + 1.0 - 0.5 / tf3 * sqrt(4*tf3*tf3 - 0.25*tf2*tf2) );

3583

// mprintf("\n%.10g",1.0 + 1.0 - 0.5 / tf3 * sqrt(4*tf3*tf3 - 0.25*tf2*tf2));

3584

// }

3585

3586

dvec3 = CrossP(dvec4,dvec2);

3587

dvec1 += dvec3 * ((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_fMass;

3588

// mprintf(" %2d: ( %g, %g, %g ) x ( %g, %g, %g ) = ( %g, %g, %g ), m = %.2f\n",z,dvec2[0],dvec2[1],dvec2[2],rot_ts.m_vaCoords[z][0],rot_ts.m_vaCoords[z][1],rot_ts.m_vaCoords[z][2],dvec3[0],dvec3[1],dvec3[2],((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_fMass);

3589

}

3590

// mprintf("Drehimpuls: %g ( %g, %g, %g )\n",dvec1.GetLength(),dvec1[0],dvec1[1],dvec1[2]);

3591

dvec3 = dvec1;

3592

dvec3.Normalize();

3593

// mprintf(" ( %g, %g, %g )\n",vec3[0],vec3[1],vec3[2]);

3594

3595

tf = 0;

3596

for (z=0;z<g_iGesAtomCount;z++)

3597

{

3598

dvec4 = (g_pTempTimestep->m_vaCoords[z] + rot_ts.m_vaCoords[z]) / 2.0;

3599

3600

// tf3 = dvec4.GetLength();

3601

// tf2 = dvec2.GetLength();

3602

// dvec4 *= (1.0 + 1.0 - 0.5 / tf3 * sqrt(4*tf3*tf3 - 0.25*tf2*tf2) );

3603

3604

dvec0 = CrossP(dvec4,dvec3);

3605

// mprintf("# ( %g, %g, %g ) x ( %g, %g, %g ) = %g\n",g_pTempTimestep->m_vaCoords[z][0],g_pTempTimestep->m_vaCoords[z][1],g_pTempTimestep->m_vaCoords[z][2],vec3[0],vec3[1],vec3[2],vec0.GetLength());

3606

tf += ((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_fMass * dvec0.GetLengthSqr();

3607

// mprintf("\n %2d: ( %g, %g, %g ) x ( %g, %g, %g ) = ( %g, %g, %g ), m = %.2f",z,vec2[0],vec2[1],vec2[2],rot_ts.m_vaCoords[z][0],rot_ts.m_vaCoords[z][1],rot_ts.m_vaCoords[z][2],vec3[0],vec3[1],vec3[2],((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_fMass);

3608

}

3609

// mprintf(" Traegheitsmoment: %g\n",tf);

3610

dvec1 /= tf;

3611

// mprintf("Angular momentum vector: ( %g, %g, %g ) (l = %g)\n",dvec1[0],dvec1[1],dvec1[2],dvec1.GetLength());

3612

// mprintf(" Winkelgeschw.: %g\n",dvec1.GetLength());

3613

// dvec3 = dvec1;

3614

// dvec3.Normalize();

3615

3616

// mprintf(" Baue Matrix: ( %g | %g | %g ), %g\n",dvec3[0],dvec3[1],dvec3[2],-dvec1.GetLength());

3617

3618

// tdmat.RotMat(dvec3,-dvec1.GetLength());

3619

3620

tq.BuildRotation(dvec3,dvec1.GetLength());

3621

3622

// mprintf(" Die Matrix:\n");

3623

// tdmat.Dump();

3624

3625

// tdmat2 = tdmat2 * tdmat;

3626

tq2 = tq2 * tq;

3627

3628

if (fabs(tq2.GetLength()-1.0) > 0.000001)

3629

{

3630

eprintf("\nRenormalizing rotation quaternion.\n");

3631

tq2.Normalize();

3632

}

3633

3634

// g_pTempTimestep->Transform(tdmat);

3635

g_pTempTimestep->Transform(tq);

3636

}

3637

3638

rot_ts.CopyFrom(g_pTempTimestep);

3639

3640

// for (z=0;z<g_iGesAtomCount;z++)

3641

// mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_sName,g_pTempTimestep->m_vaCoords[z][0]/100.0+20.0,g_pTempTimestep->m_vaCoords[z][1]/100.0,g_pTempTimestep->m_vaCoords[z][2]/100.0);

3642

3643

} else

3644

{

3645

if (g_bFold && (!g_bSaveCoordsUnchanged))

3646

{

3647

if (g_bFoldAtomwise)

3648

g_pTempTimestep->FoldAtoms();

3649

else g_pTempTimestep->FoldMolecules();

3650

}

3651

}

3652

3653

if (!g_bCenterZero && (!g_bSaveCoordsUnchanged) && g_bPeriodic)

3654

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

3655

3656

ti = g_iSaveGesAtoms;

3657

3658

if (g_bUnwrapWannier)

3659

{

3660

g_pTempTimestep->ScanWannier(false);

3661

3662

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3663

{

3664

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3665

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3666

ti += ((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_laWannier.GetSize();

3667

}

3668

}

3669

3670

mfprintf(g_fSaveJustTraj," %d\n",ti);

3671

if (g_pTempTimestep->m_pComment != NULL)

3672

mfprintf(g_fSaveJustTraj,"%s\n",g_pTempTimestep->m_pComment);

3673

else mfprintf(g_fSaveJustTraj,"\n");

3674

3675

if (g_bWriteAtomwise)

3676

{

3677

for (z7=0;z7<g_oaAtoms.GetSize();z7++)

3678

{

3679

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3680

{

3681

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3682

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3683

{

3684

for (z4=0;z4<atgr->m_baAtomType.GetSize();z4++)

3685

{

3686

if (atgr->m_baRealAtomType[z4] != z7)

3687

continue;

3688

tla = (CxIntArray*)atgr->m_oaAtoms[z4];

3689

for (z5=0;z5<tla->GetSize();z5++)

3690

{

3691

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_oaAtomOffset[atgr->m_baAtomType[z4]])->GetAt(tla->GetAt(z5))];

3692

if (g_bUnwrap)

3693

{

3694

vec0 += g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]];

3695

// mprintf("\nUnwrap: (%G|%G|%G) <-- (%G|%G|%G)",vec0[0],vec0[1],vec0[2],g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]][0],g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]][1],g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]][2]);

3696

}

3697

if (atgr->m_baRealAtomType[z4] == g_iVirtAtomType)

3698

{

3699

if (g_bSaveVirtAtoms)

3700

mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CVirtualAtom*)g_oaVirtualAtoms[atgr->m_pMolecule->m_laVirtualAtoms[tla->GetAt(z5)]])->m_sLabel,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3701

} else mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[atgr->m_baRealAtomType[z4]])->m_sName,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3702

}

3703

}

3704

}

3705

}

3706

}

3707

} else

3708

{

3709

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3710

{

3711

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3712

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3713

{

3714

for (z4=0;z4<atgr->m_baAtomType.GetSize();z4++)

3715

{

3716

tla = (CxIntArray*)atgr->m_oaAtoms[z4];

3717

for (z5=0;z5<tla->GetSize();z5++)

3718

{

3719

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_oaAtomOffset[atgr->m_baAtomType[z4]])->GetAt(tla->GetAt(z5))];

3720

if (g_bUnwrap)

3721

{

3722

vec0 += g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]];

3723

3724

}

3725

if (atgr->m_baRealAtomType[z4] == g_iVirtAtomType)

3726

{

3727

if (g_bSaveVirtAtoms)

3728

mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CVirtualAtom*)g_oaVirtualAtoms[atgr->m_pMolecule->m_laVirtualAtoms[tla->GetAt(z5)]])->m_sLabel,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3729

} else mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[atgr->m_baRealAtomType[z4]])->m_sName,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3730

}

3731

}

3732

}

3733

}

3734

}

3735

3736

if (g_bUnwrapWannier)

3737

{

3738

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3739

{

3740

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3741

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3742

{

3743

for (z4=0;z4<((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_laWannier.GetSize();z4++)

3744

{

3745

vec0 = g_pTempTimestep->m_vaCoords[((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_laWannier[z4]];

3746

if (g_bUnwrap)

3747

vec0 += g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]];

3748

mfprintf(g_fSaveJustTraj," X %8.5f %8.5f %8.5f\n",vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3749

}

3750

}

3751

}

3752

}

3753

} // END IF g_bSaveJustTraj

3754

3755

if (g_bBondACF)

3756

{

3757

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3758

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

3759

{

3760

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

3761

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

3762

{

3763

bond = (CMolBond*)sm->m_oaBonds[z3];

3764

bond->m_faData.Add(VecDist(g_pTempTimestep->m_vaCoords[bond->m_iAtomOffset[0]],g_pTempTimestep->m_vaCoords[bond->m_iAtomOffset[1]]));

3765

}

3766

}

3767

}

3768

3769

if (g_bAggregation || g_bNbExchange)

3770

{

3771

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3772

3773

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3774

{

3775

o = (CObservation*)g_oaObserv[z0];

3776

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3777

{

3778

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3779

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize();z2++)

3780

dacfsub->m_pCondition->m_iPassCounter[z2] = 0;

3781

}

3782

}

3783

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3784

{

3785

o = (CObservation*)g_oaObserv[z0];

3786

3787

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex.GetSize();z2++)

3788

{

3789

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex[z2]];

3790

3791

o->m_pDACF->m_pCondition->PreScanNeighborhoodAllOM(g_pTempTimestep,smfix);

3792

3793

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3794

{

3795

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3796

3797

dacfsub->m_pCondition->CopyResults(o->m_pDACF->m_pCondition);

3798

dacfsub->m_pCondition->m_bAnyPassed = false;

3799

dacfsub->m_pCondition->ReScan(smfix);

3800

if (dacfsub->m_pCondition->m_bAnyPassed)

3801

dacfsub->m_pCondition->m_iRMPassCounter[z2]++;

3802

3803

if (g_bDACF)

3804

o->m_pDACF->UpdateDACFSub(z2,g_pTempTimestep,dacfsub);

3805

3806

if (g_bNbExchange)

3807

o->m_pDACF->UpdateNbEx(z2,dacfsub);

3808

} // END FOR ZS

3809

} // END FOR Z2

3810

} // END FOR Z0

3811

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3812

{

3813

o = (CObservation*)g_oaObserv[z0];

3814

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3815

{

3816

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3817

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize();z2++)

3818

if (dacfsub->m_pCondition->m_iPassCounter[z2] != 0)

3819

dacfsub->m_pCondition->m_iOMPassCounter[z2]++;

3820

}

3821

}

3822

} // END IF AGGREGATION OR NBEX

3823

3824

if (g_bDens)

3825

{

3826

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3827

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3828

{

3829

o = (CObservation*)g_oaObserv[z0];

3830

m = (CMolecule*)g_oaMolecules[o->m_iShowMol];

3831

for (z3=0;z3<m->m_laSingleMolIndex.GetSize();z3++)

3832

{

3833

if (g_bRegionAnalysis)

3834

if ((!o->m_iaRMRegions.Contains(0)) && (!o->m_iaRMRegions.Contains(g_iaSMRegion[m->m_laSingleMolIndex[z3]])))

3835

continue;

3836

3837

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z3]];

3838

ti = ((CxIntArray*)sm->m_oaAtomOffset[o->m_pDensityDF->m_iCenterAtomType])->GetAt(o->m_pDensityDF->m_iCenterAtom);

3839

vec0 = g_pTempTimestep->m_vaCoords[ti];

3840

3841

g_pTempTimestep->CenterPos(vec0);

3842

g_pTempTimestep->FoldAtoms();

3843

3844

for (z4=0;z4<g_oaMolecules.GetSize();z4++)

3845

{

3846

if (!o->m_pDensityDF->m_pDensityMolSelect[z4])

3847

continue;

3848

m2 = (CMolecule*)g_oaMolecules[z4];

3849

ag = o->m_pDensityDF->m_pDensityMolAG[z4];

3850

for (z5=0;z5<m2->m_laSingleMolIndex.GetSize();z5++)

3851

{

3852

if (g_bRegionAnalysis)

3853

if ((!o->m_iaOM1Regions.Contains(0)) && (!o->m_iaOM1Regions.Contains(g_iaSMRegion[m2->m_laSingleMolIndex[z5]])))

3854

continue;

3855

3856

sm2 = (CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[z5]];

3857

for (z6=0;z6<ag->m_baAtomType.GetSize();z6++)

3858

{

3859

if (ag->m_baRealAtomType[z6] == g_iVirtAtomType)

3860

continue;

3861

if (o->m_pDensityDF->m_bDensityMass)

3862

{

3863

tf2 = ((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z6]])->m_pElement->m_fMass;

3864

for (z7=0;z7<((CxIntArray*)ag->m_oaAtoms[z6])->GetSize();z7++)

3865

{

3866

tf = g_pTempTimestep->m_vaCoords[((CxIntArray*)sm2->m_oaAtomOffset[ag->m_baAtomType[z6]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z6])->GetAt(z7))].GetLength();

3867

o->m_pDensityDF->m_pDensDF->AddToBin(tf,tf2);

3868

}

3869

} else

3870

{

3871

for (z7=0;z7<((CxIntArray*)ag->m_oaAtoms[z6])->GetSize();z7++)

3872

{

3873

tf = g_pTempTimestep->m_vaCoords[((CxIntArray*)sm2->m_oaAtomOffset[ag->m_baAtomType[z6]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z6])->GetAt(z7))].GetLength();

3874

o->m_pDensityDF->m_pDensDF->AddToBin(tf);

3875

}

3876

}

3877

}

3878

}

3879

}

3880

}

3881

}

3882

} // END IF g_bDens

3883

3884

if (g_bRDyn || g_bIRSpec)

3885

{

3886

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3887

for (z6=0;z6<g_oaObserv.GetSize();z6++)

3888

{

3889

o = (CObservation*)g_oaObserv[z6];

3890

if (g_bIRSpec)

3891

trdyn = o->m_pIRSpec;

3892

else trdyn = o->m_pRDyn;

3893

ti = 0;

3894

for (z3=0;z3<o->m_iShowMolCount;z3++) // Alle anderen Molekuele durchgehen

3895

{

3896

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

3897

3898

if (trdyn->m_iVecType == 0)

3899

{

3900

trdyn->BuildAtomList(sm,&templa);

3901

for (z4=0;z4<templa.GetSize();z4+=3)

3902

{

3903

if (trdyn->m_bOrtho)

3904

{

3905

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3906

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3907

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

3908

vec1 = CrossP(vec2-vec0,vec3-vec0);

3909

} else

3910

{

3911

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3912

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3913

vec1 = vec2-vec0;

3914

}

3915

vec1.Normalize();

3916

if (g_bRDynCacheMode)

3917

{

3918

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[0]);

3919

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[1]);

3920

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[2]);

3921

ti++;

3922

} else

3923

{

3924

for (z=0;z<trdyn->m_iDepth/trdyn->m_iStride;z++)

3925

{

3926

g_pT2Timestep = GetTimeStep(z*trdyn->m_iStride);

3927

if (g_pT2Timestep == NULL)

3928

continue;

3929

if (trdyn->m_bOrtho)

3930

{

3931

vec4 = g_pT2Timestep->m_vaCoords[templa[z4]];

3932

vec3 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

3933

vec5 = g_pT2Timestep->m_vaCoords[templa[z4+2]];

3934

vec2 = CrossP(vec3-vec4,vec5-vec4);

3935

} else

3936

{

3937

vec4 = g_pT2Timestep->m_vaCoords[templa[z4]];

3938

vec3 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

3939

vec2 = vec3-vec4;

3940

}

3941

vec2.Normalize();

3942

trdyn->m_pRDyn->AddToBin_Int(z,DotP(vec1,vec2));

3943

trdyn->m_pCount[z]++;

3944

}

3945

}

3946

}

3947

} else if (trdyn->m_iVecType == 1)

3948

{

3949

vec1 = sm->m_vDipole;

3950

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[0]);

3951

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[1]);

3952

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[2]);

3953

3954

// if (z3 == 0)

3955

// mfprintf(fff,"%f, %f, %f\n",vec1[0],vec1[1],vec1[2]);

3956

3957

ti++;

3958

} // END VECTYPE

3959

}

3960

}

3961

} // END IF RDYN

3962

3963

if (g_bVACF)

3964

{

3965

g_pT2Timestep = GetTimeStep(0);

3966

// mprintf("\nStep=%d, adding.",g_iSteps);

3967

if (g_bGlobalVACF)

3968

{

3969

if (g_bVACFCacheMode)

3970

{

3971

ti = 0;

3972

for (z2=0;z2<g_iGesAtomCount;z2++)

3973

{

3974

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z2] > 1000))

3975

continue;

3976

// mprintf("Global: Step %d, Atom %d: %.4ff | %.4ff | %.4ff\n",g_iSteps,z2+1,g_pT2Timestep->m_vaVelocities[z2][0],g_pT2Timestep->m_vaVelocities[z2][1],g_pT2Timestep->m_vaVelocities[z2][2]);

3977

((CxFloatArray*)g_pGlobalVACF->m_oaCache[ti])->Add(g_pT2Timestep->m_vaVelocities[z2][0]);

3978

((CxFloatArray*)g_pGlobalVACF->m_oaCache[ti])->Add(g_pT2Timestep->m_vaVelocities[z2][1]);

3979

((CxFloatArray*)g_pGlobalVACF->m_oaCache[ti])->Add(g_pT2Timestep->m_vaVelocities[z2][2]);

3980

ti++;

3981

}

3982

} else

3983

{

3984

for (z=0;z<g_pGlobalVACF->m_iSize;z++)

3985

{

3986

g_pTempTimestep = GetTimeStep(z);

3987

if (g_pTempTimestep == NULL)

3988

continue;

3989

if (g_pTempTimestep->m_vaVelocities.GetSize() == 0)

3990

continue;

3991

pd = &g_pGlobalVACF->m_pData[z];

3992

g_pGlobalVACF->m_pCounter[z] += g_iGesAtomCount;

3993

for (z2=0;z2<g_iGesAtomCount;z2++)

3994

*pd += DotP(g_pTempTimestep->m_vaVelocities[z2],g_pT2Timestep->m_vaVelocities[z2]);

3995

}

3996

}

3997

}

3998

for (z6=0;z6<g_oaObserv.GetSize();z6++)

3999

{

4000

o = (CObservation*)g_oaObserv[z6];

4001

for (z3=0;z3<o->m_iShowMolCount;z3++) // Alle anderen Molekuele durchgehen

4002

{

4003

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

4004

o->m_pVACF->BuildAtomList(sm,&templa);

4005

for (z4=0;z4<templa.GetSize();z4++)

4006

{

4007

if (g_bVACFCacheMode)

4008

{

4009

ti = templa[z4];

4010

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][0]);

4011

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][1]);

4012

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][2]);

4013

// mprintf("%d*%d+%d=%d\n",z3,o->m_pVACF->m_iShowAtomGes,z4,z3*o->m_pVACF->m_iShowAtomGes+z4);

4014

// mprintf("Lokal: Step %d, Atom %d: %.4ff | %.4ff | %.4ff\n",g_iSteps,ti+1,g_pT2Timestep->m_vaVelocities[ti][0],g_pT2Timestep->m_vaVelocities[ti][1],g_pT2Timestep->m_vaVelocities[ti][2]);

4015

// mprintf("Step %d: Obs %d, Mol %d, Atom %d: Index %d.\n",g_iStepHistory,z6+1,z3+1,z4+1,ti+1);

4016

} else

4017

{

4018

for (z5=0;z5<o->m_pVACF->m_iSize;z5++)

4019

{

4020

o->m_pVACF->m_pCounter[z5]++;

4021

g_pTempTimestep = GetTimeStep(z5);

4022

if (g_pTempTimestep == NULL)

4023

continue;

4024

if (g_pTempTimestep->m_vaVelocities.GetSize() == 0)

4025

continue;

4026

o->m_pVACF->m_pData[z5] += DotP(g_pTempTimestep->m_vaVelocities[templa[z4]],g_pT2Timestep->m_vaVelocities[templa[z4]]);

4027

}

4028

}

4029

}

4030

}

4031

}

4032

} // END IF VACF

4033

4034

if (g_bIRSpec && g_bGlobalIR)

4035

{

4036

for (z3=0;z3<g_oaSingleMolecules.GetSize();z3++) // Alle anderen Molekuele durchgehen

4037

{

4038

sm = (CSingleMolecule*)g_oaSingleMolecules[z3];

4039

vec1 = sm->m_vDipole;

4040

((CxFloatArray*)g_pGlobalIR->m_oaCache[z3])->Add(vec1[0]);

4041

((CxFloatArray*)g_pGlobalIR->m_oaCache[z3])->Add(vec1[1]);

4042

((CxFloatArray*)g_pGlobalIR->m_oaCache[z3])->Add(vec1[2]);

4043

}

4044

} // END IF g_bGlobalIR

4045

4046

if (g_bReact)

4047

{

4048

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4049

if (ReactSecondRun)

4050

{

4051

g_pReact->WriteTrajec(g_pTempTimestep);

4052

} else

4053

{

4054

g_pReact->ScanBonds(g_pTempTimestep,false);

4055

}

4056

}

4057

4058

if (g_bNbAnalysis)

4059

{

4060

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4061

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize();z2++)

4062

{

4063

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]];

4064

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4065

{

4066

o = (CObservation*)g_oaObserv[z6];

4067

o->m_pNbAnalysis->m_pNbSearch->ScanAllOM(smfix,g_pTempTimestep);

4068

o->m_pNbAnalysis->AnalyzeStep();

4069

}

4070

}

4071

}

4072

4073

if (g_bNbExchange)

4074

{

4075

}

4076

4077

if (g_bClusterAnalysis)

4078

{

4079

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4080

g_pClusterAnalysis->Process(g_pTempTimestep);

4081

}

4082

4083

if (g_bFESA)

4084

{

4085

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4086

g_pFESA->ProcessStep(g_pTempTimestep);

4087

}

4088

4089

if (g_bMicroHet)

4090

{

4091

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4092

g_pTempTimestep->FoldAtomsPositive();

4093

g_pMicroHet->Process(g_pTempTimestep);

4094

}

4095

4096

if (g_bThermo)

4097

{

4098

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4099

g_pThermoAnalysis->AnalyzeStep(g_pTempTimestep);

4100

}

4101

4102

if (g_bVoro)

4103

{

4104

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4105

4106

if (g_pVoroWrapper->m_bVoroStat)

4107

{

4108

g_pTempTimestep->FoldAtomsPositive();

4109

g_pVoroWrapper->Build(g_pTempTimestep);

4110

}

4111

4112

if (g_pVoroWrapper->m_bWritePOV)

4113

g_pVoroWrapper->WritePOV(g_pTempTimestep);

4114

4115

if (g_pVoroWrapper->m_bSurfCover)

4116

g_pVoroWrapper->ProcessSurfCover(g_pTempTimestep);

4117

4118

if (g_pVoroWrapper->m_bVoroMetric)

4119

{

4120

if (!g_bClusterAnalysis)

4121

g_pVoroWrapper->BuildVoroMetric(g_pTempTimestep);

4122

}

4123

4124

if (g_pVoroWrapper->m_bPOVBox)

4125

{

4126

g_pTempTimestep->FoldAtomsPositive();

4127

4128

g_pVoroWrapper->PerformChoreography(g_pTempTimestep);

4129

4130

if (g_pVoroWrapper->m_iPOVCurrentChoreographyPart >= g_pVoroWrapper->m_oaBoxChoreography.GetSize())

4131

break;

4132

}

4133

}

4134

4135

/* if (g_bSFac)

4136

{

4137

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4138

g_pSFac->ProcessStep(g_pTempTimestep);

4139

}*/

4140

4141

if (g_bVoid)

4142

{

4143

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4144

g_pTempTimestep->FoldAtomsPositive();

4145

g_pVoroAnalysis->Step(g_pTempTimestep);

4146

}

4147

4148

if (g_bVDF && (g_iFixMol == -1))

4149

{

4150

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4151

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4152

{

4153

o = (CObservation*)g_oaObserv[z6];

4154

for (z3=0;z3<o->m_iShowMolCount;z3++) // Alle anderen Molekuele durchgehen

4155

{

4156

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

4157

o->m_pVDF[0]->BuildAtomList(NULL,sm,&templa);

4158

4159

for (z4=0;z4<templa.GetSize();z4++)

4160

o->m_pVDF[0]->m_pVDF->AddToBin(g_pTempTimestep->m_vaVelocities[templa[z4]].GetLength());

4161

}

4162

}

4163

}

4164

4165

if ((!g_bCDF) && (!g_bRDF) && (!g_bSDF) && (!g_bPlDF) && (!g_bLiDF) && (!g_bVoidSDF) && (!g_bADF) && (!g_bDDF) && (!g_bVDF) && (!g_bDipDF) && (!g_bCutCluster) && (!g_bSaveRefEnv) && (!g_bVHDF) && (!g_bRevSDF) && (!g_bCond))

4166

goto _endstep;

4167

4168

if (g_bVoid)

4169

{

4170

if (g_bVoidSDF && g_pVoroAnalysis->m_bEmptySpaceSDF && g_pVoroAnalysis->m_bNewEmptyMode)

4171

{

4172

g_pVoroAnalysis->m_pTempSDF->Clear();

4173

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4174

g_pTempTimestep->FoldAtomsPositive();

4175

for (z3=0;z3<g_iGesAtomCount;z3++)

4176

{

4177

vec0 = g_pTempTimestep->m_vaCoords[z3];

4178

g_pVoroAnalysis->m_pTempSDF->AddToBin_SphereWrap(vec0,g_faVdWRadius[z3]);

4179

}

4180

// g_pVoroAnalysis->m_pTempSDF->WritePLT("","bla.plt","",true);

4181

}

4182

}

4183

4184

// tfr = 9999.0;

4185

4186

if (g_iFixMol == -1)

4187

goto _norefmol;

4188

4189

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4190

{

4191

o = (CObservation*)g_oaObserv[z6];

4192

4193

if (o->m_pConditions != NULL)

4194

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

4195

o->m_pConditions->m_iPassCounter[z2] = 0;

4196

4197

if (o->m_pConditionsOM2 != NULL)

4198

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

4199

o->m_pConditionsOM2->m_iPassCounter[z2] = 0;

4200

}

4201

4202

// Jedes Festhalte-Molekuel mal im Ursprung liegen lassen

4203

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize();z2++)

4204

{

4205

if (g_bDoubleBox && (z2 >= ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()/g_iDoubleBoxFactor))

4206

continue;

4207

4208

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]];

4209

4210

if (g_bCutCluster)

4211

{

4212

if (g_iClusterPos >= g_iClusterCount)

4213

break;

4214

4215

if (((int)g_iSteps/g_iStride) >= g_iClusterSteps)

4216

break;

4217

4218

if (g_iaClusterMol[g_iClusterPos] != z2)

4219

continue;

4220

4221

if (g_iaClusterSteps[g_iClusterPos] != ((int)g_iSteps/g_iStride))

4222

break;

4223

4224

g_iClusterPos++;

4225

}

4226

4227

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4228

4229

// Zentrieren/Falten der ganzen Box nur noch noetig bei den folgenden Analysen

4230

if (g_bSDF || g_bRevSDF || g_bCutCluster || g_bSaveRefEnv || g_bSaveJustTraj || g_bVoidSDF || g_bMiddleAvg)

4231

{

4232

vecc = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

4233

4234

if ((g_bCutCluster && !g_bRefEnvCenter) || (g_bSaveRefEnv && (!g_bRefEnvCenter) && (z2==g_iSaveRefMol)))

4235

{

1145

try { o->m_pPlProj->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pPlProj->m_baDataEnabled = NULL; }

1146

if (o->m_pPlProj->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1147

}

1148

}

1149

1150

if (g_bRDyn)

1151

{

1152

mprintf(" Creating Reorientation Dynamics...\n");

1153

o->m_pRDyn->m_pRDyn->m_fMinVal = 0;

1154

o->m_pRDyn->m_pRDyn->m_fMaxVal = o->m_pRDyn->m_iDepth * g_fTimestepLength / 1000.0f;

1155

o->m_pRDyn->m_pRDyn->m_iResolution = o->m_pRDyn->m_iDepth/o->m_pRDyn->m_iStride;

1156

o->m_pRDyn->m_pRDyn->SetLabelX("Tau [ps]");

1157

o->m_pRDyn->m_pRDyn->SetLabelY("Vector autocorrelation");

1158

o->m_pRDyn->m_pRDyn->Create();

1159

if (g_bRDynCacheMode)

1160

{

1161

if (g_iTrajSteps != -1)

1162

1163

1164

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pRDyn->m_iCombinations;z2++)

1165

{

1166

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

1167

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1168

1169

if (g_iTrajSteps != -1)

1170

{

1171

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.3));

1172

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.3));

1173

} else ptfa->SetGrow(10000);

1174

o->m_pRDyn->m_oaCache.Add(ptfa);

1175

}

1176

} else

1177

{

1178

try { o->m_pRDyn->m_pCount = new double[o->m_pRDyn->m_pRDyn->m_iResolution]; } catch(...) { o->m_pRDyn->m_pCount = NULL; }

1179

if (o->m_pRDyn->m_pCount == NULL) NewException((double)o->m_pRDyn->m_pRDyn->m_iResolution*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1180

1181

for (z2=0;z2<o->m_pRDyn->m_pRDyn->m_iResolution;z2++)

1182

o->m_pRDyn->m_pCount[z2] = 0;

1183

if (!g_bRDynCacheMode)

1184

{

1185

if (o->m_pRDyn->m_iDepth > g_iStepHistory)

1186

g_iStepHistory = o->m_pRDyn->m_iDepth;

1187

}

1188

}

1189

}

1190

1191

if (g_bIRSpec)

1192

{

1193

mprintf(" Creating IR Spectrum...\n");

1194

o->m_pIRSpec->m_pRDyn->m_fMinVal = 0;

1195

o->m_pIRSpec->m_pRDyn->m_fMaxVal = o->m_pIRSpec->m_iDepth * g_fTimestepLength / 1000.0f;

1196

o->m_pIRSpec->m_pRDyn->m_iResolution = o->m_pIRSpec->m_iDepth/o->m_pIRSpec->m_iStride;

1197

o->m_pIRSpec->m_pRDyn->SetLabelX("Tau [ps]");

1198

o->m_pIRSpec->m_pRDyn->SetLabelY("Dipole autocorrelation");

1199

o->m_pIRSpec->m_pRDyn->Create();

1200

if (g_bRDynCacheMode)

1201

{

1202

if (g_iTrajSteps != -1)

1203

mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pIRSpec->m_iCombinations*g_iTrajSteps/g_iStride*3.1*sizeof(float)));

1204

else mprintf(" RDyn Cache: Trying to allocate %s of memory...\n",FormatBytes((double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pIRSpec->m_iCombinations*10000/g_iStride*3.1*sizeof(float)));

1205

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pIRSpec->m_iCombinations;z2++)

1206

{

1207

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

1208

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1209

1210

if (g_iTrajSteps != -1)

1211

{

1212

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.3));

1213

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.3));

1214

} else ptfa->SetGrow(10000);

1215

o->m_pIRSpec->m_oaCache.Add(ptfa);

1216

}

1217

} else

1218

{

1219

try { o->m_pIRSpec->m_pCount = new double[o->m_pIRSpec->m_pRDyn->m_iResolution]; } catch(...) { o->m_pIRSpec->m_pCount = NULL; }

1220

if (o->m_pIRSpec->m_pCount == NULL) NewException((double)o->m_pIRSpec->m_pRDyn->m_iResolution*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1221

1222

for (z2=0;z2<o->m_pIRSpec->m_pRDyn->m_iResolution;z2++)

1223

o->m_pIRSpec->m_pCount[z2] = 0;

1224

if (!g_bRDynCacheMode)

1225

{

1226

if (o->m_pIRSpec->m_iDepth > g_iStepHistory)

1227

g_iStepHistory = o->m_pIRSpec->m_iDepth;

1228

}

1229

}

1230

}

1231

1232

if (g_bDens)

1233

{

1234

mprintf(" Creating Density Distribution Function...\n");

1235

o->m_pDensityDF->m_pDensDF->m_fMinVal = o->m_pDensityDF->m_fMinDist;

1236

o->m_pDensityDF->m_pDensDF->m_fMaxVal = o->m_pDensityDF->m_fMaxDist;

1237

o->m_pDensityDF->m_pDensDF->m_iResolution = o->m_pDensityDF->m_iResolution;

1238

o->m_pDensityDF->m_pDensDF->m_iHistogramRes = o->m_pDensityDF->m_iHistogramRes;

1239

o->m_pDensityDF->m_pDensDF->SetLabelX("Distance [pm]");

1240

if (o->m_pDensityDF->m_bDensityMass)

1241

o->m_pDensityDF->m_pDensDF->SetLabelY("Mass Density [g/cm^3]");

1242

else o->m_pDensityDF->m_pDensDF->SetLabelY("Particle Density [1/nm^3]");

1243

o->m_pDensityDF->m_pDensDF->Create();

1244

}

1245

1246

if (g_bVHDF)

1247

{

1248

mprintf(" Creating VHCF...\n");

1249

o->m_pVHDF->m_pVHDF->m_fMinVal[1] = o->m_pVHDF->m_fMinDist;

1250

o->m_pVHDF->m_pVHDF->m_fMaxVal[1] = o->m_pVHDF->m_fMaxDist;

1251

o->m_pVHDF->m_pVHDF->m_iRes[1] = o->m_pVHDF->m_iResolution;

1252

o->m_pVHDF->m_pVHDF->m_fMinVal[0] = 0.0;

1253

o->m_pVHDF->m_pVHDF->m_fMaxVal[0] = o->m_pVHDF->m_iDepth * g_fTimestepLength / 1000.0f;

1254

o->m_pVHDF->m_pVHDF->m_iRes[0] = o->m_pVHDF->m_iDepth / o->m_pVHDF->m_iStride;

1255

o->m_pVHDF->m_pVHDF->Create();

1256

1257

try { o->m_pVHDF->m_pCount = new double[o->m_pVHDF->m_pVHDF->m_iRes[0]]; } catch(...) { o->m_pVHDF->m_pCount = NULL; }

1258

if (o->m_pVHDF->m_pCount == NULL) NewException((double)o->m_pVHDF->m_pVHDF->m_iRes[0]*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1259

1260

for (z0=0;z0<o->m_pVHDF->m_pVHDF->m_iRes[0];z0++)

1261

o->m_pVHDF->m_pCount[z0] = 0;

1262

o->m_pVHDF->m_pVHDF->SetLabelY("Distance [pm]");

1263

o->m_pVHDF->m_pVHDF->SetLabelX("Tau [ps]");

1264

// o->m_pVHDF->m_pVHDF->m_fPlotExp = 1.0;

1265

if (o->m_pVHDF->m_iDepth > g_iStepHistory)

1266

g_iStepHistory = o->m_pVHDF->m_iDepth;

1267

mprintf(" Setting trajectory ring buffer to %s...\n",FormatBytes(g_iStepHistory*g_iGesVirtAtomCount*sizeof(float)*3));

1268

}

1269

1270

if (g_bNbAnalysis)

1271

{

1272

mprintf(" Creating Neighborhood Analysis...\n");

1273

1274

try { o->m_pNbAnalysis->m_pNPFCount = new CDF(); } catch(...) { o->m_pNbAnalysis->m_pNPFCount = NULL; }

1275

if (o->m_pNbAnalysis->m_pNPFCount == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1276

1277

o->m_pNbAnalysis->m_pNPFCount->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1278

o->m_pNbAnalysis->m_pNPFCount->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1279

o->m_pNbAnalysis->m_pNPFCount->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1280

1281

o->m_pNbAnalysis->m_pNPFCount->Create();

1282

1283

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1284

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1285

1286

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1287

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1288

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1289

tdf->SetLabelX("Distance [pm]");

1290

tdf->SetLabelY("Occurrence");

1291

tdf->Create();

1292

o->m_pNbAnalysis->m_oaNPF.Add(tdf);

1293

1294

for (z2=0;z2<=o->m_pNbAnalysis->m_iNbCount;z2++)

1295

{

1296

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1297

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1298

1299

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1300

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1301

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1302

tdf->SetLabelX("Distance [pm]");

1303

tdf->SetLabelY("Occurrence");

1304

tdf->Create();

1305

o->m_pNbAnalysis->m_oaDF.Add(tdf);

1306

1307

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

1308

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1309

1310

tdf->m_fMinVal = o->m_pNbAnalysis->m_fMinDist;

1311

tdf->m_fMaxVal = o->m_pNbAnalysis->m_fMaxDist;

1312

tdf->m_iResolution = o->m_pNbAnalysis->m_iResolution;

1313

tdf->SetLabelX("Distance [pm]");

1314

tdf->SetLabelY("Occurrence");

1315

tdf->Create();

1316

o->m_pNbAnalysis->m_oaNPF.Add(tdf);

1317

}

1318

}

1319

1320

for (z0=0;z0<g_iCDFChannels;z0++)

1321

{

1322

if (g_bRDF && (o->m_pRDF[z0] != NULL))

1323

{

1324

mprintf(" Creating RDF...\n");

1325

o->m_pRDF[z0]->m_pRDF->m_fMinVal = o->m_pRDF[z0]->m_fMinDist;

1326

o->m_pRDF[z0]->m_pRDF->m_fMaxVal = o->m_pRDF[z0]->m_fMaxDist;

1327

o->m_pRDF[z0]->m_pRDF->m_iResolution = o->m_pRDF[z0]->m_iResolution;

1328

o->m_pRDF[z0]->m_pRDF->m_iHistogramRes = o->m_pRDF[z0]->m_iHistogramRes;

1329

o->m_pRDF[z0]->m_pRDF->SetLabelX("Distance [pm]");

1330

if (o->m_pRDF[z0]->m_bProbDens)

1331

o->m_pRDF[z0]->m_pRDF->SetLabelY("g(r) [nm^(-3)]");

1332

else o->m_pRDF[z0]->m_pRDF->SetLabelY("g(r)");

1333

1334

if (o->m_bObsCertain && o->m_bDecompDist)

1335

{

1336

o->m_pRDF[z0]->m_pRDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1337

1338

/* try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = new char*[o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = NULL; }

1339

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti == NULL) NewException((double)o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize()*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1340

1341

for (z=0;z<o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize();z++)

1342

{

1343

try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = new char[128]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = NULL; }

1344

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] == NULL) NewException((double)128*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1345

}

1346

1347

for (z3=0;z3<o->m_waObsRefList.GetSize();z3++)

1348

{

1349

for (z2=0;z2<o->m_waObsShowList.GetSize();z2++)

1350

{

1351

if ((o->m_waObsRefList.GetSize() > 1) && (o->m_waObsShowList.GetSize() > 1))

1352

sprintf(buf,"RM%d-OM%d",o->m_waObsRefList[z3]+1,o->m_waObsShowList[z2]+1);

1353

else if (o->m_waObsRefList.GetSize() > 1)

1354

sprintf(buf,"RM%d",o->m_waObsRefList[z3]+1);

1355

else

1356

sprintf(buf,"OM%d",o->m_waObsShowList[z2]+1);

1357

1358

o->m_pRDF[z0]->m_pRDF->SetLabelMulti(z3*o->m_waObsShowList.GetSize()+z2,buf);

1359

}

1360

}

1361

} else if (o->m_bDecompType)

1362

{

1363

m = (CMolecule*)g_oaMolecules[g_iFixMol];

1364

o->m_waDecompTypeRefOffs.SetSize(g_iGesVirtAtomCount);

1365

for (z3=0;z3<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z3++)

1366

{

1367

ag = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z3*2];

1368

for (z2=0;z2<ag->m_baRealAtomType.GetSize();z2++)

1369

{

1370

for (z3=0;z3<o->m_waDecompTypeRefList.GetSize();z3++)

1371

if (o->m_waDecompTypeRefList[z3] == ag->m_baRealAtomType[z2])

1372

goto _decomptype1;

1373

z3 = o->m_waDecompTypeRefList.GetSize();

1374

o->m_waDecompTypeRefList.Add(ag->m_baRealAtomType[z2]);

1375

_decomptype1:

1376

for (z4=0;z4<m->m_laSingleMolIndex.GetSize();z4++)

1377

{

1378

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z4]];

1379

for (z5=0;z5<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z5++)

1380

o->m_waDecompTypeRefOffs[((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z5))] = z3;

1381

}

1382

}

1383

}

1384

1385

if (o->m_bOthers)

1386

m = (CMolecule*)g_oaMolecules[o->m_iShowMol];

1387

else m = (CMolecule*)g_oaMolecules[g_iFixMol];

1388

o->m_waDecompTypeObsOffs.SetSize(g_iGesVirtAtomCount);

1389

for (z6=0;z6<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z6++)

1390

{

1391

ag = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z6*2+1];

1392

for (z2=0;z2<ag->m_baRealAtomType.GetSize();z2++)

1393

{

1394

for (z3=0;z3<o->m_waDecompTypeObsList.GetSize();z3++)

1395

if (o->m_waDecompTypeObsList[z3] == ag->m_baRealAtomType[z2])

1396

goto _decomptype2;

1397

z3 = o->m_waDecompTypeObsList.GetSize();

1398

o->m_waDecompTypeObsList.Add(ag->m_baRealAtomType[z2]);

1399

_decomptype2:

1400

for (z4=0;z4<m->m_laSingleMolIndex.GetSize();z4++)

1401

{

1402

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z4]];

1403

for (z5=0;z5<((CxIntArray*)ag->m_oaAtoms[z2])->GetSize();z5++)

1404

o->m_waDecompTypeObsOffs[((CxIntArray*)sm->m_oaAtomOffset[ag->m_baAtomType[z2]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z2])->GetAt(z5))] = z3;

1405

}

1406

}

1407

}

1408

1409

o->m_pRDF[z0]->m_pRDF->CreateMulti(o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize());

1410

1411

/* try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = new char*[o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti = NULL; }

1412

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti == NULL) NewException((double)o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize()*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1413

1414

for (z=0;z<o->m_waDecompTypeRefList.GetSize()*o->m_waDecompTypeObsList.GetSize();z++)

1415

{

1416

try { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = new char[128]; } catch(...) { o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] = NULL; }

1417

if (o->m_pRDF[z0]->m_pRDF->m_sLabelMulti[z] == NULL) NewException((double)128*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1418

}*/

1419

1420

for (z3=0;z3<o->m_waDecompTypeRefList.GetSize();z3++)

1421

{

1422

for (z2=0;z2<o->m_waDecompTypeObsList.GetSize();z2++)

1423

{

1424

sprintf(buf,"%s-%s",((CAtom*)g_oaAtoms[o->m_waDecompTypeRefList[z3]])->m_sName,((CAtom*)g_oaAtoms[o->m_waDecompTypeObsList[z2]])->m_sName);

1425

o->m_pRDF[z0]->m_pRDF->SetLabelMulti(z*o->m_waDecompTypeObsList.GetSize()+z2,buf);

1426

}

1427

}

1428

} else o->m_pRDF[z0]->m_pRDF->Create();

1429

1430

if (o->m_bSecondShowMol && (z0 == 1))

1431

{

1432

try { o->m_pRDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pRDF[z0]->m_faData = NULL; }

1433

if (o->m_pRDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1434

1435

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1436

{

1437

try { o->m_pRDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pRDF[z0]->m_baDataEnabled = NULL; }

1438

if (o->m_pRDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1439

}

1440

} else

1441

{

1442

try { o->m_pRDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pRDF[z0]->m_faData = NULL; }

1443

if (o->m_pRDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1444

1445

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1446

{

1447

try { o->m_pRDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pRDF[z0]->m_baDataEnabled = NULL; }

1448

if (o->m_pRDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1449

}

1450

}

1451

if (o->m_bTimeDev)

1452

{

1453

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1454

{

1455

try { o->m_pRDF[z0]->m_fDist = new FILE*[1]; } catch(...) { o->m_pRDF[z0]->m_fDist = NULL; }

1456

if (o->m_pRDF[z0]->m_fDist == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1457

1458

sprintf(buf,"rdf_timedev_%s%s.csv",o->m_pRDF[z0]->m_sName,multibuf);

1459

o->m_pRDF[z0]->m_fDist[0] = OpenFileWrite(buf,true);

1460

} else

1461

{

1462

try { o->m_pRDF[z0]->m_fDist = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pRDF[z0]->m_fDist = NULL; }

1463

if (o->m_pRDF[z0]->m_fDist == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1464

1465

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1466

{

1467

sprintf(buf,"rdf_timedev_%s_ref%d%s.csv",o->m_pRDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1468

o->m_pRDF[z0]->m_fDist[z2] = OpenFileWrite(buf,true);

1469

}

1470

}

1471

if (o->m_bCombinedPlot)

1472

{

1473

// mprintf("Combined: Reflist %d, Showlist %d, Combinations %d, Steps %d.\n",o->m_waSaveRefList.GetSize(),o->m_waSaveShowList.GetSize(),o->m_pRDF[z0]->m_iCombinations,g_iTrajSteps);

1474

1475

try { o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot = NULL; }

1476

if (o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1477

1478

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetTitle("Combined distance time development/histogram");

1479

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetSubTitle(o->m_pRDF[z0]->m_sShortName);

1480

// smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]];

1481

// sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[0]];

1482

// o->m_pRDF[z0]->BuildAtomList(smfix,sm,sm,&templa);

1483

1484

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1485

{

1486

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1487

{

1488

/* for (z4=0;z4<templa.GetSize()/2;z4++)

1489

{

1490

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->AddDataset();

1491

1492

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetDatasetName(buf);

1493

if (g_iTrajSteps != -1)

1494

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize() *g_iTrajSteps);

1495

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize() *100);

1496

if (o->m_bCombinedGreyMode)

1497

{

1498

1499

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_iLineColor = ti*0x10000 + ti*0x100 + ti;

1500

}

1501

}*/

1502

1503

ti2 = 0;

1504

for (z4=0;z4<o->m_pRDF[z0]->m_oaVectors.GetSize()/2;z4++)

1505

{

1506

g1 = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z4*2];

1507

for (z1t=0;z1t<g1->m_baAtomType.GetSize();z1t++)

1508

{

1509

a1 = (CxIntArray*)g1->m_oaAtoms[z1t];

1510

for (z1a=0;z1a<a1->GetSize();z1a++)

1511

{

1512

g2 = (CAtomGroup*)o->m_pRDF[z0]->m_oaVectors[z4*2+1];

1513

for (z2t=0;z2t<g2->m_baAtomType.GetSize();z2t++)

1514

{

1515

a2 = (CxIntArray*)g2->m_oaAtoms[z2t];

1516

for (z2a=0;z2a<a2->GetSize();z2a++)

1517

{

1518

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->AddDataset();

1519

if (o->m_bOthers)

1520

1521

1522

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetDatasetName(buf);

1523

if (g_iTrajSteps != -1)

1524

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()/**o->m_pRDF[z0]->m_iCombinations*/ *g_iTrajSteps/g_iStride);

1525

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()/**o->m_pRDF[z0]->m_iCombinations*/ *100);

1526

if (o->m_bCombinedGreyMode)

1527

{

1528

1529

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1530

}

1531

ti2++;

1532

/* if (o->m_pRDF[z0]->m_iRefOrSec[0])

1533

vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));

1534

else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g1->m_baAtomType[z1t]])->GetAt(a1->GetAt(z1a)));

1535

if (o->m_pRDF[z0]->m_iRefOrSec[1])

1536

vec->Add(((CxIntArray*)obs->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));

1537

else vec->Add(((CxIntArray*)ref->m_oaAtomOffset[g2->m_baAtomType[z2t]])->GetAt(a2->GetAt(z2a)));

1538

*/ // mprintf("Vector z=%d, z1t=%d, z1a=%d, z2t=%d, z2a=%d.\n",z,z1t,z1a,z2t,z2a);

1539

}

1540

}

1541

}

1542

}

1543

}

1544

1545

}

1546

}

1547

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetLabelX("Time [ps] / g(r)");

1548

o->m_pRDF[z0]->m_pRDF->m_pCombinedPlot->SetLabelY("Distance [pm]");

1549

}

1550

} // END IF TIMEDEV

1551

1552

if (o->m_bTimeDiff)

1553

o->CreateTimeDiff(o->m_pRDF[z0]->m_pRDF,o->m_pRDF[z0]->m_iCombinations);

1554

1555

if (g_bDeriv)

1556

o->m_pRDF[z0]->InitDeriv();

1557

1558

if (o->m_pRDF[z0]->m_bCalcSD)

1559

{

1560

mprintf(" Initializing Standard Deviation Engine...\n");

1561

o->m_pRDF[z0]->m_pRDF->m_pSDEngine = new CSDEngine();

1562

o->m_pRDF[z0]->m_pRDF->m_pSDEngine->m_iaBlockSizes.SetSize(o->m_pRDF[z0]->m_iSDBlocks);

1563

mprintf(" Using the following %d trajectory block sizes:",o->m_pRDF[z0]->m_iSDBlocks);

1564

tf2 = 0;

1565

tf = 3.0;

1566

for (z4=0;z4<o->m_pRDF[z0]->m_iSDBlocks;z4++)

1567

{

1568

if ((z4 % 10) == 0)

1569

mprintf("\n ");

1570

1571

mprintf("%5d",o->m_pRDF[z0]->m_pRDF->m_pSDEngine->m_iaBlockSizes[z4]);

1572

if (z4 < o->m_pRDF[z0]->m_iSDBlocks-1)

1573

mprintf(", ");

1574

else mprintf(".");

1575

tf2 += (g_iTrajSteps/o->m_pRDF[z0]->m_pRDF->m_pSDEngine->m_iaBlockSizes[z4]) + 1;

1576

}

1577

tf2 *= o->m_pRDF[z0]->m_pRDF->m_iResolution * sizeof(double);

1578

mprintf("\n This requires %s of memory.\n\n",FormatBytes(tf2));

1579

o->m_pRDF[z0]->m_pRDF->m_pSDEngine->Init(o->m_pRDF[z0]->m_pRDF->m_iResolution);

1580

}

1581

} // END IF RDF

1582

1583

if (g_bADF && (o->m_pADF[z0] != NULL))

1584

{

1585

mprintf(" Creating ADF...\n");

1586

o->m_pADF[z0]->m_pADF->m_fMinVal = o->m_pADF[z0]->m_fMinAngle;

1587

o->m_pADF[z0]->m_pADF->m_fMaxVal = o->m_pADF[z0]->m_fMaxAngle;

1588

o->m_pADF[z0]->m_pADF->m_iResolution = o->m_pADF[z0]->m_iResolution;

1589

o->m_pADF[z0]->m_pADF->m_iHistogramRes = o->m_pADF[z0]->m_iHistogramRes;

1590

if (o->m_pADF[z0]->m_bCosine)

1591

o->m_pADF[z0]->m_pADF->SetLabelX("Cos(angle)");

1592

else o->m_pADF[z0]->m_pADF->SetLabelX("Angle (degree)");

1593

o->m_pADF[z0]->m_pADF->SetLabelY("Occurrence");

1594

if (o->m_bObsCertain && o->m_bDecompDist)

1595

o->m_pADF[z0]->m_pADF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1596

else o->m_pADF[z0]->m_pADF->Create();

1597

if (o->m_bSecondShowMol && (z0 == 1))

1598

{

1599

try { o->m_pADF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pADF[z0]->m_faData = NULL; }

1600

if (o->m_pADF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1601

1602

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1603

{

1604

try { o->m_pADF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pADF[z0]->m_baDataEnabled = NULL; }

1605

if (o->m_pADF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1606

}

1607

} else

1608

{

1609

try { o->m_pADF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pADF[z0]->m_faData = NULL; }

1610

if (o->m_pADF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1611

1612

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1613

{

1614

try { o->m_pADF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pADF[z0]->m_baDataEnabled = NULL; }

1615

if (o->m_pADF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1616

}

1617

}

1618

if (o->m_bTimeDev)

1619

{

1620

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1621

{

1622

try { o->m_pADF[z0]->m_fAngle = new FILE*[1]; } catch(...) { o->m_pADF[z0]->m_fAngle = NULL; }

1623

if (o->m_pADF[z0]->m_fAngle == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1624

1625

sprintf(buf,"adf_timedev_%s%s.csv",o->m_pADF[z0]->m_sName,multibuf);

1626

o->m_pADF[z0]->m_fAngle[0] = OpenFileWrite(buf,true);

1627

} else

1628

{

1629

try { o->m_pADF[z0]->m_fAngle = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pADF[z0]->m_fAngle = NULL; }

1630

if (o->m_pADF[z0]->m_fAngle == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1631

1632

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1633

{

1634

sprintf(buf,"adf_timedev_%s_ref%d%s.csv",o->m_pADF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1635

o->m_pADF[z0]->m_fAngle[z2] = OpenFileWrite(buf,true);

1636

}

1637

}

1638

if (o->m_bCombinedPlot)

1639

{

1640

try { o->m_pADF[z0]->m_pADF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pADF[z0]->m_pADF->m_pCombinedPlot = NULL; }

1641

if (o->m_pADF[z0]->m_pADF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1642

1643

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetTitle("Combined angle time development/histogram");

1644

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSubTitle(o->m_pADF[z0]->m_sShortName);

1645

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1646

{

1647

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1648

{

1649

for (z4=0;z4<o->m_pADF[z0]->m_iCombinations;z4++)

1650

{

1651

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->AddDataset();

1652

if (g_iTrajSteps != -1)

1653

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pADF[z0]->m_iCombinations*g_iTrajSteps);

1654

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pADF[z0]->m_iCombinations*100);

1655

if (o->m_bCombinedGreyMode)

1656

{

1657

1658

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1659

}

1660

// o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetSetLineWidth((z2*o->m_waSaveRefList.GetSize()+z3)*o->m_pADF[z0]->m_iCombinations+z4,2.0f);

1661

}

1662

}

1663

}

1664

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetLabelX("Time [ps] / ADF(r)");

1665

o->m_pADF[z0]->m_pADF->m_pCombinedPlot->SetLabelY("Angle [Degree]");

1666

}

1667

} // END IF TIMEDEV

1668

1669

if (o->m_bTimeDiff)

1670

o->CreateTimeDiff(o->m_pADF[z0]->m_pADF,o->m_pADF[z0]->m_iCombinations);

1671

1672

if (g_bDeriv)

1673

o->m_pADF[z0]->InitDeriv();

1674

} // END IF ADF

1675

1676

if (g_bDipDF && (o->m_pDipDF[z0] != NULL))

1677

{

1678

mprintf(" Creating DipDF...\n");

1679

o->m_pDipDF[z0]->m_pDipoleDF->m_fMinVal = o->m_pDipDF[z0]->m_fDipoleMin;

1680

o->m_pDipDF[z0]->m_pDipoleDF->m_fMaxVal = o->m_pDipDF[z0]->m_fDipoleMax;

1681

o->m_pDipDF[z0]->m_pDipoleDF->m_iResolution = o->m_pDipDF[z0]->m_iResolution;

1682

o->m_pDipDF[z0]->m_pDipoleDF->m_iHistogramRes = o->m_pDipDF[z0]->m_iHistogramRes;

1683

o->m_pDipDF[z0]->m_pDipoleDF->SetLabelX("Dipole moment (Debye)");

1684

o->m_pDipDF[z0]->m_pDipoleDF->SetLabelY("Occurrence");

1685

if (o->m_bObsCertain && o->m_bDecompDist)

1686

o->m_pDipDF[z0]->m_pDipoleDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1687

else o->m_pDipDF[z0]->m_pDipoleDF->Create();

1688

if (o->m_bSecondShowMol && (z0 == 1))

1689

{

1690

try { o->m_pDipDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDipDF[z0]->m_faData = NULL; }

1691

if (o->m_pDipDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1692

1693

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1694

{

1695

try { o->m_pDipDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDipDF[z0]->m_baDataEnabled = NULL; }

1696

if (o->m_pDipDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1697

}

1698

} else

1699

{

1700

try { o->m_pDipDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pDipDF[z0]->m_faData = NULL; }

1701

if (o->m_pDipDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1702

1703

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1704

{

1705

try { o->m_pDipDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pDipDF[z0]->m_baDataEnabled = NULL; }

1706

if (o->m_pDipDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1707

}

1708

}

1709

if (o->m_bTimeDev)

1710

{

1711

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1712

{

1713

try { o->m_pDipDF[z0]->m_fDipole = new FILE*[1]; } catch(...) { o->m_pDipDF[z0]->m_fDipole = NULL; }

1714

if (o->m_pDipDF[z0]->m_fDipole == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1715

1716

sprintf(buf,"dipole_timedev_%s%s.csv",o->m_pDipDF[z0]->m_sName,multibuf);

1717

o->m_pDipDF[z0]->m_fDipole[0] = OpenFileWrite(buf,true);

1718

} else

1719

{

1720

try { o->m_pDipDF[z0]->m_fDipole = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pDipDF[z0]->m_fDipole = NULL; }

1721

if (o->m_pDipDF[z0]->m_fDipole == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1722

1723

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1724

{

1725

sprintf(buf,"dipole_timedev_%s_ref%d%s.csv",o->m_pDipDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1726

o->m_pDipDF[z0]->m_fDipole[z2] = OpenFileWrite(buf,true);

1727

}

1728

}

1729

if (o->m_bCombinedPlot)

1730

{

1731

try { o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot = NULL; }

1732

if (o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1733

1734

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetTitle("Combined dipole moment time development/histogram");

1735

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetSubTitle(o->m_pDipDF[z0]->m_sShortName);

1736

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1737

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1738

{

1739

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->AddDataset();

1740

if (g_iTrajSteps != -1)

1741

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*g_iTrajSteps);

1742

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*100);

1743

if (o->m_bCombinedGreyMode)

1744

{

1745

ti = o->m_iCombinedGreyMin + ((z3+z2*o->m_waSaveShowList.GetSize())%o->m_iCombinedGreyShades)*(o->m_iCombinedGreyMax-o->m_iCombinedGreyMin)/o->m_iCombinedGreyShades;

1746

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1747

}

1748

}

1749

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetLabelX("Time [ps] / DipDF(r)");

1750

o->m_pDipDF[z0]->m_pDipoleDF->m_pCombinedPlot->SetLabelY("Dipole moment [Debye]");

1751

}

1752

} // END IF TIMEDEV

1753

1754

if (o->m_bTimeDiff)

1755

o->CreateTimeDiff(o->m_pDipDF[z0]->m_pDipoleDF,1);

1756

1757

if (g_bDeriv)

1758

o->m_pDipDF[z0]->InitDeriv();

1759

} // END IF DIPOLE

1760

1761

if (g_bVDF && (o->m_pVDF[z0] != NULL))

1762

{

1763

mprintf(" Creating VDF...\n");

1764

o->m_pVDF[z0]->m_pVDF->m_fMinVal = o->m_pVDF[z0]->m_fMinSpeed;

1765

o->m_pVDF[z0]->m_pVDF->m_fMaxVal = o->m_pVDF[z0]->m_fMaxSpeed;

1766

o->m_pVDF[z0]->m_pVDF->m_iResolution = o->m_pVDF[z0]->m_iResolution;

1767

o->m_pVDF[z0]->m_pVDF->m_iHistogramRes = o->m_pVDF[z0]->m_iHistogramRes;

1768

o->m_pVDF[z0]->m_pVDF->SetLabelX("Velocity [pm/ps]");

1769

o->m_pVDF[z0]->m_pVDF->SetLabelY("Occurrence");

1770

if (o->m_bObsCertain && o->m_bDecompDist)

1771

o->m_pVDF[z0]->m_pVDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1772

else o->m_pVDF[z0]->m_pVDF->Create();

1773

if (o->m_bSecondShowMol && (z0 == 1))

1774

{

1775

try { o->m_pVDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pVDF[z0]->m_faData = NULL; }

1776

if (o->m_pVDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1777

1778

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1779

{

1780

try { o->m_pVDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pVDF[z0]->m_baDataEnabled = NULL; }

1781

if (o->m_pVDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1782

}

1783

} else

1784

{

1785

try { o->m_pVDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pVDF[z0]->m_faData = NULL; }

1786

if (o->m_pVDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1787

1788

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1789

{

1790

try { o->m_pVDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pVDF[z0]->m_baDataEnabled = NULL; }

1791

if (o->m_pVDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1792

}

1793

}

1794

if (o->m_bTimeDev)

1795

{

1796

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1797

{

1798

try { o->m_pVDF[z0]->m_fSpeed = new FILE*[1]; } catch(...) { o->m_pVDF[z0]->m_fSpeed = NULL; }

1799

if (o->m_pVDF[z0]->m_fSpeed == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1800

1801

sprintf(buf,"vdf_timedev_%s%s.csv",o->m_pVDF[z0]->m_sName,multibuf);

1802

o->m_pVDF[z0]->m_fSpeed[0] = OpenFileWrite(buf,true);

1803

} else

1804

{

1805

try { o->m_pVDF[z0]->m_fSpeed = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pVDF[z0]->m_fSpeed = NULL; }

1806

if (o->m_pVDF[z0]->m_fSpeed == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1807

1808

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1809

{

1810

sprintf(buf,"vdf_timedev_%s_ref%d%s.csv",o->m_pVDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1811

o->m_pVDF[z0]->m_fSpeed[z2] = OpenFileWrite(buf,true);

1812

}

1813

}

1814

if (o->m_bCombinedPlot)

1815

{

1816

try { o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot = NULL; }

1817

if (o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1818

1819

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetTitle("Combined velocity time development/histogram");

1820

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSubTitle(o->m_pVDF[z0]->m_sShortName);

1821

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1822

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1823

for (z4=0;z4<o->m_pVDF[z0]->m_iCombinations;z4++)

1824

{

1825

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->AddDataset();

1826

if (g_iTrajSteps != -1)

1827

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pVDF[z0]->m_iCombinations*g_iTrajSteps);

1828

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pVDF[z0]->m_iCombinations*100);

1829

if (o->m_bCombinedGreyMode)

1830

{

1831

1832

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1833

}

1834

// o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetSetLineWidth(z2*o->m_waSaveRefList.GetSize()+z3,3.0f);

1835

}

1836

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetLabelX("Time [ps] / VDF(r)");

1837

o->m_pVDF[z0]->m_pVDF->m_pCombinedPlot->SetLabelY("Velocity [pm/ps]");

1838

}

1839

} // END IF TIMEDEV

1840

1841

if (o->m_bTimeDiff)

1842

o->CreateTimeDiff(o->m_pVDF[z0]->m_pVDF,o->m_pVDF[z0]->m_iCombinations);

1843

1844

if (g_bDeriv)

1845

o->m_pVDF[z0]->InitDeriv();

1846

} // END IF VDF

1847

1848

if (g_bDDF && (o->m_pDDF[z0] != NULL))

1849

{

1850

mprintf(" Creating DDF...\n");

1851

o->m_pDDF[z0]->m_pDDF->m_fMinVal = o->m_pDDF[z0]->m_fMinAngle;

1852

o->m_pDDF[z0]->m_pDDF->m_fMaxVal = o->m_pDDF[z0]->m_fMaxAngle;

1853

o->m_pDDF[z0]->m_pDDF->m_iResolution = o->m_pDDF[z0]->m_iResolution;

1854

o->m_pDDF[z0]->m_pDDF->m_iHistogramRes = o->m_pDDF[z0]->m_iHistogramRes;

1855

if (o->m_pDDF[z0]->m_bCosine)

1856

o->m_pDDF[z0]->m_pDDF->SetLabelX("Cos(Dihedral Angle)");

1857

else o->m_pDDF[z0]->m_pDDF->SetLabelX("Dihedral Angle (Degree)");

1858

o->m_pDDF[z0]->m_pDDF->SetLabelY("Occurrence");

1859

if (o->m_bObsCertain && o->m_bDecompDist)

1860

o->m_pDDF[z0]->m_pDDF->CreateMulti(o->m_waObsRefList.GetSize()*o->m_waObsShowList.GetSize());

1861

else o->m_pDDF[z0]->m_pDDF->Create();

1862

if (o->m_bSecondShowMol && (z0 == 1))

1863

{

1864

try { o->m_pDDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDDF[z0]->m_faData = NULL; }

1865

if (o->m_pDDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1866

1867

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1868

{

1869

try { o->m_pDDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pDDF[z0]->m_baDataEnabled = NULL; }

1870

if (o->m_pDDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1871

}

1872

} else

1873

{

1874

try { o->m_pDDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pDDF[z0]->m_faData = NULL; }

1875

if (o->m_pDDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1876

1877

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1878

{

1879

try { o->m_pDDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pDDF[z0]->m_baDataEnabled = NULL; }

1880

if (o->m_pDDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1881

}

1882

1883

if (o->m_pDDF[z0]->m_bRotate)

1884

{

1885

for (z2=0;z2<o->m_iShowMolCount * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() * o->m_pDDF[z0]->m_iCombinations;z2++)

1886

{

1887

o->m_pDDF[z0]->m_faLastData.Add(0);

1888

o->m_pDDF[z0]->m_laRotation.Add(0);

1889

}

1890

}

1891

}

1892

if (o->m_bTimeDev)

1893

{

1894

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

1895

{

1896

try { o->m_pDDF[z0]->m_fAngle = new FILE*[1]; } catch(...) { o->m_pDDF[z0]->m_fAngle = NULL; }

1897

if (o->m_pDDF[z0]->m_fAngle == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1898

1899

sprintf(buf,"ddf_timedev_%s%s.csv",o->m_pDDF[z0]->m_sName,multibuf);

1900

o->m_pDDF[z0]->m_fAngle[0] = OpenFileWrite(buf,true);

1901

} else

1902

{

1903

try { o->m_pDDF[z0]->m_fAngle = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pDDF[z0]->m_fAngle = NULL; }

1904

if (o->m_pDDF[z0]->m_fAngle == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1905

1906

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1907

{

1908

sprintf(buf,"ddf_timedev_%s_ref%d%s.csv",o->m_pDDF[z0]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

1909

o->m_pDDF[z0]->m_fAngle[z2] = OpenFileWrite(buf,true);

1910

}

1911

}

1912

if (o->m_bCombinedPlot)

1913

{

1914

try { o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot = new CGrace(); } catch(...) { o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot = NULL; }

1915

if (o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1916

1917

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetTitle("Combined dihedral time development/histogram");

1918

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSubTitle(o->m_pDDF[z0]->m_sShortName);

1919

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

1920

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

1921

for (z4=0;z4<o->m_pDDF[z0]->m_iCombinations;z4++)

1922

{

1923

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->AddDataset();

1924

if (g_iTrajSteps != -1)

1925

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pDDF[z0]->m_iCombinations*g_iTrajSteps);

1926

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pDDF[z0]->m_iCombinations*100);

1927

if (o->m_bCombinedGreyMode)

1928

{

1929

1930

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSetLineColor(ti,ti,ti);

1931

}

1932

// o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetSetLineWidth((z2*o->m_waSaveRefList.GetSize()+z3)*o->m_pDDF[z0]->m_iCombinations+z4,2.0f);

1933

}

1934

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetLabelX("Time [ps] / DDF(r)");

1935

o->m_pDDF[z0]->m_pDDF->m_pCombinedPlot->SetLabelY("Dihedral [Degree]");

1936

}

1937

} // END IF TIMEDEV

1938

1939

if (o->m_bTimeDiff)

1940

o->CreateTimeDiff(o->m_pDDF[z0]->m_pDDF,o->m_pDDF[z0]->m_iCombinations);

1941

1942

if (g_bDeriv)

1943

o->m_pDDF[z0]->InitDeriv();

1944

} // END IF DDF

1945

1946

if (g_bPlDF && (o->m_pPlDF[z0] != NULL))

1947

{

1948

mprintf(" Creating PlDF...\n");

1949

o->m_pPlDF[z0]->m_pPlDF->m_fMinVal = o->m_pPlDF[z0]->m_fMinDist;

1950

o->m_pPlDF[z0]->m_pPlDF->m_fMaxVal = o->m_pPlDF[z0]->m_fMaxDist;

1951

o->m_pPlDF[z0]->m_pPlDF->m_iResolution = o->m_pPlDF[z0]->m_iResolution;

1952

o->m_pPlDF[z0]->m_pPlDF->m_iHistogramRes = o->m_pPlDF[z0]->m_iHistogramRes;

1953

o->m_pPlDF[z0]->m_pPlDF->SetLabelX("Distance from plane [pm]");

1954

o->m_pPlDF[z0]->m_pPlDF->SetLabelY("Occurrence");

1955

o->m_pPlDF[z0]->m_pPlDF->Create();

1956

if (o->m_bSecondShowMol && (z0 == 1))

1957

{

1958

try { o->m_pPlDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pPlDF[z0]->m_faData = NULL; }

1959

if (o->m_pPlDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1960

1961

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1962

{

1963

try { o->m_pPlDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pPlDF[z0]->m_baDataEnabled = NULL; }

1964

if (o->m_pPlDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1965

}

1966

} else

1967

{

1968

try { o->m_pPlDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pPlDF[z0]->m_faData = NULL; }

1969

if (o->m_pPlDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1970

1971

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1972

{

1973

try { o->m_pPlDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pPlDF[z0]->m_baDataEnabled = NULL; }

1974

if (o->m_pPlDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1975

}

1976

}

1977

} // END IF PlDF

1978

1979

if (g_bLiDF && (o->m_pLiDF[z0] != NULL))

1980

{

1981

mprintf(" Creating LiDF...\n");

1982

o->m_pLiDF[z0]->m_pLiDF->m_fMinVal = o->m_pLiDF[z0]->m_fMinDist;

1983

o->m_pLiDF[z0]->m_pLiDF->m_fMaxVal = o->m_pLiDF[z0]->m_fMaxDist;

1984

o->m_pLiDF[z0]->m_pLiDF->m_iResolution = o->m_pLiDF[z0]->m_iResolution;

1985

o->m_pLiDF[z0]->m_pLiDF->m_iHistogramRes = o->m_pLiDF[z0]->m_iHistogramRes;

1986

o->m_pLiDF[z0]->m_pLiDF->SetLabelX("Distance from line [pm]");

1987

o->m_pLiDF[z0]->m_pLiDF->SetLabelY("Occurrence");

1988

o->m_pLiDF[z0]->m_pLiDF->Create();

1989

if (o->m_bSecondShowMol && (z0 == 1))

1990

{

1991

try { o->m_pLiDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMol2Count]; } catch(...) { o->m_pLiDF[z0]->m_faData = NULL; }

1992

if (o->m_pLiDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1993

1994

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

1995

{

1996

try { o->m_pLiDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMol2Count]; } catch(...) { o->m_pLiDF[z0]->m_baDataEnabled = NULL; }

1997

if (o->m_pLiDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMol2Count*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

1998

}

1999

} else

2000

{

2001

try { o->m_pLiDF[z0]->m_faData = new CxDoubleArray[o->m_iShowMolCount]; } catch(...) { o->m_pLiDF[z0]->m_faData = NULL; }

2002

if (o->m_pLiDF[z0]->m_faData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxDoubleArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2003

2004

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

2005

{

2006

try { o->m_pLiDF[z0]->m_baDataEnabled = new CxByteArray[o->m_iShowMolCount]; } catch(...) { o->m_pLiDF[z0]->m_baDataEnabled = NULL; }

2007

if (o->m_pLiDF[z0]->m_baDataEnabled == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxByteArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2008

}

2009

}

2010

} // END IF LiDF

2011

2012

} // END FOR z0

2013

2014

if (g_bCDF)

2015

{

2016

mprintf(" Creating CDF...\n");

2017

if (g_iCDFChannels == 2)

2018

{

2019

try { o->m_pCDF->m_p2DF = new C2DF(); } catch(...) { o->m_pCDF->m_p2DF = NULL; }

2020

if (o->m_pCDF->m_p2DF == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2021

2022

buf[0] = 0;

2023

for (z2=0;z2<2;z2++)

2024

{

2025

o->m_pCDF->m_p2DF->m_iRes[z2] = o->m_pCDF->m_iResolution[z2];

2026

switch(g_iObsChannel[z2])

2027

{

2028

case 0:

2029

strcat(buf,"_rdf");

2030

strcat(buf,o->m_pRDF[z2]->m_sShortName);

2031

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pRDF[z2]->m_fMinDist;

2032

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pRDF[z2]->m_fMaxDist;

2033

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pRDF[z2]->m_pRDF;

2034

break;

2035

2036

case 1:

2037

strcat(buf,"_adf");

2038

strcat(buf,o->m_pADF[z2]->m_sShortName);

2039

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pADF[z2]->m_fMinAngle;

2040

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pADF[z2]->m_fMaxAngle;

2041

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pADF[z2]->m_pADF;

2042

break;

2043

2044

case 2:

2045

strcat(buf,"_ddf");

2046

strcat(buf,o->m_pDDF[z2]->m_sShortName);

2047

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pDDF[z2]->m_fMinAngle;

2048

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pDDF[z2]->m_fMaxAngle;

2049

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pDDF[z2]->m_pDDF;

2050

break;

2051

2052

case 3:

2053

strcat(buf,"_dipole");

2054

strcat(buf,o->m_pDipDF[z2]->m_sShortName);

2055

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pDipDF[z2]->m_fDipoleMin;

2056

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pDipDF[z2]->m_fDipoleMax;

2057

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pDipDF[z2]->m_pDipoleDF;

2058

break;

2059

2060

case 4:

2061

strcat(buf,"_vdf");

2062

strcat(buf,o->m_pVDF[z2]->m_sShortName);

2063

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pVDF[z2]->m_fMinSpeed;

2064

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pVDF[z2]->m_fMaxSpeed;

2065

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pVDF[z2]->m_pVDF;

2066

break;

2067

2068

case 5:

2069

strcat(buf,"_pldf");

2070

strcat(buf,o->m_pPlDF[z2]->m_sShortName);

2071

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pPlDF[z2]->m_fMinDist;

2072

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pPlDF[z2]->m_fMaxDist;

2073

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pPlDF[z2]->m_pPlDF;

2074

break;

2075

2076

case 6:

2077

strcat(buf,"_lidf");

2078

strcat(buf,o->m_pLiDF[z2]->m_sShortName);

2079

o->m_pCDF->m_p2DF->m_fMinVal[z2] = o->m_pLiDF[z2]->m_fMinDist;

2080

o->m_pCDF->m_p2DF->m_fMaxVal[z2] = o->m_pLiDF[z2]->m_fMaxDist;

2081

o->m_pCDF->m_p2DF->m_pChannels[z2] = o->m_pLiDF[z2]->m_pLiDF;

2082

break;

2083

}

2084

}

2085

o->m_pCDF->m_p2DF->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

2086

o->m_pCDF->m_p2DF->Create();

2087

switch(g_iObsChannel[0])

2088

{

2089

case 0:

2090

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[0]->m_sShortName);

2091

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2092

break;

2093

case 1:

2094

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[0]->m_sShortName);

2095

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2096

break;

2097

case 2:

2098

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[0]->m_sShortName);

2099

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2100

break;

2101

case 3:

2102

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[0]->m_sShortName);

2103

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2104

break;

2105

case 4:

2106

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[0]->m_sShortName);

2107

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2108

break;

2109

case 5:

2110

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[0]->m_sShortName);

2111

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2112

break;

2113

case 6:

2114

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[0]->m_sShortName);

2115

o->m_pCDF->m_p2DF->SetLabelX(buf2);

2116

break;

2117

}

2118

switch(g_iObsChannel[1])

2119

{

2120

case 0:

2121

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[1]->m_sShortName);

2122

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2123

break;

2124

case 1:

2125

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[1]->m_sShortName);

2126

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2127

break;

2128

case 2:

2129

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[1]->m_sShortName);

2130

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2131

break;

2132

case 3:

2133

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[1]->m_sShortName);

2134

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2135

break;

2136

case 4:

2137

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[1]->m_sShortName);

2138

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2139

break;

2140

case 5:

2141

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[1]->m_sShortName);

2142

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2143

break;

2144

case 6:

2145

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[1]->m_sShortName);

2146

o->m_pCDF->m_p2DF->SetLabelY(buf2);

2147

break;

2148

}

2149

} // END IF CHANNELS == 2

2150

2151

if (g_iCDFChannels == 3)

2152

{

2153

try { o->m_pCDF->m_p3DF = new C3DF(); } catch(...) { o->m_pCDF->m_p3DF = NULL; }

2154

if (o->m_pCDF->m_p3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2155

2156

buf[0] = 0;

2157

for (z2=0;z2<g_iCDFChannels;z2++)

2158

{

2159

o->m_pCDF->m_p3DF->m_iRes[z2] = o->m_pCDF->m_iResolution[z2];

2160

switch(g_iObsChannel[z2])

2161

{

2162

case 0:

2163

strcat(buf,"_rdf");

2164

strcat(buf,o->m_pRDF[z2]->m_sShortName);

2165

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pRDF[z2]->m_fMinDist;

2166

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pRDF[z2]->m_fMaxDist;

2167

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pRDF[z2]->m_pRDF;

2168

break;

2169

case 1:

2170

strcat(buf,"_adf");

2171

strcat(buf,o->m_pADF[z2]->m_sShortName);

2172

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pADF[z2]->m_fMinAngle;

2173

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pADF[z2]->m_fMaxAngle;

2174

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pADF[z2]->m_pADF;

2175

break;

2176

case 2:

2177

strcat(buf,"_ddf");

2178

strcat(buf,o->m_pDDF[z2]->m_sShortName);

2179

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pDDF[z2]->m_fMinAngle;

2180

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pDDF[z2]->m_fMaxAngle;

2181

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pDDF[z2]->m_pDDF;

2182

break;

2183

case 3:

2184

strcat(buf,"_dipole");

2185

strcat(buf,o->m_pDipDF[z2]->m_sShortName);

2186

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pDipDF[z2]->m_fDipoleMin;

2187

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pDipDF[z2]->m_fDipoleMax;

2188

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pDipDF[z2]->m_pDipoleDF;

2189

break;

2190

case 4:

2191

strcat(buf,"_vdf");

2192

strcat(buf,o->m_pVDF[z2]->m_sShortName);

2193

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pVDF[z2]->m_fMinSpeed;

2194

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pVDF[z2]->m_fMaxSpeed;

2195

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pVDF[z2]->m_pVDF;

2196

break;

2197

case 5:

2198

strcat(buf,"_pldf");

2199

strcat(buf,o->m_pPlDF[z2]->m_sShortName);

2200

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pPlDF[z2]->m_fMinDist;

2201

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pPlDF[z2]->m_fMaxDist;

2202

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pPlDF[z2]->m_pPlDF;

2203

break;

2204

case 6:

2205

strcat(buf,"_lidf");

2206

strcat(buf,o->m_pLiDF[z2]->m_sShortName);

2207

o->m_pCDF->m_p3DF->m_fMinVal[z2] = o->m_pLiDF[z2]->m_fMinDist;

2208

o->m_pCDF->m_p3DF->m_fMaxVal[z2] = o->m_pLiDF[z2]->m_fMaxDist;

2209

o->m_pCDF->m_p3DF->m_pChannels[z2] = o->m_pLiDF[z2]->m_pLiDF;

2210

break;

2211

}

2212

}

2213

o->m_pCDF->m_p3DF->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

2214

o->m_pCDF->m_p3DF->Create();

2215

switch(g_iObsChannel[0])

2216

{

2217

case 0:

2218

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[0]->m_sShortName);

2219

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2220

break;

2221

case 1:

2222

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[0]->m_sShortName);

2223

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2224

break;

2225

case 2:

2226

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[0]->m_sShortName);

2227

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2228

break;

2229

case 3:

2230

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[0]->m_sShortName);

2231

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2232

break;

2233

case 4:

2234

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[0]->m_sShortName);

2235

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2236

break;

2237

case 5:

2238

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[0]->m_sShortName);

2239

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2240

break;

2241

case 6:

2242

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[0]->m_sShortName);

2243

o->m_pCDF->m_p3DF->SetLabelX(buf2);

2244

break;

2245

}

2246

switch(g_iObsChannel[1])

2247

{

2248

case 0:

2249

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[1]->m_sShortName);

2250

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2251

break;

2252

case 1:

2253

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[1]->m_sShortName);

2254

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2255

break;

2256

case 2:

2257

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[1]->m_sShortName);

2258

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2259

break;

2260

case 3:

2261

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[1]->m_sShortName);

2262

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2263

break;

2264

case 4:

2265

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[1]->m_sShortName);

2266

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2267

break;

2268

case 5:

2269

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[1]->m_sShortName);

2270

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2271

break;

2272

case 6:

2273

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[1]->m_sShortName);

2274

o->m_pCDF->m_p3DF->SetLabelY(buf2);

2275

break;

2276

}

2277

switch(g_iObsChannel[2])

2278

{

2279

case 0:

2280

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[2]->m_sShortName);

2281

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2282

break;

2283

case 1:

2284

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[2]->m_sShortName);

2285

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2286

break;

2287

case 2:

2288

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[2]->m_sShortName);

2289

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2290

break;

2291

case 3:

2292

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[2]->m_sShortName);

2293

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2294

break;

2295

case 4:

2296

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[2]->m_sShortName);

2297

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2298

break;

2299

case 5:

2300

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[2]->m_sShortName);

2301

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2302

break;

2303

case 6:

2304

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[2]->m_sShortName);

2305

o->m_pCDF->m_p3DF->SetLabelZ(buf2);

2306

break;

2307

}

2308

2309

// Fuer jede C3DF noch die 3 C2DFs erzeugen

2310

for (z3=0;z3<3;z3++)

2311

{

2312

try { o->m_pCDF->m_p3DF->m_p2DF[z3] = new C2DF(); } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3] = NULL; }

2313

if (o->m_pCDF->m_p3DF->m_p2DF[z3] == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2314

2315

buf3[0] = 0;

2316

switch(z3)

2317

{

2318

case 0:

2319

tia[0] = 0;

2320

tia[1] = 1;

2321

break;

2322

case 1:

2323

tia[0] = 0;

2324

tia[1] = 2;

2325

break;

2326

case 2:

2327

tia[0] = 1;

2328

tia[1] = 2;

2329

break;

2330

}

2331

for (z2=0;z2<2;z2++)

2332

{

2333

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_iRes[z2] = o->m_pCDF->m_iResolution[tia[z2]];

2334

switch(g_iObsChannel[tia[z2]])

2335

{

2336

case 0:

2337

strcat(buf3,"_rdf");

2338

strcat(buf3,o->m_pRDF[tia[z2]]->m_sShortName);

2339

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pRDF[tia[z2]]->m_fMinDist;

2340

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pRDF[tia[z2]]->m_fMaxDist;

2341

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pRDF[tia[z2]]->m_pRDF;

2342

break;

2343

case 1:

2344

strcat(buf3,"_adf");

2345

strcat(buf3,o->m_pADF[tia[z2]]->m_sShortName);

2346

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pADF[tia[z2]]->m_fMinAngle;

2347

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pADF[tia[z2]]->m_fMaxAngle;

2348

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pADF[tia[z2]]->m_pADF;

2349

break;

2350

case 2:

2351

strcat(buf3,"_ddf");

2352

strcat(buf3,o->m_pDDF[tia[z2]]->m_sShortName);

2353

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pDDF[tia[z2]]->m_fMinAngle;

2354

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pDDF[tia[z2]]->m_fMaxAngle;

2355

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pDDF[tia[z2]]->m_pDDF;

2356

break;

2357

case 3:

2358

strcat(buf3,"_dipole");

2359

strcat(buf3,o->m_pDipDF[tia[z2]]->m_sShortName);

2360

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pDipDF[tia[z2]]->m_fDipoleMin;

2361

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pDipDF[tia[z2]]->m_fDipoleMax;

2362

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pDipDF[tia[z2]]->m_pDipoleDF;

2363

break;

2364

case 4:

2365

strcat(buf3,"_vdf");

2366

strcat(buf3,o->m_pVDF[tia[z2]]->m_sShortName);

2367

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pVDF[tia[z2]]->m_fMinSpeed;

2368

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pVDF[tia[z2]]->m_fMaxSpeed;

2369

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pVDF[tia[z2]]->m_pVDF;

2370

break;

2371

case 5:

2372

strcat(buf3,"_pldf");

2373

strcat(buf3,o->m_pPlDF[tia[z2]]->m_sShortName);

2374

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pPlDF[tia[z2]]->m_fMinDist;

2375

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pPlDF[tia[z2]]->m_fMaxDist;

2376

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pPlDF[tia[z2]]->m_pPlDF;

2377

break;

2378

case 6:

2379

strcat(buf3,"_lidf");

2380

strcat(buf3,o->m_pLiDF[tia[z2]]->m_sShortName);

2381

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMinVal[z2] = o->m_pLiDF[tia[z2]]->m_fMinDist;

2382

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fMaxVal[z2] = o->m_pLiDF[tia[z2]]->m_fMaxDist;

2383

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_pChannels[z2] = o->m_pLiDF[tia[z2]]->m_pLiDF;

2384

break;

2385

}

2386

}

2387

o->m_pCDF->m_p3DF->m_p2DF[z3]->m_iHistogramRes = o->m_pCDF->m_iHistogramRes;

2388

o->m_pCDF->m_p3DF->m_p2DF[z3]->Create();

2389

switch(g_iObsChannel[tia[0]])

2390

{

2391

case 0:

2392

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[tia[0]]->m_sShortName);

2393

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2394

break;

2395

case 1:

2396

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[tia[0]]->m_sShortName);

2397

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2398

break;

2399

case 2:

2400

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[tia[0]]->m_sShortName);

2401

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2402

break;

2403

case 3:

2404

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[tia[0]]->m_sShortName);

2405

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2406

break;

2407

case 4:

2408

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[tia[0]]->m_sShortName);

2409

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2410

break;

2411

case 5:

2412

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[tia[0]]->m_sShortName);

2413

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2414

break;

2415

case 6:

2416

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[tia[0]]->m_sShortName);

2417

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelX(buf2);

2418

break;

2419

}

2420

switch(g_iObsChannel[tia[1]])

2421

{

2422

case 0:

2423

sprintf(buf2,"%s Distance [pm]",o->m_pRDF[tia[1]]->m_sShortName);

2424

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2425

break;

2426

case 1:

2427

sprintf(buf2,"%s Angle [Degree]",o->m_pADF[tia[1]]->m_sShortName);

2428

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2429

break;

2430

case 2:

2431

sprintf(buf2,"%s Dihedral [Degree]",o->m_pDDF[tia[1]]->m_sShortName);

2432

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2433

break;

2434

case 3:

2435

sprintf(buf2,"%s Dipole moment [Debye]",o->m_pDipDF[tia[1]]->m_sShortName);

2436

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2437

break;

2438

case 4:

2439

sprintf(buf2,"%s Velocity [pm/ps]",o->m_pVDF[tia[1]]->m_sShortName);

2440

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2441

break;

2442

case 5:

2443

sprintf(buf2,"%s Distance from Plane [pm]",o->m_pPlDF[tia[1]]->m_sShortName);

2444

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2445

break;

2446

case 6:

2447

sprintf(buf2,"%s Distance from Line [pm]",o->m_pLiDF[tia[1]]->m_sShortName);

2448

o->m_pCDF->m_p3DF->m_p2DF[z3]->SetLabelY(buf2);

2449

break;

2450

}

2451

try { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName = new char[strlen(buf3)+1]; } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName = NULL; }

2452

if (o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName == NULL) NewException((double)(strlen(buf3)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2453

2454

strcpy(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName,buf3);

2455

sprintf(buf3,"cdf_2");

2456

strcat(buf3,o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sShortName);

2457

2458

try { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName = new char[strlen(buf3)+1]; } catch(...) { o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName = NULL; }

2459

if (o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName == NULL) NewException((double)(strlen(buf3)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2460

2461

strcpy(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,buf3);

2462

} // END FOR z3

2463

} // END IF CHANNELS == 3

2464

2465

try { o->m_pCDF->m_sShortName = new char[strlen(buf)+1]; } catch(...) { o->m_pCDF->m_sShortName = NULL; }

2466

if (o->m_pCDF->m_sShortName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2467

2468

strcpy(o->m_pCDF->m_sShortName,buf);

2469

sprintf(buf,"cdf_%d",g_iCDFChannels);

2470

strcat(buf,o->m_pCDF->m_sShortName);

2471

2472

try { o->m_pCDF->m_sName = new char[strlen(buf)+1]; } catch(...) { o->m_pCDF->m_sName = NULL; }

2473

if (o->m_pCDF->m_sName == NULL) NewException((double)(strlen(buf)+1)*sizeof(char),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2474

2475

strcpy(o->m_pCDF->m_sName,buf);

2476

if (o->m_pCDF->m_bDumpDat)

2477

{

2478

sprintf(buf,"cdfdump_%dd%s%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

2479

o->m_pCDF->m_fDump = OpenFileWrite(buf,true);

2480

mfprintf(o->m_pCDF->m_fDump,"# step; RM; OM1; OM2; channels\n");

2481

}

2482

if (o->m_bTimeDev)

2483

{

2484

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

2485

{

2486

try { o->m_pCDF->m_fTimeDev = new FILE*[1]; } catch(...) { o->m_pCDF->m_fTimeDev = NULL; }

2487

if (o->m_pCDF->m_fTimeDev == NULL) NewException((double)sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2488

2489

sprintf(buf,"cdf_timedev_%dd%s%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

2490

o->m_pCDF->m_fTimeDev[0] = OpenFileWrite(buf,true);

2491

} else

2492

{

2493

try { o->m_pCDF->m_fTimeDev = new FILE*[o->m_waSaveRefList.GetSize()]; } catch(...) { o->m_pCDF->m_fTimeDev = NULL; }

2494

if (o->m_pCDF->m_fTimeDev == NULL) NewException((double)o->m_waSaveRefList.GetSize()*sizeof(FILE*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2495

2496

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

2497

{

2498

sprintf(buf,"cdf_timedev_%dd%s_ref%d%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

2499

o->m_pCDF->m_fTimeDev[z2] = OpenFileWrite(buf,true);

2500

}

2501

}

2502

if (o->m_pCDF->m_bTDAnimation)

2503

{

2504

try { o->m_pCDF->m_pTDAPlot = new CGrace(); } catch(...) { o->m_pCDF->m_pTDAPlot = NULL; }

2505

if (o->m_pCDF->m_pTDAPlot == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2506

2507

o->m_pCDF->m_pTDAPlot->SetTitle("CDF Time Development");

2508

o->m_pCDF->m_pTDAPlot->SetSubTitle(&o->m_pCDF->m_sShortName[1]);

2509

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

2510

{

2511

for (z3=0;z3<o->m_waSaveShowList.GetSize();z3++)

2512

{

2513

for (z4=0;z4<o->m_pCDF->m_iCombinationsEnabled;z4++)

2514

{

2515

o->m_pCDF->m_pTDAPlot->AddDataset();

2516

if (g_iTrajSteps != -1)

2517

o->m_pCDF->m_pTDAPlot->LastDataset()->m_faValues.SetMaxSize(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled*g_iTrajSteps);

2518

o->m_pCDF->m_pTDAPlot->LastDataset()->m_faValues.SetGrow(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled*100);

2519

}

2520

}

2521

}

2522

o->m_pCDF->m_pTDAPlot->SetRangeX(o->m_pCDF->m_p2DF->m_fMinVal[0],o->m_pCDF->m_p2DF->m_fMaxVal[0]);

2523

o->m_pCDF->m_pTDAPlot->SetRangeY(o->m_pCDF->m_p2DF->m_fMinVal[1],o->m_pCDF->m_p2DF->m_fMaxVal[1]);

2524

o->m_pCDF->m_pTDAPlot->MakeTicks();

2525

o->m_pCDF->m_pTDAPlot->SetLabelX(o->m_pCDF->m_p2DF->m_sLabelX);

2526

o->m_pCDF->m_pTDAPlot->SetLabelY(o->m_pCDF->m_p2DF->m_sLabelY);

2527

}

2528

}

2529

} // END IF CDF

2530

2531

if (g_bVACF)

2532

{

2533

mprintf(" Creating VACF...\n");

2534

o->m_pVACF->Create();

2535

if (g_bVACFCacheMode)

2536

{

2537

2538

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

2539

{

2540

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

2541

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2542

2543

if (g_iTrajSteps != -1)

2544

{

2545

ptfa->SetMaxSize((long)(g_iTrajSteps*3.1));

2546

ptfa->SetGrow((long)(g_iTrajSteps*0.1));

2547

} else ptfa->SetGrow(1000);

2548

o->m_pVACF->m_oaCache.Add(ptfa);

2549

}

2550

} else

2551

{

2552

if (o->m_pVACF->m_iSize > g_iStepHistory)

2553

g_iStepHistory = o->m_pVACF->m_iSize;

2554

}

2555

}

2556

2557

/* if (g_bDipACF)

2558

{

2559

mprintf(" Creating DipACF...\n");

2560

o->m_pDipACF->Create();

2561

}*/

2562

2563

if (g_bMSD)

2564

{

2565

mprintf(" Creating MSD...\n");

2566

o->m_pMSD->m_pMSD->m_fMinVal = 0.0f;

2567

o->m_pMSD->m_pMSD->m_fMaxVal = o->m_pMSD->m_iResolution*g_fTimestepLength*g_iStride/1000.0;

2568

o->m_pMSD->m_pMSD->m_iResolution = o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;

2569

o->m_pMSD->m_pMSD->Create();

2570

if (g_bMSDCacheMode)

2571

{

2572

2573

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

2574

{

2575

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

2576

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2577

2578

if (g_iTrajSteps != -1)

2579

{

2580

ptfa->SetMaxSize((long)(g_iTrajSteps/g_iStride*3.1));

2581

ptfa->SetGrow((long)(g_iTrajSteps/g_iStride*0.1));

2582

} else ptfa->SetGrow(1000);

2583

o->m_pMSD->m_oaCache.Add(ptfa);

2584

}

2585

if (o->m_pMSD->m_bSplit)

2586

{

2587

2588

try { o->m_pMSD->m_pSplitMSD = new CAF*[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms]; } catch(...) { o->m_pMSD->m_pSplitMSD = NULL; }

2589

2590

2591

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

2592

{

2593

try { o->m_pMSD->m_pSplitMSD[z2] = new CAF(); } catch(...) { o->m_pMSD->m_pSplitMSD[z2] = NULL; }

2594

if (o->m_pMSD->m_pSplitMSD[z2] == NULL) NewException((double)sizeof(CAF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2595

2596

o->m_pMSD->m_pSplitMSD[z2]->m_fMinVal = 0.0f;

2597

o->m_pMSD->m_pSplitMSD[z2]->m_fMaxVal = o->m_pMSD->m_iResolution*g_fTimestepLength/1000.0;

2598

o->m_pMSD->m_pSplitMSD[z2]->m_iResolution = o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;

2599

o->m_pMSD->m_pSplitMSD[z2]->Create();

2600

}

2601

}

2602

} else

2603

{

2604

if (!g_bMSDCacheMode)

2605

{

2606

if (o->m_pMSD->m_iResolution > g_iStepHistory)

2607

g_iStepHistory = o->m_pMSD->m_iResolution;

2608

}

2609

}

2610

}

2611

2612

if (g_bRevSDF)

2613

{

2614

mprintf(" Creating Pseudo SDF...\n");

2615

o->m_pRevSDF->m_p2DF->m_fMinVal[0] = -o->m_pRevSDF->m_fRadius;

2616

o->m_pRevSDF->m_p2DF->m_fMaxVal[0] = o->m_pRevSDF->m_fRadius;

2617

o->m_pRevSDF->m_p2DF->m_fMinVal[1] = -o->m_pRevSDF->m_fRadius;

2618

o->m_pRevSDF->m_p2DF->m_fMaxVal[1] = o->m_pRevSDF->m_fRadius;

2619

o->m_pRevSDF->m_p2DF->m_iRes[0] = o->m_pRevSDF->m_iResolution;

2620

o->m_pRevSDF->m_p2DF->m_iRes[1] = o->m_pRevSDF->m_iResolution;

2621

o->m_pRevSDF->m_p2DF->SetLabelX("X [pm]");

2622

o->m_pRevSDF->m_p2DF->SetLabelY("Y [pm]");

2623

o->m_pRevSDF->m_p2DF->m_iHistogramRes = o->m_pRevSDF->m_iHistogramRes;

2624

o->m_pRevSDF->m_p2DF->Create();

2625

2626

try { o->m_pRevSDF->m_vaData = new CxVec3Array[o->m_iShowMolCount]; } catch(...) { o->m_pRevSDF->m_vaData = NULL; }

2627

if (o->m_pRevSDF->m_vaData == NULL) NewException((double)o->m_iShowMolCount*sizeof(CxVec3Array),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2628

}

2629

}

2630

2631

if (g_bBondACF)

2632

{

2633

mprintf(" Creating BondACF...\n");

2634

for (z=0;z<g_oaSingleMolecules.GetSize();z++)

2635

{

2636

sm = (CSingleMolecule*)g_oaSingleMolecules[z];

2637

for (z2=0;z2<sm->m_oaBondGroups.GetSize();z2++)

2638

{

2639

bg = (CMolBondGroup*)sm->m_oaBondGroups[z2];

2640

for (z3=0;z3<bg->m_oaBonds.GetSize();z3++)

2641

{

2642

if (g_iTrajSteps != -1)

2643

{

2644

((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetMaxSize(g_iTrajSteps);

2645

((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetGrow(g_iTrajSteps/10);

2646

} else ((CMolBond*)bg->m_oaBonds[z3])->m_faData.SetGrow(10000);

2647

}

2648

}

2649

}

2650

}

2651

2652

if (g_bClusterAnalysis)

2653

{

2654

mprintf(" Creating Cluster Analysis...\n");

2655

g_pClusterAnalysis->Create();

2656

}

2657

2658

if (g_bFESA)

2659

{

2660

mprintf(" Creating FES Analysis...\n");

2661

g_pFESA->Create();

2662

}

2663

2664

if (g_bMicroHet)

2665

{

2666

mprintf(" Creating Microheterogeneity Analysis...\n");

2667

g_pMicroHet->Create();

2668

}

2669

2670

if (g_bThermo)

2671

{

2672

mprintf(" Creating Thermodynamic Analysis...\n");

2673

g_pThermoAnalysis->Create();

2674

}

2675

2676

if (g_iRefSystemDim == 3)

2677

g_pRefMol.SetSize(((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes);

2678

if ((g_iRefSystemDim == 3) && !g_bMiddleAvg) // Einfach das erstbeste Molekuel als Referenz nehmen

2679

{

2680

mprintf("Creating reference molecule from first time step...");

2681

g_TimeStep.CalcCenters();

2682

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[0]];

2683

vec1 = g_TimeStep.m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

2684

g_TimeStep.CenterPos(vec1);

2685

vec2 = g_TimeStep.m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

2686

vec3 = g_TimeStep.m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

2687

// vec2 -= vec1;

2688

// vec3 -= vec1;

2689

mat.MatUltra(vec2,vec3);

2690

cc = 0;

2691

// Jeden Atomtyp des Zielmolekuels durchgehen

2692

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z3++)

2693

{

2694

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z4++)

2695

{

2696

vec2 = g_TimeStep.m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[z3])->GetAt(z4)];

2697

// vec2 -= vec1;

2698

g_pRefMol[cc] = mat * vec2;

2699

cc++;

2700

}

2701

}

2702

if (g_bPlProj)

2703

{

2704

g_TimeStep.FoldAtoms();

2705

g_TimeStep.Transform(mat);

2706

for (z3=0;z3<g_oaObserv.GetSize();z3++)

2707

{

2708

o = (CObservation*)g_oaObserv[z3];

2709

if (!o->m_pPlProj->m_bAverageAtomPos)

2710

{

2711

ti = 0;

2712

for (z3=0;z3<o->m_pPlProj->m_oDrawAtoms.m_oaAtoms.GetSize();z3++)

2713

{

2714

for (z4=0;z4<((CxIntArray*)o->m_pPlProj->m_oDrawAtoms.m_oaAtoms[z3])->GetSize();z4++)

2715

{

2716

o->m_pPlProj->m_vaAtomPos[ti] = g_TimeStep.m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[o->m_pPlProj->m_oDrawAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)o->m_pPlProj->m_oDrawAtoms.m_oaAtoms[z3])->GetAt(z4))];

2717

ti++;

2718

}

2719

}

2720

}

2721

}

2722

}

2723

mprintf("Done.\n");

2724

} // Ende Referenzbestimmung

2725

2726

if (g_iSwapAtoms)

2727

{

2728

mprintf("Creating Reference Molecule Swap Matrix...\n");

2729

2730

try { pSwapMatrix = new unsigned int[((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes]; } catch(...) { pSwapMatrix = NULL; }

2731

2732

2733

for (z=0;z<((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes;z++)

2734

pSwapMatrix[z] = 0;

2735

}

2736

2737

g_iCurrentTimeStep = -1;

2738

g_iNextTimeStep = -1;

2739

g_iLastTimeStep = -1;

2740

2741

try { g_pTempTimestep = new CTimeStep(); } catch(...) { g_pTempTimestep = NULL; }

2742

if (g_pTempTimestep == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2743

2744

if ((g_bSaveRefEnv) && (g_iNbhMode == 3) && (!g_bStreamInput))

2745

{

2746

mprintf(WHITE,"\n>>> Pre-analysis for neighborhood search >>>\n");

2747

2748

g_fPos = fopen(g_sInputTraj,"rt"); // Eingabedatei erneut Oeffnen

2749

if (g_fPos == NULL)

2750

{

2751

eprintf("\nError. Input Trajectory suddenly vanished ^^\n");

2752

return 0;

2753

}

2754

g_iSteps = 0; // Der Zaehler der Zeitschritte

2755

if (g_iScanNbhStart != 0)

2756

{

2757

mprintf("\nFast-forwarding to step %d...\n",g_iScanNbhStart+1);

2758

mprintf(WHITE," [");

2759

for (z=0;z<g_iScanNbhStart;z++)

2760

{

2761

if (fmod(z,g_iScanNbhStart/60.0) < 1.0)

2762

mprintf(WHITE,"#");

2763

if (!g_TimeStep.SkipTimestep(g_fPos))

2764

break;

2765

}

2766

mprintf(WHITE,"]\n");

2767

}

2768

while (!feof(g_fPos)) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

2769

{

2770

for (z=0;z<(g_iScanNbhStride-1);z++)

2771

if (!g_TimeStep.SkipTimestep(g_fPos))

2772

goto _endnbs;

2773

if (!g_TimeStep.ReadTimestep(g_fPos,false))

2774

goto _endnbs;

2775

if (g_TimeStep.m_iGesAtomCount == 0)

2776

goto _endnbs;

2777

// g_TimeStep.m_vaCoords.SetSize(g_iGesVirtAtomCount);

2778

// g_TimeStep.UniteMolecules();

2779

// !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

2780

g_TimeStep.CalcCenters();

2781

2782

if ((g_iSteps % (4*g_iScanNbhStride)) == 0)

2783

{

2784

if ((g_iSteps % (200*g_iScanNbhStride)) == 0)

2785

mprintf("\nStep %6d...",g_iSteps);

2786

else mprintf(".");

2787

}

2788

2789

g_iSteps+=g_iScanNbhStride;

2790

2791

2792

2793

// g_TimeStep.CenterPos(vec1);

2794

2795

// if (g_bFold)

2796

// g_TimeStep.FoldMolecules();

2797

2798

// for (z=0;z<g_oaNbSearches.GetSize();z++)

2799

g_pNbSet->Scan((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[g_iSaveRefMol]],&g_TimeStep);

2800

2801

if ((g_iScanNbhSteps > 0) && ((int)g_iSteps >= g_iScanNbhSteps))

2802

break;

2803

}

2804

_endnbs:

2805

2806

fclose(g_fPos);

2807

mprintf(WHITE,"\n\n<<< Neighborhood search done <<<\n");

2808

// for (z0=0;z0<g_oaNbSearches.GetSize();z0++)

2809

{

2810

mprintf(YELLOW,"\n*** Choose Neighbors\n");

2811

// nbset = (CNbSet*)g_oaNbSearches[z0];

2812

// Sort Neighbors after time they have been neighbors

2813

for (z=0;z<g_pNbSet->m_oaConditionGroups.GetSize();z++)

2814

{

2815

if (g_pNbSet->m_oaConditionGroups[z] == NULL)

2816

continue;

2817

cg = (CConditionGroup*)g_pNbSet->m_oaConditionGroups[z];

2818

2819

try { tpi = new int[((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize()]; } catch(...) { tpi = NULL; }

2820

if (tpi == NULL) NewException((double)((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize()*sizeof(int),__FILE__,__LINE__,__PRETTY_FUNCTION__);

2821

2822

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)

2823

{

2824

cg->m_bAlwaysTrue[z2] = false;

2825

tpi[z2] = -1;

2826

}

2827

ti3 = 0;

2828

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z2++)

2829

{

2830

ti = 0;

2831

for (z3=z2;z3<((CMolecule*)g_oaMolecules[z])->m_laSingleMolIndex.GetSize();z3++)

2832

{

2833

for (z4=0;z4<z2;z4++)

2834

if (tpi[z4] == z3)

2835

goto _nbhave;

2836

if (cg->m_iPassCounter[z3] > ti)

2837

{

2838

ti = cg->m_iPassCounter[z3];

2839

ti2 = z3;

2840

}

2841

_nbhave:;

2842

}

2843

if (ti == 0)

2844

break;

2845

ti3++;

2846

tpi[z2] = ti2;

2847

}

2848

mprintf(WHITE,"\n Molecule type %s. %d neighbors found in total:\n",((CMolecule*)g_oaMolecules[z])->m_sName,ti3);

2849

for (z2=0;z2<ti3;z2++)

2850

mprintf(" %2d.) Molecule %3d (%8.4f percent of the time, %d hits)\n",z2+1,tpi[z2]+1,((double)cg->m_iPassCounter[tpi[z2]])*g_iScanNbhStride/g_iSteps*100.0,cg->m_iPassCounter[tpi[z2]]);

2851

2852

if (ti3 != 0)

2853

{

2854

z3 = AskUnsignedInteger("\nUse how many of the frequentiest neighbors for molecule %s? [%d] ",ti3,((CMolecule*)g_oaMolecules[z])->m_sName,ti3);

2855

for (z2=0;z2<z3;z2++)

2856

cg->m_bAlwaysTrue[tpi[z2]] = true;

2857

}

2858

2859

delete[] tpi;

2860

cg->m_bInactive = true;

2861

}

2862

}

2863

mprintf("\n");

2864

// for (z0=0;z0<g_oaNbSearches.GetSize();z0++)

2865

if (g_bSaveRefWithEnv)

2866

{

2867

mprintf("Adding reference molecule to neighborhood...\n");

2868

g_pNbSet->AddMolecule(g_iFixMol,g_iSaveRefMol);

2869

}

2870

2871

g_pNbSet->Reset();

2872

g_pNbSet->Dump();

2873

}

2874

2875

if (g_bVFDF)

2876

{

2877

g_iVFCorrCount = 0;

2878

for (z=0;z<g_oaMolecules.GetSize();z++)

2879

{

2880

for (z2=0;z2<((CMolecule*)g_oaMolecules[z])->m_baAtomIndex.GetSize();z2++)

2881

{

2882

sprintf(buf,"vfcorr_%s_%s%s.dat",((CMolecule*)g_oaMolecules[z])->m_sName,((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[z])->m_baAtomIndex[z2]])->m_sName,multibuf);

2883

// FreeFileName(buf);

2884

g_fVFCorr[g_iVFCorrCount] = OpenFileWrite(buf,true);

2885

g_iVFCorrCount++;

2886

}

2887

}

2888

}

2889

2890

if (g_bReact)

2891

{

2892

g_pReact->Create();

2893

g_pReact->InitMolecules(&g_TimeStep);

2894

}

2895

2896

if (g_bSaveRefEnv)

2897

{

2898

mprintf("\n");

2899

sprintf(g_sRefEnv,"refenv_%s.%d.",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1);

2900

/* for (z=0;z<g_oaMolecules.GetSize();z++)

2901

if (g_pNbAll->m_waMolCount[z] != 0)

2902

{

2903

sprintf(buf2,"%dx%s.",g_pNbAll->m_waMolCount[z],((CMolecule*)g_oaMolecules[z])->m_sName);

2904

strcat(g_sRefEnv,buf2);

2905

}*/

2906

/* if (!g_bDynamicNeighbor)

2907

strcat(g_sRefEnv,"static.");

2908

if (g_bRefEnvCenter)

2909

strcat(g_sRefEnv,"center.");

2910

if (g_bRefEnvFix)

2911

strcat(g_sRefEnv,"fix.");

2912

if (g_bScanNeighbors)

2913

strcat(g_sRefEnv,"scannb.");*/

2914

strcat(g_sRefEnv,multibuf);

2915

strcat(g_sRefEnv,"xyz");

2916

mprintf(">>> Saving reference environment as %s\n",g_sRefEnv);

2917

// FreeFileName(g_sRefEnv);

2918

g_fRefEnv = OpenFileWrite(g_sRefEnv,true);

2919

mprintf("\n");

2920

}

2921

2922

if (g_bCutCluster)

2923

{

2924

mprintf("\n");

2925

sprintf(g_sRefEnv,"cluster_%s.",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);

2926

/* for (z=0;z<g_oaMolecules.GetSize();z++)

2927

if (g_pNbAll->m_waMolCount[z] != 0)

2928

{

2929

sprintf(buf2,"%dx%s.",g_pNbAll->m_waMolCount[z],((CMolecule*)g_oaMolecules[z])->m_sName);

2930

strcat(g_sRefEnv,buf2);

2931

}*/

2932

/* if (g_bRefEnvCenter)

2933

strcat(g_sRefEnv,"center.");

2934

if (g_bRefEnvFix)

2935

strcat(g_sRefEnv,"fix.");*/

2936

strcat(g_sRefEnv,multibuf);

2937

strcat(g_sRefEnv,"xyz");

2938

mprintf(">>> Saving cluster list as %s\n",g_sRefEnv);

2939

// FreeFileName(g_sRefEnv);

2940

g_fRefEnv = OpenFileWrite(g_sRefEnv,true);

2941

mprintf("\n");

2942

}

2943

2944

if (g_bSaveJustTraj)

2945

{

2946

strcpy(buf,g_sInputTraj);

2947

p = strrchr(buf,'/');

2948

q = strrchr(buf,'\\');

2949

if (q > p)

2950

p = q;

2951

if (p == NULL)

2952

p = buf;

2953

else p++;

2954

strcpy(buf2,p);

2955

p = strrchr(buf2,'.');

2956

if (p != NULL)

2957

*p = 0;

2958

strcat(buf2,multibuf);

2959

strcat(buf2,"_out.xyz");

2960

// FreeFileName(buf);

2961

// sprintf(buf,"traj_out.xyz");

2962

mprintf("Saving processed trajectory as %s ...\n",buf2);

2963

g_fSaveJustTraj = OpenFileWrite(buf2,true);

2964

}

2965

2966

2967

/******* Interface *******************/

2968

if (!Interface_Initialization())

2969

goto _ende;

2970

2971

2972

mprintf(WHITE,"\n<<< End of Initialization <<<\n\n");

2973

2974

_beginmain:

2975

if (ReactSecondRun)

2976

{

2977

mprintf(WHITE,"\n### Starting Second Pass ###\n");

2978

} else

2979

{

2980

mprintf(WHITE,"\n### Starting Main Analysis ###\n");

2981

if (g_bVHDF)

2982

mprintf("\n Please note: The VHCF analysis will become slower while it proceeds.\n");

2983

}

2984

2985

#ifdef TARGET_LINUX

2986

if (!g_bMultiInterval || (multicounter == 0))

2987

{

2988

mprintf(WHITE,"\nHint: ");

2989

mprintf("Press CTRL+C once to softly interrupt analysis and still write the results.\n");

2990

mprintf(" Creating an empty file named EXIT (\"touch EXIT\") has the same effect.\n");

2991

}

2992

#endif

2993

2994

if (!g_bStreamInput)

2995

{

2996

g_fPos = fopen(g_sInputTraj,"rb");

2997

if (g_fPos == NULL)

2998

{

2999

eprintf("\nCould not open position trajectory.\n");

3000

goto _ende;

3001

}

3002

}

3003

3004

if ((g_bNPT) && (g_sNPTFile[0] != 0))

3005

{

3006

g_fNPTFile = fopen(g_sNPTFile,"rt");

3007

if (g_fNPTFile == NULL)

3008

{

3009

eprintf("\nCould not open cell vector file.\n");

3010

goto _ende;

3011

}

3012

}

3013

3014

if (g_bUseVelocities && (g_sInputVel[0] != 0))

3015

{

3016

g_fVel = fopen(g_sInputVel,"rt");

3017

if (g_fVel == NULL)

3018

{

3019

eprintf("\nCould not open velocity trajectory.\n");

3020

goto _ende;

3021

}

3022

}

3023

if (g_bUseForces && (g_sInputForce[0] != 0))

3024

{

3025

g_fForce = fopen(g_sInputForce,"rt");

3026

if (g_fForce == NULL)

3027

{

3028

eprintf("\nCould not open force trajectory.\n");

3029

goto _ende;

3030

}

3031

}

3032

3033

// fff = fopen("dipole.txt","wt");

3034

3035

if (g_iBeginStep != 0)

3036

{

3037

mprintf("\nFast-forwarding to step %d...\n",g_iBeginStep+1);

3038

// mprintf("Seek: %d.\n",g_iFastForwardPos);

3039

fseek(g_fPos,g_iFastForwardPos,SEEK_SET);

3040

if ((g_fVel != NULL) || (g_fForce != NULL) || ((g_bNPT) && (g_sNPTFile[0] != 0)))

3041

{

3042

mprintf(WHITE," [");

3043

for (z=0;z<g_iBeginStep;z++)

3044

{

3045

/* if (!g_TimeStep.SkipTimestep(g_fPos))

3046

{

3047

eprintf("Error. Unexpected end of position trajectory.\n");

3048

goto _endmainloop;

3049

}*/

3050

if (fmod(z,g_iBeginStep/60.0) < 1.0)

3051

mprintf(WHITE,"#");

3052

if (g_fVel != NULL)

3053

{

3054

if (!g_TimeStep.SkipTimestep(g_fVel))

3055

{

3056

eprintf("Error. Unexpected end of velocity trajectory.\n");

3057

goto _endmainloop;

3058

}

3059

}

3060

if (g_fForce != NULL)

3061

{

3062

if (!g_TimeStep.SkipTimestep(g_fForce))

3063

{

3064

eprintf("Error. Unexpected end of force trajectory.\n");

3065

goto _endmainloop;

3066

}

3067

}

3068

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

3069

fgets(buf,256,g_fNPTFile);

3070

}

3071

mprintf(WHITE,"]\n");

3072

}

3073

}

3074

3075

g_oaTimeSteps.SetSize(g_iStepHistory);

3076

for (z=0;z<g_iStepHistory;z++)

3077

g_oaTimeSteps[z] = NULL;

3078

3079

g_iSteps = 0; // Der Zaehler der Zeitschritte

3080

g_iCurrentTimeStep = 0;

3081

t0 = time(NULL);

3082

g_iClusterPos = 0;

3083

sic = 0;

3084

g_iSaveCondCount = 0;

3085

3086

try { apfa = new CxDoubleArray*[g_iCDFChannels]; } catch(...) { apfa = NULL; }

3087

if (apfa == NULL) NewException((double)g_iCDFChannels*sizeof(CxDoubleArray*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3088

3089

try { apba = new CxByteArray*[g_iCDFChannels]; } catch(...) { apba = NULL; }

3090

if (apba == NULL) NewException((double)g_iCDFChannels*sizeof(CxByteArray*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3091

3092

try { tda = new double[g_iCDFChannels]; } catch(...) { tda = NULL; }

3093

if (tda == NULL) NewException((double)g_iCDFChannels*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3094

3095

if (g_bDeriv)

3096

{

3097

g_iDerivNext = 2;

3098

g_iDerivCurr = 1;

3099

g_iDerivLast = 0;

3100

}

3101

3102

if (g_bDipole && g_bDumpDipoleVector)

3103

{

3104

g_fDumpDipole = OpenFileWrite("dipole_vectors.csv",true);

3105

fprintf(g_fDumpDipole,"#Step");

3106

for (z=0;z<g_oaMolecules.GetSize();z++)

3107

{

3108

if (g_oaDumpDipoleVector[z] == NULL)

3109

continue;

3110

for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)

3111

{

3112

fprintf(g_fDumpDipole,"; %s[%d]_X; Y; Z",((CMolecule*)g_oaMolecules[z])->m_sName,((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)+1);

3113

if (g_bDumpDipoleAbs)

3114

fprintf(g_fDumpDipole,"; Abs");

3115

}

3116

}

3117

fprintf(g_fDumpDipole,"\n");

3118

3119

if (g_bDumpDipoleXYZ)

3120

{

3121

g_fDumpDipoleXYZ = OpenFileWrite("dipole_vectors.xyz",true);

3122

3123

fprintf(g_fDumpDipoleXYZ,"%d\n\n",g_iDumpDipoleXYZAtoms);

3124

3125

for (z=0;z<g_oaMolecules.GetSize();z++)

3126

{

3127

if (g_oaDumpDipoleVector[z] == NULL)

3128

continue;

3129

m = (CMolecule*)g_oaMolecules[z];

3130

for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)

3131

{

3132

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[((CxIntArray*)g_oaDumpDipoleVector[z])->GetAt(z2)]];

3133

3134

for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)

3135

{

3136

if (m->m_baAtomIndex[z3] == g_iVirtAtomType)

3137

continue;

3138

for (z4=0;z4<((CxIntArray*)sm->m_oaAtomOffset[z3])->GetSize();z4++)

3139

{

3140

ti = ((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(z4);

3141

3142

}

3143

}

3144

}

3145

}

3146

3147

ti2 = 0;

3148

for (z=0;z<g_oaMolecules.GetSize();z++)

3149

{

3150

if (g_oaDumpDipoleVector[z] == NULL)

3151

continue;

3152

m = (CMolecule*)g_oaMolecules[z];

3153

for (z2=0;z2<((CxIntArray*)g_oaDumpDipoleVector[z])->GetSize();z2++)

3154

{

3155

fprintf(g_fDumpDipoleXYZ,"B %12f 0 0\n",100.0+ti2*3.0);

3156

fprintf(g_fDumpDipoleXYZ,"B %12f 0.5 0\n",100.0+ti2*3.0);

3157

ti2++;

3158

}

3159

}

3160

}

3161

}

3162

3163

3164

/*****************************************************************************

3165

*************** Beginn Hauptschleife *****************************************

3166

*****************************************************************************/

3167

3168

g_iLastTimeStep = -1;

3169

g_iDotCounter = 0;

3170

g_bStepSkipped = false;

3171

g_iFirstStepSkipped = -1;

3172

tbs = false;

3173

3174

while (true) // Zeitschritt fuer Zeitschritt die Trajektorie durchgehen

3175

{

3176

if (feof(g_fPos))

3177

{

3178

mprintf("\nEnd of trajectory file reached.\n");

3179

break;

3180

}

3181

if (g_bAbortAnalysis)

3182

{

3183

mprintf("\nAnalysis aborted by user.\n");

3184

break;

3185

}

3186

g_iCurrentTimeStep++;

3187

if (g_iCurrentTimeStep >= g_iStepHistory)

3188

g_iCurrentTimeStep = 0;

3189

3190

if (g_bDeriv)

3191

{

3192

g_iDerivNext++;

3193

if (g_iDerivNext > 2)

3194

g_iDerivNext = 0;

3195

g_iDerivCurr++;

3196

if (g_iDerivCurr > 2)

3197

g_iDerivCurr = 0;

3198

g_iDerivLast++;

3199

if (g_iDerivLast > 2)

3200

g_iDerivLast = 0;

3201

}

3202

3203

for (z=0;z<(g_iStride-1);z++)

3204

{

3205

if (!g_TimeStep.SkipTimestep(g_fPos))

3206

{

3207

if (!feof(g_fPos))

3208

eprintf("\nError while skipping time step %d.\n",g_iSteps+z+1);

3209

goto _endmainloop;

3210

}

3211

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

3212

fgets(buf,256,g_fNPTFile);

3213

if (g_fVel != NULL)

3214

{

3215

if (!g_TimeStep.SkipTimestep(g_fVel))

3216

{

3217

eprintf("\nError while skipping velocity time step %d.\n",g_iSteps+z+1);

3218

goto _endmainloop;

3219

}

3220

}

3221

if (g_fForce != NULL)

3222

{

3223

if (!g_TimeStep.SkipTimestep(g_fForce))

3224

{

3225

eprintf("\nError while skipping force time step %d.\n",g_iSteps+z+1);

3226

goto _endmainloop;

3227

}

3228

}

3229

}

3230

_readagain:

3231

if (g_bUseVelocities || g_bUseForces)

3232

{

3233

if (GetTimeStep(-1) == NULL)

3234

{

3235

try { *GetTimeStepAddress(-1) = new CTimeStep(); } catch(...) { *GetTimeStepAddress(-1) = NULL; }

3236

if (*GetTimeStepAddress(-1) == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3237

}

3238

if (!GetTimeStep(-1)->ReadTimestep(g_fPos,false))

3239

{

3240

if (feof(g_fPos))

3241

{

3242

mprintf("\nEnd of Trajectory File reached.\n");

3243

break;

3244

}

3245

eprintf("\nError while reading time step %d.\n",g_iSteps+1);

3246

goto _endmainloop;

3247

}

3248

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

3249

GetTimeStep(-1)->ReadCellVector(g_fNPTFile);

3250

if (g_bSkipDoubleSteps)

3251

{

3252

if (GetTimeStep(-1)->ExtractNumber(g_iNumberPos) <= g_iLastTimeStep)

3253

{

3254

if (!g_bStepSkipped)

3255

{

3256

g_bStepSkipped = true;

3257

g_iFirstStepSkipped = GetTimeStep(-1)->ExtractNumber(g_iNumberPos);

3258

mprintf("\nSkipping:");

3259

}

3260

mprintf("*");

3261

goto _readagain;

3262

} else if (g_iFirstStepSkipped != -1)

3263

{

3264

if (g_iFirstStepSkipped == GetTimeStep(-1)->ExtractNumber(g_iNumberPos))

3265

mprintf("\nRepeated step %d skipped.",g_iFirstStepSkipped);

3266

else mprintf("\nRepeated steps %d-%d skipped.",g_iFirstStepSkipped,GetTimeStep(-1)->ExtractNumber(g_iNumberPos));

3267

g_iDotCounter = 0;

3268

g_iFirstStepSkipped = -1;

3269

}

3270

3271

if (g_iLastTimeStep != -1)

3272

{

3273

if (g_iStrideDetect == -1)

3274

{

3275

g_iStrideDetect = GetTimeStep(-1)->ExtractNumber(g_iNumberPos) - g_iLastTimeStep;

3276

} else

3277

{

3278

if (g_iStrideDetect != (GetTimeStep(-1)->ExtractNumber(g_iNumberPos) - g_iLastTimeStep))

3279

{

3280

if (!tbs)

3281

eprintf("\n");

3282

3283

tbs = true;

3284

} else tbs = false;

3285

}

3286

}

3287

3288

if (GetTimeStep(-1)->ExtractNumber(g_iNumberPos) > g_iLastTimeStep)

3289

g_iLastTimeStep = GetTimeStep(-1)->ExtractNumber(g_iNumberPos);

3290

}

3291

if (GetTimeStep(-1)->m_iGesAtomCount == 0)

3292

{

3293

eprintf("\nError: Atom count = 0 at time step %d.\n",g_iSteps+1);

3294

goto _endmainloop;

3295

}

3296

GetTimeStep(-1)->UniteMolecules(false);

3297

if (g_bRemoveCOM)

3298

GetTimeStep(-1)->CenterCOM();

3299

GetTimeStep(-1)->CalcCenters();

3300

if (g_bDipole)

3301

{

3302

if (g_bWannier)

3303

GetTimeStep(-1)->ScanWannier(false);

3304

GetTimeStep(-1)->CalcDipoles();

3305

if (g_bDumpDipoleVector)

3306

GetTimeStep(-1)->DumpDipoles();

3307

}

3308

} else

3309

{

3310

if (GetTimeStep(0) == NULL)

3311

{

3312

try { *GetTimeStepAddress(0) = new CTimeStep(); } catch(...) { *GetTimeStepAddress(0) = NULL; }

3313

if (*GetTimeStepAddress(0) == NULL) NewException((double)sizeof(CTimeStep),__FILE__,__LINE__,__PRETTY_FUNCTION__);

3314

}

3315

if (!GetTimeStep(0)->ReadTimestep(g_fPos,false))

3316

{

3317

if (feof(g_fPos))

3318

{

3319

mprintf("\nEnd of trajectory file reached.\n");

3320

break;

3321

}

3322

eprintf("\nError while reading time step %d.\n",g_iSteps+1);

3323

goto _endmainloop;

3324

}

3325

if (((g_bNPT) && (g_sNPTFile[0] != 0)))

3326

GetTimeStep(0)->ReadCellVector(g_fNPTFile);

3327

if (g_bSkipDoubleSteps)

3328

{

3329

if (GetTimeStep(0)->ExtractNumber(g_iNumberPos) <= g_iLastTimeStep)

3330

{

3331

// mprintf("\n[Skip %d/%d]",GetTimeStep(0)->ExtractNumber(),g_iLastTimeStep);

3332

if (!g_bStepSkipped)

3333

{

3334

g_bStepSkipped = true;

3335

g_iFirstStepSkipped = GetTimeStep(0)->ExtractNumber(g_iNumberPos);

3336

mprintf("\nSkipping:");

3337

}

3338

mprintf("*");

3339

goto _readagain;

3340

} else if (g_iFirstStepSkipped != -1)

3341

{

3342

if (g_iFirstStepSkipped == GetTimeStep(0)->ExtractNumber(g_iNumberPos))

3343

mprintf("\nRepeated step %d skipped.",g_iFirstStepSkipped);

3344

else mprintf("\nRepeated steps %d-%d skipped.",g_iFirstStepSkipped,GetTimeStep(0)->ExtractNumber(g_iNumberPos));

3345

g_iDotCounter = 0;

3346

g_iFirstStepSkipped = -1;

3347

}

3348

// mprintf("\nNumber %d.",GetTimeStep(0)->ExtractNumber());

3349

3350

if (g_iLastTimeStep != -1)

3351

{

3352

if (g_iStrideDetect == -1)

3353

{

3354

g_iStrideDetect = GetTimeStep(0)->ExtractNumber(g_iNumberPos) - g_iLastTimeStep;

3355

} else

3356

{

3357

if (g_iStrideDetect != (GetTimeStep(0)->ExtractNumber(g_iNumberPos) - g_iLastTimeStep))

3358

{

3359

if (!tbs)

3360

eprintf("\n");

3361

3362

tbs = true;

3363

} else tbs = false;

3364

}

3365

}

3366

3367

if (GetTimeStep(0)->ExtractNumber(g_iNumberPos) > g_iLastTimeStep)

3368

g_iLastTimeStep = GetTimeStep(0)->ExtractNumber(g_iNumberPos);

3369

}

3370

if (GetTimeStep(0)->m_iGesAtomCount == 0)

3371

{

3372

eprintf("\nError: Atom count = 0 at time step %d.\n",g_iSteps+1);

3373

goto _endmainloop;

3374

}

3375

if (!g_bSaveCoordsUnchanged)

3376

{

3377

GetTimeStep(0)->UniteMolecules(false);

3378

if (g_bRemoveCOM)

3379

GetTimeStep(0)->CenterCOM();

3380

}

3381

GetTimeStep(0)->CalcCenters();

3382

if (g_bDipole)

3383

{

3384

if (g_bWannier)

3385

GetTimeStep(0)->ScanWannier(false);

3386

GetTimeStep(0)->CalcDipoles();

3387

if (g_bDumpDipoleVector)

3388

GetTimeStep(0)->DumpDipoles();

3389

}

3390

}

3391

g_bWarnUnsteady = false;

3392

3393

if (((g_iSteps-(sic*g_iStride*50)) % (showinterval*g_iStride)) == 0)

3394

{

3395

if ((g_iSteps == 0) || g_bStepSkipped)

3396

{

3397

g_bStepSkipped = false;

3398

if (!g_bSilentProgress)

3399

mprintf("\nStep %6d ",g_iSteps);

3400

}

3401

if (g_bAsciiArt && (!g_bSilentProgress))

3402

{

3403

tc = g_oAsciiArt.GetChar();

3404

if (tc == 0)

3405

{

3406

if ((g_iSteps != 0) && (g_iTrajSteps != -1))

3407

{

3408

if ((time(NULL) - t0) > 5)

3409

{

3410

eta = (unsigned long)(((double)time(NULL) - t0) / g_iSteps * ((double)max(long(0),(((g_iMaxStep > 0)?g_iMaxStep:g_iTrajSteps) - ((long)g_iSteps)))));

3411

FormatTime(eta,buf);

3412

mprintf(" ETA %s",buf);

3413

}

3414

}

3415

mprintf("\nStep %6d ",g_iSteps);

3416

if (g_iSteps != 0)

3417

g_oAsciiArt.NewLine();

3418

} else mprintf("%c",tc);

3419

} else

3420

{

3421

if (g_iDotCounter >= 50)

3422

{

3423

g_iDotCounter = 0;

3424

if (!g_bSilentProgress)

3425

{

3426

if ((g_iSteps != 0) && (g_iTrajSteps != -1))

3427

{

3428

if ((time(NULL) - t0) > 5)

3429

{

3430

eta = (unsigned long)(((double)time(NULL) - t0) / g_iSteps * ((double)max(long(0),g_iTrajSteps - ((long)g_iSteps))));

3431

FormatTime(eta,buf);

3432

mprintf(" ETA %s",buf);

3433

}

3434

}

3435

mprintf("\nStep %6d ",g_iSteps);

3436

}

3437

}

3438

g_iDotCounter++;

3439

if (!g_bSilentProgress)

3440

mprintf(".");

3441

}

3442

if (FileExist("EXIT"))

3443

{

3444

mprintf("\n\n*** File \"EXIT\" detected. Aborting analysis. ***\n\n");

3445

remove("EXIT");

3446

break;

3447

}

3448

}

3449

3450

if ((int)g_iSteps == /*showinterval**/g_iStride*50)

3451

{

3452

t1 = time(NULL);

3453

if (t1 == t0)

3454

showinterval = 20;

3455

else showinterval = (int)(20.0f/(t1-t0));

3456

if (showinterval == 0)

3457

showinterval = 1;

3458

sic = 1;

3459

}

3460

3461

g_iSteps += g_iStride;

3462

3463

if (GetTimeStep(0)==NULL)

3464

continue;

3465

3466

if ((g_bUseVelocities || g_bUseForces) && (GetTimeStep(1)==NULL))

3467

continue;

3468

3469

if (g_bUseVelocities)

3470

{

3471

if (g_fVel == NULL)

3472

{

3473

CalcVelocities();

3474

} else if (!GetTimeStep(-1)->ReadTimestepVel(g_fVel))

3475

{

3476

eprintf("\nError reading velocity time step %d.\n",g_iSteps+1);

3477

goto _endmainloop;

3478

}

3479

}

3480

if (g_bUseForces)

3481

{

3482

if (g_fForce == NULL)

3483

{

3484

CalcForces();

3485

} else if (!GetTimeStep(-1)->ReadTimestepForce(g_fForce))

3486

{

3487

eprintf("\nError reading force time step %d.\n",g_iSteps+1);

3488

goto _endmainloop;

3489

}

3490

}

3491

3492

if (g_bCutCluster)

3493

{

3494

if (((int)g_iSteps/g_iStride) >= g_iClusterSteps)

3495

break;

3496

3497

if (g_iClusterPos >= g_iClusterCount)

3498

break;

3499

3500

if (g_iaClusterSteps[g_iClusterPos] != ((int)g_iSteps/g_iStride))

3501

continue;

3502

}

3503

// mprintf("\nStep %d for clusters.",((int)g_iSteps/g_iStride));

3504

3505

if (g_bUnwrap && ((int)g_iSteps > g_iStride))

3506

// Nicht im ersten Schritt

3507

{

3508

for (z=0;z<g_oaMolecules.GetSize();z++)

3509

{

3510

m = (CMolecule*)g_oaMolecules[z];

3511

for (z3=0;z3<m->m_baAtomIndex.GetSize();z3++)

3512

{

3513

if (m->m_baAtomIndex[z3] != g_iVirtAtomType)

3514

continue;

3515

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

3516

{

3517

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];

3518

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] > g_fBoxX/2.0f)

3519

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][0] -= g_fBoxX;

3520

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][0] < -g_fBoxX/2.0f)

3521

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][0] += g_fBoxX;

3522

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] > g_fBoxY/2.0f)

3523

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][1] -= g_fBoxY;

3524

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][1] < -g_fBoxY/2.0f)

3525

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][1] += g_fBoxY;

3526

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] > g_fBoxZ/2.0f)

3527

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][2] -= g_fBoxZ;

3528

if (GetTimeStep(0)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] - GetTimeStep(1)->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z3])->GetAt(0)][2] < -g_fBoxZ/2.0f)

3529

g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][2] += g_fBoxZ;

3530

// mprintf("\n%2d.%2d: %f, %f, %f",z,z2,g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][0],g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][1],g_vaUnwrapArray[m->m_laSingleMolIndex[z2]][2]);

3531

}

3532

}

3533

}

3534

}

3535

3536

if (g_bKeepUnfoldedCoords)

3537

GetTimeStep(0)->m_vaCoords_Unfolded.CopyFrom(&GetTimeStep(0)->m_vaCoords);

3538

3539

/******* Interface *********/

3540

Interface_ProcessStep(GetTimeStep(0));

3541

3542

if (g_bMSD)

3543

{

3544

g_pT2Timestep = GetTimeStep(0);

3545

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3546

{

3547

ti2 = 0;

3548

o = (CObservation*)g_oaObserv[z0];

3549

if (g_bMSDCacheMode)

3550

{

3551

for (z2=0;z2<o->m_pMSD->m_pAtomGroup->m_oaAtoms.GetSize();z2++)

3552

{

3553

for (z3=0;z3<((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetSize();z3++)

3554

{

3555

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z4++)

3556

{

3557

3558

ptfa = (CxFloatArray*)o->m_pMSD->m_oaCache[ti2];

3559

3560

if (g_bPeriodic && (ptfa->GetSize() > 0))

3561

{

3562

ti3 = ptfa->GetSize()-3;

3563

vec1[0] = ptfa->GetAt(ti3++);

3564

vec1[1] = ptfa->GetAt(ti3++);

3565

vec1[2] = ptfa->GetAt(ti3);

3566

tf = (g_pT2Timestep->m_vaCoords[ti]-vec1).GetLength();

3567

if (tf > g_fMinPeriodic/2.0)

3568

3569

}

3570

3571

ptfa->Add(g_pT2Timestep->m_vaCoords[ti][0]);

3572

ptfa->Add(g_pT2Timestep->m_vaCoords[ti][1]);

3573

ptfa->Add(g_pT2Timestep->m_vaCoords[ti][2]);

3574

3575

ti2++;

3576

}

3577

}

3578

}

3579

} else

3580

{

3581

for (z=0;z<o->m_pMSD->m_iResolution/o->m_pMSD->m_iStride;z++)

3582

{

3583

g_pTempTimestep = GetTimeStep(z*o->m_pMSD->m_iStride);

3584

if (g_pTempTimestep == NULL)

3585

continue;

3586

for (z2=0;z2<o->m_pMSD->m_pAtomGroup->m_oaAtoms.GetSize();z2++)

3587

{

3588

for (z3=0;z3<((CxIntArray*)o->m_pMSD->m_pAtomGroup->m_oaAtoms[z2])->GetSize();z3++)

3589

{

3590

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z4++)

3591

{

3592

3593

3594

}

3595

}

3596

}

3597

}

3598

}

3599

}

3600

} // END IF MSD

3601

3602

if (g_bSaveJustTraj)

3603

{

3604

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3605

3606

if (g_bSaveJustCenter && (!g_bSaveCoordsUnchanged))

3607

{

3608

3609

g_pTempTimestep->CenterPos(vec0);

3610

}

3611

3612

if (g_bSaveTrajNoRot)

3613

{

3614

g_pTempTimestep->CenterCOM();

3615

3616

// mfprintf(g_fSaveJustTraj," %d\n\n",(int)g_iSaveGesAtoms*3);

3617

3618

// for (z=0;z<g_iGesAtomCount;z++)

3619

3620

3621

// g_pTempTimestep->Transform(tdmat2);

3622

g_pTempTimestep->Transform(tq2);

3623

3624

// for (z=0;z<g_iGesAtomCount;z++)

3625

3626

3627

if ((int)g_iSteps > g_iStride)

3628

{

3629

dvec1 = 0;

3630

for (z=0;z<g_iGesAtomCount;z++)

3631

{

3632

dvec2 = (g_pTempTimestep->m_vaCoords[z] - rot_ts.m_vaCoords[z]);

3633

dvec4 = (g_pTempTimestep->m_vaCoords[z] + rot_ts.m_vaCoords[z]) / 2.0;

3634

3635

// tf3 = dvec4.GetLength();

3636

// tf2 = dvec2.GetLength();

3637

// if (4*tf3*tf3 > 0.25*tf2*tf2)

3638

// {

3639

// dvec4 *= (1.0 + 1.0 - 0.5 / tf3 * sqrt(4*tf3*tf3 - 0.25*tf2*tf2) );

3640

// mprintf("\n%.10g",1.0 + 1.0 - 0.5 / tf3 * sqrt(4*tf3*tf3 - 0.25*tf2*tf2));

3641

// }

3642

3643

dvec3 = CrossP(dvec4,dvec2);

3644

dvec1 += dvec3 * ((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_fMass;

3645

3646

}

3647

// mprintf("Drehimpuls: %g ( %g, %g, %g )\n",dvec1.GetLength(),dvec1[0],dvec1[1],dvec1[2]);

3648

dvec3 = dvec1;

3649

dvec3.Normalize();

3650

// mprintf(" ( %g, %g, %g )\n",vec3[0],vec3[1],vec3[2]);

3651

3652

tf = 0;

3653

for (z=0;z<g_iGesAtomCount;z++)

3654

{

3655

dvec4 = (g_pTempTimestep->m_vaCoords[z] + rot_ts.m_vaCoords[z]) / 2.0;

3656

3657

// tf3 = dvec4.GetLength();

3658

// tf2 = dvec2.GetLength();

3659

// dvec4 *= (1.0 + 1.0 - 0.5 / tf3 * sqrt(4*tf3*tf3 - 0.25*tf2*tf2) );

3660

3661

dvec0 = CrossP(dvec4,dvec3);

3662

// mprintf("# ( %g, %g, %g ) x ( %g, %g, %g ) = %g\n",g_pTempTimestep->m_vaCoords[z][0],g_pTempTimestep->m_vaCoords[z][1],g_pTempTimestep->m_vaCoords[z][2],vec3[0],vec3[1],vec3[2],vec0.GetLength());

3663

tf += ((CAtom*)g_oaAtoms[g_waAtomRealElement[z]])->m_pElement->m_fMass * dvec0.GetLengthSqr();

3664

3665

}

3666

// mprintf(" Traegheitsmoment: %g\n",tf);

3667

dvec1 /= tf;

3668

// mprintf("Angular momentum vector: ( %g, %g, %g ) (l = %g)\n",dvec1[0],dvec1[1],dvec1[2],dvec1.GetLength());

3669

// mprintf(" Winkelgeschw.: %g\n",dvec1.GetLength());

3670

// dvec3 = dvec1;

3671

// dvec3.Normalize();

3672

3673

// mprintf(" Baue Matrix: ( %g | %g | %g ), %g\n",dvec3[0],dvec3[1],dvec3[2],-dvec1.GetLength());

3674

3675

// tdmat.RotMat(dvec3,-dvec1.GetLength());

3676

3677

tq.BuildRotation(dvec3,dvec1.GetLength());

3678

3679

// mprintf(" Die Matrix:\n");

3680

// tdmat.Dump();

3681

3682

// tdmat2 = tdmat2 * tdmat;

3683

tq2 = tq2 * tq;

3684

3685

if (fabs(tq2.GetLength()-1.0) > 0.000001)

3686

{

3687

eprintf("\nRenormalizing rotation quaternion.\n");

3688

tq2.Normalize();

3689

}

3690

3691

// g_pTempTimestep->Transform(tdmat);

3692

g_pTempTimestep->Transform(tq);

3693

}

3694

3695

rot_ts.CopyFrom(g_pTempTimestep);

3696

3697

// for (z=0;z<g_iGesAtomCount;z++)

3698

3699

3700

} else

3701

{

3702

if (g_bFold && (!g_bSaveCoordsUnchanged))

3703

{

3704

if (g_bFoldAtomwise)

3705

g_pTempTimestep->FoldAtoms();

3706

else g_pTempTimestep->FoldMolecules();

3707

}

3708

}

3709

3710

if (!g_bCenterZero && (!g_bSaveCoordsUnchanged) && g_bPeriodic)

3711

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

3712

3713

ti = g_iSaveGesAtoms;

3714

3715

if (g_bUnwrapWannier)

3716

{

3717

g_pTempTimestep->ScanWannier(false);

3718

3719

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3720

{

3721

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3722

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3723

ti += ((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_laWannier.GetSize();

3724

}

3725

}

3726

3727

mfprintf(g_fSaveJustTraj," %d\n",ti);

3728

if (g_pTempTimestep->m_pComment != NULL)

3729

mfprintf(g_fSaveJustTraj,"%s\n",g_pTempTimestep->m_pComment);

3730

else mfprintf(g_fSaveJustTraj,"\n");

3731

3732

if (g_bWriteInputOrder) // This implies that all non-virtual atoms are to be written

3733

{

3734

for (z7=0;z7<g_iGesAtomCount;z7++)

3735

{

3736

z3 = g_waAtomMolIndex[z7]; // Molecule

3737

z6 = g_laAtomSMLocalIndex[z7]; // SingleMolecule

3738

z4 = g_waAtomElement[z7]; // AtomType

3739

z5 = g_waAtomMolNumber[z7]; // Atom

3740

3741

m = (CMolecule*)g_oaMolecules[z3];

3742

3743

vec0 = g_pTempTimestep->m_vaCoords[z7];

3744

if (g_bUnwrap)

3745

{

3746

vec0 += g_vaUnwrapArray[m->m_laSingleMolIndex[z6]];

3747

3748

}

3749

mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[g_waAtomRealElement[z7]])->m_sName,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3750

}

3751

} else

3752

{

3753

if (g_bWriteAtomwise)

3754

{

3755

for (z7=0;z7<g_oaAtoms.GetSize();z7++)

3756

{

3757

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3758

{

3759

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3760

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3761

{

3762

for (z4=0;z4<atgr->m_baAtomType.GetSize();z4++)

3763

{

3764

if (atgr->m_baRealAtomType[z4] != z7)

3765

continue;

3766

tla = (CxIntArray*)atgr->m_oaAtoms[z4];

3767

for (z5=0;z5<tla->GetSize();z5++)

3768

{

3769

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_oaAtomOffset[atgr->m_baAtomType[z4]])->GetAt(tla->GetAt(z5))];

3770

if (g_bUnwrap)

3771

{

3772

vec0 += g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]];

3773

3774

}

3775

if (atgr->m_baRealAtomType[z4] == g_iVirtAtomType)

3776

{

3777

if (g_bSaveVirtAtoms)

3778

mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CVirtualAtom*)g_oaVirtualAtoms[atgr->m_pMolecule->m_laVirtualAtoms[tla->GetAt(z5)]])->m_sLabel,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3779

} else mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[atgr->m_baRealAtomType[z4]])->m_sName,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3780

}

3781

}

3782

}

3783

}

3784

}

3785

} else

3786

{

3787

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3788

{

3789

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3790

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3791

{

3792

for (z4=0;z4<atgr->m_baAtomType.GetSize();z4++)

3793

{

3794

tla = (CxIntArray*)atgr->m_oaAtoms[z4];

3795

for (z5=0;z5<tla->GetSize();z5++)

3796

{

3797

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_oaAtomOffset[atgr->m_baAtomType[z4]])->GetAt(tla->GetAt(z5))];

3798

if (g_bUnwrap)

3799

{

3800

vec0 += g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]];

3801

3802

}

3803

if (atgr->m_baRealAtomType[z4] == g_iVirtAtomType)

3804

{

3805

if (g_bSaveVirtAtoms)

3806

mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CVirtualAtom*)g_oaVirtualAtoms[atgr->m_pMolecule->m_laVirtualAtoms[tla->GetAt(z5)]])->m_sLabel,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3807

} else mfprintf(g_fSaveJustTraj,"%2s %8.5f %8.5f %8.5f\n",((CAtom*)g_oaAtoms[atgr->m_baRealAtomType[z4]])->m_sName,vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3808

}

3809

}

3810

}

3811

}

3812

}

3813

}

3814

3815

if (g_bUnwrapWannier)

3816

{

3817

for (z3=0;z3<g_oaSaveMolecules.GetSize();z3++)

3818

{

3819

atgr = (CAtomGroup*)g_oaSaveMolecules[z3];

3820

for (z6=0;z6<atgr->m_pMolecule->m_laSingleMolIndex.GetSize();z6++)

3821

{

3822

for (z4=0;z4<((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_laWannier.GetSize();z4++)

3823

{

3824

vec0 = g_pTempTimestep->m_vaCoords[((CSingleMolecule*)g_oaSingleMolecules[atgr->m_pMolecule->m_laSingleMolIndex[z6]])->m_laWannier[z4]];

3825

if (g_bUnwrap)

3826

vec0 += g_vaUnwrapArray[atgr->m_pMolecule->m_laSingleMolIndex[z6]];

3827

mfprintf(g_fSaveJustTraj," X %8.5f %8.5f %8.5f\n",vec0[0]/100.0,vec0[1]/100.0,vec0[2]/100.0);

3828

}

3829

}

3830

}

3831

}

3832

} // END IF g_bSaveJustTraj

3833

3834

if (g_bBondACF)

3835

{

3836

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3837

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

3838

{

3839

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

3840

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

3841

{

3842

bond = (CMolBond*)sm->m_oaBonds[z3];

3843

bond->m_faData.Add(VecDist(g_pTempTimestep->m_vaCoords[bond->m_iAtomOffset[0]],g_pTempTimestep->m_vaCoords[bond->m_iAtomOffset[1]]));

3844

}

3845

}

3846

}

3847

3848

if (g_bAggregation || g_bNbExchange)

3849

{

3850

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3851

3852

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3853

{

3854

o = (CObservation*)g_oaObserv[z0];

3855

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3856

{

3857

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3858

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize();z2++)

3859

dacfsub->m_pCondition->m_iPassCounter[z2] = 0;

3860

}

3861

}

3862

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3863

{

3864

o = (CObservation*)g_oaObserv[z0];

3865

3866

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex.GetSize();z2++)

3867

{

3868

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex[z2]];

3869

3870

o->m_pDACF->m_pCondition->PreScanNeighborhoodAllOM(g_pTempTimestep,smfix);

3871

3872

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3873

{

3874

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3875

3876

dacfsub->m_pCondition->CopyResults(o->m_pDACF->m_pCondition);

3877

dacfsub->m_pCondition->m_bAnyPassed = false;

3878

dacfsub->m_pCondition->ReScan(smfix);

3879

if (dacfsub->m_pCondition->m_bAnyPassed)

3880

dacfsub->m_pCondition->m_iRMPassCounter[z2]++;

3881

3882

if (g_bDACF)

3883

o->m_pDACF->UpdateDACFSub(z2,g_pTempTimestep,dacfsub);

3884

3885

if (g_bNbExchange)

3886

o->m_pDACF->UpdateNbEx(z2,dacfsub);

3887

} // END FOR ZS

3888

} // END FOR Z2

3889

} // END FOR Z0

3890

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3891

{

3892

o = (CObservation*)g_oaObserv[z0];

3893

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

3894

{

3895

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

3896

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize();z2++)

3897

if (dacfsub->m_pCondition->m_iPassCounter[z2] != 0)

3898

dacfsub->m_pCondition->m_iOMPassCounter[z2]++;

3899

}

3900

}

3901

} // END IF AGGREGATION OR NBEX

3902

3903

if (g_bDens)

3904

{

3905

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3906

for (z0=0;z0<g_oaObserv.GetSize();z0++)

3907

{

3908

o = (CObservation*)g_oaObserv[z0];

3909

m = (CMolecule*)g_oaMolecules[o->m_iShowMol];

3910

for (z3=0;z3<m->m_laSingleMolIndex.GetSize();z3++)

3911

{

3912

if (g_bRegionAnalysis)

3913

if ((!o->m_iaRMRegions.Contains(0)) && (!o->m_iaRMRegions.Contains(g_iaSMRegion[m->m_laSingleMolIndex[z3]])))

3914

continue;

3915

3916

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z3]];

3917

ti = ((CxIntArray*)sm->m_oaAtomOffset[o->m_pDensityDF->m_iCenterAtomType])->GetAt(o->m_pDensityDF->m_iCenterAtom);

3918

vec0 = g_pTempTimestep->m_vaCoords[ti];

3919

3920

g_pTempTimestep->CenterPos(vec0);

3921

g_pTempTimestep->FoldAtoms();

3922

3923

for (z4=0;z4<g_oaMolecules.GetSize();z4++)

3924

{

3925

if (!o->m_pDensityDF->m_pDensityMolSelect[z4])

3926

continue;

3927

m2 = (CMolecule*)g_oaMolecules[z4];

3928

ag = o->m_pDensityDF->m_pDensityMolAG[z4];

3929

for (z5=0;z5<m2->m_laSingleMolIndex.GetSize();z5++)

3930

{

3931

if (g_bRegionAnalysis)

3932

if ((!o->m_iaOM1Regions.Contains(0)) && (!o->m_iaOM1Regions.Contains(g_iaSMRegion[m2->m_laSingleMolIndex[z5]])))

3933

continue;

3934

3935

sm2 = (CSingleMolecule*)g_oaSingleMolecules[m2->m_laSingleMolIndex[z5]];

3936

for (z6=0;z6<ag->m_baAtomType.GetSize();z6++)

3937

{

3938

if (ag->m_baRealAtomType[z6] == g_iVirtAtomType)

3939

continue;

3940

if (o->m_pDensityDF->m_bDensityMass)

3941

{

3942

tf2 = ((CAtom*)g_oaAtoms[ag->m_baRealAtomType[z6]])->m_pElement->m_fMass;

3943

for (z7=0;z7<((CxIntArray*)ag->m_oaAtoms[z6])->GetSize();z7++)

3944

{

3945

tf = g_pTempTimestep->m_vaCoords[((CxIntArray*)sm2->m_oaAtomOffset[ag->m_baAtomType[z6]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z6])->GetAt(z7))].GetLength();

3946

o->m_pDensityDF->m_pDensDF->AddToBin(tf,tf2);

3947

}

3948

} else

3949

{

3950

for (z7=0;z7<((CxIntArray*)ag->m_oaAtoms[z6])->GetSize();z7++)

3951

{

3952

tf = g_pTempTimestep->m_vaCoords[((CxIntArray*)sm2->m_oaAtomOffset[ag->m_baAtomType[z6]])->GetAt(((CxIntArray*)ag->m_oaAtoms[z6])->GetAt(z7))].GetLength();

3953

o->m_pDensityDF->m_pDensDF->AddToBin(tf);

3954

}

3955

}

3956

}

3957

}

3958

}

3959

}

3960

}

3961

} // END IF g_bDens

3962

3963

if (g_bRDyn || g_bIRSpec)

3964

{

3965

g_pTempTimestep->CopyFrom(GetTimeStep(0));

3966

for (z6=0;z6<g_oaObserv.GetSize();z6++)

3967

{

3968

o = (CObservation*)g_oaObserv[z6];

3969

if (g_bIRSpec)

3970

trdyn = o->m_pIRSpec;

3971

else trdyn = o->m_pRDyn;

3972

ti = 0;

3973

for (z3=0;z3<o->m_iShowMolCount;z3++) // Alle anderen Molekuele durchgehen

3974

{

3975

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

3976

3977

if (trdyn->m_iVecType == 0)

3978

{

3979

trdyn->BuildAtomList(sm,&templa);

3980

for (z4=0;z4<templa.GetSize();z4+=3)

3981

{

3982

if (trdyn->m_bOrtho)

3983

{

3984

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3985

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3986

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

3987

vec1 = CrossP(vec2-vec0,vec3-vec0);

3988

} else

3989

{

3990

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

3991

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

3992

vec1 = vec2-vec0;

3993

}

3994

vec1.Normalize();

3995

if (g_bRDynCacheMode)

3996

{

3997

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[0]);

3998

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[1]);

3999

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[2]);

4000

ti++;

4001

} else

4002

{

4003

for (z=0;z<trdyn->m_iDepth/trdyn->m_iStride;z++)

4004

{

4005

g_pT2Timestep = GetTimeStep(z*trdyn->m_iStride);

4006

if (g_pT2Timestep == NULL)

4007

continue;

4008

if (trdyn->m_bOrtho)

4009

{

4010

vec4 = g_pT2Timestep->m_vaCoords[templa[z4]];

4011

vec3 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

4012

vec5 = g_pT2Timestep->m_vaCoords[templa[z4+2]];

4013

vec2 = CrossP(vec3-vec4,vec5-vec4);

4014

} else

4015

{

4016

vec4 = g_pT2Timestep->m_vaCoords[templa[z4]];

4017

vec3 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

4018

vec2 = vec3-vec4;

4019

}

4020

vec2.Normalize();

4021

trdyn->m_pRDyn->AddToBin_Int(z,DotP(vec1,vec2));

4022

trdyn->m_pCount[z]++;

4023

}

4024

}

4025

}

4026

} else if (trdyn->m_iVecType == 1)

4027

{

4028

vec1 = sm->m_vDipole;

4029

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[0]);

4030

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[1]);

4031

((CxFloatArray*)trdyn->m_oaCache[ti])->Add(vec1[2]);

4032

4033

// if (z3 == 0)

4034

// mfprintf(fff,"%f, %f, %f\n",vec1[0],vec1[1],vec1[2]);

4035

4036

ti++;

4037

} // END VECTYPE

4038

}

4039

}

4040

} // END IF RDYN

4041

4042

if (g_bVACF)

4043

{

4044

g_pT2Timestep = GetTimeStep(0);

4045

// mprintf("\nStep=%d, adding.",g_iSteps);

4046

if (g_bGlobalVACF)

4047

{

4048

if (g_bVACFCacheMode)

4049

{

4050

ti = 0;

4051

for (z2=0;z2<g_iGesAtomCount;z2++)

4052

{

4053

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z2] > 1000))

4054

continue;

4055

// mprintf("Global: Step %d, Atom %d: %.4ff | %.4ff | %.4ff\n",g_iSteps,z2+1,g_pT2Timestep->m_vaVelocities[z2][0],g_pT2Timestep->m_vaVelocities[z2][1],g_pT2Timestep->m_vaVelocities[z2][2]);

4056

((CxFloatArray*)g_pGlobalVACF->m_oaCache[ti])->Add(g_pT2Timestep->m_vaVelocities[z2][0]);

4057

((CxFloatArray*)g_pGlobalVACF->m_oaCache[ti])->Add(g_pT2Timestep->m_vaVelocities[z2][1]);

4058

((CxFloatArray*)g_pGlobalVACF->m_oaCache[ti])->Add(g_pT2Timestep->m_vaVelocities[z2][2]);

4059

ti++;

4060

}

4061

} else

4062

{

4063

for (z=0;z<g_pGlobalVACF->m_iSize;z++)

4064

{

4065

g_pTempTimestep = GetTimeStep(z);

4066

if (g_pTempTimestep == NULL)

4067

continue;

4068

if (g_pTempTimestep->m_vaVelocities.GetSize() == 0)

4069

continue;

4070

pd = &g_pGlobalVACF->m_pData[z];

4071

g_pGlobalVACF->m_pCounter[z] += g_iGesAtomCount;

4072

for (z2=0;z2<g_iGesAtomCount;z2++)

4073

*pd += DotP(g_pTempTimestep->m_vaVelocities[z2],g_pT2Timestep->m_vaVelocities[z2]);

4074

}

4075

}

4076

}

4077

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4078

{

4079

o = (CObservation*)g_oaObserv[z6];

4080

for (z3=0;z3<o->m_iShowMolCount;z3++) // Alle anderen Molekuele durchgehen

4081

{

4082

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

4083

o->m_pVACF->BuildAtomList(sm,&templa);

4084

for (z4=0;z4<templa.GetSize();z4++)

4085

{

4086

if (g_bVACFCacheMode)

4087

{

4088

ti = templa[z4];

4089

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][0]);

4090

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][1]);

4091

((CxFloatArray*)o->m_pVACF->m_oaCache[z3*o->m_pVACF->m_iShowAtomGes+z4])->Add(g_pT2Timestep->m_vaVelocities[ti][2]);

4092

// mprintf("%d*%d+%d=%d\n",z3,o->m_pVACF->m_iShowAtomGes,z4,z3*o->m_pVACF->m_iShowAtomGes+z4);

4093

// mprintf("Lokal: Step %d, Atom %d: %.4ff | %.4ff | %.4ff\n",g_iSteps,ti+1,g_pT2Timestep->m_vaVelocities[ti][0],g_pT2Timestep->m_vaVelocities[ti][1],g_pT2Timestep->m_vaVelocities[ti][2]);

4094

// mprintf("Step %d: Obs %d, Mol %d, Atom %d: Index %d.\n",g_iStepHistory,z6+1,z3+1,z4+1,ti+1);

4095

} else

4096

{

4097

for (z5=0;z5<o->m_pVACF->m_iSize;z5++)

4098

{

4099

o->m_pVACF->m_pCounter[z5]++;

4100

g_pTempTimestep = GetTimeStep(z5);

4101

if (g_pTempTimestep == NULL)

4102

continue;

4103

if (g_pTempTimestep->m_vaVelocities.GetSize() == 0)

4104

continue;

4105

o->m_pVACF->m_pData[z5] += DotP(g_pTempTimestep->m_vaVelocities[templa[z4]],g_pT2Timestep->m_vaVelocities[templa[z4]]);

4106

}

4107

}

4108

}

4109

}

4110

}

4111

} // END IF VACF

4112

4113

if (g_bIRSpec && g_bGlobalIR)

4114

{

4115

for (z3=0;z3<g_oaSingleMolecules.GetSize();z3++) // Alle anderen Molekuele durchgehen

4116

{

4117

sm = (CSingleMolecule*)g_oaSingleMolecules[z3];

4118

vec1 = sm->m_vDipole;

4119

((CxFloatArray*)g_pGlobalIR->m_oaCache[z3])->Add(vec1[0]);

4120

((CxFloatArray*)g_pGlobalIR->m_oaCache[z3])->Add(vec1[1]);

4121

((CxFloatArray*)g_pGlobalIR->m_oaCache[z3])->Add(vec1[2]);

4122

}

4123

} // END IF g_bGlobalIR

4124

4125

if (g_bReact)

4126

{

4127

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4128

if (ReactSecondRun)

4129

{

4130

g_pReact->WriteTrajec(g_pTempTimestep);

4131

} else

4132

{

4133

g_pReact->ScanBonds(g_pTempTimestep,false);

4134

}

4135

}

4136

4137

if (g_bNbAnalysis)

4138

{

4139

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4140

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize();z2++)

4141

{

4142

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]];

4143

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4144

{

4145

o = (CObservation*)g_oaObserv[z6];

4146

o->m_pNbAnalysis->m_pNbSearch->ScanAllOM(smfix,g_pTempTimestep);

4147

o->m_pNbAnalysis->AnalyzeStep();

4148

}

4149

}

4150

}

4151

4152

if (g_bNbExchange)

4153

{

4154

}

4155

4156

if (g_bClusterAnalysis)

4157

{

4158

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4159

g_pClusterAnalysis->Process(g_pTempTimestep);

4160

}

4161

4162

if (g_bFESA)

4163

{

4164

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4165

g_pFESA->ProcessStep(g_pTempTimestep);

4166

}

4167

4168

if (g_bMicroHet)

4169

{

4170

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4171

g_pTempTimestep->FoldAtomsPositive();

4172

g_pMicroHet->Process(g_pTempTimestep);

4173

}

4174

4175

if (g_bThermo)

4176

{

4177

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4178

g_pThermoAnalysis->AnalyzeStep(g_pTempTimestep);

4179

}

4180

4181

if (g_bVoro)

4182

{

4183

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4184

4185

if (g_pVoroWrapper->m_bVoroStat)

4186

{

4187

g_pTempTimestep->FoldAtomsPositive();

4188

g_pVoroWrapper->Build(g_pTempTimestep);

4189

}

4190

4191

if (g_pVoroWrapper->m_bWritePOV)

4192

{

4193

// g_pVoroWrapper->WritePOV(g_pTempTimestep);

4194

// g_pTempTimestep->FoldAtomsPositive();

4195

4196

g_pVoroWrapper->PerformChoreography_Single(g_pTempTimestep);

4197

4198

if (g_pVoroWrapper->m_bWritePOVMovie)

4199

{

4200

if (g_pVoroWrapper->m_iPOVCurrentChoreographyPart >= g_pVoroWrapper->m_oaBoxChoreography.GetSize())

4201

break;

4202

} else break;

4203

}

4204

4205

if (g_pVoroWrapper->m_bSurfCover)

4206

g_pVoroWrapper->ProcessSurfCover(g_pTempTimestep);

4207

4208

if (g_pVoroWrapper->m_bVoroMetric)

4209

{

4210

if (!g_bClusterAnalysis)

4211

g_pVoroWrapper->BuildVoroMetric(g_pTempTimestep);

4212

}

4213

4214

if (g_pVoroWrapper->m_bPOVBox)

4215

{

4216

g_pTempTimestep->FoldAtomsPositive();

4217

4218

g_pVoroWrapper->PerformChoreography_Box(g_pTempTimestep);

4219

4220

if (g_pVoroWrapper->m_bWritePOVMovie)

4221

{

4222

if (g_pVoroWrapper->m_iPOVCurrentChoreographyPart >= g_pVoroWrapper->m_oaBoxChoreography.GetSize())

4223

break;

4224

} else break;

4225

}

4226

}

4227

4228

/* if (g_bSFac)

4229

{

4230

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4231

g_pSFac->ProcessStep(g_pTempTimestep);

4232

}*/

4233

4234

if (g_bVoid)

4235

{

4236

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4237

g_pTempTimestep->FoldAtomsPositive();

4238

g_pVoroAnalysis->Step(g_pTempTimestep);

4239

}

4240

4241

if (g_bVDF && (g_iFixMol == -1))

4242

{

4243

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4244

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4245

{

4246

o = (CObservation*)g_oaObserv[z6];

4247

for (z3=0;z3<o->m_iShowMolCount;z3++) // Alle anderen Molekuele durchgehen

4248

{

4249

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

4250

o->m_pVDF[0]->BuildAtomList(NULL,sm,&templa);

4251

4252

for (z4=0;z4<templa.GetSize();z4++)

4253

o->m_pVDF[0]->m_pVDF->AddToBin(g_pTempTimestep->m_vaVelocities[templa[z4]].GetLength());

4254

}

4255

}

4256

}

4257

4258

if ((!g_bCDF) && (!g_bRDF) && (!g_bSDF) && (!g_bPlProj) && (!g_bPlDF) && (!g_bLiDF) && (!g_bVoidSDF) && (!g_bADF) && (!g_bDDF) && (!g_bVDF) && (!g_bDipDF) && (!g_bCutCluster) && (!g_bSaveRefEnv) && (!g_bVHDF) && (!g_bRevSDF) && (!g_bCond))

4259

goto _endstep;

4260

4261

if (g_bVoid)

4262

{

4263

if (g_bVoidSDF && g_pVoroAnalysis->m_bEmptySpaceSDF && g_pVoroAnalysis->m_bNewEmptyMode)

4264

{

4265

g_pVoroAnalysis->m_pTempSDF->Clear();

4266

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4267

g_pTempTimestep->FoldAtomsPositive();

4268

for (z3=0;z3<g_iGesAtomCount;z3++)

4269

{

4270

vec0 = g_pTempTimestep->m_vaCoords[z3];

4271

g_pVoroAnalysis->m_pTempSDF->AddToBin_SphereWrap(vec0,g_faVdWRadius[z3]);

4272

}

4273

// g_pVoroAnalysis->m_pTempSDF->WritePLT("","bla.plt","",true);

4274

}

4275

}

4276

4277

// tfr = 9999.0;

4278

4279

if (g_iFixMol == -1)

4280

goto _norefmol;

4281

4282

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4283

{

4284

o = (CObservation*)g_oaObserv[z6];

4285

4286

if (o->m_pConditions != NULL)

4287

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

4288

o->m_pConditions->m_iPassCounter[z2] = 0;

4289

4290

if (o->m_pConditionsOM2 != NULL)

4291

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

4292

o->m_pConditionsOM2->m_iPassCounter[z2] = 0;

4293

}

4294

4295

// Jedes Festhalte-Molekuel mal im Ursprung liegen lassen

4296

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize();z2++)

4297

{

4298

if (g_bDoubleBox && (z2 >= ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()/g_iDoubleBoxFactor))

4299

continue;

4300

4301

smfix = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]];

4302

4303

if (g_bCutCluster)

4304

{

4305

if (g_iClusterPos >= g_iClusterCount)

4306

break;

4307

4308

if (((int)g_iSteps/g_iStride) >= g_iClusterSteps)

4309

break;

4310

4311

if (g_iaClusterMol[g_iClusterPos] != z2)

4312

continue;

4313

4314

if (g_iaClusterSteps[g_iClusterPos] != ((int)g_iSteps/g_iStride))

4315

break;

4316

4317

g_iClusterPos++;

4318

}

4319

4320

g_pTempTimestep->CopyFrom(GetTimeStep(0));

4321

4322

// Zentrieren/Falten der ganzen Box nur noch noetig bei den folgenden Analysen

4323

if (g_bPlProj || g_bSDF || g_bRevSDF || g_bCutCluster || g_bSaveRefEnv || g_bSaveJustTraj || g_bVoidSDF || g_bMiddleAvg)

4324

{

4325

vecc = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

4326

4327

if ((g_bCutCluster && !g_bRefEnvCenter) || (g_bSaveRefEnv && (!g_bRefEnvCenter) && (z2==g_iSaveRefMol)))

4328

{

4329

if (g_bFold)

4330

{

4331

g_pTempTimestep->CenterPos(vecc);

4332

4333

if (g_bFoldAtomwise)

4334

g_pTempTimestep->FoldAtoms();

4335

else g_pTempTimestep->FoldMolecules();

4336

4337

vec2 = -1.0f * vecc;

4338

4339

g_pTempTimestep->CenterPos(vec2);

4340

}

4341

4342

if (g_bCutCluster || (g_iNbhMode == 2))

4343

{

4344

g_pNbSet->Reset();

4345

4346

if (g_bCutCluster)

4347

g_pNbSet->ResetAlwaysTrue();

4348

4349

g_pNbSet->Scan(smfix,g_pTempTimestep);

4350

4351

if (g_bSaveRefWithEnv)

4352

g_pNbSet->AddMolecule(g_iFixMol,z2);

4353

}

4354

4355

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet);

4356

4357

if (g_bTDO)

4358

{

4359

if (g_laTDOSteps.Contains(g_iSteps-1))

4360

{

4361

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

4362

mprintf("\nSaving TDO step as %s.\n",buf);

4363

tfi = OpenFileWrite(buf,true);

4364

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

4365

fclose(tfi);

4366

}

4367

}

4368

}

4369

4370

// Legt vecc genau in den Ursprung des Koordinatensystems

4371

g_pTempTimestep->CenterPos(vecc);

4372

4373

4374

if ((g_bCutCluster && g_bRefEnvCenter && (!g_bRefEnvFix)) || (g_bSaveRefEnv && g_bRefEnvCenter && (!g_bRefEnvFix) && (z2==g_iSaveRefMol)))

4375

{

4236

4376

if (g_bFold)

4237

4377

{

4238

g_pTempTimestep->CenterPos(vecc);

4239

4240

4378

if (g_bFoldAtomwise)

4241

4379

g_pTempTimestep->FoldAtoms();

4242

4380

else g_pTempTimestep->FoldMolecules();

4243

4244

vec2 = -1.0f * vecc;

4245

4246

g_pTempTimestep->CenterPos(vec2);

4247

}

4248

4249

if (g_bCutCluster || (g_iNbhMode == 2))

4250

{

4251

g_pNbSet->Reset();

4252

4253

if (g_bCutCluster)

4254

g_pNbSet->ResetAlwaysTrue();

4255

4256

g_pNbSet->Scan(smfix,g_pTempTimestep);

4257

4258

if (g_bSaveRefWithEnv)

4259

g_pNbSet->AddMolecule(g_iFixMol,z2);

4260

}

4261

4262

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet);

4263

4264

if (g_bTDO)

4265

{

4266

if (g_laTDOSteps.Contains(g_iSteps-1))

4381

}

4382

4383

if (g_bCutCluster || (g_iNbhMode == 2))

4384

{

4385

g_pNbSet->Reset();

4386

4387

if (g_bCutCluster)

4388

g_pNbSet->ResetAlwaysTrue();

4389

4390

g_pNbSet->Scan(smfix,g_pTempTimestep);

4391

4392

if (g_bSaveRefWithEnv)

4393

g_pNbSet->AddMolecule(g_iFixMol,z2);

4394

}

4395

4396

if (!g_bCenterZero && g_bPeriodic)

4397

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

4398

4399

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet,((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]);

4400

4401

if (g_bTDO)

4402

{

4403

if (g_laTDOSteps.Contains(g_iSteps-1))

4404

{

4405

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

4406

mprintf("\nSaving TDO step as %s.\n",buf);

4407

tfi = OpenFileWrite(buf,true);

4408

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

4409

fclose(tfi);

4410

}

4411

}

4412

}

4413

4414

if (g_bPlProj || g_bSDF || g_bVoidSDF || g_bAvg || ((g_bSaveRefEnv || g_bCutCluster) && g_bRefEnvCenter && g_bRefEnvFix)) // Wir brauchen ein neues Koordinatensystem und eine Drehmatrix

4415

{

4416

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

4417

vec3 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

4418

mat.MatUltra(vec2,vec3); // Dies erstellt uns die Drehmatrix

4419

g_pTempTimestep->Transform(mat);

4420

4421

if (g_bPlProj)

4422

{

4423

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4267

4424

{

4268

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

4269

mprintf("\nSaving TDO step as %s.\n",buf);

4270

tfi = OpenFileWrite(buf,true);

4271

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

4272

fclose(tfi);

4425

o = (CObservation*)g_oaObserv[z6];

4426

4427

if (o->m_pPlProj->m_bAverageAtomPos)

4428

{

4429

o->m_pPlProj->m_iAverageCounter++;

4430

ti = 0;

4431

for (z3=0;z3<o->m_pPlProj->m_oDrawAtoms.m_oaAtoms.GetSize();z3++)

4432

{

4433

for (z4=0;z4<((CxIntArray*)o->m_pPlProj->m_oDrawAtoms.m_oaAtoms[z3])->GetSize();z4++)

4434

{

4435

o->m_pPlProj->m_vaAtomPos[ti] += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[o->m_pPlProj->m_oDrawAtoms.m_baAtomType[z3]])->GetAt(((CxIntArray*)o->m_pPlProj->m_oDrawAtoms.m_oaAtoms[z3])->GetAt(z4))];

4436

ti++;

4437

}

4438

}

4439

}

4273

4440

}

4274

4441

}

4275

4442

}

4276

4277

// Legt vecc genau in den Ursprung des Koordinatensystems

4278

g_pTempTimestep->CenterPos(vecc);

4279

4443

4280

4444

if (g_bFold)

4281

4445

{

4282

4446

if (g_bFoldAtomwise)

4284

4448

else g_pTempTimestep->FoldMolecules();

4285

4449

}

4286

4450

4287

if ((g_bCutCluster && g_bRefEnvCenter && (!g_bRefEnvFix)) || (g_bSaveRefEnv && g_bRefEnvCenter && (!g_bRefEnvFix) && (z2==g_iSaveRefMol)))

4288

{

4289

if (g_bCutCluster || (g_iNbhMode == 2))

4290

{

4291

g_pNbSet->Reset();

4292

4293

if (g_bCutCluster)

4294

g_pNbSet->ResetAlwaysTrue();

4295

4296

g_pNbSet->Scan(smfix,g_pTempTimestep);

4297

4298

if (g_bSaveRefWithEnv)

4299

g_pNbSet->AddMolecule(g_iFixMol,z2);

4300

}

4301

4302

if (!g_bCenterZero && g_bPeriodic)

4303

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

4304

4305

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet,((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]);

4306

4307

if (g_bTDO)

4308

{

4309

if (g_laTDOSteps.Contains(g_iSteps-1))

4310

{

4311

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

4312

mprintf("\nSaving TDO step as %s.\n",buf);

4313

tfi = OpenFileWrite(buf,true);

4314

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

4315

fclose(tfi);

4316

}

4317

}

4318

}

4319

4320

if (g_bSDF || g_bVoidSDF || g_bAvg || ((g_bSaveRefEnv || g_bCutCluster) && g_bRefEnvCenter && g_bRefEnvFix)) // Wir brauchen ein neues Koordinatensystem und eine Drehmatrix

4321

{

4322

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

4323

vec3 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

4324

mat.MatUltra(vec2,vec3); // Dies erstellt uns die Drehmatrix

4325

g_pTempTimestep->Transform(mat);

4326

}

4327

4328

if ((g_bCutCluster && g_bRefEnvCenter && g_bRefEnvFix) || (g_bSaveRefEnv && g_bRefEnvCenter && g_bRefEnvFix && (z2==g_iSaveRefMol)))

4329

{

4330

if (g_bCutCluster || (g_iNbhMode == 2))

4331

{

4332

g_pNbSet->Reset();

4333

if (g_bCutCluster)

4334

g_pNbSet->ResetAlwaysTrue();

4335

g_pNbSet->Scan(smfix,g_pTempTimestep);

4336

if (g_bSaveRefWithEnv)

4337

g_pNbSet->AddMolecule(g_iFixMol,z2);

4338

}

4339

4340

if (!g_bCenterZero && g_bPeriodic)

4341

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

4342

4343

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet,((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]);

4344

4345

if (g_bTDO)

4346

{

4347

if (g_laTDOSteps.Contains(g_iSteps-1))

4348

{

4349

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

4350

mprintf("\nSaving TDO step as %s.\n",buf);

4351

tfi = OpenFileWrite(buf,true);

4352

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

4353

fclose(tfi);

4354

}

4355

}

4356

}

4357

} // END IF SDF, RevEnv, ...

4358

4359

/***************************************************************************************************************************/

4360

4361

if (g_bVoidSDF)

4362

{

4363

if (g_pVoroAnalysis->m_bEmptySpaceSDF)

4364

{

4365

if (!g_pVoroAnalysis->m_bNewEmptyMode)

4366

{

4367

g_pVoroAnalysis->m_pTempSDF->Clear();

4368

4369

for (z3=0;z3<g_oaMolecules.GetSize();z3++)

4370

{

4371

tm = (CMolecule*)g_oaMolecules[z3];

4372

for (z4=0;z4<tm->m_laSingleMolIndex.GetSize();z4++)

4373

{

4374

if (!g_pVoroAnalysis->m_bEmptySpaceSDF_RefMol)

4375

if ((z3 == g_iFixMol) && (z4 == z2))

4376

continue;

4377

4378

tsm = (CSingleMolecule*)g_oaSingleMolecules[tm->m_laSingleMolIndex[z4]];

4379

4380

for (z5=0;z5<tsm->m_oaAtomOffset.GetSize();z5++)

4381

{

4382

if (tm->m_baAtomIndex[z5] == g_iVirtAtomType)

4383

continue;

4384

4385

for (z6=0;z6<((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetSize();z6++)

4386

{

4387

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetAt(z6)];

4388

4389

g_pVoroAnalysis->m_pTempSDF->AddToBin_Sphere(vec0,g_faVdWRadius[((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetAt(z6)]);

4390

}

4391

}

4392

}

4393

}

4394

g_pVoroAnalysis->BinEmptySDF_New(&mat,&vecc);

4395

} else

4396

{

4397

g_pVoroAnalysis->BinEmptySDF();

4398

}

4399

}

4400

4401

if (g_pVoroAnalysis->m_bSphereHoleSDF)

4402

{

4403

g_pVoroAnalysis->BinSphereHoleSDF(&mat,&vecc);

4404

}

4405

}

4406

4407

if (g_bDipDF || g_bRevSDF || g_bVHDF || g_bRDF || g_bPlDF || g_bLiDF || g_bSDF || g_bADF || g_bDDF || g_bVDF || g_bCond)

4408

{

4409

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4410

{

4411

o = (CObservation*)g_oaObserv[z6];

4412

4413

// mprintf("\nStep %d, z2=%d, Obs=%d, Reg=%d, ObsReg=%d.",g_iSteps,z2,z6,g_iaSMRegion[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]],o->m_iaRMRegions[0]);

4414

4415

if (g_bRegionAnalysis)

4416

if ((!o->m_iaRMRegions.Contains(0)) && (!o->m_iaRMRegions.Contains(g_iaSMRegion[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])))

4417

continue;

4418

4419

// mprintf("\n ...RM ist in Region.");

4420

4421

ti2 = o->m_waSaveRefList.GetPosition(z2);

4422

4423

if (o->m_bObsCertain)

4424

{

4425

// mprintf("\n RefList: ");

4426

// for (z7=0;z7<o->m_waObsRefList.GetSize();z7++)

4427

// mprintf("%d, ",o->m_waObsRefList[z7]);

4428

4429

if (!o->m_waObsRefList.Contains(z2))

4430

continue;

4431

// mprintf("\n ...RM ist auch in RefList.");

4432

tic_r = o->m_waObsRefList.GetPosition(z2);

4433

}

4434

4435

if (g_bUseVelocities)

4436

{

4437

tempvel.CopyFrom(&g_pTempTimestep->m_vaVelocities);

4438

if (o->m_bVelocityRelToRef)

4439

{

4440

vecv = g_pTempTimestep->m_vaVelocities[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

4441

for (z3=0;z3<g_iGesVirtAtomCount;z3++)

4442

tempvel[z3] -= vecv;

4443

}

4444

}

4445

4446

if ((g_bCDF) && (o->m_bTimeDev) && (ti2 != -1))

4447

{

4448

if (o->m_bSaveSeparateFiles)

4449

mfprintf(o->m_pCDF->m_fTimeDev[ti2],"%d",(int)g_iSteps);

4450

else if (ti2 == 0)

4451

mfprintf(o->m_pCDF->m_fTimeDev[0],"%d",(int)g_iSteps);

4452

}

4453

4454

for (zr=0;zr<g_iCDFChannels;zr++)

4455

{

4456

if (g_bRDF && (o->m_pRDF[zr] != NULL))

4457

{

4458

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4459

o->m_pRDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4460

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4461

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4462

o->m_pRDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4463

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4464

{

4465

if (o->m_bSaveSeparateFiles)

4466

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"%d",(int)g_iSteps);

4467

else if (ti2 == 0)

4468

mfprintf(o->m_pRDF[zr]->m_fDist[0],"%d",(int)g_iSteps);

4469

}

4470

}

4471

4472

if (g_bADF && (o->m_pADF[zr] != NULL))

4473

{

4474

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4475

o->m_pADF[zr]->m_faData[z3].RemoveAll_KeepSize();

4476

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4477

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4478

o->m_pADF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4479

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4480

{

4481

if (o->m_bSaveSeparateFiles)

4482

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

4483

else if (ti2 == 0)

4484

mfprintf(o->m_pADF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

4485

}

4486

}

4487

4488

if (g_bDDF && (o->m_pDDF[zr] != NULL))

4489

{

4490

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4491

o->m_pDDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4492

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4493

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4494

o->m_pDDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4495

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4496

{

4497

if (o->m_bSaveSeparateFiles)

4498

mfprintf(o->m_pDDF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

4499

else if (ti2 == 0)

4500

mfprintf(o->m_pDDF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

4501

}

4502

}

4503

4504

if (g_bPlDF && (o->m_pPlDF[zr] != NULL))

4505

{

4506

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4507

o->m_pPlDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4508

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4509

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4510

o->m_pPlDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4511

/* if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4512

{

4513

if (o->m_bSaveSeparateFiles)

4514

mfprintf(o->m_pPlDF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

4515

else if (ti2 == 0)

4516

mfprintf(o->m_pDDF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

4517

}*/

4518

}

4519

4520

if (g_bLiDF && (o->m_pLiDF[zr] != NULL))

4521

{

4522

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4523

o->m_pLiDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4524

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4525

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4526

o->m_pLiDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4527

/* if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4528

{

4529

if (o->m_bSaveSeparateFiles)

4530

mfprintf(o->m_pPlDF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

4531

else if (ti2 == 0)

4532

mfprintf(o->m_pDDF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

4533

}*/

4534

}

4535

4536

if (g_bDipDF && (o->m_pDipDF[zr] != NULL))

4537

{

4538

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4539

o->m_pDipDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4540

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4541

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4542

o->m_pDipDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4543

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4544

{

4545

if (o->m_bSaveSeparateFiles)

4546

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"%d",(int)g_iSteps);

4547

else if (ti2 == 0)

4548

mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"%d",(int)g_iSteps);

4549

}

4550

}

4551

4552

if (g_bVDF && (o->m_pVDF[zr] != NULL))

4553

{

4554

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4555

o->m_pVDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4556

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4557

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4558

o->m_pVDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4559

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4560

{

4561

if (o->m_bSaveSeparateFiles)

4562

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"%d",(int)g_iSteps);

4563

else if (ti2 == 0)

4564

mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"%d",(int)g_iSteps);

4565

}

4566

}

4567

} // END FOR zr

4568

4569

if (g_bSDF)

4570

{

4571

for (z3=0;z3<o->m_iShowMolCount;z3++)

4572

{

4573

o->m_pSDF->m_vaData[z3].RemoveAll_KeepSize();

4574

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4575

o->m_pSDF->m_baDataEnabled[z3].RemoveAll_KeepSize();

4576

}

4577

}

4578

4579

if (g_bRevSDF)

4580

{

4581

for (z3=0;z3<o->m_iShowMolCount;z3++)

4582

{

4583

o->m_pRevSDF->m_vaData[z3].RemoveAll_KeepSize();

4584

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4585

o->m_pRevSDF->m_baDataEnabled[z3].RemoveAll_KeepSize();

4586

}

4587

}

4588

4589

if (o->m_bSelf)

4590

{

4591

if (g_bADF)

4592

{

4593

for (zr=0;zr<g_iCDFChannels;zr++)

4594

{

4595

if (o->m_pADF[zr] == NULL)

4596

continue;

4597

o->m_pADF[zr]->BuildAtomList(smfix,NULL,&templa);

4598

for (z4=0;z4<templa.GetSize();z4+=6)

4599

{

4600

if (o->m_pADF[zr]->m_bOrtho[0])

4601

{

4602

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4603

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4604

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

4605

vec1 = CrossP(FoldVector(vec2-vec0),FoldVector(vec3-vec0));

4606

} else

4607

{

4608

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4609

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4610

vec1 = FoldVector(vec2-vec0);

4611

}

4612

if (o->m_pADF[zr]->m_bOrtho[1])

4613

{

4614

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4615

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4616

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

4617

vec2 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

4618

} else

4619

{

4620

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4621

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4622

vec2 = FoldVector(vec3-vec4);

4623

}

4624

tf = Angle_Deg(vec1,vec2);

4625

if ((tf > 90.0f) && (o->m_pADF[zr]->m_bFoldAngle))

4626

tf = 180.0f-tf;

4627

if (o->m_pADF[zr]->m_bCosine)

4628

tf = cos(tf/180.0*Pi);

4629

4630

if (g_bDeriv)

4631

{

4632

o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) = tf;

4633

switch(o->m_pADF[zr]->m_iDeriv)

4634

{

4635

case 0:

4636

tf = o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6);

4637

break;

4638

case 1:

4639

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) - o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6)) / (2*g_fTimestepLength);

4640

break;

4641

case 2:

4642

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) + o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) - 2*o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6)) / (g_fTimestepLength * g_fTimestepLength);

4643

break;

4644

}

4645

}

4646

4647

if (!g_bDeriv || (g_iSteps > 2))

4648

{

4649

if (o->m_bObsCertain && o->m_bDecompDist)

4650

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r,tf);

4651

4652

o->m_pADF[zr]->m_faData[0].Add(tf);

4653

4654

if (o->m_pADF[zr]->m_bACF)

4655

o->m_pADF[zr]->m_pfaACFBuffer[z2*o->m_pADF[zr]->m_iCombinations+z4/6]->Add((float)tf);

4656

4657

/* if (o->m_pADF[zr]->m_bMirror)

4658

{

4659

if (o->m_bObsCertain && o->m_bDecompDist)

4660

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r,180.0-tf);

4661

o->m_pADF[zr]->m_faData[0].Add(180.0-tf);

4662

}*/

4663

4664

if (o->m_bTimeDev && (ti2 != -1))

4665

{

4666

if (o->m_bSaveSeparateFiles)

4667

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"; %8.3f",tf);

4668

else mfprintf(o->m_pADF[zr]->m_fAngle[0],"; %8.3f",tf);

4669

if (o->m_bCombinedPlot)

4670

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pADF[zr]->m_iCombinations+z4/6,g_iSteps*g_fTimestepLength/1000.0,tf);

4671

}

4672

if (o->m_bTimeDiff)

4673

((CxFloatArray*)o->m_pADF[zr]->m_pADF->m_oaTimeDiffBuf[z2*o->m_pADF[zr]->m_iCombinations+z4/6])->Add((float)tf);

4674

}

4675

} // END FOR z4

4676

} // END FOR zr

4677

} // Ende IF ADF

4678

4679

if (g_bDDF)

4680

{

4681

for (zr=0;zr<g_iCDFChannels;zr++)

4682

{

4683

if (o->m_pDDF[zr] == NULL)

4684

continue;

4685

o->m_pDDF[zr]->BuildAtomList(smfix,smfix,&templa);

4686

for (z4=0;z4<templa.GetSize();z4+=9)

4687

{

4688

if (o->m_pDDF[zr]->m_bOrtho[0])

4689

{

4690

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4691

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4692

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

4693

vec1 = CrossP(FoldVector(vec2-vec0),FoldVector(vec3-vec0));

4694

} else

4695

{

4696

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4697

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4698

vec1 = FoldVector(vec2-vec0);

4699

}

4700

if (o->m_pDDF[zr]->m_bOrtho[1])

4701

{

4702

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4703

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4704

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

4705

vec2 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

4706

} else

4707

{

4708

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4709

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4710

vec2 = FoldVector(vec3-vec4);

4711

}

4712

if (o->m_pDDF[zr]->m_bOrtho[2])

4713

{

4714

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

4715

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

4716

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+8]];

4717

vec3 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

4718

} else

4719

{

4720

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

4721

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

4722

vec3 = FoldVector(vec3-vec4);

4723

}

4724

tf = Dihedral(vec1,vec2,vec3,o->m_pDDF[zr]->m_bAbs);

4725

if (o->m_pDDF[zr]->m_bCosine)

4726

tf = cos(tf/180.0*Pi);

4727

else if (o->m_pDDF[zr]->m_bPositive)

4728

if (tf < 0)

4729

tf += 360.0;

4730

if (g_bDeriv)

4731

{

4732

o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) = tf;

4733

switch(o->m_pDDF[zr]->m_iDeriv)

4734

{

4735

case 0:

4736

tf = o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9);

4737

break;

4738

case 1:

4739

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) - o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9)) / (2*g_fTimestepLength);

4740

break;

4741

case 2:

4742

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) + o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) - 2*o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9)) / (g_fTimestepLength * g_fTimestepLength);

4743

break;

4744

}

4745

}

4746

if (!g_bDeriv || (g_iSteps > 2))

4747

{

4748

if (o->m_bObsCertain && o->m_bDecompDist)

4749

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r,tf);

4750

4751

o->m_pDDF[zr]->m_faData[0].Add(tf);

4752

4753

if (o->m_pDDF[zr]->m_bACF)

4754

o->m_pDDF[zr]->m_pfaACFBuffer[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]->Add((float)tf);

4755

4756

if (/*(!o->m_pDDF[zr]->m_bAbs) && */o->m_pDDF[zr]->m_bSymm)

4757

{

4758

o->m_pDDF[zr]->m_faData[0].Add(-tf);

4759

if (o->m_bObsCertain && o->m_bDecompDist)

4760

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r,-tf);

4761

}

4762

4763

if (o->m_bTimeDiff)

4764

((CxFloatArray*)o->m_pDDF[zr]->m_pDDF->m_oaTimeDiffBuf[z2*o->m_pDDF[zr]->m_iCombinations+z4/9])->Add((float)tf);

4765

4766

if (o->m_bTimeDev && (ti2 != -1))

4767

{

4768

if (o->m_pDDF[zr]->m_bRotate)

4769

{

4770

if (g_iSteps > 1)

4771

{

4772

if ((tf - o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]) > 180.0)

4773

o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]--;

4774

if ((tf - o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]) < -180.0)

4775

o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]++;

4776

}

4777

o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9] = tf;

4778

tf2 = tf + o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9] * 360.0;

4779

} else tf2 = tf;

4780

if (o->m_bSaveSeparateFiles)

4781

mfprintf(o->m_pDDF[zr]->m_fAngle[ti2],"; %8.3f",tf2);

4782

else mfprintf(o->m_pDDF[zr]->m_fAngle[0],"; %8.3f",tf2);

4783

if (o->m_bCombinedPlot)

4784

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pDDF[zr]->m_iCombinations+z4/9,g_iSteps*g_fTimestepLength/1000.0,tf);

4785

}

4786

}

4787

}

4788

}

4789

} // END IF DDF

4790

4791

if (g_bVHDF)

4792

{

4793

o->m_pVHDF->BuildAtomList(smfix,smfix,&templa);

4794

for (z4=0;z4<templa.GetSize();z4+=2)

4795

{

4796

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];// + vecc;

4797

for (z0=0;z0<o->m_pVHDF->m_iDepth/o->m_pVHDF->m_iStride;z0++)

4798

{

4799

g_pT2Timestep = GetTimeStep(z0*o->m_pVHDF->m_iStride);

4800

if (g_pT2Timestep == NULL)

4801

continue;

4802

vec1 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

4803

tf = FoldedLength(vec0-vec1);

4804

o->m_pVHDF->m_pVHDF->AddToBin_IntX_fast(z0,tf);

4805

o->m_pVHDF->m_pCount[z0]++;

4806

}

4807

}

4808

} // Ende IF VHDF

4809

4810

if (g_bRDF)

4811

{

4812

for (zr=0;zr<g_iCDFChannels;zr++)

4813

{

4814

if (o->m_pRDF[zr] == NULL)

4815

continue;

4816

o->m_pRDF[zr]->BuildAtomList(smfix,smfix,&templa);

4817

for (z4=0;z4<templa.GetSize();z4+=2)

4818

{

4819

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4820

vec1 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4821

tf = FoldedLength(vec0-vec1);

4822

if (g_bDeriv)

4823

{

4824

o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) = tf;

4825

switch(o->m_pRDF[zr]->m_iDeriv)

4826

{

4827

case 0:

4828

tf = o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2);

4829

break;

4830

case 1:

4831

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) - o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2)) / (2*g_fTimestepLength);

4832

break;

4833

case 2:

4834

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) + o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) - 2*o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2)) / (g_fTimestepLength * g_fTimestepLength);

4835

break;

4836

}

4837

}

4838

if (!g_bDeriv || (g_iSteps > 2))

4839

{

4840

if (o->m_bObsCertain && o->m_bDecompDist)

4841

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(tic_r,tf);

4842

4843

if (o->m_bDecompType)

4844

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(o->m_waDecompTypeRefOffs[templa[z4]]*o->m_waDecompTypeObsOffs.GetSize()+o->m_waDecompTypeObsOffs[templa[z4+1]],tf);

4845

4846

o->m_pRDF[zr]->m_faData[0].Add(tf);

4847

4848

if (o->m_pRDF[zr]->m_bACF)

4849

o->m_pRDF[zr]->m_pfaACFBuffer[z2*o->m_pRDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

4850

4851

if (o->m_bTimeDev && (ti2 != -1))

4852

{

4853

if (o->m_bSaveSeparateFiles)

4854

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"; %10.3f",tf);

4855

else mfprintf(o->m_pRDF[zr]->m_fDist[0],"; %10.3f",tf);

4856

if (o->m_bCombinedPlot)

4857

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pRDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

4858

}

4859

if (o->m_bTimeDiff)

4860

((CxFloatArray*)o->m_pRDF[zr]->m_pRDF->m_oaTimeDiffBuf[z2*o->m_pRDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

4861

}

4862

}

4863

}

4864

} // Ende IF RDF

4865

4866

if (g_bPlDF)

4867

{

4868

for (zr=0;zr<g_iCDFChannels;zr++)

4869

{

4870

if (o->m_pPlDF[zr] == NULL)

4871

continue;

4872

o->m_pPlDF[zr]->BuildAtomList(smfix,smfix,&templa);

4873

for (z4=0;z4<templa.GetSize();z4+=4)

4874

{

4875

if (o->m_pPlDF[zr]->m_bNormal)

4876

{

4877

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4878

vec0.Normalize();

4879

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4880

tf = DotP(vec0,vec1);

4881

} else

4882

{

4883

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4884

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+2]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4885

vec3 = CrossP(vec0,vec1);

4886

vec3.Normalize();

4887

vec2 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4888

tf = DotP(vec2,vec3);

4889

}

4890

4891

if (!g_bDeriv || (g_iSteps > 2))

4892

{

4893

if (o->m_bObsCertain && o->m_bDecompDist)

4894

o->m_pPlDF[zr]->m_pPlDF->AddToBin_Multi(tic_r,tf);

4895

4896

o->m_pPlDF[zr]->m_faData[0].Add(tf);

4897

}

4898

}

4899

}

4900

} // END IF PlDF

4901

4902

if (g_bLiDF)

4903

{

4904

for (zr=0;zr<g_iCDFChannels;zr++)

4905

{

4906

if (o->m_pLiDF[zr] == NULL)

4907

continue;

4908

o->m_pLiDF[zr]->BuildAtomList(smfix,smfix,&templa);

4909

for (z4=0;z4<templa.GetSize();z4+=4)

4910

{

4911

if (o->m_pLiDF[zr]->m_bNormal)

4912

{

4913

vec2 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4914

vec3 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+2]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4915

vec0 = CrossP(vec2,vec3);

4916

vec0.Normalize();

4917

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4918

vec0 *= DotP(vec0,vec1);

4919

tf = (vec1 - vec0).GetLength();

4920

} else

4921

{

4922

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4923

vec0.Normalize();

4924

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

4925

vec0 *= DotP(vec0,vec1);

4926

tf = (vec1 - vec0).GetLength();

4927

}

4928

4929

if (!g_bDeriv || (g_iSteps > 2))

4930

{

4931

if (o->m_bObsCertain && o->m_bDecompDist)

4932

o->m_pLiDF[zr]->m_pLiDF->AddToBin_Multi(tic_r,tf);

4933

4934

o->m_pLiDF[zr]->m_faData[0].Add(tf);

4935

}

4936

}

4937

}

4938

} // END IF LiDF

4939

4940

if (g_bDipDF)

4941

{

4942

for (zr=0;zr<g_iCDFChannels;zr++)

4943

{

4944

if (o->m_pDipDF[zr] == NULL)

4945

continue;

4946

tf = smfix->m_vDipole.GetLength();

4947

if (g_bDeriv)

4948

{

4949

o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2) = tf;

4950

switch(o->m_pDipDF[zr]->m_iDeriv)

4951

{

4952

case 0:

4953

tf = o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2);

4954

break;

4955

case 1:

4956

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2) - o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2)) / (2*g_fTimestepLength);

4957

break;

4958

case 2:

4959

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2) + o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2) - 2*o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2)) / (g_fTimestepLength * g_fTimestepLength);

4960

break;

4961

}

4962

}

4963

if (!g_bDeriv || (g_iSteps > 2))

4964

{

4965

if (o->m_bObsCertain && o->m_bDecompDist)

4966

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin_Multi(tic_r,tf);

4967

4968

o->m_pDipDF[zr]->m_faData[0].Add(tf);

4969

4970

if (o->m_pDipDF[zr]->m_bACF)

4971

o->m_pDipDF[zr]->m_pfaACFBuffer[z2]->Add((float)tf);

4972

4973

if (o->m_bTimeDev && (ti2 != -1))

4974

{

4975

if (o->m_bSaveSeparateFiles)

4976

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; %8.3f",tf);

4977

else mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"; %8.3f",tf);

4978

if (o->m_bCombinedPlot)

4979

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->AddXYTupel(ti2,g_iSteps*g_fTimestepLength/1000.0,tf);

4980

}

4981

if (o->m_bTimeDiff)

4982

((CxFloatArray*)o->m_pDipDF[zr]->m_pDipoleDF->m_oaTimeDiffBuf[z2])->Add((float)tf);

4983

}

4984

}

4985

} // Ende IF DIPDF

4986

4987

if (g_bVDF)

4988

{

4989

for (zr=0;zr<g_iCDFChannels;zr++)

4990

{

4991

if (o->m_pVDF[zr] == NULL)

4992

continue;

4993

o->m_pVDF[zr]->BuildAtomList(smfix,smfix,&templa);

4994

for (z4=0;z4<templa.GetSize();z4++)

4995

{

4996

tf = tempvel[templa[z4]].GetLength();

4997

if (g_bDeriv)

4998

{

4999

o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) = tf;

5000

switch(o->m_pVDF[zr]->m_iDeriv)

5001

{

5002

case 0:

5003

tf = o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2);

5004

break;

5005

case 1:

5006

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) - o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2)) / (2*g_fTimestepLength);

5007

break;

5008

case 2:

5009

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) + o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) - 2*o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2)) / (g_fTimestepLength * g_fTimestepLength);

5010

break;

5011

}

5012

}

5013

if (!g_bDeriv || (g_iSteps > 2))

5014

{

5015

if (o->m_bObsCertain && o->m_bDecompDist)

5016

o->m_pVDF[zr]->m_pVDF->AddToBin_Multi(tic_r,tf);

5017

5018

o->m_pVDF[zr]->m_faData[0].Add(tf);

5019

5020

if (o->m_pVDF[zr]->m_bACF)

5021

o->m_pVDF[zr]->m_pfaACFBuffer[z2*o->m_pVDF[zr]->m_iCombinations+z4]->Add((float)tf);

5022

5023

if (o->m_bTimeDev && (ti2 != -1))

5024

{

5025

if (o->m_bSaveSeparateFiles)

5026

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; %8.3f",tf);

5027

else mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"; %8.3f",tf);

5028

if (o->m_bCombinedPlot)

5029

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pVDF[zr]->m_iCombinations+z4,g_iSteps*g_fTimestepLength/1000.0,tf);

5030

}

5031

if (o->m_bTimeDiff)

5032

((CxFloatArray*)o->m_pVDF[zr]->m_pVDF->m_oaTimeDiffBuf[z2*o->m_pVDF[zr]->m_iCombinations+z4])->Add((float)tf);

5033

}

5034

}

5035

}

5036

} // Ende IF VDF

5037

5038

if (g_bSDF)

5039

{

5040

o->m_pSDF->BuildAtomList(smfix,smfix,&templa);

5041

for (z4=0;z4<templa.GetSize();z4++)

5042

{

5043

o->m_pSDF->m_vaData[0].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

5044

5045

if (o->m_pSDF->m_bVdWSpheres)

5046

o->m_pSDF->m_faRadius[0].Add(g_faVdWRadius[templa[z4]]);

5047

}

5048

} // Ende IF SDF

5049

5050

if (g_bRevSDF)

5051

{

5052

o->m_pRevSDF->BuildAtomList(smfix,smfix,&templa);

5053

for (z4=0;z4<templa.GetSize();z4++)

5054

o->m_pRevSDF->m_vaData[0].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

5055

} // Ende IF RevSDF

5056

5057

} // Ende IF m_bSelf

5058

5059

if (o->m_bOthers)

5060

{

5061

secondmolrun = false;

5062

_secondmolstart:

5063

if ((!secondmolrun) && (o->m_pConditions != NULL))

5064

{

5065

o->m_pConditions->m_bAnyPassed = false;

5066

o->m_pConditions->ScanNeighborhoodAllOM(g_pTempTimestep,smfix);

5067

if (o->m_pConditions->m_bAnyPassed)

5068

o->m_pConditions->m_iRMPassCounter[z2]++;

5069

}

5070

5071

if ((secondmolrun) && (o->m_pConditionsOM2 != NULL))

5072

{

5073

o->m_pConditionsOM2->m_bAnyPassed = false;

5074

o->m_pConditionsOM2->ScanNeighborhoodAllOM(g_pTempTimestep,smfix);

5075

if (o->m_pConditionsOM2->m_bAnyPassed)

5076

o->m_pConditionsOM2->m_iRMPassCounter[z2]++;

5077

}

5078

5079

for (z3=0;z3<(secondmolrun?o->m_iShowMol2Count:o->m_iShowMolCount);z3++) // Alle anderen Molekuele durchgehen

5080

{

5081

if (secondmolrun)

5082

{

5083

if ((g_iFixMol == o->m_iShowMol2) && (z3 == z2)) // Wir wollen nicht das Referenzmolekuel mitzaehlen

5084

continue;

5085

if (o->m_bObsCertain)

5086

{

5087

if (!o->m_waObsShow2List.Contains(z3))

5088

continue;

5089

tic_o = o->m_waObsShow2List.GetPosition(z3);

5090

}

5091

} else

5092

{

5093

if ((g_iFixMol == o->m_iShowMol) && (z3 == z2)) // Wir wollen nicht das Referenzmolekuel mitzaehlen

5094

continue;

5095

if (o->m_bObsCertain)

5096

{

5097

if (!o->m_waObsShowList.Contains(z3))

5098

continue;

5099

tic_o = o->m_waObsShowList.GetPosition(z3);

5100

}

5101

}

5102

5103

if (g_bRegionAnalysis)

5104

{

5105

if (secondmolrun)

5106

{

5107

if ((!o->m_iaOM2Regions.Contains(0)) && (!o->m_iaOM2Regions.Contains(g_iaSMRegion[((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex[z3]])))

5108

continue;

5109

} else

5110

{

5111

if ((!o->m_iaOM1Regions.Contains(0)) && (!o->m_iaOM1Regions.Contains(g_iaSMRegion[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]])))

5112

continue;

5113

}

5114

}

5115

// mprintf("\n ... OM %d ist drin!",z3);

5116

5117

if (secondmolrun)

5118

{

5119

ti = -1;

5120

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex[z3]];

5121

} else

5122

{

5123

ti = o->m_waSaveShowList.GetPosition(z3);

5124

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

5125

}

5126

5127

if (o->m_bTimeDev && (o->m_pConditions != NULL))

5128

{

5129

if (!o->m_pConditions->Contains(z3) && (!g_bDeriv || (g_iSteps > 2)))

5130

{

5131

for (zr=0;zr<g_iCDFChannels;zr++)

5132

{

5133

if (g_bADF && (o->m_pADF[zr] != NULL))

5134

{

5135

if ((ti2 != -1) && (ti != -1))

5136

{

5137

if (o->m_bSaveSeparateFiles)

5138

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"; - ");

5139

else mfprintf(o->m_pADF[zr]->m_fAngle[0],"; - ");

5140

}

5141

}

5142

5143

if (g_bDDF && (o->m_pDDF[zr] != NULL))

5144

{

5145

if ((ti2 != -1) && (ti != -1))

5146

{

5147

if (o->m_bSaveSeparateFiles)

5148

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"; - ");

5149

else mfprintf(o->m_pDDF[zr]->m_fAngle[0],"; - ");

5150

}

5151

}

5152

5153

if (g_bDipDF && (o->m_pDipDF[zr] != NULL))

5154

{

5155

if ((ti2 != -1) && (ti != -1))

5156

{

5157

if (o->m_bSaveSeparateFiles)

5158

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; - ");

5159

else mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"; - ");

5160

}

5161

}

5162

5163

if (g_bVDF && (o->m_pVDF[zr] != NULL))

5164

{

5165

if ((ti2 != -1) && (ti != -1))

5166

{

5167

if (o->m_bSaveSeparateFiles)

5168

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; - ");

5169

else mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"; - ");

5170

}

5171

}

5172

5173

if (g_bRDF && (o->m_pRDF[zr] != NULL))

5174

{

5175

if ((ti2 != -1) && (ti != -1))

5176

{

5177

if (o->m_bSaveSeparateFiles)

5178

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"; - ");

5179

else mfprintf(o->m_pRDF[zr]->m_fDist[0],"; - ");

5180

}

5181

}

5182

}

5183

continue;

5184

}

5185

}

5186

5187

if ((!secondmolrun) && (o->m_pConditions != NULL))

5188

{

5189

if (!o->m_pConditions->Contains(z3))

5190

continue;

5191

5192

if (o->m_bBinOnlyPassedAtoms)

5193

o->m_pConditions->MarkPassedAtoms(z3,true);

5194

5195

if (o->m_bBinOnlyNotPassedAtoms)

5196

o->m_pConditions->MarkPassedAtoms(z3,false);

5197

5198

if (g_bSaveCondSnapshot)

5199

{

5200

g_iSaveCondCount++;

5201

if (g_bSaveCondWholeBox)

5202

{

5203

g_pTempTimestep->WriteTimestep(g_fSaveCondFile);

5204

} else

5205

{

5206

mfprintf(g_fSaveCondFile,"%d\nTimestep %lu, RM %d, OM %d\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes - ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laVirtualAtoms.GetSize() + ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_iAtomGes - ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laVirtualAtoms.GetSize(),g_iSteps,z2+1,z3+1);

5207

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z4++)

5208

{

5209

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

5210

continue;

5211

for (z5=0;z5<((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetSize();z5++)

5212

mfprintf(g_fSaveCondFile,"%s %f %f %f\n",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z4]])->m_sName,g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetAt(z5)][0]/100.0,g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetAt(z5)][1]/100.0,g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetAt(z5)][2]/100.0);

5213

}

5214

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex.GetSize();z4++)

5215

{

5216

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

5217

continue;

5218

for (z5=0;z5<((CxIntArray*)sm->m_oaAtomOffset[z4])->GetSize();z5++)

5219

mfprintf(g_fSaveCondFile,"%s %f %f %f\n",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[z4]])->m_sName,g_pTempTimestep->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z4])->GetAt(z5)][0]/100.0,g_pTempTimestep->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z4])->GetAt(z5)][1]/100.0,g_pTempTimestep->m_vaCoords[((CxIntArray*)sm->m_oaAtomOffset[z4])->GetAt(z5)][2]/100.0);

5220

}

5221

}

5222

}

5223

}

5224

5225

if (secondmolrun && (o->m_pConditionsOM2 != NULL))

5226

{

5227

if (!o->m_pConditionsOM2->Contains(z3))

5228

continue;

5229

5230

// mprintf("\nStep %d: z2=%d, z3=%d passed.",g_iSteps,z2,z3);

5231

5232

if (o->m_bBinOnlyPassedAtoms)

5233

o->m_pConditionsOM2->MarkPassedAtoms(z3,true);

5234

5235

if (o->m_bBinOnlyNotPassedAtoms)

5236

o->m_pConditionsOM2->MarkPassedAtoms(z3,false);

5237

5238

/* if (g_bSaveCondSnapshot)

5239

{

5240

g_iSaveCondCount++;

5241

if (g_bSaveCondWholeBox)

5242

{

5243

g_pTempTimestep->WriteTimestep(g_fSaveCondFile);

5244

} else

5245

{

5246

5247

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z4++)

5248

{

5249

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

5250

continue;

5251

for (z5=0;z5<((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetSize();z5++)

5252

5253

}

5254

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex.GetSize();z4++)

5255

{

5256

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

5257

continue;

5258

for (z5=0;z5<((CxIntArray*)sm->m_oaAtomOffset[z4])->GetSize();z5++)

5259

5260

}

5261

}

5262

}*/

5263

}

5264

5265

if (g_bVHDF)

5266

{

5267

o->m_pVHDF->BuildAtomList(smfix,sm,&templa);

5268

for (z4=0;z4<templa.GetSize();z4+=2)

5269

{

5270

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];// + vecc;

5271

for (z0=0;z0<o->m_pVHDF->m_iDepth/o->m_pVHDF->m_iStride;z0++)

5272

{

5273

g_pT2Timestep = GetTimeStep(z0*o->m_pVHDF->m_iStride);

5274

if (g_pT2Timestep == NULL)

5275

continue;

5276

vec1 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

5277

tf = FoldedLength(vec0-vec1);

5278

o->m_pVHDF->m_pVHDF->AddToBin_IntX_fast(z0,tf);

5279

o->m_pVHDF->m_pCount[z0]++;

5280

}

5281

}

5282

} // Ende IF VHDF

5283

5284

if (g_bADF)

5285

{

5286

for (zr=0;zr<g_iCDFChannels;zr++)

5287

{

5288

if (o->m_pADF[zr] == NULL)

5289

continue;

5290

if (o->m_bSecondShowMol)

5291

{

5292

if (secondmolrun && (zr == 0))

5293

continue;

5294

if (!secondmolrun && (zr == 1))

5295

continue;

5296

}

5297

o->m_pADF[zr]->BuildAtomList(smfix,sm,&templa);

5298

for (z4=0;z4<templa.GetSize();z4+=6)

5299

{

5300

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5301

{

5302

tb = true;

5303

if (g_baAtomPassedCondition[templa[z4]] == 0)

5304

tb = false;

5305

if (g_baAtomPassedCondition[templa[z4+1]] == 0)

5306

tb = false;

5307

if (o->m_pADF[zr]->m_bOrtho[0])

5308

if (g_baAtomPassedCondition[templa[z4+2]] == 0)

5309

tb = false;

5310

if (g_baAtomPassedCondition[templa[z4+3]] == 0)

5311

tb = false;

5312

if (g_baAtomPassedCondition[templa[z4+4]] == 0)

5313

tb = false;

5314

if (o->m_pADF[zr]->m_bOrtho[1])

5315

if (g_baAtomPassedCondition[templa[z4+5]] == 0)

5316

tb = false;

5317

if (tb)

5318

{

5319

o->m_pADF[zr]->m_baDataEnabled[z3].Add(1);

5320

} else

5321

{

5322

// mprintf("Nicht bestanden; z2=%d, z3=%d; (%d,%d,%d) (%d,%d,%d).\n",z2,z3,g_baAtomPassedCondition[tempwa[z4]],g_baAtomPassedCondition[tempwa[z4+1]],g_baAtomPassedCondition[tempwa[z4+2]],g_baAtomPassedCondition[tempwa[z4+3]],g_baAtomPassedCondition[tempwa[z4+4]],g_baAtomPassedCondition[tempwa[z4+5]]);

5323

o->m_pADF[zr]->m_baDataEnabled[z3].Add(0);

5324

}

5325

}

5326

if (o->m_pADF[zr]->m_bOrtho[0])

5327

{

5328

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5329

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5330

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

5331

vec1 = CrossP(FoldVector(vec2-vec0),FoldVector(vec3-vec0));

5332

} else

5333

{

5334

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5335

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5336

vec1 = FoldVector(vec2-vec0);

5337

}

5338

if (o->m_pADF[zr]->m_bOrtho[1])

5339

{

5340

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

5341

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

5342

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

5343

vec2 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

5344

} else

5345

{

5346

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

5347

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

5348

vec2 = FoldVector(vec3-vec4);

5349

}

5350

5351

tf = Angle_Deg(vec1,vec2);

5352

if ((tf > 90.0f) && (o->m_pADF[zr]->m_bFoldAngle))

5353

tf = 180.0f-tf;

5354

if (o->m_pADF[zr]->m_bCosine)

5355

tf = cos(tf/180.0*Pi);

5356

5357

if (g_bDeriv)

5358

{

5359

zi = (z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6;

5360

o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5361

switch(o->m_pADF[zr]->m_iDeriv)

5362

{

5363

case 0:

5364

tf = o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5365

break;

5366

case 1:

5367

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5368

break;

5369

case 2:

5370

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

5371

break;

5372

}

5373

}

5374

if (!g_bDeriv || (g_iSteps > 2))

5375

{

5376

if (o->m_bObsCertain && o->m_bDecompDist)

5377

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5378

5379

o->m_pADF[zr]->m_faData[z3].Add(tf);

5380

5381

if (o->m_pADF[zr]->m_bACF)

5382

o->m_pADF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6]->Add((float)tf);

5383

5384

/* if (o->m_pADF[zr]->m_bMirror)

5385

{

5386

if (o->m_bObsCertain && o->m_bDecompDist)

5387

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,180.0-tf);

5388

o->m_pADF[zr]->m_faData[z3].Add(180.0-tf);

5389

}*/

5390

5391

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5392

{

5393

// o->m_pAngleStat->AddValue(ti2,ti,tf);

5394

if (o->m_bSaveSeparateFiles)

5395

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"; %8.3f",tf);

5396

else mfprintf(o->m_pADF[zr]->m_fAngle[0],"; %8.3f",tf);

5397

if (o->m_bCombinedPlot)

5398

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pADF[zr]->m_iCombinations+z4/6,g_iSteps*g_fTimestepLength/1000.0,tf);

5399

}

5400

if (o->m_bTimeDiff)

5401

((CxFloatArray*)o->m_pADF[zr]->m_pADF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6])->Add((float)tf);

5402

}

5403

}

5404

}

5405

} // Ende IF ADF

5406

5407

if (g_bDDF)

5408

{

5409

for (zr=0;zr<g_iCDFChannels;zr++)

5410

{

5411

if (o->m_pDDF[zr] == NULL)

5412

continue;

5413

if (o->m_bSecondShowMol)

5414

{

5415

if (secondmolrun && (zr == 0))

5416

continue;

5417

if (!secondmolrun && (zr == 1))

5418

continue;

5419

}

5420

o->m_pDDF[zr]->BuildAtomList(smfix,sm,&templa);

5421

for (z4=0;z4<templa.GetSize();z4+=9)

5422

{

5423

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5424

{

5425

tb = true;

5426

for (z5=z4;z5<z4+9;z5++)

5427

if (g_baAtomPassedCondition[templa[z5]] == 0)

5428

tb = false;

5429

if (tb)

5430

o->m_pDDF[zr]->m_baDataEnabled[z3].Add(1);

5431

else o->m_pDDF[zr]->m_baDataEnabled[z3].Add(0);

5432

}

5433

if (o->m_pDDF[zr]->m_bOrtho[0])

5434

{

5435

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5436

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5437

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

5438

vec1 = CrossP(FoldVector(vec2-vec0),FoldVector(vec3-vec0));

5439

} else

5440

{

5441

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5442

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5443

vec1 = FoldVector(vec2-vec0);

5444

}

5445

if (o->m_pDDF[zr]->m_bOrtho[1])

5446

{

5447

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

5448

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

5449

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

5450

vec2 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

5451

} else

5452

{

5453

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

5454

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

5455

vec2 = FoldVector(vec3-vec4);

5456

}

5457

if (o->m_pDDF[zr]->m_bOrtho[2])

5458

{

5459

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

5460

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

5461

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+8]];

5462

vec3 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

5463

} else

5464

{

5465

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

5466

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

5467

vec3 = FoldVector(vec3-vec4);

5468

}

5469

tf = Dihedral(vec1,vec2,vec3,o->m_pDDF[zr]->m_bAbs);

5470

if (o->m_pDDF[zr]->m_bCosine)

5471

tf = cos(tf/180.0*Pi);

5472

else if (o->m_pDDF[zr]->m_bPositive)

5473

if (tf < 0)

5474

tf += 360.0;

5475

if (g_bDeriv)

5476

{

5477

zi = (z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9;

5478

o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5479

switch(o->m_pDDF[zr]->m_iDeriv)

5480

{

5481

case 0:

5482

tf = o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5483

break;

5484

case 1:

5485

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5486

break;

5487

case 2:

5488

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

5489

break;

5490

}

5491

}

5492

if (!g_bDeriv || (g_iSteps > 2))

5493

{

5494

if (o->m_bObsCertain && o->m_bDecompDist)

5495

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5496

5497

o->m_pDDF[zr]->m_faData[z3].Add(tf);

5498

5499

if (o->m_pDDF[zr]->m_bACF)

5500

o->m_pDDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]->Add((float)tf);

5501

5502

if (/*(!o->m_pDDF[zr]->m_bAbs) && */o->m_pDDF[zr]->m_bSymm)

5503

{

5504

o->m_pDDF[zr]->m_faData[z3].Add(-tf);

5505

if (o->m_bObsCertain && o->m_bDecompDist)

5506

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,-tf);

5507

}

5508

5509

if (o->m_bTimeDiff)

5510

((CxFloatArray*)o->m_pDDF[zr]->m_pDDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9])->Add((float)tf);

5511

5512

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5513

{

5514

if (o->m_pDDF[zr]->m_bRotate)

5515

{

5516

if (g_iSteps > 1)

5517

{

5518

if ((tf - o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]) > 180.0)

5519

o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]--;

5520

if ((tf - o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]) < -180.0)

5521

o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]++;

5522

}

5523

o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9] = tf;

5524

tf2 = tf + o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9] * 360.0;

5525

} else tf2 = tf;

5526

if (o->m_bSaveSeparateFiles)

5527

mfprintf(o->m_pDDF[zr]->m_fAngle[ti2],"; %8.3f",tf2);

5528

else mfprintf(o->m_pDDF[zr]->m_fAngle[0],"; %8.3f",tf2);

5529

if (o->m_bCombinedPlot)

5530

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pDDF[zr]->m_iCombinations+z4/9,g_iSteps*g_fTimestepLength/1000.0,tf);

5531

}

5532

}

5533

}

5534

}

5535

} // Ende IF DDF

5536

5537

if (g_bPlDF)

5538

{

5539

for (zr=0;zr<g_iCDFChannels;zr++)

5540

{

5541

if (o->m_pPlDF[zr] == NULL)

5542

continue;

5543

if (o->m_bSecondShowMol)

5544

{

5545

if (secondmolrun && (zr == 0))

5546

continue;

5547

if (!secondmolrun && (zr == 1))

5548

continue;

5549

}

5550

o->m_pPlDF[zr]->BuildAtomList(smfix,sm,&templa);

5551

for (z4=0;z4<templa.GetSize();z4+=4)

5552

{

5553

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5554

{

5555

tb = true;

5556

for (z5=z4;z5<z4+4;z5++)

5557

if (g_baAtomPassedCondition[templa[z5]] == 0)

5558

tb = false;

5559

if (tb)

5560

o->m_pPlDF[zr]->m_baDataEnabled[z3].Add(1);

5561

else o->m_pPlDF[zr]->m_baDataEnabled[z3].Add(0);

5562

}

5563

if (o->m_pPlDF[zr]->m_bNormal)

5564

{

5565

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5566

vec0.Normalize();

5567

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5568

tf = DotP(vec0,vec1);

5569

} else

5570

{

5571

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5572

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+2]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5573

vec3 = CrossP(vec0,vec1);

5574

vec3.Normalize();

5575

vec2 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5576

tf = DotP(vec2,vec3);

5577

}

5578

5579

if (!g_bDeriv || (g_iSteps > 2))

5580

{

5581

if (o->m_bObsCertain && o->m_bDecompDist)

5582

o->m_pPlDF[zr]->m_pPlDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5583

5584

o->m_pPlDF[zr]->m_faData[z3].Add(tf);

5585

}

5586

}

5587

}

5588

} // Ende IF PlDF

5589

5590

if (g_bLiDF)

5591

{

5592

for (zr=0;zr<g_iCDFChannels;zr++)

5593

{

5594

if (o->m_pLiDF[zr] == NULL)

5595

continue;

5596

if (o->m_bSecondShowMol)

5597

{

5598

if (secondmolrun && (zr == 0))

5599

continue;

5600

if (!secondmolrun && (zr == 1))

5601

continue;

5602

}

5603

o->m_pLiDF[zr]->BuildAtomList(smfix,sm,&templa);

5604

for (z4=0;z4<templa.GetSize();z4+=4)

5605

{

5606

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5607

{

5608

tb = true;

5609

for (z5=z4;z5<z4+4;z5++)

5610

if (g_baAtomPassedCondition[templa[z5]] == 0)

5611

tb = false;

5612

if (tb)

5613

o->m_pLiDF[zr]->m_baDataEnabled[z3].Add(1);

5614

else o->m_pLiDF[zr]->m_baDataEnabled[z3].Add(0);

5615

}

5616

5617

if (o->m_pLiDF[zr]->m_bNormal)

5618

{

5619

vec2 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5620

vec3 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+2]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5621

vec0 = CrossP(vec2,vec3);

5622

vec0.Normalize();

5623

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5624

vec0 *= DotP(vec0,vec1);

5625

tf = (vec1 - vec0).GetLength();

5626

} else

5627

{

5628

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5629

vec0.Normalize();

5630

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5631

vec0 *= DotP(vec0,vec1);

5632

tf = (vec1 - vec0).GetLength();

5633

}

5634

5635

if (!g_bDeriv || (g_iSteps > 2))

5636

{

5637

if (o->m_bObsCertain && o->m_bDecompDist)

5638

o->m_pLiDF[zr]->m_pLiDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5639

5640

o->m_pLiDF[zr]->m_faData[z3].Add(tf);

5641

}

5642

}

5643

}

5644

} // Ende IF LilDF

5645

5646

if (g_bDipDF)

5647

{

5648

for (zr=0;zr<g_iCDFChannels;zr++)

5649

{

5650

if (o->m_pDipDF[zr] == NULL)

5651

continue;

5652

if (o->m_bSecondShowMol)

5653

{

5654

if (secondmolrun && (zr == 0))

5655

continue;

5656

if (!secondmolrun && (zr == 1))

5657

continue;

5658

}

5659

if (o->m_pDipDF[zr]->m_iRefOrSec == 0)

5660

tf = smfix->m_vDipole.GetLength();

5661

else tf = sm->m_vDipole.GetLength();

5662

if (g_bDeriv)

5663

{

5664

zi = z2*o->m_iShowMolCount+z3;

5665

o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5666

switch(o->m_pDipDF[zr]->m_iDeriv)

5667

{

5668

case 0:

5669

tf = o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5670

break;

5671

case 1:

5672

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5673

break;

5674

case 2:

5675

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

5676

break;

5677

}

5678

}

5679

if (!g_bDeriv || (g_iSteps > 2))

5680

{

5681

if (o->m_bObsCertain && o->m_bDecompDist)

5682

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5683

5684

o->m_pDipDF[zr]->m_faData[z3].Add(tf);

5685

5686

if (o->m_pDipDF[zr]->m_bACF)

5687

o->m_pDipDF[zr]->m_pfaACFBuffer[z2*o->m_iShowMolCount+z3]->Add((float)tf);

5688

5689

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5690

{

5691

if (o->m_bSaveSeparateFiles)

5692

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; %8.3f",tf);

5693

else mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"; %8.3f",tf);

5694

if (o->m_bCombinedPlot)

5695

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_waSaveShowList.GetSize()+ti,g_iSteps*g_fTimestepLength/1000.0,tf);

5696

}

5697

if (o->m_bTimeDiff)

5698

((CxFloatArray*)o->m_pDipDF[zr]->m_pDipoleDF->m_oaTimeDiffBuf[z2*o->m_iShowMolCount+z3])->Add((float)tf);

5699

}

5700

}

5701

} // Ende IF DIPOLE

5702

5703

if (g_bVDF)

5704

{

5705

for (zr=0;zr<g_iCDFChannels;zr++)

5706

{

5707

if (o->m_pVDF[zr] == NULL)

5708

continue;

5709

if (o->m_bSecondShowMol)

5710

{

5711

if (secondmolrun && (zr == 0))

5712

continue;

5713

if (!secondmolrun && (zr == 1))

5714

continue;

5715

}

5716

o->m_pVDF[zr]->BuildAtomList(smfix,sm,&templa);

5717

for (z4=0;z4<templa.GetSize();z4++)

5718

{

5719

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5720

{

5721

tb = true;

5722

for (z5=z4;z5<z4+2;z5++)

5723

if (g_baAtomPassedCondition[templa[z5]] == 0)

5724

tb = false;

5725

if (tb)

5726

o->m_pVDF[zr]->m_baDataEnabled[z3].Add(1);

5727

else o->m_pVDF[zr]->m_baDataEnabled[z3].Add(0);

5728

}

5729

tf = tempvel[templa[z4]].GetLength();

5730

if (g_bDeriv)

5731

{

5732

zi = (z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2;

5733

o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5734

switch(o->m_pVDF[zr]->m_iDeriv)

5735

{

5736

case 0:

5737

tf = o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5738

break;

5739

case 1:

5740

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5741

break;

5742

case 2:

5743

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

5744

break;

5745

}

5746

}

5747

if (!g_bDeriv || (g_iSteps > 2))

5748

{

5749

if (o->m_bObsCertain && o->m_bDecompDist)

5750

o->m_pVDF[zr]->m_pVDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5751

5752

o->m_pVDF[zr]->m_faData[z3].Add(tf);

5753

5754

if (o->m_pVDF[zr]->m_bACF)

5755

o->m_pVDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

5756

5757

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5758

{

5759

if (o->m_bSaveSeparateFiles)

5760

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; %8.3f",tf);

5761

else mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"; %8.3f",tf);

5762

if (o->m_bCombinedPlot)

5763

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pVDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

5764

}

5765

if (o->m_bTimeDiff)

5766

((CxFloatArray*)o->m_pVDF[zr]->m_pVDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

5767

}

5768

}

5769

}

5770

} // Ende IF VDF

5771

5772

if (g_bRDF)

5773

{

5774

for (zr=0;zr<g_iCDFChannels;zr++)

5775

{

5776

if (o->m_pRDF[zr] == NULL)

5777

continue;

5778

if (o->m_bSecondShowMol)

5779

{

5780

if (secondmolrun && (zr == 0))

5781

continue;

5782

if (!secondmolrun && (zr == 1))

5783

continue;

5784

}

5785

o->m_pRDF[zr]->BuildAtomList(smfix,sm,&templa);

5786

for (z4=0;z4<templa.GetSize();z4+=2)

5787

{

5788

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5789

{

5790

tb = true;

5791

for (z5=z4;z5<z4+2;z5++)

5792

if (g_baAtomPassedCondition[templa[z5]] == 0)

5793

tb = false;

5794

if (tb)

5795

o->m_pRDF[zr]->m_baDataEnabled[z3].Add(1);

5796

else o->m_pRDF[zr]->m_baDataEnabled[z3].Add(0);

5797

}

5798

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5799

vec1 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5800

tf = FoldedLength(vec0-vec1);

5801

/* if (tf > 2000)

5802

{

5803

mprintf("\n@ z2=%d, z3=%d, z4=%d, templa[z4]=%d, templa[z4+1]=%d, dist=%f ",z2,z3,z4,templa[z4],templa[z4+1],tf);

5804

mprintf("\n vec0: "); vec0.Dump(); mprintf(", vec1: "); vec1.Dump(); mprintf(", vec2: "); vec2.Dump();

5805

}

5806

*/ // mprintf("\n@ z2=%d, z3=%d, z4=%d, templa[z4]=%d, templa[z4+1]=%d, dist=%f ",z2,z3,z4,templa[z4],templa[z4+1],tf);

5807

// mprintf("\n vec0: "); vec0.Dump(); mprintf(", vec1: "); vec1.Dump(); mprintf(", vec2: "); vec2.Dump();

5808

if (g_bDeriv)

5809

{

5810

zi = (z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2;

5811

o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5812

switch(o->m_pRDF[zr]->m_iDeriv)

5813

{

5814

case 0:

5815

tf = o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5816

break;

5817

case 1:

5818

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5819

break;

5820

case 2:

5821

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi) + o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - 2*o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi)) / (g_fTimestepLength * g_fTimestepLength);

5822

break;

5823

}

5824

}

5825

if (!g_bDeriv || (g_iSteps > 2))

5826

{

5827

if (o->m_bObsCertain && o->m_bDecompDist)

5828

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5829

5830

if (o->m_bDecompType)

5831

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(o->m_waDecompTypeRefOffs[templa[z4]]*o->m_waDecompTypeObsOffs.GetSize()+o->m_waDecompTypeObsOffs[templa[z4+1]],tf);

5832

5833

o->m_pRDF[zr]->m_faData[z3].Add(tf);

5834

5835

if (o->m_pRDF[zr]->m_bACF)

5836

o->m_pRDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

5837

5838

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5839

{

5840

if (o->m_bSaveSeparateFiles)

5841

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"; %10.3f",tf);

5842

else mfprintf(o->m_pRDF[zr]->m_fDist[0],"; %10.3f",tf);

5843

if (o->m_bCombinedPlot)

5844

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pRDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

5845

}

5846

if (o->m_bTimeDiff)

5847

((CxFloatArray*)o->m_pRDF[zr]->m_pRDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

5848

}

5849

}

5850

}

5851

} // Ende IF RDF

5852

5853

if (g_bSDF)

5854

{

5855

o->m_pSDF->BuildAtomList(smfix,sm,&templa);

5856

for (z4=0;z4<templa.GetSize();z4++)

5857

{

5858

o->m_pSDF->m_vaData[z3].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

5859

5860

if (o->m_pSDF->m_bVdWSpheres)

5861

o->m_pSDF->m_faRadius[z3].Add(g_faVdWRadius[templa[z4]]);

5862

}

4451

if ((g_bCutCluster && g_bRefEnvCenter && g_bRefEnvFix) || (g_bSaveRefEnv && g_bRefEnvCenter && g_bRefEnvFix && (z2==g_iSaveRefMol)))

4452

{

4453

if (g_bCutCluster || (g_iNbhMode == 2))

4454

{

4455

g_pNbSet->Reset();

4456

if (g_bCutCluster)

4457

g_pNbSet->ResetAlwaysTrue();

4458

g_pNbSet->Scan(smfix,g_pTempTimestep);

4459

if (g_bSaveRefWithEnv)

4460

g_pNbSet->AddMolecule(g_iFixMol,z2);

4461

}

4462

4463

if (!g_bCenterZero && g_bPeriodic)

4464

g_pTempTimestep->CenterPos(CxVector3(-g_fBoxX/2,-g_fBoxY/2,-g_fBoxZ/2));

4465

4466

g_pTempTimestep->WriteTimestepNb(g_fRefEnv,g_pNbSet,((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]);

4467

4468

if (g_bTDO)

4469

{

4470

if (g_laTDOSteps.Contains(g_iSteps-1))

4471

{

4472

sprintf(buf,"tdo_%s_%d_%06lu%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_iSteps-1,multibuf);

4473

mprintf("\nSaving TDO step as %s.\n",buf);

4474

tfi = OpenFileWrite(buf,true);

4475

g_pTempTimestep->WriteTimestepNb(tfi,g_pNbSet);

4476

fclose(tfi);

4477

}

4478

}

4479

}

4480

} // END IF SDF, RevEnv, ...

4481

4482

/***************************************************************************************************************************/

4483

4484

if (g_bVoidSDF)

4485

{

4486

if (g_pVoroAnalysis->m_bEmptySpaceSDF)

4487

{

4488

if (!g_pVoroAnalysis->m_bNewEmptyMode)

4489

{

4490

g_pVoroAnalysis->m_pTempSDF->Clear();

4491

4492

for (z3=0;z3<g_oaMolecules.GetSize();z3++)

4493

{

4494

tm = (CMolecule*)g_oaMolecules[z3];

4495

for (z4=0;z4<tm->m_laSingleMolIndex.GetSize();z4++)

4496

{

4497

if (!g_pVoroAnalysis->m_bEmptySpaceSDF_RefMol)

4498

if ((z3 == g_iFixMol) && (z4 == z2))

4499

continue;

4500

4501

tsm = (CSingleMolecule*)g_oaSingleMolecules[tm->m_laSingleMolIndex[z4]];

4502

4503

for (z5=0;z5<tsm->m_oaAtomOffset.GetSize();z5++)

4504

{

4505

if (tm->m_baAtomIndex[z5] == g_iVirtAtomType)

4506

continue;

4507

4508

for (z6=0;z6<((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetSize();z6++)

4509

{

4510

vec0 = g_pTempTimestep->m_vaCoords[((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetAt(z6)];

4511

4512

g_pVoroAnalysis->m_pTempSDF->AddToBin_Sphere(vec0,g_faVdWRadius[((CxIntArray*)tsm->m_oaAtomOffset[z5])->GetAt(z6)]);

4513

}

4514

}

4515

}

4516

}

4517

g_pVoroAnalysis->BinEmptySDF_New(&mat,&vecc);

4518

} else

4519

{

4520

g_pVoroAnalysis->BinEmptySDF();

4521

}

4522

}

4523

4524

if (g_pVoroAnalysis->m_bSphereHoleSDF)

4525

{

4526

g_pVoroAnalysis->BinSphereHoleSDF(&mat,&vecc);

4527

}

4528

}

4529

4530

if (g_bPlProj || g_bDipDF || g_bRevSDF || g_bVHDF || g_bRDF || g_bPlDF || g_bLiDF || g_bSDF || g_bADF || g_bDDF || g_bVDF || g_bCond)

4531

{

4532

for (z6=0;z6<g_oaObserv.GetSize();z6++)

4533

{

4534

o = (CObservation*)g_oaObserv[z6];

4535

4536

// mprintf("\nStep %d, z2=%d, Obs=%d, Reg=%d, ObsReg=%d.",g_iSteps,z2,z6,g_iaSMRegion[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]],o->m_iaRMRegions[0]);

4537

4538

if (g_bRegionAnalysis)

4539

if ((!o->m_iaRMRegions.Contains(0)) && (!o->m_iaRMRegions.Contains(g_iaSMRegion[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])))

4540

continue;

4541

4542

// mprintf("\n ...RM ist in Region.");

4543

4544

ti2 = o->m_waSaveRefList.GetPosition(z2);

4545

4546

if (o->m_bObsCertain)

4547

{

4548

// mprintf("\n RefList: ");

4549

// for (z7=0;z7<o->m_waObsRefList.GetSize();z7++)

4550

// mprintf("%d, ",o->m_waObsRefList[z7]);

4551

4552

if (!o->m_waObsRefList.Contains(z2))

4553

continue;

4554

// mprintf("\n ...RM ist auch in RefList.");

4555

tic_r = o->m_waObsRefList.GetPosition(z2);

4556

}

4557

4558

if (g_bUseVelocities)

4559

{

4560

tempvel.CopyFrom(&g_pTempTimestep->m_vaVelocities);

4561

if (o->m_bVelocityRelToRef)

4562

{

4563

vecv = g_pTempTimestep->m_vaVelocities[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[0]])->GetAt(g_iFixAtom[0])];

4564

for (z3=0;z3<g_iGesVirtAtomCount;z3++)

4565

tempvel[z3] -= vecv;

4566

}

4567

}

4568

4569

if ((g_bCDF) && (o->m_bTimeDev) && (ti2 != -1))

4570

{

4571

if (o->m_bSaveSeparateFiles)

4572

mfprintf(o->m_pCDF->m_fTimeDev[ti2],"%d",(int)g_iSteps);

4573

else if (ti2 == 0)

4574

mfprintf(o->m_pCDF->m_fTimeDev[0],"%d",(int)g_iSteps);

4575

}

4576

4577

for (zr=0;zr<g_iCDFChannels;zr++)

4578

{

4579

if (g_bRDF && (o->m_pRDF[zr] != NULL))

4580

{

4581

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4582

o->m_pRDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4583

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4584

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4585

o->m_pRDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4586

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4587

{

4588

if (o->m_bSaveSeparateFiles)

4589

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"%d",(int)g_iSteps);

4590

else if (ti2 == 0)

4591

mfprintf(o->m_pRDF[zr]->m_fDist[0],"%d",(int)g_iSteps);

4592

}

4593

}

4594

4595

if (g_bADF && (o->m_pADF[zr] != NULL))

4596

{

4597

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4598

o->m_pADF[zr]->m_faData[z3].RemoveAll_KeepSize();

4599

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4600

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4601

o->m_pADF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4602

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4603

{

4604

if (o->m_bSaveSeparateFiles)

4605

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

4606

else if (ti2 == 0)

4607

mfprintf(o->m_pADF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

4608

}

4609

}

4610

4611

if (g_bDDF && (o->m_pDDF[zr] != NULL))

4612

{

4613

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4614

o->m_pDDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4615

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4616

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4617

o->m_pDDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4618

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4619

{

4620

if (o->m_bSaveSeparateFiles)

4621

mfprintf(o->m_pDDF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

4622

else if (ti2 == 0)

4623

mfprintf(o->m_pDDF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

4624

}

4625

}

4626

4627

if (g_bPlDF && (o->m_pPlDF[zr] != NULL))

4628

{

4629

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4630

o->m_pPlDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4631

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4632

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4633

o->m_pPlDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4634

/* if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4635

{

4636

if (o->m_bSaveSeparateFiles)

4637

mfprintf(o->m_pPlDF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

4638

else if (ti2 == 0)

4639

mfprintf(o->m_pDDF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

4640

}*/

4641

}

4642

4643

if (g_bLiDF && (o->m_pLiDF[zr] != NULL))

4644

{

4645

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4646

o->m_pLiDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4647

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4648

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4649

o->m_pLiDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4650

/* if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4651

{

4652

if (o->m_bSaveSeparateFiles)

4653

mfprintf(o->m_pPlDF[zr]->m_fAngle[ti2],"%d",(int)g_iSteps);

4654

else if (ti2 == 0)

4655

mfprintf(o->m_pDDF[zr]->m_fAngle[0],"%d",(int)g_iSteps);

4656

}*/

4657

}

4658

4659

if (g_bDipDF && (o->m_pDipDF[zr] != NULL))

4660

{

4661

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4662

o->m_pDipDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4663

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4664

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4665

o->m_pDipDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4666

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4667

{

4668

if (o->m_bSaveSeparateFiles)

4669

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"%d",(int)g_iSteps);

4670

else if (ti2 == 0)

4671

mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"%d",(int)g_iSteps);

4672

}

4673

}

4674

4675

if (g_bVDF && (o->m_pVDF[zr] != NULL))

4676

{

4677

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4678

o->m_pVDF[zr]->m_faData[z3].RemoveAll_KeepSize();

4679

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4680

for (z3=0;z3<((o->m_bSecondShowMol && (zr == 1))?o->m_iShowMol2Count:o->m_iShowMolCount);z3++)

4681

o->m_pVDF[zr]->m_baDataEnabled[z3].RemoveAll_KeepSize();

4682

if ((o->m_bTimeDev) && (ti2 != -1) && (!g_bDeriv || (g_iSteps > 2)))

4683

{

4684

if (o->m_bSaveSeparateFiles)

4685

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"%d",(int)g_iSteps);

4686

else if (ti2 == 0)

4687

mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"%d",(int)g_iSteps);

4688

}

4689

}

4690

} // END FOR zr

4691

4692

if (g_bSDF)

4693

{

4694

for (z3=0;z3<o->m_iShowMolCount;z3++)

4695

{

4696

o->m_pSDF->m_vaData[z3].RemoveAll_KeepSize();

4697

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4698

o->m_pSDF->m_baDataEnabled[z3].RemoveAll_KeepSize();

4699

}

4700

}

4701

4702

if (g_bPlProj)

4703

{

4704

for (z3=0;z3<o->m_iShowMolCount;z3++)

4705

{

4706

o->m_pPlProj->m_vaData[z3].RemoveAll_KeepSize();

4707

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4708

o->m_pPlProj->m_baDataEnabled[z3].RemoveAll_KeepSize();

4709

}

4710

}

4711

4712

if (g_bRevSDF)

4713

{

4714

for (z3=0;z3<o->m_iShowMolCount;z3++)

4715

{

4716

o->m_pRevSDF->m_vaData[z3].RemoveAll_KeepSize();

4717

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

4718

o->m_pRevSDF->m_baDataEnabled[z3].RemoveAll_KeepSize();

4719

}

4720

}

4721

4722

if (o->m_bSelf)

4723

{

4724

if (g_bADF)

4725

{

4726

for (zr=0;zr<g_iCDFChannels;zr++)

4727

{

4728

if (o->m_pADF[zr] == NULL)

4729

continue;

4730

o->m_pADF[zr]->BuildAtomList(smfix,NULL,&templa);

4731

for (z4=0;z4<templa.GetSize();z4+=6)

4732

{

4733

if (o->m_pADF[zr]->m_bOrtho[0])

4734

{

4735

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4736

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4737

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

4738

vec1 = CrossP(FoldVector(vec2-vec0),FoldVector(vec3-vec0));

4739

} else

4740

{

4741

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4742

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4743

vec1 = FoldVector(vec2-vec0);

4744

}

4745

if (o->m_pADF[zr]->m_bOrtho[1])

4746

{

4747

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4748

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4749

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

4750

vec2 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

4751

} else

4752

{

4753

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4754

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4755

vec2 = FoldVector(vec3-vec4);

4756

}

4757

tf = Angle_Deg(vec1,vec2);

4758

if ((tf > 90.0f) && (o->m_pADF[zr]->m_bFoldAngle))

4759

tf = 180.0f-tf;

4760

if (o->m_pADF[zr]->m_bCosine)

4761

tf = cos(tf/180.0*Pi);

4762

4763

if (g_bDeriv)

4764

{

4765

o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6) = tf;

4766

switch(o->m_pADF[zr]->m_iDeriv)

4767

{

4768

case 0:

4769

tf = o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pADF[zr]->m_iCombinations+z4/6);

4770

break;

4771

case 1:

4772

4773

break;

4774

case 2:

4775

4776

break;

4777

}

4778

}

4779

4780

if (!g_bDeriv || (g_iSteps > 2))

4781

{

4782

if (o->m_bObsCertain && o->m_bDecompDist)

4783

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r,tf);

4784

4785

o->m_pADF[zr]->m_faData[0].Add(tf);

4786

4787

if (o->m_pADF[zr]->m_bACF)

4788

o->m_pADF[zr]->m_pfaACFBuffer[z2*o->m_pADF[zr]->m_iCombinations+z4/6]->Add((float)tf);

4789

4790

/* if (o->m_pADF[zr]->m_bMirror)

4791

{

4792

if (o->m_bObsCertain && o->m_bDecompDist)

4793

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r,180.0-tf);

4794

o->m_pADF[zr]->m_faData[0].Add(180.0-tf);

4795

}*/

4796

4797

if (o->m_bTimeDev && (ti2 != -1))

4798

{

4799

if (o->m_bSaveSeparateFiles)

4800

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"; %8.3f",tf);

4801

else mfprintf(o->m_pADF[zr]->m_fAngle[0],"; %8.3f",tf);

4802

if (o->m_bCombinedPlot)

4803

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pADF[zr]->m_iCombinations+z4/6,g_iSteps*g_fTimestepLength/1000.0,tf);

4804

}

4805

if (o->m_bTimeDiff)

4806

((CxFloatArray*)o->m_pADF[zr]->m_pADF->m_oaTimeDiffBuf[z2*o->m_pADF[zr]->m_iCombinations+z4/6])->Add((float)tf);

4807

}

4808

} // END FOR z4

4809

} // END FOR zr

4810

} // Ende IF ADF

4811

4812

if (g_bDDF)

4813

{

4814

for (zr=0;zr<g_iCDFChannels;zr++)

4815

{

4816

if (o->m_pDDF[zr] == NULL)

4817

continue;

4818

o->m_pDDF[zr]->BuildAtomList(smfix,smfix,&templa);

4819

for (z4=0;z4<templa.GetSize();z4+=9)

4820

{

4821

if (o->m_pDDF[zr]->m_bOrtho[0])

4822

{

4823

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4824

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4825

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

4826

vec1 = CrossP(FoldVector(vec2-vec0),FoldVector(vec3-vec0));

4827

} else

4828

{

4829

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4830

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4831

vec1 = FoldVector(vec2-vec0);

4832

}

4833

if (o->m_pDDF[zr]->m_bOrtho[1])

4834

{

4835

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4836

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4837

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

4838

vec2 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

4839

} else

4840

{

4841

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

4842

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

4843

vec2 = FoldVector(vec3-vec4);

4844

}

4845

if (o->m_pDDF[zr]->m_bOrtho[2])

4846

{

4847

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

4848

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

4849

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+8]];

4850

vec3 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

4851

} else

4852

{

4853

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

4854

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

4855

vec3 = FoldVector(vec3-vec4);

4856

}

4857

tf = Dihedral(vec1,vec2,vec3,o->m_pDDF[zr]->m_bAbs);

4858

if (o->m_pDDF[zr]->m_bCosine)

4859

tf = cos(tf/180.0*Pi);

4860

else if (o->m_pDDF[zr]->m_bPositive)

4861

if (tf < 0)

4862

tf += 360.0;

4863

if (g_bDeriv)

4864

{

4865

o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9) = tf;

4866

switch(o->m_pDDF[zr]->m_iDeriv)

4867

{

4868

case 0:

4869

tf = o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pDDF[zr]->m_iCombinations+z4/9);

4870

break;

4871

case 1:

4872

4873

break;

4874

case 2:

4875

4876

break;

4877

}

4878

}

4879

if (!g_bDeriv || (g_iSteps > 2))

4880

{

4881

if (o->m_bObsCertain && o->m_bDecompDist)

4882

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r,tf);

4883

4884

o->m_pDDF[zr]->m_faData[0].Add(tf);

4885

4886

if (o->m_pDDF[zr]->m_bACF)

4887

o->m_pDDF[zr]->m_pfaACFBuffer[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]->Add((float)tf);

4888

4889

if (/*(!o->m_pDDF[zr]->m_bAbs) && */o->m_pDDF[zr]->m_bSymm)

4890

{

4891

o->m_pDDF[zr]->m_faData[0].Add(-tf);

4892

if (o->m_bObsCertain && o->m_bDecompDist)

4893

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r,-tf);

4894

}

4895

4896

if (o->m_bTimeDiff)

4897

((CxFloatArray*)o->m_pDDF[zr]->m_pDDF->m_oaTimeDiffBuf[z2*o->m_pDDF[zr]->m_iCombinations+z4/9])->Add((float)tf);

4898

4899

if (o->m_bTimeDev && (ti2 != -1))

4900

{

4901

if (o->m_pDDF[zr]->m_bRotate)

4902

{

4903

if (g_iSteps > 1)

4904

{

4905

if ((tf - o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]) > 180.0)

4906

o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]--;

4907

if ((tf - o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]) < -180.0)

4908

o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9]++;

4909

}

4910

o->m_pDDF[zr]->m_faLastData[z2*o->m_pDDF[zr]->m_iCombinations+z4/9] = tf;

4911

tf2 = tf + o->m_pDDF[zr]->m_laRotation[z2*o->m_pDDF[zr]->m_iCombinations+z4/9] * 360.0;

4912

} else tf2 = tf;

4913

if (o->m_bSaveSeparateFiles)

4914

mfprintf(o->m_pDDF[zr]->m_fAngle[ti2],"; %8.3f",tf2);

4915

else mfprintf(o->m_pDDF[zr]->m_fAngle[0],"; %8.3f",tf2);

4916

if (o->m_bCombinedPlot)

4917

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pDDF[zr]->m_iCombinations+z4/9,g_iSteps*g_fTimestepLength/1000.0,tf);

4918

}

4919

}

4920

}

4921

}

4922

} // END IF DDF

4923

4924

if (g_bVHDF)

4925

{

4926

o->m_pVHDF->BuildAtomList(smfix,smfix,&templa);

4927

for (z4=0;z4<templa.GetSize();z4+=2)

4928

{

4929

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];// + vecc;

4930

for (z0=0;z0<o->m_pVHDF->m_iDepth/o->m_pVHDF->m_iStride;z0++)

4931

{

4932

g_pT2Timestep = GetTimeStep(z0*o->m_pVHDF->m_iStride);

4933

if (g_pT2Timestep == NULL)

4934

continue;

4935

vec1 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

4936

tf = FoldedLength(vec0-vec1);

4937

o->m_pVHDF->m_pVHDF->AddToBin_IntX_fast(z0,tf);

4938

o->m_pVHDF->m_pCount[z0]++;

4939

}

4940

}

4941

} // Ende IF VHDF

4942

4943

if (g_bRDF)

4944

{

4945

for (zr=0;zr<g_iCDFChannels;zr++)

4946

{

4947

if (o->m_pRDF[zr] == NULL)

4948

continue;

4949

o->m_pRDF[zr]->BuildAtomList(smfix,smfix,&templa);

4950

for (z4=0;z4<templa.GetSize();z4+=2)

4951

{

4952

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

4953

vec1 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

4954

tf = FoldedLength(vec0-vec1);

4955

if (g_bDeriv)

4956

{

4957

o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2) = tf;

4958

switch(o->m_pRDF[zr]->m_iDeriv)

4959

{

4960

case 0:

4961

tf = o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pRDF[zr]->m_iCombinations+z4/2);

4962

break;

4963

case 1:

4964

4965

break;

4966

case 2:

4967

4968

break;

4969

}

4970

}

4971

if (!g_bDeriv || (g_iSteps > 2))

4972

{

4973

if (o->m_bObsCertain && o->m_bDecompDist)

4974

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(tic_r,tf);

4975

4976

if (o->m_bDecompType)

4977

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(o->m_waDecompTypeRefOffs[templa[z4]]*o->m_waDecompTypeObsOffs.GetSize()+o->m_waDecompTypeObsOffs[templa[z4+1]],tf);

4978

4979

o->m_pRDF[zr]->m_faData[0].Add(tf);

4980

4981

if (o->m_pRDF[zr]->m_bACF)

4982

o->m_pRDF[zr]->m_pfaACFBuffer[z2*o->m_pRDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

4983

4984

if (o->m_bTimeDev && (ti2 != -1))

4985

{

4986

if (o->m_bSaveSeparateFiles)

4987

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"; %10.3f",tf);

4988

else mfprintf(o->m_pRDF[zr]->m_fDist[0],"; %10.3f",tf);

4989

if (o->m_bCombinedPlot)

4990

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pRDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

4991

}

4992

if (o->m_bTimeDiff)

4993

((CxFloatArray*)o->m_pRDF[zr]->m_pRDF->m_oaTimeDiffBuf[z2*o->m_pRDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

4994

}

4995

}

4996

}

4997

} // Ende IF RDF

4998

4999

if (g_bPlDF)

5000

{

5001

for (zr=0;zr<g_iCDFChannels;zr++)

5002

{

5003

if (o->m_pPlDF[zr] == NULL)

5004

continue;

5005

o->m_pPlDF[zr]->BuildAtomList(smfix,smfix,&templa);

5006

for (z4=0;z4<templa.GetSize();z4+=4)

5007

{

5008

if (o->m_pPlDF[zr]->m_bNormal)

5009

{

5010

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5011

vec0.Normalize();

5012

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5013

tf = DotP(vec0,vec1);

5014

} else

5015

{

5016

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5017

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+2]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5018

vec3 = CrossP(vec0,vec1);

5019

vec3.Normalize();

5020

vec2 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5021

tf = DotP(vec2,vec3);

5022

}

5023

5024

if (!g_bDeriv || (g_iSteps > 2))

5025

{

5026

if (o->m_bObsCertain && o->m_bDecompDist)

5027

o->m_pPlDF[zr]->m_pPlDF->AddToBin_Multi(tic_r,tf);

5028

5029

o->m_pPlDF[zr]->m_faData[0].Add(tf);

5030

}

5031

}

5032

}

5033

} // END IF PlDF

5034

5035

if (g_bLiDF)

5036

{

5037

for (zr=0;zr<g_iCDFChannels;zr++)

5038

{

5039

if (o->m_pLiDF[zr] == NULL)

5040

continue;

5041

o->m_pLiDF[zr]->BuildAtomList(smfix,smfix,&templa);

5042

for (z4=0;z4<templa.GetSize();z4+=4)

5043

{

5044

if (o->m_pLiDF[zr]->m_bNormal)

5045

{

5046

vec2 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5047

vec3 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+2]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5048

vec0 = CrossP(vec2,vec3);

5049

vec0.Normalize();

5050

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5051

vec0 *= DotP(vec0,vec1);

5052

tf = (vec1 - vec0).GetLength();

5053

} else

5054

{

5055

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5056

vec0.Normalize();

5057

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5058

vec0 *= DotP(vec0,vec1);

5059

tf = (vec1 - vec0).GetLength();

5060

}

5061

5062

if (!g_bDeriv || (g_iSteps > 2))

5063

{

5064

if (o->m_bObsCertain && o->m_bDecompDist)

5065

o->m_pLiDF[zr]->m_pLiDF->AddToBin_Multi(tic_r,tf);

5066

5067

o->m_pLiDF[zr]->m_faData[0].Add(tf);

5068

}

5069

}

5070

}

5071

} // END IF LiDF

5072

5073

if (g_bDipDF)

5074

{

5075

for (zr=0;zr<g_iCDFChannels;zr++)

5076

{

5077

if (o->m_pDipDF[zr] == NULL)

5078

continue;

5079

tf = smfix->m_vDipole.GetLength();

5080

if (g_bDeriv)

5081

{

5082

o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2) = tf;

5083

switch(o->m_pDipDF[zr]->m_iDeriv)

5084

{

5085

case 0:

5086

tf = o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2);

5087

break;

5088

case 1:

5089

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2) - o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(z2)) / (2*g_fTimestepLength);

5090

break;

5091

case 2:

5092

5093

break;

5094

}

5095

}

5096

if (!g_bDeriv || (g_iSteps > 2))

5097

{

5098

if (o->m_bObsCertain && o->m_bDecompDist)

5099

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin_Multi(tic_r,tf);

5100

5101

o->m_pDipDF[zr]->m_faData[0].Add(tf);

5102

5103

if (o->m_pDipDF[zr]->m_bACF)

5104

o->m_pDipDF[zr]->m_pfaACFBuffer[z2]->Add((float)tf);

5105

5106

if (o->m_bTimeDev && (ti2 != -1))

5107

{

5108

if (o->m_bSaveSeparateFiles)

5109

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; %8.3f",tf);

5110

else mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"; %8.3f",tf);

5111

if (o->m_bCombinedPlot)

5112

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->AddXYTupel(ti2,g_iSteps*g_fTimestepLength/1000.0,tf);

5113

}

5114

if (o->m_bTimeDiff)

5115

((CxFloatArray*)o->m_pDipDF[zr]->m_pDipoleDF->m_oaTimeDiffBuf[z2])->Add((float)tf);

5116

}

5117

}

5118

} // Ende IF DIPDF

5119

5120

if (g_bVDF)

5121

{

5122

for (zr=0;zr<g_iCDFChannels;zr++)

5123

{

5124

if (o->m_pVDF[zr] == NULL)

5125

continue;

5126

o->m_pVDF[zr]->BuildAtomList(smfix,smfix,&templa);

5127

for (z4=0;z4<templa.GetSize();z4++)

5128

{

5129

tf = tempvel[templa[z4]].GetLength();

5130

if (g_bDeriv)

5131

{

5132

o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2) = tf;

5133

switch(o->m_pVDF[zr]->m_iDeriv)

5134

{

5135

case 0:

5136

tf = o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(z2*o->m_pVDF[zr]->m_iCombinations+z4/2);

5137

break;

5138

case 1:

5139

5140

break;

5141

case 2:

5142

5143

break;

5144

}

5145

}

5146

if (!g_bDeriv || (g_iSteps > 2))

5147

{

5148

if (o->m_bObsCertain && o->m_bDecompDist)

5149

o->m_pVDF[zr]->m_pVDF->AddToBin_Multi(tic_r,tf);

5150

5151

o->m_pVDF[zr]->m_faData[0].Add(tf);

5152

5153

if (o->m_pVDF[zr]->m_bACF)

5154

o->m_pVDF[zr]->m_pfaACFBuffer[z2*o->m_pVDF[zr]->m_iCombinations+z4]->Add((float)tf);

5155

5156

if (o->m_bTimeDev && (ti2 != -1))

5157

{

5158

if (o->m_bSaveSeparateFiles)

5159

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; %8.3f",tf);

5160

else mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"; %8.3f",tf);

5161

if (o->m_bCombinedPlot)

5162

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_pVDF[zr]->m_iCombinations+z4,g_iSteps*g_fTimestepLength/1000.0,tf);

5163

}

5164

if (o->m_bTimeDiff)

5165

((CxFloatArray*)o->m_pVDF[zr]->m_pVDF->m_oaTimeDiffBuf[z2*o->m_pVDF[zr]->m_iCombinations+z4])->Add((float)tf);

5166

}

5167

}

5168

}

5169

} // Ende IF VDF

5170

5171

if (g_bSDF)

5172

{

5173

o->m_pSDF->BuildAtomList(smfix,smfix,&templa);

5174

for (z4=0;z4<templa.GetSize();z4++)

5175

{

5176

o->m_pSDF->m_vaData[0].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

5177

5178

if (o->m_pSDF->m_bVdWSpheres)

5179

o->m_pSDF->m_faRadius[0].Add(g_faVdWRadius[templa[z4]]);

5180

}

5181

} // Ende IF SDF

5182

5183

if (g_bPlProj)

5184

{

5185

o->m_pPlProj->BuildAtomList(smfix,smfix,&templa);

5186

for (z4=0;z4<templa.GetSize();z4++)

5187

o->m_pPlProj->m_vaData[0].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

5188

} // Ende IF PlProj

5189

5190

if (g_bRevSDF)

5191

{

5192

o->m_pRevSDF->BuildAtomList(smfix,smfix,&templa);

5193

for (z4=0;z4<templa.GetSize();z4++)

5194

o->m_pRevSDF->m_vaData[0].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

5195

} // Ende IF RevSDF

5196

5197

} // Ende IF m_bSelf

5198

5199

if (o->m_bOthers)

5200

{

5201

secondmolrun = false;

5202

_secondmolstart:

5203

if ((!secondmolrun) && (o->m_pConditions != NULL))

5204

{

5205

o->m_pConditions->m_bAnyPassed = false;

5206

o->m_pConditions->ScanNeighborhoodAllOM(g_pTempTimestep,smfix);

5207

if (o->m_pConditions->m_bAnyPassed)

5208

o->m_pConditions->m_iRMPassCounter[z2]++;

5209

}

5210

5211

if ((secondmolrun) && (o->m_pConditionsOM2 != NULL))

5212

{

5213

o->m_pConditionsOM2->m_bAnyPassed = false;

5214

o->m_pConditionsOM2->ScanNeighborhoodAllOM(g_pTempTimestep,smfix);

5215

if (o->m_pConditionsOM2->m_bAnyPassed)

5216

o->m_pConditionsOM2->m_iRMPassCounter[z2]++;

5217

}

5218

5219

for (z3=0;z3<(secondmolrun?o->m_iShowMol2Count:o->m_iShowMolCount);z3++) // Alle anderen Molekuele durchgehen

5220

{

5221

if (secondmolrun)

5222

{

5223

if ((g_iFixMol == o->m_iShowMol2) && (z3 == z2)) // Wir wollen nicht das Referenzmolekuel mitzaehlen

5224

continue;

5225

if (o->m_bObsCertain)

5226

{

5227

if (!o->m_waObsShow2List.Contains(z3))

5228

continue;

5229

tic_o = o->m_waObsShow2List.GetPosition(z3);

5230

}

5231

} else

5232

{

5233

if ((g_iFixMol == o->m_iShowMol) && (z3 == z2)) // Wir wollen nicht das Referenzmolekuel mitzaehlen

5234

continue;

5235

if (o->m_bObsCertain)

5236

{

5237

if (!o->m_waObsShowList.Contains(z3))

5238

continue;

5239

tic_o = o->m_waObsShowList.GetPosition(z3);

5240

}

5241

}

5242

5243

if (g_bRegionAnalysis)

5244

{

5245

if (secondmolrun)

5246

{

5247

if ((!o->m_iaOM2Regions.Contains(0)) && (!o->m_iaOM2Regions.Contains(g_iaSMRegion[((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex[z3]])))

5248

continue;

5249

} else

5250

{

5251

if ((!o->m_iaOM1Regions.Contains(0)) && (!o->m_iaOM1Regions.Contains(g_iaSMRegion[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]])))

5252

continue;

5253

}

5254

}

5255

// mprintf("\n ... OM %d ist drin!",z3);

5256

5257

if (secondmolrun)

5258

{

5259

ti = -1;

5260

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol2])->m_laSingleMolIndex[z3]];

5261

} else

5262

{

5263

ti = o->m_waSaveShowList.GetPosition(z3);

5264

sm = (CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex[z3]];

5265

}

5266

5267

if (o->m_bTimeDev && (o->m_pConditions != NULL))

5268

{

5269

if (!o->m_pConditions->Contains(z3) && (!g_bDeriv || (g_iSteps > 2)))

5270

{

5271

for (zr=0;zr<g_iCDFChannels;zr++)

5272

{

5273

if (g_bADF && (o->m_pADF[zr] != NULL))

5274

{

5275

if ((ti2 != -1) && (ti != -1))

5276

{

5277

if (o->m_bSaveSeparateFiles)

5278

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"; - ");

5279

else mfprintf(o->m_pADF[zr]->m_fAngle[0],"; - ");

5280

}

5281

}

5282

5283

if (g_bDDF && (o->m_pDDF[zr] != NULL))

5284

{

5285

if ((ti2 != -1) && (ti != -1))

5286

{

5287

if (o->m_bSaveSeparateFiles)

5288

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"; - ");

5289

else mfprintf(o->m_pDDF[zr]->m_fAngle[0],"; - ");

5290

}

5291

}

5292

5293

if (g_bDipDF && (o->m_pDipDF[zr] != NULL))

5294

{

5295

if ((ti2 != -1) && (ti != -1))

5296

{

5297

if (o->m_bSaveSeparateFiles)

5298

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; - ");

5299

else mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"; - ");

5300

}

5301

}

5302

5303

if (g_bVDF && (o->m_pVDF[zr] != NULL))

5304

{

5305

if ((ti2 != -1) && (ti != -1))

5306

{

5307

if (o->m_bSaveSeparateFiles)

5308

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; - ");

5309

else mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"; - ");

5310

}

5311

}

5312

5313

if (g_bRDF && (o->m_pRDF[zr] != NULL))

5314

{

5315

if ((ti2 != -1) && (ti != -1))

5316

{

5317

if (o->m_bSaveSeparateFiles)

5318

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"; - ");

5319

else mfprintf(o->m_pRDF[zr]->m_fDist[0],"; - ");

5320

}

5321

}

5322

}

5323

continue;

5324

}

5325

}

5326

5327

if ((!secondmolrun) && (o->m_pConditions != NULL))

5328

{

5329

if (!o->m_pConditions->Contains(z3))

5330

continue;

5331

5332

if (o->m_bBinOnlyPassedAtoms)

5333

o->m_pConditions->MarkPassedAtoms(z3,true);

5334

5335

if (o->m_bBinOnlyNotPassedAtoms)

5336

o->m_pConditions->MarkPassedAtoms(z3,false);

5337

5338

if (g_bSaveCondSnapshot)

5339

{

5340

g_iSaveCondCount++;

5341

if (g_bSaveCondWholeBox)

5342

{

5343

g_pTempTimestep->WriteTimestep(g_fSaveCondFile);

5344

} else

5345

{

5346

5347

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z4++)

5348

{

5349

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

5350

continue;

5351

for (z5=0;z5<((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetSize();z5++)

5352

5353

}

5354

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex.GetSize();z4++)

5355

{

5356

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

5357

continue;

5358

for (z5=0;z5<((CxIntArray*)sm->m_oaAtomOffset[z4])->GetSize();z5++)

5359

5360

}

5361

}

5362

}

5363

}

5364

5365

if (secondmolrun && (o->m_pConditionsOM2 != NULL))

5366

{

5367

if (!o->m_pConditionsOM2->Contains(z3))

5368

continue;

5369

5370

// mprintf("\nStep %d: z2=%d, z3=%d passed.",g_iSteps,z2,z3);

5371

5372

if (o->m_bBinOnlyPassedAtoms)

5373

o->m_pConditionsOM2->MarkPassedAtoms(z3,true);

5374

5375

if (o->m_bBinOnlyNotPassedAtoms)

5376

o->m_pConditionsOM2->MarkPassedAtoms(z3,false);

5377

5378

/* if (g_bSaveCondSnapshot)

5379

{

5380

g_iSaveCondCount++;

5381

if (g_bSaveCondWholeBox)

5382

{

5383

g_pTempTimestep->WriteTimestep(g_fSaveCondFile);

5384

} else

5385

{

5386

5387

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z4++)

5388

{

5389

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

5390

continue;

5391

for (z5=0;z5<((CxIntArray*)smfix->m_oaAtomOffset[z4])->GetSize();z5++)

5392

5393

}

5394

for (z4=0;z4<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex.GetSize();z4++)

5395

{

5396

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_baAtomIndex[z4] == g_iVirtAtomType))

5397

continue;

5398

for (z5=0;z5<((CxIntArray*)sm->m_oaAtomOffset[z4])->GetSize();z5++)

5399

5400

}

5401

}

5402

}*/

5403

}

5404

5405

if (g_bVHDF)

5406

{

5407

o->m_pVHDF->BuildAtomList(smfix,sm,&templa);

5408

for (z4=0;z4<templa.GetSize();z4+=2)

5409

{

5410

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];// + vecc;

5411

for (z0=0;z0<o->m_pVHDF->m_iDepth/o->m_pVHDF->m_iStride;z0++)

5412

{

5413

g_pT2Timestep = GetTimeStep(z0*o->m_pVHDF->m_iStride);

5414

if (g_pT2Timestep == NULL)

5415

continue;

5416

vec1 = g_pT2Timestep->m_vaCoords[templa[z4+1]];

5417

tf = FoldedLength(vec0-vec1);

5418

o->m_pVHDF->m_pVHDF->AddToBin_IntX_fast(z0,tf);

5419

o->m_pVHDF->m_pCount[z0]++;

5420

}

5421

}

5422

} // Ende IF VHDF

5423

5424

if (g_bADF)

5425

{

5426

for (zr=0;zr<g_iCDFChannels;zr++)

5427

{

5428

if (o->m_pADF[zr] == NULL)

5429

continue;

5430

if (o->m_bSecondShowMol)

5431

{

5432

if (secondmolrun && (zr == 0))

5433

continue;

5434

if (!secondmolrun && (zr == 1))

5435

continue;

5436

}

5437

o->m_pADF[zr]->BuildAtomList(smfix,sm,&templa);

5438

for (z4=0;z4<templa.GetSize();z4+=6)

5439

{

5440

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5441

{

5442

tb = true;

5443

if (g_baAtomPassedCondition[templa[z4]] == 0)

5444

tb = false;

5445

if (g_baAtomPassedCondition[templa[z4+1]] == 0)

5446

tb = false;

5447

if (o->m_pADF[zr]->m_bOrtho[0])

5448

if (g_baAtomPassedCondition[templa[z4+2]] == 0)

5449

tb = false;

5450

if (g_baAtomPassedCondition[templa[z4+3]] == 0)

5451

tb = false;

5452

if (g_baAtomPassedCondition[templa[z4+4]] == 0)

5453

tb = false;

5454

if (o->m_pADF[zr]->m_bOrtho[1])

5455

if (g_baAtomPassedCondition[templa[z4+5]] == 0)

5456

tb = false;

5457

if (tb)

5458

{

5459

o->m_pADF[zr]->m_baDataEnabled[z3].Add(1);

5460

} else

5461

{

5462

5463

o->m_pADF[zr]->m_baDataEnabled[z3].Add(0);

5464

}

5465

}

5466

if (o->m_pADF[zr]->m_bOrtho[0])

5467

{

5468

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5469

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5470

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

5471

vec1 = CrossP(FoldVector(vec2-vec0),FoldVector(vec3-vec0));

5472

} else

5473

{

5474

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5475

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5476

vec1 = FoldVector(vec2-vec0);

5477

}

5478

if (o->m_pADF[zr]->m_bOrtho[1])

5479

{

5480

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

5481

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

5482

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

5483

vec2 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

5484

} else

5485

{

5486

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

5487

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

5488

vec2 = FoldVector(vec3-vec4);

5489

}

5490

5491

tf = Angle_Deg(vec1,vec2);

5492

if ((tf > 90.0f) && (o->m_pADF[zr]->m_bFoldAngle))

5493

tf = 180.0f-tf;

5494

if (o->m_pADF[zr]->m_bCosine)

5495

tf = cos(tf/180.0*Pi);

5496

5497

if (g_bDeriv)

5498

{

5499

zi = (z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6;

5500

o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5501

switch(o->m_pADF[zr]->m_iDeriv)

5502

{

5503

case 0:

5504

tf = o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5505

break;

5506

case 1:

5507

tf = (o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pADF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5508

break;

5509

case 2:

5510

5511

break;

5512

}

5513

}

5514

if (!g_bDeriv || (g_iSteps > 2))

5515

{

5516

if (o->m_bObsCertain && o->m_bDecompDist)

5517

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5518

5519

o->m_pADF[zr]->m_faData[z3].Add(tf);

5520

5521

if (o->m_pADF[zr]->m_bACF)

5522

o->m_pADF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6]->Add((float)tf);

5523

5524

/* if (o->m_pADF[zr]->m_bMirror)

5525

{

5526

if (o->m_bObsCertain && o->m_bDecompDist)

5527

o->m_pADF[zr]->m_pADF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,180.0-tf);

5528

o->m_pADF[zr]->m_faData[z3].Add(180.0-tf);

5529

}*/

5530

5531

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5532

{

5533

// o->m_pAngleStat->AddValue(ti2,ti,tf);

5534

if (o->m_bSaveSeparateFiles)

5535

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"; %8.3f",tf);

5536

else mfprintf(o->m_pADF[zr]->m_fAngle[0],"; %8.3f",tf);

5537

if (o->m_bCombinedPlot)

5538

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pADF[zr]->m_iCombinations+z4/6,g_iSteps*g_fTimestepLength/1000.0,tf);

5539

}

5540

if (o->m_bTimeDiff)

5541

((CxFloatArray*)o->m_pADF[zr]->m_pADF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pADF[zr]->m_iCombinations+z4/6])->Add((float)tf);

5542

}

5543

}

5544

}

5545

} // Ende IF ADF

5546

5547

if (g_bDDF)

5548

{

5549

for (zr=0;zr<g_iCDFChannels;zr++)

5550

{

5551

if (o->m_pDDF[zr] == NULL)

5552

continue;

5553

if (o->m_bSecondShowMol)

5554

{

5555

if (secondmolrun && (zr == 0))

5556

continue;

5557

if (!secondmolrun && (zr == 1))

5558

continue;

5559

}

5560

o->m_pDDF[zr]->BuildAtomList(smfix,sm,&templa);

5561

for (z4=0;z4<templa.GetSize();z4+=9)

5562

{

5563

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5564

{

5565

tb = true;

5566

for (z5=z4;z5<z4+9;z5++)

5567

if (g_baAtomPassedCondition[templa[z5]] == 0)

5568

tb = false;

5569

if (tb)

5570

o->m_pDDF[zr]->m_baDataEnabled[z3].Add(1);

5571

else o->m_pDDF[zr]->m_baDataEnabled[z3].Add(0);

5572

}

5573

if (o->m_pDDF[zr]->m_bOrtho[0])

5574

{

5575

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5576

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5577

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+2]];

5578

vec1 = CrossP(FoldVector(vec2-vec0),FoldVector(vec3-vec0));

5579

} else

5580

{

5581

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5582

vec2 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5583

vec1 = FoldVector(vec2-vec0);

5584

}

5585

if (o->m_pDDF[zr]->m_bOrtho[1])

5586

{

5587

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

5588

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

5589

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+5]];

5590

vec2 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

5591

} else

5592

{

5593

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+3]];

5594

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+4]];

5595

vec2 = FoldVector(vec3-vec4);

5596

}

5597

if (o->m_pDDF[zr]->m_bOrtho[2])

5598

{

5599

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

5600

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

5601

vec5 = g_pTempTimestep->m_vaCoords[templa[z4+8]];

5602

vec3 = CrossP(FoldVector(vec3-vec4),FoldVector(vec5-vec4));

5603

} else

5604

{

5605

vec4 = g_pTempTimestep->m_vaCoords[templa[z4+6]];

5606

vec3 = g_pTempTimestep->m_vaCoords[templa[z4+7]];

5607

vec3 = FoldVector(vec3-vec4);

5608

}

5609

tf = Dihedral(vec1,vec2,vec3,o->m_pDDF[zr]->m_bAbs);

5610

if (o->m_pDDF[zr]->m_bCosine)

5611

tf = cos(tf/180.0*Pi);

5612

else if (o->m_pDDF[zr]->m_bPositive)

5613

if (tf < 0)

5614

tf += 360.0;

5615

if (g_bDeriv)

5616

{

5617

zi = (z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9;

5618

o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5619

switch(o->m_pDDF[zr]->m_iDeriv)

5620

{

5621

case 0:

5622

tf = o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5623

break;

5624

case 1:

5625

tf = (o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pDDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5626

break;

5627

case 2:

5628

5629

break;

5630

}

5631

}

5632

if (!g_bDeriv || (g_iSteps > 2))

5633

{

5634

if (o->m_bObsCertain && o->m_bDecompDist)

5635

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5636

5637

o->m_pDDF[zr]->m_faData[z3].Add(tf);

5638

5639

if (o->m_pDDF[zr]->m_bACF)

5640

o->m_pDDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]->Add((float)tf);

5641

5642

if (/*(!o->m_pDDF[zr]->m_bAbs) && */o->m_pDDF[zr]->m_bSymm)

5643

{

5644

o->m_pDDF[zr]->m_faData[z3].Add(-tf);

5645

if (o->m_bObsCertain && o->m_bDecompDist)

5646

o->m_pDDF[zr]->m_pDDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,-tf);

5647

}

5648

5649

if (o->m_bTimeDiff)

5650

((CxFloatArray*)o->m_pDDF[zr]->m_pDDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9])->Add((float)tf);

5651

5652

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5653

{

5654

if (o->m_pDDF[zr]->m_bRotate)

5655

{

5656

if (g_iSteps > 1)

5657

{

5658

if ((tf - o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]) > 180.0)

5659

o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]--;

5660

if ((tf - o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]) < -180.0)

5661

o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9]++;

5662

}

5663

o->m_pDDF[zr]->m_faLastData[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9] = tf;

5664

tf2 = tf + o->m_pDDF[zr]->m_laRotation[(z2*o->m_iShowMolCount+z3)*o->m_pDDF[zr]->m_iCombinations+z4/9] * 360.0;

5665

} else tf2 = tf;

5666

if (o->m_bSaveSeparateFiles)

5667

mfprintf(o->m_pDDF[zr]->m_fAngle[ti2],"; %8.3f",tf2);

5668

else mfprintf(o->m_pDDF[zr]->m_fAngle[0],"; %8.3f",tf2);

5669

if (o->m_bCombinedPlot)

5670

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pDDF[zr]->m_iCombinations+z4/9,g_iSteps*g_fTimestepLength/1000.0,tf);

5671

}

5672

}

5673

}

5674

}

5675

} // Ende IF DDF

5676

5677

if (g_bPlDF)

5678

{

5679

for (zr=0;zr<g_iCDFChannels;zr++)

5680

{

5681

if (o->m_pPlDF[zr] == NULL)

5682

continue;

5683

if (o->m_bSecondShowMol)

5684

{

5685

if (secondmolrun && (zr == 0))

5686

continue;

5687

if (!secondmolrun && (zr == 1))

5688

continue;

5689

}

5690

o->m_pPlDF[zr]->BuildAtomList(smfix,sm,&templa);

5691

for (z4=0;z4<templa.GetSize();z4+=4)

5692

{

5693

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5694

{

5695

tb = true;

5696

for (z5=z4;z5<z4+4;z5++)

5697

if (g_baAtomPassedCondition[templa[z5]] == 0)

5698

tb = false;

5699

if (tb)

5700

o->m_pPlDF[zr]->m_baDataEnabled[z3].Add(1);

5701

else o->m_pPlDF[zr]->m_baDataEnabled[z3].Add(0);

5702

}

5703

if (o->m_pPlDF[zr]->m_bNormal)

5704

{

5705

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5706

vec0.Normalize();

5707

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5708

tf = DotP(vec0,vec1);

5709

} else

5710

{

5711

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5712

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+2]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5713

vec3 = CrossP(vec0,vec1);

5714

vec3.Normalize();

5715

vec2 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5716

tf = DotP(vec2,vec3);

5717

}

5718

5719

if (!g_bDeriv || (g_iSteps > 2))

5720

{

5721

if (o->m_bObsCertain && o->m_bDecompDist)

5722

o->m_pPlDF[zr]->m_pPlDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5723

5724

o->m_pPlDF[zr]->m_faData[z3].Add(tf);

5725

}

5726

}

5727

}

5728

} // Ende IF PlDF

5729

5730

if (g_bLiDF)

5731

{

5732

for (zr=0;zr<g_iCDFChannels;zr++)

5733

{

5734

if (o->m_pLiDF[zr] == NULL)

5735

continue;

5736

if (o->m_bSecondShowMol)

5737

{

5738

if (secondmolrun && (zr == 0))

5739

continue;

5740

if (!secondmolrun && (zr == 1))

5741

continue;

5742

}

5743

o->m_pLiDF[zr]->BuildAtomList(smfix,sm,&templa);

5744

for (z4=0;z4<templa.GetSize();z4+=4)

5745

{

5746

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5747

{

5748

tb = true;

5749

for (z5=z4;z5<z4+4;z5++)

5750

if (g_baAtomPassedCondition[templa[z5]] == 0)

5751

tb = false;

5752

if (tb)

5753

o->m_pLiDF[zr]->m_baDataEnabled[z3].Add(1);

5754

else o->m_pLiDF[zr]->m_baDataEnabled[z3].Add(0);

5755

}

5756

5757

if (o->m_pLiDF[zr]->m_bNormal)

5758

{

5759

vec2 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5760

vec3 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+2]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5761

vec0 = CrossP(vec2,vec3);

5762

vec0.Normalize();

5763

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5764

vec0 *= DotP(vec0,vec1);

5765

tf = (vec1 - vec0).GetLength();

5766

} else

5767

{

5768

vec0 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+1]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5769

vec0.Normalize();

5770

vec1 = FoldVector(g_pTempTimestep->m_vaCoords[templa[z4+3]] - g_pTempTimestep->m_vaCoords[templa[z4]]);

5771

vec0 *= DotP(vec0,vec1);

5772

tf = (vec1 - vec0).GetLength();

5773

}

5774

5775

if (!g_bDeriv || (g_iSteps > 2))

5776

{

5777

if (o->m_bObsCertain && o->m_bDecompDist)

5778

o->m_pLiDF[zr]->m_pLiDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5779

5780

o->m_pLiDF[zr]->m_faData[z3].Add(tf);

5781

}

5782

}

5783

}

5784

} // Ende IF LilDF

5785

5786

if (g_bDipDF)

5787

{

5788

for (zr=0;zr<g_iCDFChannels;zr++)

5789

{

5790

if (o->m_pDipDF[zr] == NULL)

5791

continue;

5792

if (o->m_bSecondShowMol)

5793

{

5794

if (secondmolrun && (zr == 0))

5795

continue;

5796

if (!secondmolrun && (zr == 1))

5797

continue;

5798

}

5799

if (o->m_pDipDF[zr]->m_iRefOrSec == 0)

5800

tf = smfix->m_vDipole.GetLength();

5801

else tf = sm->m_vDipole.GetLength();

5802

if (g_bDeriv)

5803

{

5804

zi = z2*o->m_iShowMolCount+z3;

5805

o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5806

switch(o->m_pDipDF[zr]->m_iDeriv)

5807

{

5808

case 0:

5809

tf = o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5810

break;

5811

case 1:

5812

tf = (o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pDipDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5813

break;

5814

case 2:

5815

5816

break;

5817

}

5818

}

5819

if (!g_bDeriv || (g_iSteps > 2))

5820

{

5821

if (o->m_bObsCertain && o->m_bDecompDist)

5822

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5823

5824

o->m_pDipDF[zr]->m_faData[z3].Add(tf);

5825

5826

if (o->m_pDipDF[zr]->m_bACF)

5827

o->m_pDipDF[zr]->m_pfaACFBuffer[z2*o->m_iShowMolCount+z3]->Add((float)tf);

5828

5829

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5830

{

5831

if (o->m_bSaveSeparateFiles)

5832

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"; %8.3f",tf);

5833

else mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"; %8.3f",tf);

5834

if (o->m_bCombinedPlot)

5835

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->AddXYTupel(ti2*o->m_waSaveShowList.GetSize()+ti,g_iSteps*g_fTimestepLength/1000.0,tf);

5836

}

5837

if (o->m_bTimeDiff)

5838

((CxFloatArray*)o->m_pDipDF[zr]->m_pDipoleDF->m_oaTimeDiffBuf[z2*o->m_iShowMolCount+z3])->Add((float)tf);

5839

}

5840

}

5841

} // Ende IF DIPOLE

5842

5843

if (g_bVDF)

5844

{

5845

for (zr=0;zr<g_iCDFChannels;zr++)

5846

{

5847

if (o->m_pVDF[zr] == NULL)

5848

continue;

5849

if (o->m_bSecondShowMol)

5850

{

5851

if (secondmolrun && (zr == 0))

5852

continue;

5853

if (!secondmolrun && (zr == 1))

5854

continue;

5855

}

5856

o->m_pVDF[zr]->BuildAtomList(smfix,sm,&templa);

5857

for (z4=0;z4<templa.GetSize();z4++)

5858

{

5859

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5860

{

5861

tb = true;

5862

for (z5=z4;z5<z4+2;z5++)

5863

if (g_baAtomPassedCondition[templa[z5]] == 0)

5864

tb = false;

5865

if (tb)

5866

o->m_pVDF[zr]->m_baDataEnabled[z3].Add(1);

5867

else o->m_pVDF[zr]->m_baDataEnabled[z3].Add(0);

5868

}

5869

tf = tempvel[templa[z4]].GetLength();

5870

if (g_bDeriv)

5871

{

5872

zi = (z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2;

5873

o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5874

switch(o->m_pVDF[zr]->m_iDeriv)

5875

{

5876

case 0:

5877

tf = o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5878

break;

5879

case 1:

5880

tf = (o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pVDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5881

break;

5882

case 2:

5883

5884

break;

5885

}

5886

}

5887

if (!g_bDeriv || (g_iSteps > 2))

5888

{

5889

if (o->m_bObsCertain && o->m_bDecompDist)

5890

o->m_pVDF[zr]->m_pVDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5891

5892

o->m_pVDF[zr]->m_faData[z3].Add(tf);

5893

5894

if (o->m_pVDF[zr]->m_bACF)

5895

o->m_pVDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

5896

5897

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5898

{

5899

if (o->m_bSaveSeparateFiles)

5900

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"; %8.3f",tf);

5901

else mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"; %8.3f",tf);

5902

if (o->m_bCombinedPlot)

5903

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pVDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

5904

}

5905

if (o->m_bTimeDiff)

5906

((CxFloatArray*)o->m_pVDF[zr]->m_pVDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pVDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

5907

}

5908

}

5909

}

5910

} // Ende IF VDF

5911

5912

if (g_bRDF)

5913

{

5914

for (zr=0;zr<g_iCDFChannels;zr++)

5915

{

5916

if (o->m_pRDF[zr] == NULL)

5917

continue;

5918

if (o->m_bSecondShowMol)

5919

{

5920

if (secondmolrun && (zr == 0))

5921

continue;

5922

if (!secondmolrun && (zr == 1))

5923

continue;

5924

}

5925

o->m_pRDF[zr]->BuildAtomList(smfix,sm,&templa);

5926

for (z4=0;z4<templa.GetSize();z4+=2)

5927

{

5928

if (o->m_bBinOnlyPassedAtoms || o->m_bBinOnlyNotPassedAtoms)

5929

{

5930

tb = true;

5931

for (z5=z4;z5<z4+2;z5++)

5932

if (g_baAtomPassedCondition[templa[z5]] == 0)

5933

tb = false;

5934

if (tb)

5935

o->m_pRDF[zr]->m_baDataEnabled[z3].Add(1);

5936

else o->m_pRDF[zr]->m_baDataEnabled[z3].Add(0);

5937

}

5938

vec0 = g_pTempTimestep->m_vaCoords[templa[z4]];

5939

vec1 = g_pTempTimestep->m_vaCoords[templa[z4+1]];

5940

tf = FoldedLength(vec0-vec1);

5941

/* if (tf > 2000)

5942

{

5943

mprintf("\n@ z2=%d, z3=%d, z4=%d, templa[z4]=%d, templa[z4+1]=%d, dist=%f ",z2,z3,z4,templa[z4],templa[z4+1],tf);

5944

mprintf("\n vec0: "); vec0.Dump(); mprintf(", vec1: "); vec1.Dump(); mprintf(", vec2: "); vec2.Dump();

5945

}

5946

*/ // mprintf("\n@ z2=%d, z3=%d, z4=%d, templa[z4]=%d, templa[z4+1]=%d, dist=%f ",z2,z3,z4,templa[z4],templa[z4+1],tf);

5947

// mprintf("\n vec0: "); vec0.Dump(); mprintf(", vec1: "); vec1.Dump(); mprintf(", vec2: "); vec2.Dump();

5948

if (g_bDeriv)

5949

{

5950

zi = (z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2;

5951

o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) = tf;

5952

switch(o->m_pRDF[zr]->m_iDeriv)

5953

{

5954

case 0:

5955

tf = o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivCurr]->GetAt(zi);

5956

break;

5957

case 1:

5958

tf = (o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivNext]->GetAt(zi) - o->m_pRDF[zr]->m_pfaDerivBuffer[g_iDerivLast]->GetAt(zi)) / (2*g_fTimestepLength);

5959

break;

5960

case 2:

5961

5962

break;

5963

}

5964

}

5965

if (!g_bDeriv || (g_iSteps > 2))

5966

{

5967

if (o->m_bObsCertain && o->m_bDecompDist)

5968

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(tic_r*o->m_waObsShowList.GetSize()+tic_o,tf);

5969

5970

if (o->m_bDecompType)

5971

o->m_pRDF[zr]->m_pRDF->AddToBin_Multi(o->m_waDecompTypeRefOffs[templa[z4]]*o->m_waDecompTypeObsOffs.GetSize()+o->m_waDecompTypeObsOffs[templa[z4+1]],tf);

5972

5973

o->m_pRDF[zr]->m_faData[z3].Add(tf);

5974

5975

if (o->m_pRDF[zr]->m_bACF)

5976

o->m_pRDF[zr]->m_pfaACFBuffer[(z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2]->Add((float)tf);

5977

5978

if (o->m_bTimeDev && (ti2 != -1) && (ti != -1))

5979

{

5980

if (o->m_bSaveSeparateFiles)

5981

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"; %10.3f",tf);

5982

else mfprintf(o->m_pRDF[zr]->m_fDist[0],"; %10.3f",tf);

5983

if (o->m_bCombinedPlot)

5984

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pRDF[zr]->m_iCombinations+z4/2,g_iSteps*g_fTimestepLength/1000.0,tf);

5985

}

5986

if (o->m_bTimeDiff)

5987

((CxFloatArray*)o->m_pRDF[zr]->m_pRDF->m_oaTimeDiffBuf[(z2*o->m_iShowMolCount+z3)*o->m_pRDF[zr]->m_iCombinations+z4/2])->Add((float)tf);

5988

}

5989

}

5990

}

5991

} // Ende IF RDF

5992

5993

if (g_bSDF)

5994

{

5995

o->m_pSDF->BuildAtomList(smfix,sm,&templa);

5996

for (z4=0;z4<templa.GetSize();z4++)

5997

{

5998

o->m_pSDF->m_vaData[z3].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

5999

6000

if (o->m_pSDF->m_bVdWSpheres)

6001

o->m_pSDF->m_faRadius[z3].Add(g_faVdWRadius[templa[z4]]);

6002

}

5863

6003

} // Ende IF SDF

5864

5865

if (g_bRevSDF)

6004

6005

if (g_bPlProj)

5866

6006

{

5867

o->m_pRevSDF->BuildAtomList(smfix,sm,&templa);

6007

o->m_pPlProj->BuildAtomList(smfix,sm,&templa);

5868

6008

for (z4=0;z4<templa.GetSize();z4++)

5869

o->m_pRevSDF->m_vaData[z3].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

5870

} // Ende IF RevSDF

5871

5872

} // Ende FOR Alle anderen Molekuele durchgehen

5873

if (o->m_bSecondShowMol && (!secondmolrun))

5874

{

5875

secondmolrun = true;

5876

goto _secondmolstart;

5877

}

5878

} // Ende IF m_bOthers

5879

5880

if (g_bSDF)

5881

{

5882

if (o->m_pSDF->m_bSDFMirrorBisect)

5883

{

5884

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

5885

vec3 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

5886

vec1 = CrossP(vec2,vec3);

5887

vec2 += vec3;

5888

}

5889

5890

if (o->m_pSDF->m_bCutPlane)

5891

{

5892

o->m_pSDF->m_fAtom2PosX += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])][0];

5893

o->m_pSDF->m_fAtom3PosX += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])][0];

5894

o->m_pSDF->m_fAtom3PosY += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])][1];

5895

o->m_pSDF->m_fPosCounter++;

5896

}

5897

5898

if (o->m_bSelf)

5899

{

5900

for (z5=0;z5<o->m_pSDF->m_vaData[0].GetSize();z5++)

5901

{

5902

vec0 = o->m_pSDF->m_vaData[0][z5];

5903

5904

if (o->m_pSDF->m_bVdWSpheres)

5905

o->m_pSDF->m_pSDF->AddToBin_Sphere(vec0,o->m_pSDF->m_faRadius[0][z5]);

5906

else o->m_pSDF->m_pSDF->AddToBin(vec0);

5907

5908

if (o->m_pSDF->m_bSDFMirrorXY)

5909

{

5910

vec0[2] = -vec0[2];

5911

o->m_pSDF->m_pSDF->AddToBin(vec0);

5912

}

5913

5914

if (o->m_pSDF->m_bSDFMirrorBisect)

5915

{

5916

vec3.PointRoot(vec1,vec2,vec0);

5917

vec3 -= vec0;

5918

vec3 *= 2.0f;

5919

vec0 += vec3;

5920

o->m_pSDF->m_pSDF->AddToBin(vec0);

5921

if (o->m_pSDF->m_bSDFMirrorXY)

5922

{

5923

vec0[2] = -vec0[2];

5924

o->m_pSDF->m_pSDF->AddToBin(vec0);

5925

}

5926

}

5927

}

5928

} else

5929

{

5930

for (z4=0;z4<o->m_iShowMolCount;z4++)

5931

{

5932

for (z5=0;z5<o->m_pSDF->m_vaData[z4].GetSize();z5++)

5933

{

5934

vec0 = o->m_pSDF->m_vaData[z4][z5];

5935

5936

if (o->m_pSDF->m_bVdWSpheres)

5937

o->m_pSDF->m_pSDF->AddToBin_Sphere(vec0,o->m_pSDF->m_faRadius[z4][z5]);

5938

else o->m_pSDF->m_pSDF->AddToBin(vec0);

5939

5940

if (o->m_pSDF->m_bSDFMirrorXY)

5941

{

5942

vec0[2] = -vec0[2];

5943

o->m_pSDF->m_pSDF->AddToBin(vec0);

5944

}

5945

5946

if (o->m_pSDF->m_bSDFMirrorBisect)

5947

{

5948

vec3.PointRoot(vec1,vec2,vec0);

5949

vec3 -= vec0;

5950

vec3 *= 2.0f;

5951

vec0 += vec3;

5952

o->m_pSDF->m_pSDF->AddToBin(vec0);

5953

if (o->m_pSDF->m_bSDFMirrorXY)

5954

{

5955

vec0[2] = -vec0[2];

5956

o->m_pSDF->m_pSDF->AddToBin(vec0);

5957

}

5958

}

5959

}

5960

}

5961

}

5962

}

5963

5964

if (g_bRevSDF)

5965

{

5966

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

5967

tf4 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])].GetLength();

5968

o->m_pRevSDF->m_fSecondAtomPosX += tf4;

5969

o->m_pRevSDF->m_fSecondAtomCount++;

5970

if (o->m_bSelf)

5971

{

5972

for (z5=0;z5<o->m_pRevSDF->m_vaData[0].GetSize();z5++)

5973

{

5974

vec0 = o->m_pRevSDF->m_vaData[0][z5];

5975

tf = fabs(Angle(vec2,vec0));

5976

tf2 = vec0.GetLength();

5977

tf3 = 1.0;

5978

if (o->m_pRevSDF->m_bCorrectAngle)

5979

{

5980

if ((tf < 0.001) || (tf > Pi-0.001))

5981

tf3 /= 0.001;

5982

else tf3 /= sin(tf);

5983

}

5984

if (o->m_pRevSDF->m_bCorrectRadial)

5985

tf3 /= tf2; // Erste Potenz, da 2D-Grid (SDF hat "nullte Potenz" ^^)

5986

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,cos(tf)*tf2,tf3);

5987

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,cos(tf)*tf2,tf3);

5988

if (o->m_pRevSDF->m_bMirrorY)

5989

{

5990

if (o->m_pRevSDF->m_bMirrorBond)

5991

{

5992

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

5993

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

5994

} else

5995

{

5996

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,-cos(tf)*tf2,tf3);

5997

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,-cos(tf)*tf2,tf3);

5998

}

5999

}

6000

}

6001

} else

6002

{

6003

for (z4=0;z4<o->m_iShowMolCount;z4++)

6004

{

6005

for (z5=0;z5<o->m_pRevSDF->m_vaData[z4].GetSize();z5++)

6006

{

6007

vec0 = o->m_pRevSDF->m_vaData[z4][z5];

6008

tf = fabs(Angle(vec2,vec0));

6009

tf2 = vec0.GetLength();

6010

tf3 = 1.0;

6011

if (o->m_pRevSDF->m_bCorrectAngle)

6012

{

6013

if ((tf < 0.001) || (tf > Pi-0.001))

6014

tf3 /= 0.001;

6015

else tf3 /= sin(tf);

6016

}

6017

if (o->m_pRevSDF->m_bCorrectRadial)

6018

tf3 /= tf2; // Erste Potenz, da 2D-Grid (SDF hat "nullte Potenz" ^^)

6019

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,cos(tf)*tf2,tf3);

6020

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,cos(tf)*tf2,tf3);

6021

if (o->m_pRevSDF->m_bMirrorY)

6022

{

6023

if (o->m_pRevSDF->m_bMirrorBond)

6024

{

6025

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

6026

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

6027

} else

6028

{

6029

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,-cos(tf)*tf2,tf3);

6030

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,-cos(tf)*tf2,tf3);

6031

}

6032

}

6033

}

6034

}

6035

}

6036

} // END IF REVSDF

6037

6038

if (g_bCDF && (!g_bDeriv || (g_iSteps > 2)))

6039

{

6040

if (o->m_bSecondShowMol)

6041

{

6042

for (zr=0;zr<g_iCDFChannels;zr++)

6043

{

6044

switch(g_iObsChannel[zr])

6045

{

6046

case 0:

6047

apfa[zr] = o->m_pRDF[zr]->m_faData;

6048

apba[zr] = o->m_pRDF[zr]->m_baDataEnabled;

6049

break;

6050

case 1:

6051

apfa[zr] = o->m_pADF[zr]->m_faData;

6052

apba[zr] = o->m_pADF[zr]->m_baDataEnabled;

6053

break;

6054

case 2:

6055

apfa[zr] = o->m_pDDF[zr]->m_faData;

6056

apba[zr] = o->m_pDDF[zr]->m_baDataEnabled;

6057

break;

6058

case 3:

6059

apfa[zr] = o->m_pDipDF[zr]->m_faData;

6060

apba[zr] = o->m_pDipDF[zr]->m_baDataEnabled;

6061

break;

6062

case 4:

6063

apfa[zr] = o->m_pVDF[zr]->m_faData;

6064

apba[zr] = o->m_pVDF[zr]->m_baDataEnabled;

6065

break;

6066

case 5:

6067

apfa[zr] = o->m_pPlDF[zr]->m_faData;

6068

apba[zr] = o->m_pPlDF[zr]->m_baDataEnabled;

6069

break;

6070

case 6:

6071

apfa[zr] = o->m_pLiDF[zr]->m_faData;

6072

apba[zr] = o->m_pLiDF[zr]->m_baDataEnabled;

6073

break;

6074

}

6075

}

6076

6077

if (g_iCDFChannels == 2)

6078

{

6079

for (z4=0;z4<o->m_iShowMolCount;z4++)

6080

{

6081

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

6082

{

6083

for (z8=0;z8<o->m_iShowMol2Count;z8++)

6084

{

6085

if (o->m_bExclude1eq2 && (z4 == z8))

6086

continue;

6087

6088

for (z7=0;z7<apfa[1][z8].GetSize();z7++)

6089

{

6090

if (o->m_bBinOnlyPassedAtoms)

6091

{

6092

if ((apba[0][z4][z5] == 0) || (apba[1][z8][z7] == 0))

6093

goto _nocdfbin2;

6094

}

6095

if (o->m_bBinOnlyNotPassedAtoms)

6096

{

6097

if ((apba[0][z4][z5] != 0) && (apba[1][z8][z7] != 0))

6098

goto _nocdfbin2;

6099

}

6100

6101

o->m_pCDF->m_p2DF->AddToBin(apfa[0][z4][z5],apfa[1][z8][z7]);

6102

_nocdfbin2:

6103

6104

if (o->m_pCDF->m_bDumpDat)

6105

mfprintf(o->m_pCDF->m_fDump,"%d; %d; %d; %d; %10.3f; %10.3f\n",(int)g_iSteps,z2+1,z4+1,z5+1,apfa[0][z4][z5],apfa[1][z8][z7]);

6106

}

6107

}

6108

}

6109

}

6110

}

6111

} else // IF NOT SECOND_OM

6112

{

6113

for (zr=0;zr<g_iCDFChannels;zr++)

6114

{

6115

switch(g_iObsChannel[zr])

6116

{

6117

case 0:

6118

apfa[zr] = o->m_pRDF[zr]->m_faData;

6119

apba[zr] = o->m_pRDF[zr]->m_baDataEnabled;

6120

break;

6121

case 1:

6122

apfa[zr] = o->m_pADF[zr]->m_faData;

6123

apba[zr] = o->m_pADF[zr]->m_baDataEnabled;

6124

break;

6125

case 2:

6126

apfa[zr] = o->m_pDDF[zr]->m_faData;

6127

apba[zr] = o->m_pDDF[zr]->m_baDataEnabled;

6128

break;

6129

case 3:

6130

apfa[zr] = o->m_pDipDF[zr]->m_faData;

6131

apba[zr] = o->m_pDipDF[zr]->m_baDataEnabled;

6132

break;

6133

case 4:

6134

apfa[zr] = o->m_pVDF[zr]->m_faData;

6135

apba[zr] = o->m_pVDF[zr]->m_baDataEnabled;

6136

break;

6137

case 5:

6138

apfa[zr] = o->m_pPlDF[zr]->m_faData;

6139

apba[zr] = o->m_pPlDF[zr]->m_baDataEnabled;

6140

break;

6141

case 6:

6142

apfa[zr] = o->m_pLiDF[zr]->m_faData;

6143

apba[zr] = o->m_pLiDF[zr]->m_baDataEnabled;

6144

break;

6145

}

6146

}

6147

6148

if (g_iCDFChannels == 2)

6149

{

6150

for (z4=0;z4<o->m_iShowMolCount;z4++)

6151

{

6152

ticomb = 0;

6153

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

6154

{

6155

for (z7=0;z7<apfa[1][z4].GetSize();z7++)

6156

{

6157

6158

/* Workaround for symmetrical DDFs (double data amount) */

6159

if (g_iObsChannel[0] == 2)

6160

{

6161

if (o->m_pDDF[0]->m_bSymm)

6162

{

6163

if (g_iObsChannel[1] == 2)

6164

{

6165

if (o->m_pDDF[1]->m_bSymm)

6166

{

6167

if (o->m_pCDF->m_pCombineList[(z5/2)*o->m_pCDF->m_iCombinations[1]+(z7/2)] == 0)

6168

continue;

6169

goto _ddfsymmdone;

6170

}

6171

}

6172

}

6173

if (o->m_pCDF->m_pCombineList[(z5/2)*o->m_pCDF->m_iCombinations[1]+z7] == 0)

6174

continue;

6175

} else

6176

{

6177

if (g_iObsChannel[1] == 2)

6178

{

6179

if (o->m_pDDF[1]->m_bSymm)

6180

{

6181

if (o->m_pCDF->m_pCombineList[z5*o->m_pCDF->m_iCombinations[1]+(z7/2)] == 0)

6182

continue;

6183

goto _ddfsymmdone;

6184

}

6185

}

6186

if (o->m_pCDF->m_pCombineList[z5*o->m_pCDF->m_iCombinations[1]+z7] == 0)

6187

continue;

6188

}

6189

_ddfsymmdone:

6190

6191

if (o->m_bBinOnlyPassedAtoms)

6192

{

6193

if ((apba[0][z4][z5] == 0) || (apba[1][z4][z7] == 0))

6194

goto _nocdfbin;

6195

}

6196

if (o->m_bBinOnlyNotPassedAtoms)

6197

{

6198

if ((apba[0][z4][z5] != 0) && (apba[1][z4][z7] != 0))

6199

goto _nocdfbin;

6200

}

6201

o->m_pCDF->m_p2DF->AddToBin(apfa[0][z4][z5],apfa[1][z4][z7]);

6202

_nocdfbin:;

6203

if (o->m_pCDF->m_bDumpDat)

6204

mfprintf(o->m_pCDF->m_fDump,"%d; %d; %d; ; %10.3f; %10.3f\n",(int)g_iSteps,z2+1,z4+1,apfa[0][z4][z5],apfa[1][z4][z7]);

6205

if (o->m_bTimeDev)

6206

{

6207

ti = o->m_waSaveShowList.GetPosition(z4);

6208

if ((ti2 != -1) && (ti != -1))

6209

{

6210

if (o->m_bSaveSeparateFiles)

6211

mfprintf(o->m_pCDF->m_fTimeDev[ti2],"; %10.3f; %10.3f",apfa[0][z4][z5],apfa[1][z4][z7]);

6212

else mfprintf(o->m_pCDF->m_fTimeDev[0],"; %10.3f; %10.3f",apfa[0][z4][z5],apfa[1][z4][z7]);

6213

if (o->m_pCDF->m_bTDAnimation)

6214

o->m_pCDF->m_pTDAPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pCDF->m_iCombinationsEnabled+ticomb,apfa[0][z4][z5],apfa[1][z4][z7]);

6215

}

6216

ticomb++;

6217

}

6218

}

6219

}

6220

}

6221

if (o->m_bTimeDev && (ti2 != -1))

6222

{

6223

if (o->m_bSaveSeparateFiles)

6224

mfprintf(o->m_pCDF->m_fTimeDev[ti2],"\n");

6225

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6226

mfprintf(o->m_pCDF->m_fTimeDev[0],"\n");

6227

}

6228

} // END IF CHANNELS == 2

6229

6230

if (g_iCDFChannels == 3)

6231

{

6232

for (z4=0;z4<o->m_iShowMolCount;z4++)

6233

{

6234

ticomb = 0;

6235

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

6236

{

6237

for (z8=0;z8<apfa[1][z4].GetSize();z8++)

6238

{

6239

for (z7=0;z7<apfa[2][z4].GetSize();z7++)

6240

{

6241

if (o->m_pCDF->m_pCombineList[z5*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+z8*o->m_pCDF->m_iCombinations[1]+z7] == 0)

6242

continue;

6243

if (o->m_bBinOnlyPassedAtoms)

6244

{

6245

if ((apba[0][z4][z5] == 0) || (apba[1][z4][z8] == 0) || (apba[2][z4][z7] == 0))

6246

goto _3nocdfbin;

6247

}

6248

if (o->m_bBinOnlyNotPassedAtoms)

6249

{

6250

if ((apba[0][z4][z5] != 0) && (apba[1][z4][z8] != 0) && (apba[2][z4][z7] != 0))

6251

goto _3nocdfbin;

6252

}

6253

o->m_pCDF->m_p3DF->AddToBin(apfa[0][z4][z5],apfa[1][z4][z8],apfa[2][z4][z7]);

6254

6255

o->m_pCDF->m_p3DF->m_p2DF[0]->AddToBin(apfa[0][z4][z5],apfa[1][z4][z8]);

6256

o->m_pCDF->m_p3DF->m_p2DF[1]->AddToBin(apfa[0][z4][z5],apfa[2][z4][z7]);

6257

o->m_pCDF->m_p3DF->m_p2DF[2]->AddToBin(apfa[1][z4][z8],apfa[2][z4][z7]);

6258

_3nocdfbin:;

6259

if (o->m_pCDF->m_bDumpDat)

6260

mfprintf(o->m_pCDF->m_fDump,"%d; %d; %d; ; %10.3f; %10.3f; %10.3f\n",(int)g_iSteps,z2+1,z4+1,apfa[0][z4][z5],apfa[1][z4][z8],apfa[2][z4][z7]);

6261

}

6262

}

6263

}

6264

}

6265

} // END IF CHANNELS == 3

6266

} // IF NOT SECOND_OM

6267

} // IF CDF

6268

6269

for (zr=0;zr<g_iCDFChannels;zr++)

6270

{

6271

if (g_bRDF && !(o->m_bObsCertain && o->m_bDecompDist) && (!o->m_bDecompType) && (o->m_pRDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6272

{

6273

if (o->m_bOthers)

6274

{

6275

if (o->m_bSecondShowMol && (zr == 1))

6276

{

6277

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6278

{

6279

for (z5=0;z5<o->m_pRDF[zr]->m_faData[z4].GetSize();z5++)

6280

{

6281

if (o->m_bBinOnlyPassedAtoms)

6282

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] == 0)

6283

continue;

6284

if (o->m_bBinOnlyNotPassedAtoms)

6285

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] != 0)

6286

continue;

6287

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[z4][z5]);

6288

}

6289

}

6290

} else

6291

{

6292

for (z4=0;z4<o->m_iShowMolCount;z4++)

6293

{

6294

for (z5=0;z5<o->m_pRDF[zr]->m_faData[z4].GetSize();z5++)

6295

{

6296

if (o->m_bBinOnlyPassedAtoms)

6297

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] == 0)

6298

continue;

6299

if (o->m_bBinOnlyNotPassedAtoms)

6300

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] != 0)

6301

continue;

6302

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[z4][z5]);

6303

}

6304

}

6305

}

6306

} else

6307

{

6308

for (z5=0;z5<o->m_pRDF[zr]->m_faData[0].GetSize();z5++)

6309

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[0][z5]);

6310

}

6311

if (o->m_bTimeDev && (ti2 != -1))

6312

{

6313

if (o->m_bSaveSeparateFiles)

6314

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"\n");

6315

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6316

mfprintf(o->m_pRDF[zr]->m_fDist[0],"\n");

6317

}

6318

}

6319

6320

if (g_bVDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pVDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6321

{

6322

if (o->m_bOthers)

6323

{

6324

if (o->m_bSecondShowMol && (zr == 1))

6325

{

6326

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6327

for (z5=0;z5<o->m_pVDF[zr]->m_faData[z4].GetSize();z5++)

6328

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[z4][z5]);

6329

} else

6330

{

6331

for (z4=0;z4<o->m_iShowMolCount;z4++)

6332

{

6333

for (z5=0;z5<o->m_pVDF[zr]->m_faData[z4].GetSize();z5++)

6334

{

6335

if (o->m_bBinOnlyPassedAtoms)

6336

if (o->m_pVDF[zr]->m_baDataEnabled[z4][z5] == 0)

6337

continue;

6338

if (o->m_bBinOnlyNotPassedAtoms)

6339

if (o->m_pVDF[zr]->m_baDataEnabled[z4][z5] != 0)

6340

continue;

6341

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[z4][z5]);

6342

}

6343

}

6344

}

6345

} else

6346

{

6347

for (z5=0;z5<o->m_pVDF[zr]->m_faData[0].GetSize();z5++)

6348

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[0][z5]);

6349

}

6350

if (o->m_bTimeDev && (ti2 != -1))

6351

{

6352

if (o->m_bSaveSeparateFiles)

6353

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"\n");

6354

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6355

mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"\n");

6356

}

6357

}

6358

6359

if (g_bDipDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pDipDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6360

{

6361

if (o->m_bOthers)

6362

{

6363

if (o->m_bSecondShowMol && (zr == 1))

6364

{

6365

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6366

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[z4].GetSize();z5++)

6367

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[z4][z5]);

6368

} else

6369

{

6370

for (z4=0;z4<o->m_iShowMolCount;z4++)

6371

{

6372

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[z4].GetSize();z5++)

6373

{

6374

if (o->m_bBinOnlyPassedAtoms)

6375

if (o->m_pDipDF[zr]->m_baDataEnabled[z4][z5] == 0)

6376

continue;

6377

if (o->m_bBinOnlyNotPassedAtoms)

6378

if (o->m_pDipDF[zr]->m_baDataEnabled[z4][z5] != 0)

6379

continue;

6380

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[z4][z5]);

6381

}

6382

}

6383

}

6384

} else

6385

{

6386

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[0].GetSize();z5++)

6387

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[0][z5]);

6388

}

6389

if (o->m_bTimeDev && (ti2 != -1))

6390

{

6391

if (o->m_bSaveSeparateFiles)

6392

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"\n");

6393

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6394

mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"\n");

6395

}

6396

}

6397

6398

if (g_bADF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pADF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6399

{

6400

if (o->m_bOthers)

6401

{

6402

if (o->m_bSecondShowMol && (zr == 1))

6403

{

6404

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6405

for (z5=0;z5<o->m_pADF[zr]->m_faData[z4].GetSize();z5++)

6406

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[z4][z5]);

6407

} else

6408

{

6409

for (z4=0;z4<o->m_iShowMolCount;z4++)

6410

{

6411

for (z5=0;z5<o->m_pADF[zr]->m_faData[z4].GetSize();z5++)

6412

{

6413

if (o->m_bBinOnlyPassedAtoms)

6414

if (o->m_pADF[zr]->m_baDataEnabled[z4][z5] == 0)

6415

continue;

6416

if (o->m_bBinOnlyNotPassedAtoms)

6417

if (o->m_pADF[zr]->m_baDataEnabled[z4][z5] != 0)

6418

continue;

6419

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[z4][z5]);

6420

}

6421

}

6422

}

6423

} else

6424

{

6425

for (z5=0;z5<o->m_pADF[zr]->m_faData[0].GetSize();z5++)

6426

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[0][z5]);

6427

}

6428

if (o->m_bTimeDev && (ti2 != -1))

6429

{

6430

if (o->m_bSaveSeparateFiles)

6431

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"\n");

6432

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6433

mfprintf(o->m_pADF[zr]->m_fAngle[0],"\n");

6434

}

6435

}

6436

6437

if (g_bDDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pDDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6438

{

6439

if (o->m_bOthers)

6440

{

6441

if (o->m_bSecondShowMol && (zr == 1))

6442

{

6443

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6444

for (z5=0;z5<o->m_pDDF[zr]->m_faData[z4].GetSize();z5++)

6445

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[z4][z5]);

6446

} else

6447

{

6448

for (z4=0;z4<o->m_iShowMolCount;z4++)

6449

{

6450

for (z5=0;z5<o->m_pDDF[zr]->m_faData[z4].GetSize();z5++)

6451

{

6452

if (o->m_bBinOnlyPassedAtoms)

6453

if (o->m_pDDF[zr]->m_baDataEnabled[z4][z5] == 0)

6454

continue;

6455

if (o->m_bBinOnlyNotPassedAtoms)

6456

if (o->m_pDDF[zr]->m_baDataEnabled[z4][z5] != 0)

6457

continue;

6458

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[z4][z5]);

6459

}

6460

}

6461

}

6462

} else

6463

{

6464

for (z5=0;z5<o->m_pDDF[zr]->m_faData[0].GetSize();z5++)

6465

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[0][z5]);

6466

}

6467

if (o->m_bTimeDev && (ti2 != -1))

6468

{

6469

if (o->m_bSaveSeparateFiles)

6470

mfprintf(o->m_pDDF[zr]->m_fAngle[ti2],"\n");

6471

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6472

mfprintf(o->m_pDDF[zr]->m_fAngle[0],"\n");

6473

}

6474

} // End IF DDF

6475

6476

if (g_bPlDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pPlDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6477

{

6478

if (o->m_bOthers)

6479

{

6480

if (o->m_bSecondShowMol && (zr == 1))

6481

{

6482

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6483

for (z5=0;z5<o->m_pPlDF[zr]->m_faData[z4].GetSize();z5++)

6484

o->m_pPlDF[zr]->m_pPlDF->AddToBin(o->m_pPlDF[zr]->m_faData[z4][z5]);

6485

} else

6486

{

6487

for (z4=0;z4<o->m_iShowMolCount;z4++)

6488

{

6489

for (z5=0;z5<o->m_pPlDF[zr]->m_faData[z4].GetSize();z5++)

6490

{

6491

if (o->m_bBinOnlyPassedAtoms)

6492

if (o->m_pPlDF[zr]->m_baDataEnabled[z4][z5] == 0)

6493

continue;

6494

if (o->m_bBinOnlyNotPassedAtoms)

6495

if (o->m_pPlDF[zr]->m_baDataEnabled[z4][z5] != 0)

6496

continue;

6497

o->m_pPlDF[zr]->m_pPlDF->AddToBin(o->m_pPlDF[zr]->m_faData[z4][z5]);

6498

}

6499

}

6500

}

6501

} else

6502

{

6503

for (z5=0;z5<o->m_pPlDF[zr]->m_faData[0].GetSize();z5++)

6504

o->m_pPlDF[zr]->m_pPlDF->AddToBin(o->m_pPlDF[zr]->m_faData[0][z5]);

6505

}

6506

} // End IF PlDF

6507

6508

if (g_bLiDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pLiDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6509

{

6510

if (o->m_bOthers)

6511

{

6512

if (o->m_bSecondShowMol && (zr == 1))

6513

{

6514

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6515

for (z5=0;z5<o->m_pLiDF[zr]->m_faData[z4].GetSize();z5++)

6516

o->m_pLiDF[zr]->m_pLiDF->AddToBin(o->m_pLiDF[zr]->m_faData[z4][z5]);

6517

} else

6518

{

6519

for (z4=0;z4<o->m_iShowMolCount;z4++)

6520

{

6521

for (z5=0;z5<o->m_pLiDF[zr]->m_faData[z4].GetSize();z5++)

6522

{

6523

if (o->m_bBinOnlyPassedAtoms)

6524

if (o->m_pLiDF[zr]->m_baDataEnabled[z4][z5] == 0)

6525

continue;

6526

if (o->m_bBinOnlyNotPassedAtoms)

6527

if (o->m_pLiDF[zr]->m_baDataEnabled[z4][z5] != 0)

6528

continue;

6529

o->m_pLiDF[zr]->m_pLiDF->AddToBin(o->m_pLiDF[zr]->m_faData[z4][z5]);

6530

}

6531

}

6532

}

6533

} else

6534

{

6535

for (z5=0;z5<o->m_pLiDF[zr]->m_faData[0].GetSize();z5++)

6536

o->m_pLiDF[zr]->m_pLiDF->AddToBin(o->m_pLiDF[zr]->m_faData[0][z5]);

6537

}

6538

} // End IF LiDF

6539

6540

} // FOR CDFChannels

6541

6542

} // Ende FOR g_oaObserv.GetSize

6543

} // Ende IF [blabla]

6544

6545

if (g_bMiddleAvg) // Referenzmolekuel mitteln

6546

{

6547

cc = 0;

6548

ti2 = (g_iSteps-2)*((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()+z2;

6549

// Jeden Atomtyp des Zielmolekuels durchgehen

6550

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z3++)

6551

{

6552

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z4++)

6553

{

6554

// Atome vertauschen, aber nicht im allerersten Durchgang hier, und nur wenn mehr als 1 Atom dieser Sorte

6555

if ((g_iSwapAtoms) && (ti2 != 0) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3]>1))

6556

{

6557

vec4 = g_pRefMol[cc];

6558

vec4 /= (float)ti2; // der bisherige Mittelwert des Referenzmolekuels

6559

tf = VecDist(g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z4)],vec4); // der Abstand dieses Atoms von seinem Aequivalent im Referenzmolekuel

6560

ti3 = -1;

6561

for (z5=z4+1;z5<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z5++) // Alle folgenden Atome dieser Sorte durchgehen

6562

{

6563

tf2 = VecDist(g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z5)],vec4);

6564

if (tf2 < tf) // Das andere Atom ist naeher am Platz im Referenzmolekuel als das eigentlich vorgesehene

6565

{

6566

ti3 = z5;

6567

tf = tf2;

6568

}

6569

}

6570

if (ti3 != -1) // Ein Anderes ist naeher dran als unseres: Vertausche diese beiden

6571

{

6572

Swap(g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z4)],g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(ti3)]);

6573

pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+(cc-z4+ti3)] += 1;

6574

pSwapMatrix[(cc-z4+ti3)*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc] += 1;

6575

}

6576

} // Ende IF SwapAtoms

6577

g_pRefMol[cc] += g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z4)];

6578

cc++;

6579

} // Ende FOR Atom des Referenzmolekuels

6580

} // Ende FOR Atomtyp des Referenzmolekuels

6581

} // Ende IF Referenzmolekuel mitteln

6582

} // Ende FOR RefMol (z2)

6583

6584

for (z6=0;z6<g_oaObserv.GetSize();z6++)

6585

{

6586

o = (CObservation*)g_oaObserv[z6];

6587

6588

if (o->m_pConditions != NULL)

6589

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

6590

if (o->m_pConditions->m_iPassCounter[z2] != 0)

6591

o->m_pConditions->m_iOMPassCounter[z2]++;

6592

6593

if (o->m_pConditionsOM2 != NULL)

6594

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

6595

if (o->m_pConditionsOM2->m_iPassCounter[z2] != 0)

6596

o->m_pConditionsOM2->m_iOMPassCounter[z2]++;

6597

6598

if (g_bRDF)

6599

{

6600

for (zr=0;zr<g_iCDFChannels;zr++)

6601

{

6602

if (o->m_pRDF[zr] != NULL)

6603

if (o->m_pRDF[zr]->m_bCalcSD)

6604

o->m_pRDF[zr]->m_pRDF->m_pSDEngine->FinishStep();

6605

}

6606

}

6607

}

6608

6609

6610

//_end:;

6611

_endstep:

6612

_norefmol:

6613

if ((g_iMaxStep > 0) && ((int)g_iSteps >= g_iMaxStep))

6614

{

6615

mprintf("\n\nMaximum step count of %d reached, stopping.",g_iMaxStep);

6616

break;

6617

}

6618

} // Ende while

6619

6620

/*************************************************************************

6621

*************** Ende Hauptschleife ***************************************

6622

*************************************************************************/

6623

6624

// fclose(fff);

6625

6626

_endmainloop:

6627

if (g_bUseVelocities)

6628

g_iSteps -= 2;

6629

6630

mprintf(WHITE,"\n\n########## Analysis finished ##########\n");

6631

6632

if (g_iStride != 1)

6633

mprintf("\n%d time steps processed (every %dth from %d).\n\n",g_iSteps/g_iStride,g_iStride,g_iSteps);

6634

else mprintf("\n%d time steps processed.\n\n",g_iSteps);

6635

6636

fclose(g_fPos);

6637

if (g_fVel != NULL)

6638

fclose(g_fVel);

6639

if (g_fForce != NULL)

6640

fclose(g_fForce);

6641

if ((g_bNPT) && (g_sNPTFile[0] != 0))

6642

fclose(g_fNPTFile);

6643

6644

if (g_bDipole && g_bDumpDipoleVector)

6645

{

6646

fclose(g_fDumpDipole);

6647

mprintf(" Dipole vectors written to file \"dipole_vectors.csv\".\n");

6648

if (g_bDumpDipoleXYZ)

6649

{

6650

fclose(g_fDumpDipoleXYZ);

6651

mprintf(" Dipole XYZ trajectory written to file \"dipole_vectors.xyz\".\n");

6652

}

6653

mprintf("\n");

6654

}

6655

6656

6657

/************ Interface **************/

6658

Interface_AfterAnalysis();

6659

6660

6661

if (g_bVoro)

6662

{

6663

g_pVoroWrapper->Finish();

6664

}

6665

6666

if (g_bVoid)

6667

{

6668

g_pVoroAnalysis->Finish();

6669

}

6670

6671

if (g_bReact)

6672

{

6673

if (!ReactSecondRun)

6674

{

6675

g_pReact->Finish();

6676

g_pReact->DumpMolecules();

6677

g_pReact->CreateOutput();

6678

}

6679

if (g_pReact->m_oaReactTrajectories.GetSize() != 0)

6680

{

6681

if (!ReactSecondRun)

6682

{

6683

mprintf(WHITE,"Starting second pass for Reaction Analysis...\n\n");

6684

ReactSecondRun = true;

6685

goto _beginmain;

6686

} else

6687

{

6688

mprintf(WHITE,"Second pass for Reaction Analysis finished.\n\n");

6689

}

6690

}

6691

}

6692

g_bAbortAnalysis = true;

6693

6694

if (g_bSaveCondSnapshot)

6695

{

6696

fclose(g_fSaveCondFile);

6697

mprintf("%d condition snapshots saved as savecondition.xyz\n\n",g_iSaveCondCount);

6698

}

6699

6700

if (g_bMicroHet)

6701

{

6702

mprintf(WHITE,"*** Microheterogeneity Analysis\n\n");

6703

for (z=0;z<g_pMicroHet->m_oaObservations.GetSize();z++)

6704

{

6705

mho = (CMicroHetObservation*)g_pMicroHet->m_oaObservations[z];

6706

mprintf(WHITE," * Observation %d: %s\n",z+1,mho->m_sName);

6707

6708

if (mho->m_bCSV)

6709

{

6710

/* mprintf(" Creating Microheterogeneity plot...\n");

6711

sprintf(buf,"microhet_df_obs%d%s",z+1,multibuf);

6712

mho->BuildSlices(buf);*/

6713

6714

mprintf(" Creating entry plot...\n");

6715

sprintf(buf,"microhet_entry_obs%d%s",z+1,multibuf);

6716

mho->BuildZeroPlot(buf,true);

6717

}

6718

6719

if (mho->m_bCDF)

6720

{

6721

if (mho->m_bCDF_Dens)

6722

mho->BuildCDF(0,z,multibuf);

6723

6724

if (mho->m_bCDF_Tot)

6725

mho->BuildCDF(1,z,multibuf);

6726

6727

if (mho->m_bCDF_Mode3)

6728

mho->BuildCDF(2,z,multibuf);

6729

}

6730

}

6731

mprintf("\n");

6732

}

6733

6734

if (g_bClusterAnalysis)

6735

{

6736

mprintf(WHITE,"*** Cluster Analysis\n\n");

6737

g_pClusterAnalysis->BuildClusterDistribution();

6738

g_pClusterAnalysis->WriteOutput(multibuf);

6739

}

6740

6741

if (g_bFESA)

6742

{

6743

mprintf(WHITE,"*** FES Analysis\n\n");

6744

g_pFESA->Finish();

6745

}

6746

6747

/* if (g_bSFac)

6748

{

6749

g_pSFac->Finish();

6750

}*/

6751

6752

if (g_bBondACF)

6753

{

6754

mprintf(WHITE,"*** Bond autocorrelation function\n");

6755

if (g_bBondACFDebug)

6756

{

6757

mprintf(" Writing \"bondacf.agr\"...\n");

6758

6759

try { gc = new CGrace(); } catch(...) { gc = NULL; }

6760

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6761

6762

gc->SetRangeX(0,g_iSteps*g_fTimestepLength/1000.0);

6763

gc->SetRangeY(0,250);

6764

gc->MakeTicks();

6765

gc->SetLabelX("Time [ps]");

6766

gc->SetLabelY("Bond length [pm]");

6767

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6768

{

6769

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6770

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

6771

{

6772

bond = (CMolBond*)sm->m_oaBonds[z3];

6773

gc->AddDataset();

6774

for (z4=0;z4<bond->m_faData.GetSize();z4++)

6775

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

6776

}

6777

}

6778

gc->WriteAgr("bondacf.agr",false);

6779

delete gc;

6780

}

6781

mprintf(" Differentiating bond length developments...\n");

6782

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6783

{

6784

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6785

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

6786

{

6787

bond = (CMolBond*)sm->m_oaBonds[z3];

6788

for (z4=0;z4<bond->m_faData.GetSize()-1;z4++)

6789

bond->m_faData[z4] = bond->m_faData[z4+1] - bond->m_faData[z4];

6790

}

6791

}

6792

if (g_bBondACFDebug)

6793

{

6794

mprintf(" Writing \"bondacf_diff.agr\"...\n");

6795

6796

try { gc = new CGrace(); } catch(...) { gc = NULL; }

6797

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6798

6799

gc->SetRangeX(0,g_iSteps*g_fTimestepLength/1000.0);

6800

gc->SetRangeY(-15,15);

6801

gc->MakeTicks();

6802

gc->SetLabelX("Time [ps]");

6803

gc->SetLabelY("Bond length change rate");

6804

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6805

{

6806

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6807

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

6808

{

6809

bond = (CMolBond*)sm->m_oaBonds[z3];

6810

gc->AddDataset();

6811

for (z4=0;z4<bond->m_faData.GetSize();z4++)

6812

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

6813

}

6814

}

6815

gc->WriteAgr("bondacf_diff.agr",false);

6816

delete gc;

6817

}

6818

mprintf(" Autocorrelating bond length developments...\n");

6819

mprintf(WHITE," [");

6820

tfs = 0;

6821

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6822

{

6823

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6824

tfs += sm->m_oaBonds.GetSize();

6825

}

6826

tfs /= 60.0;

6827

ti2 = 0;

6828

/* fft = new CFFT();

6829

fft->PrepareFFT_C2C(g_iSteps*2);

6830

fft2 = new CFFT();

6831

fft2->PrepareInverseFFT_C2C(g_iSteps*2);*/

6832

6833

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

6834

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6835

6836

ac->Init(g_iSteps,g_iBondACFDepth,g_bACFFFT);

6837

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6838

{

6839

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6840

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

6841

{

6842

if (fmod(ti2,tfs) < 1.0)

6843

mprintf(WHITE,"#");

6844

bond = (CMolBond*)sm->m_oaBonds[z3];

6845

ac->AutoCorrelate(&bond->m_faData,&tempfa);

6846

bond->m_faData.CopyFrom(&tempfa);

6847

ti2++;

6848

}

6849

}

6850

delete ac;

6851

mprintf(WHITE,"]\n");

6852

if (g_bBondACFDebug)

6853

{

6854

mprintf(" Writing \"bondacf_autocorr.agr\"...\n");

6855

6856

try { gc = new CGrace(); } catch(...) { gc = NULL; }

6857

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6858

6859

gc->SetRangeX(0,g_iBondACFDepth*g_fTimestepLength/1000.0);

6860

gc->SetRangeY(-25,25);

6861

gc->MakeTicks();

6862

gc->SetLabelX("Time [ps]");

6863

gc->SetLabelY("ACF(Bond length change rate)");

6864

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6865

{

6866

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6867

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

6868

{

6869

bond = (CMolBond*)sm->m_oaBonds[z3];

6870

gc->AddDataset();

6871

for (z4=0;z4<g_iBondACFDepth;z4++)

6872

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

6873

}

6874

}

6875

gc->WriteAgr("bondacf_autocorr.agr",false);

6876

delete gc;

6877

}

6878

mprintf(" Merging equivalent Bonds...\n");

6879

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

6880

{

6881

m = (CMolecule*)g_oaMolecules[z0];

6882

sm2 = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

6883

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

6884

{

6885

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];

6886

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

6887

{

6888

bg = (CMolBondGroup*)sm->m_oaBondGroups[z3];

6889

for (z4=1;z4<bg->m_oaBonds.GetSize();z4++)

6890

{

6891

bond = (CMolBond*)bg->m_oaBonds[z4];

6892

for (z5=0;z5<g_iBondACFDepth;z5++)

6893

((CMolBond*)((CMolBondGroup*)sm2->m_oaBondGroups[z3])->m_oaBonds[0])->m_faData[z5] += bond->m_faData[z5];

6894

}

6895

}

6896

}

6897

}

6898

if (g_bBondACFSymmetrize)

6899

{

6900

mprintf(" Symmetrizing bond ACFs...\n");

6901

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

6902

{

6903

m = (CMolecule*)g_oaMolecules[z0];

6904

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

6905

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

6906

{

6907

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

6908

bond->m_faData.SetSize(2*g_iBondACFDepth);

6909

for (z4=0;z4<g_iBondACFDepth;z4++)

6910

bond->m_faData[z4+g_iBondACFDepth] = bond->m_faData[z4];

6911

for (z4=0;z4<g_iBondACFDepth;z4++)

6912

bond->m_faData[z4] = bond->m_faData[2*g_iBondACFDepth-z4-1];

6913

}

6914

}

6915

g_iBondACFDepth *= 2;

6916

}

6917

if (g_bBondACFWindow)

6918

{

6919

mprintf(" Applying Window Function...\n");

6920

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

6921

{

6922

m = (CMolecule*)g_oaMolecules[z0];

6923

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

6924

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

6925

{

6926

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

6927

for (z4=0;z4<g_iBondACFDepth;z4++)

6928

bond->m_faData[z4] *= (float)pow(sin(z4*Pi/(bond->m_faData.GetSize()-1)),2);

6929

}

6930

}

6931

}

6932

if (g_bBondACFNormalize)

6933

{

6934

mprintf(" Normalizing bond ACFs...\n");

6935

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

6936

{

6937

m = (CMolecule*)g_oaMolecules[z0];

6938

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

6939

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

6940

{

6941

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

6942

tf = 0;

6943

for (z4=0;z4<g_iBondACFDepth;z4++)

6944

if (tf < bond->m_faData[z4])

6945

tf = bond->m_faData[z4];

6946

for (z4=0;z4<g_iBondACFDepth;z4++)

6947

bond->m_faData[z4] /= (float)tf;

6948

}

6949

}

6950

}

6951

mprintf(" Writing \"bondacf_ac_merged.agr\"...\n");

6952

6953

try { gc = new CGrace(); } catch(...) { gc = NULL; }

6954

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6955

6956

gc->SetRangeX(0,g_iBondACFDepth*g_fTimestepLength/1000.0);

6957

gc->SetRangeY(-200,200);

6958

gc->MakeTicks();

6959

gc->SetLabelX("Time [ps]");

6960

gc->SetLabelY("Sum ACF(Bond length change rate)");

6961

gc->CurrentGraph()->m_bLegend = true;

6962

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

6963

{

6964

m = (CMolecule*)g_oaMolecules[z0];

6965

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

6966

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

6967

{

6968

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

6969

gc->AddDataset();

6970

sprintf(buf,"%s %s%d - %s%d",m->m_sName,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[0]]])->m_sName,bond->m_iAtom[0]+1,((CAtom*)g_oaAtoms[sm->m_baAtomIndex[bond->m_iAtomType[1]]])->m_sName,bond->m_iAtom[1]+1);

6971

gc->SetDatasetName(buf);

6972

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth*2);

6973

for (z4=0;z4<g_iBondACFDepth;z4++)

6974

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

6975

}

6976

}

6977

gc->WriteAgr("bondacf_ac_merged.agr",false);

6978

delete gc;

6979

mprintf(" Applying Fourier Transformation...\n");

6980

6981

try { fft = new CFFT(); } catch(...) { fft = NULL; }

6982

if (fft == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6983

6984

fft->PrepareFFT_C2C(g_iBondACFDepth);

6985

tf3 = 0;

6986

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

6987

{

6988

m = (CMolecule*)g_oaMolecules[z0];

6989

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

6990

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

6991

{

6992

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

6993

for (z4=0;z4<g_iBondACFDepth;z4++)

6994

{

6995

fft->m_pInput[z4*2] = bond->m_faData[z4];

6996

fft->m_pInput[z4*2+1] = 0;

6997

}

6998

fft->DoFFT();

6999

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7000

{

7001

bond->m_faData[z4] = (float)(pow(fft->m_pOutput[z4*2],2) + pow(fft->m_pOutput[z4*2+1],2)) / g_iBondACFDepth;

7002

if (bond->m_faData[z4] > tf3)

7003

tf3 = bond->m_faData[z4];

7004

}

7005

}

7006

}

7007

delete fft;

7008

mprintf(" Writing \"bond_spectrum.agr\"...\n");

7009

7010

try { gc = new CGrace(); } catch(...) { gc = NULL; }

7011

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7012

7013

gc->SetRangeX(0,4000.0);

7014

gc->SetRangeY(0,tf3*1.1);

7015

gc->MakeTicks();

7016

gc->SetLabelX("Wave number [1/cm]");

7017

gc->SetLabelY("Intensity");

7018

gc->CurrentGraph()->m_bInvertXAxis = true;

7019

gc->CurrentGraph()->m_bLegend = true;

7020

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7021

{

7022

m = (CMolecule*)g_oaMolecules[z0];

7023

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7024

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7025

{

7026

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7027

gc->AddDataset();

7028

7029

gc->SetDatasetName(buf);

7030

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth*2);

7031

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7032

gc->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,bond->m_faData[z4]);

7033

}

7034

}

7035

gc->WriteAgr("bond_spectrum.agr",false);

7036

delete gc;

7037

for (z5=1;z5<5;z5++)

7038

{

7039

mprintf(" Smoothing spectrum, degree %d...\n",z5);

7040

mprintf(" Writing \"bond_spectrum_s%d.agr\"...\n",z5);

7041

7042

try { gc = new CGrace(); } catch(...) { gc = NULL; }

7043

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7044

7045

gc->SetRangeX(0,4000.0);

7046

gc->SetRangeY(0,tf3*1.1);

7047

gc->MakeTicks();

7048

gc->SetLabelX("Wave number [1/cm]");

7049

gc->SetLabelY("Intensity");

7050

gc->CurrentGraph()->m_bInvertXAxis = true;

7051

gc->CurrentGraph()->m_bLegend = true;

7052

7053

try { gc2 = new CGrace(); } catch(...) { gc2 = NULL; }

7054

if (gc2 == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7055

7056

gc2->SetRangeX(0,4000.0);

7057

gc2->SetRangeY(0,tf3*1.1);

7058

gc2->MakeTicks();

7059

gc2->SetLabelX("Wave number [1/cm]");

7060

gc2->SetLabelY("Intensity");

7061

gc2->CurrentGraph()->m_bInvertXAxis = true;

7062

gc2->CurrentGraph()->m_bLegend = true;

7063

7064

tempfa.SetSize(g_iBondACFDepth/2);

7065

tempfa2.SetSize(g_iBondACFDepth/2);

7066

7067

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7068

tempfa2[z4] = 0;

7069

7070

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7071

{

7072

m = (CMolecule*)g_oaMolecules[z0];

7073

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7074

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7075

{

7076

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7077

7078

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7079

{

7080

tf = 0;

7081

tf2 = 0;

7082

for (z6=-z5;z6<=z5;z6++)

7083

{

7084

if ((z4+z6 < 0) || (z4+z6 >= g_iBondACFDepth/2))

7085

continue;

7086

tf += bond->m_faData[z4+z6] / (pow((double)z6,2)+1.0);

7087

tf2 += 1.0 / (pow((double)z6,2)+1.0);

7088

}

7089

tempfa[z4] = (float)(tf / tf2);

7090

tempfa2[z4] += tempfa[z4];

7091

}

7092

7093

gc->AddDataset();

7094

gc2->AddDataset();

7095

7096

gc->SetDatasetName(buf);

7097

gc2->SetDatasetName(buf);

7098

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth);

7099

((CGraceDataset*)gc2->CurrentGraph()->m_oaDatasets[gc2->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth);

7100

7101

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7102

gc->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,tempfa[z4]);

7103

7104

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7105

gc2->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,tempfa2[z4]);

7106

}

7107

}

7108

7109

sprintf(buf,"bond_spectrum_s%d.agr",z5);

7110

gc->WriteAgr(buf,false);

7111

delete gc;

7112

7113

mprintf(" Writing \"bond_spectrum_cumulative_s%d.agr\"...\n",z5);

7114

sprintf(buf,"bond_spectrum_cumulative_s%d.agr",z5);

7115

gc2->WriteAgr(buf,false);

7116

delete gc2;

7117

}

7118

}

7119

7120

if (g_bSaveRefEnv)

7121

{

7122

fclose(g_fRefEnv);

7123

mprintf("\nTrajectory of reference molecule was saved as %s.\n",g_sRefEnv);

7124

if (g_bTDO)

7125

{

7126

#ifdef TARGET_WINDOWS

7127

sprintf(buf,"tdo_pymol_%s_%d%s.bat",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

7128

#else

7129

sprintf(buf,"tdo_pymol_%s_%d%s.sh",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

7130

#endif

7131

mprintf("Saving TDO PyMol script as %s.\n",buf);

7132

tfi = OpenFileWrite(buf,true);

7133

#ifdef TARGET_WINDOWS

7134

mfprintf(tfi,"pymolwin ");

7135

#else

7136

mfprintf(tfi,"pymol ");

7137

#endif

7138

for (z=0;z<g_laTDOSteps.GetSize();z++)

7139

mfprintf(tfi,"tdo_%s_%d_%06d%s.xyz ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_laTDOSteps[z],multibuf);

7140

mfprintf(tfi,"-d \"set sphere_scale,0.25\" ");

7141

mfprintf(tfi,"-d \"set stick_radius,0.17\" ");

7142

mfprintf(tfi,"-d \"set ray_trace_mode,1\" ");

7143

mfprintf(tfi,"-d \"set fog,0\" ");

7144

mfprintf(tfi,"-d \"set ray_trace_fog,0\" ");

7145

mfprintf(tfi,"-d \"set bg_rgb,(1,1,1)\" ");

7146

mfprintf(tfi,"-d \"set ray_shadow,0\" ");

7147

mfprintf(tfi,"-d \"set ray_shadows,0\" ");

7148

mfprintf(tfi,"-d \"set ray_interior_shadows,0\" ");

7149

mfprintf(tfi,"-d \"show sticks; show spheres\" ");

7150

7151

for (z=0;z<g_laTDOSteps.GetSize();z++)

7152

{

7153

for (z2=0;z2<g_oaAtoms.GetSize();z2++)

7154

{

7155

if ((z2 == g_iVirtAtomType) && (!g_bSaveVirtAtoms))

7156

continue;

7157

mfprintf(tfi,"-d \"set_color mol_%s_%d, [%d,%d,%d]\" ",((CAtom*)g_oaAtoms[z2])->m_sName,z+1,((CAtom*)g_oaAtoms[z2])->m_pElement->ColorR((float)z/(g_laTDOSteps.GetSize()-1)*g_fTDOBleaching),((CAtom*)g_oaAtoms[z2])->m_pElement->ColorG((float)z/(g_laTDOSteps.GetSize()-1)*g_fTDOBleaching),((CAtom*)g_oaAtoms[z2])->m_pElement->ColorB((float)z/(g_laTDOSteps.GetSize()-1)*g_fTDOBleaching));

7158

}

7159

}

7160

for (z=0;z<g_laTDOSteps.GetSize();z++)

7161

{

7162

for (z2=0;z2<g_oaAtoms.GetSize();z2++)

7163

{

7164

if ((z2 == g_iVirtAtomType) && (!g_bSaveVirtAtoms))

7165

continue;

7166

mfprintf(tfi,"-d \"color mol_%s_%d, tdo_%s_%d_%06d and name %s\" ",((CAtom*)g_oaAtoms[z2])->m_sName,z+1,((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_laTDOSteps[z],((CAtom*)g_oaAtoms[z2])->m_sName);

7167

}

7168

}

7169

mfprintf(tfi,"\n");

7170

fclose(tfi);

7171

#ifdef TARGET_LINUX

7172

sprintf(buf,"chmod 755 tdo_pymol_%s_%d%s.sh",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

7173

mprintf("Executing \"%s\"...\n",buf);

7174

system(buf);

7175

#endif

7176

}

7177

}

7178

if (g_bCutCluster)

7179

{

7180

fclose(g_fRefEnv);

7181

mprintf("\nCluster trajectory was saved as %s.\n",g_sRefEnv);

7182

}

7183

7184

if (g_bSaveJustTraj)

7185

{

7186

fclose(g_fSaveJustTraj);

7187

/* strcpy(buf,g_sInputTraj);

7188

p = strrchr(buf,'.');

7189

*p = 0;

7190

strcat(buf,multibuf);

7191

strcat(buf,".out.xyz");*/

7192

// mprintf("\nProcessed output trajectory was saved as traj_out.xyz\n",buf);

7193

}

7194

7195

if (g_bIRSpec && g_bGlobalIR)

7196

{

7197

mprintf(WHITE,"\n*** Global IR Spectrum\n");

7198

g_pGlobalIR->Finish(multibuf);

7199

}

7200

7201

if (g_bVACF && g_bGlobalVACF)

7202

{

7203

mprintf(WHITE,"\n*** Global velocity autocorrelation function\n");

7204

if (g_pGlobalVACF->m_bDerivative)

7205

{

7206

mprintf(" Deriving velocities...\n");

7207

mprintf(WHITE," [");

7208

tfs = g_iGesAtomCount/60.0;

7209

ti = 0;

7210

for (z2=0;z2<g_iGesAtomCount;z2++)

7211

{

7212

if (fmod(z2,tfs) < 1)

7213

mprintf(WHITE,"#");

7214

7215

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z2] > 1000))

7216

continue;

7217

7218

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[ti];

7219

7220

for (z3=0;z3<(int)g_iSteps*3-3;z3++)

7221

(*ptfa)[z3] = (*ptfa)[z3+3] - (*ptfa)[z3];

7222

7223

ti++;

7224

}

7225

mprintf(WHITE,"]\n");

7226

}

7227

if (g_bVACFCacheMode)

7228

{

7229

tfs = g_iGesAtomCount/60.0;

7230

/* if (g_bACFFFT)

7231

{*/

7232

mprintf(" Autocorrelating cached vectors...\n");

7233

mprintf(WHITE," [");

7234

/* fft = new CFFT();

7235

fft->PrepareFFT_C2C(2*g_iSteps);

7236

fft2 = new CFFT();

7237

fft2->PrepareInverseFFT_C2C(2*g_iSteps);*/

7238

7239

try { ptfa2 = new CxFloatArray("main():ptfa2"); } catch(...) { ptfa2 = NULL; }

7240

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7241

7242

ptfa2->SetSize(g_iSteps);

7243

7244

try { ptfa3 = new CxFloatArray("main():ptfa3"); } catch(...) { ptfa3 = NULL; }

7245

if (ptfa3 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7246

7247

ptfa3->SetSize(g_iSteps);

7248

7249

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

7250

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7251

7252

ac->Init(g_iSteps,g_pGlobalVACF->m_iSize,g_bACFFFT);

7253

ti = 0;

7254

for (z2=0;z2<g_iGesAtomCount;z2++)

7255

{

7256

if (fmod(z2,tfs) < 1.0)

7257

mprintf(WHITE,"#");

7258

7259

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z2] > 1000))

7260

continue;

7261

7262

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[ti];

7263

7264

if (g_pGlobalVACF->m_bMassWeight)

7265

tf = ((CAtom*)g_oaAtoms[g_waAtomRealElement[z2]])->m_pElement->m_fMass;

7266

else tf = 1.0f;

7267

7268

/* X */

7269

for (z3=0;z3<(int)g_iSteps;z3++)

7270

(*ptfa2)[z3] = (*ptfa)[z3*3];

7271

ac->AutoCorrelate(ptfa2,ptfa3);

7272

// mprintf("Global Atom %d X: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

7273

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

7274

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

7275

7276

/* Y */

7277

for (z3=0;z3<(int)g_iSteps;z3++)

7278

(*ptfa2)[z3] = (*ptfa)[z3*3+1];

7279

ac->AutoCorrelate(ptfa2,ptfa3);

7280

// mprintf("Global Atom %d Y: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

7281

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

7282

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

7283

7284

/* Z */

7285

for (z3=0;z3<(int)g_iSteps;z3++)

7286

(*ptfa2)[z3] = (*ptfa)[z3*3+2];

7287

ac->AutoCorrelate(ptfa2,ptfa3);

7288

// mprintf("Global Atom %d Z: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

7289

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

7290

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

7291

7292

ti++;

7293

}

7294

delete ac;

7295

delete ptfa2;

7296

delete ptfa3;

7297

/* delete fft2;

7298

delete fft;*/

7299

/* } else

7300

{

7301

mprintf(" Autocorrelating cached vectors...\n");

7302

mprintf(WHITE," [");

7303

for (z2=0;z2<g_iGesAtomCount;z2++)

7304

{

7305

if (fmod(z2,tfs) < 1.0)

7306

mprintf(WHITE,"#");

7307

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[z2];

7308

for (z3=0;z3<g_pGlobalVACF->m_iSize;z3+=g_pGlobalVACF->m_iStride) // Das ist das Tau

7309

{

7310

tf = 0;

7311

for (z4=0;z4<(int)g_iSteps-z3;z4++) // Das ist der Startpunkt

7312

tf += (*ptfa)[z4*3]*(*ptfa)[(z4+z3)*3] + (*ptfa)[z4*3+1]*(*ptfa)[(z4+z3)*3+1] + (*ptfa)[z4*3+2]*(*ptfa)[(z4+z3)*3+2];

7313

g_pGlobalVACF->m_pData[z3/g_pGlobalVACF->m_iStride] += tf/(g_iSteps-z3);

7314

}

7315

}

7316

}*/

7317

mprintf(WHITE,"]\n");

7318

mprintf(" %d atoms, %d time steps and %d correlation depths processed.\n",g_pGlobalVACF->m_oaCache.GetSize(),g_iSteps,g_pGlobalVACF->m_iSize);

7319

g_pGlobalVACF->MultiplyCached(1.0/g_iGesAtomCount);

7320

7321

if (g_pGlobalVACF->m_bDecomposeModes)

7322

{

7323

tfs = g_iGesAtomCount*g_iGesAtomCount*3/60.0;

7324

7325

mprintf(" Allocating cross-correlation matrix (%s)...\n",FormatBytes((double)sizeof(float)*g_pGlobalVACF->m_iSize*g_pGlobalVACF->m_iParticles*3*g_pGlobalVACF->m_iParticles*3));

7326

7327

g_pGlobalVACF->m_oaCCRMatrix.SetMaxSize(g_pGlobalVACF->m_iParticles*3*g_pGlobalVACF->m_iParticles*3);

7328

for (z2=0;z2<g_pGlobalVACF->m_iParticles*3;z2++)

7329

{

7330

for (z3=0;z3<g_pGlobalVACF->m_iParticles*3;z3++)

7331

{

7332

// mprintf("X: %X\n",g_pGlobalVACF);

7333

// mprintf("%d - %d -->\n",z2,z3);

7334

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

7335

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7336

7337

// mprintf("A\n");

7338

ptfa->SetSize(g_pGlobalVACF->m_iSize);

7339

// mprintf("B\n");

7340

// mprintf("X2: %X\n",g_pGlobalVACF);

7341

g_pGlobalVACF->m_oaCCRMatrix.Add(ptfa);

7342

// mprintf("%d - %d <--\n",z2,z3);

7343

}

7344

}

7345

7346

mprintf(" Computing %d cross-correlations...\n",g_pGlobalVACF->m_iParticles*3*g_pGlobalVACF->m_iParticles*3);

7347

mprintf(WHITE," [");

7348

7349

try { ptfa2 = new CxFloatArray("main():ptfa2"); } catch(...) { ptfa2 = NULL; }

7350

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7351

7352

ptfa2->SetSize(g_iSteps);

7353

7354

try { ptfa2b = new CxFloatArray("main():ptfa2b"); } catch(...) { ptfa2b = NULL; }

7355

if (ptfa2b == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7356

7357

ptfa2b->SetSize(g_iSteps);

7358

7359

try { ccr = new CCrossCorrelation(); } catch(...) { ccr = NULL; }

7360

if (ccr == NULL) NewException((double)sizeof(CCrossCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7361

7362

ccr->Init(g_iSteps,g_pGlobalVACF->m_iSize,g_bACFFFT);

7363

7364

ti = 0;

7365

7366

for (z2=0;z2<g_iGesAtomCount;z2++)

7367

{

7368

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z2] > 1000))

7369

continue;

7370

7371

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[ti];

7372

7373

for (z2b=0;z2b<3;z2b++)

7374

{

7375

ti2 = 0;

7376

for (z3=0;z3<g_iGesAtomCount;z3++)

7377

{

7378

if (fmod(z2*g_iGesAtomCount*3+z2b*g_iGesAtomCount+z3,tfs) < 1.0)

7379

mprintf(WHITE,"#");

7380

7381

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z3] > 1000))

7382

continue;

7383

7384

ptfab = (CxFloatArray*)g_pGlobalVACF->m_oaCache[ti2];

7385

7386

if (g_pGlobalVACF->m_bMassWeight)

7387

tf = ((CAtom*)g_oaAtoms[g_waAtomRealElement[z2]])->m_pElement->m_fMass;

7388

else tf = 1.0f;

7389

7390

for (z3b=0;z3b<3;z3b++)

7391

{

7392

for (z4=0;z4<(int)g_iSteps;z4++)

7393

{

7394

(*ptfa2)[z4] = (*ptfa)[z4*3+z2b];

7395

(*ptfa2b)[z4] = (*ptfab)[z4*3+z3b];

7396

}

7397

ccr->CrossCorrelate(ptfa2,ptfa2b,(CxFloatArray*)g_pGlobalVACF->m_oaCCRMatrix[ti*g_pGlobalVACF->m_iParticles*9 + z2b*g_pGlobalVACF->m_iParticles*3 + ti2*3 + z3b]);

7398

// mprintf("z2=%d, z2b=%d, z3=%d, z3b=%d, I=%d\n",z2,z2b,z3,z3b,ti*g_pGlobalVACF->m_iParticles*9 + z2b*g_pGlobalVACF->m_iParticles*3 + ti2*3 + z3b);

7399

}

7400

7401

ti2++;

7402

}

7403

}

7404

ti++;

7405

}

7406

delete ccr;

7407

delete ptfa2;

7408

delete ptfa2b;

7409

7410

mprintf(WHITE,"]\n");

7411

7412

/* for (z2=0;z2<g_pGlobalVACF->m_iParticles*3;z2++)

7413

{

7414

for (z3=0;z3<g_pGlobalVACF->m_iParticles*3;z3++)

7415

mprintf("%6G ",((CxFloatArray*)g_pGlobalVACF->m_oaCCRMatrix[z2*g_pGlobalVACF->m_iParticles*3+z3])->GetAt(0));

7416

mprintf("\n");

7417

}*/

7418

7419

Interface_DecomposeModes(g_pGlobalVACF->m_iParticles*3, &g_pGlobalVACF->m_oaCCRMatrix);

7420

7421

} // END IF m_bDecomposeModes

7422

7423

} else g_pGlobalVACF->Multiply(1.0/g_iGesAtomCount);

7424

7425

mprintf(" Saving global VACF as acf_global%s.csv ...\n",multibuf);

7426

g_pGlobalVACF->WriteACF("acf_global",multibuf,".csv");

7427

7428

if (g_pGlobalVACF->m_iMirror != 0)

7429

{

7430

mprintf(" Mirroring global VACF...\n");

7431

g_pGlobalVACF->Mirror(g_pGlobalVACF->m_iMirror);

7432

mprintf(" Saving mirrored global VACF as acf_global.m%s.csv ...\n",multibuf);

7433

g_pGlobalVACF->WriteACF("acf_global.m",multibuf,".csv");

7434

}

7435

7436

if (g_pGlobalVACF->m_bWindowFunction)

7437

{

7438

mprintf(" Applying window function...\n");

7439

g_pGlobalVACF->Window();

7440

mprintf(" Saving windowed global VACF as acf_global.w%s.csv ...\n",multibuf);

7441

g_pGlobalVACF->WriteACF("acf_global.w",multibuf,".csv");

7442

}

7443

7444

if (g_pGlobalVACF->m_bSpectrum)

7445

{

7446

mprintf(" Performing Fourier transformation...\n");

7447

7448

try { g_pFFT = new CFFT(); } catch(...) { g_pFFT = NULL; }

7449

if (g_pFFT == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7450

7451

g_pFFT->PrepareFFT_C2C(g_pGlobalVACF->m_iSize+g_pGlobalVACF->m_iZeroPadding);

7452

g_pGlobalVACF->Transform(g_pFFT);

7453

delete g_pFFT;

7454

g_pGlobalVACF->m_pSpectrum->SetMaxRWL(1E7f/299.792f/g_fTimestepLength/g_iStride);

7455

if (g_pGlobalVACF->m_bACF_DB)

7456

{

7457

mprintf(" Normalising spectrum to decibel...\n");

7458

g_pGlobalVACF->m_pSpectrum->MakeDB();

7459

}/* else

7460

{

7461

mprintf(" Normalising integral of spectrum...\n");

7462

g_pGlobalVACF->m_pSpectrum->SetIntegral(1000000.0f);

7463

}*/

7464

if (g_pGlobalVACF->m_bWindowFunction)

7465

{

7466

mprintf(" Saving spectrum as power_global_w%s.csv ...\n",multibuf);

7467

g_pGlobalVACF->m_pSpectrum->Write("power_global_w",multibuf,".csv");

7468

} else

7469

{

7470

mprintf(" Saving spectrum as power_global%s.csv ...\n",multibuf);

7471

g_pGlobalVACF->m_pSpectrum->Write("power_global",multibuf,".csv");

7472

}

7473

}

7474

mprintf("\n");

7475

}

7476

7477

if (g_bVFDF)

7478

{

7479

for (z=0;z<g_iVFCorrCount;z++)

7480

fclose(g_fVFCorr[z]);

7481

}

7482

7483

7484

// fclose(ff);

7485

7486

for (z=0;z<g_oaObserv.GetSize();z++)

7487

{

7488

o = (CObservation*)g_oaObserv[z];

7489

mprintf(YELLOW,"\n>>> Observation %d >>>\n",z+1);

7490

7491

if (o->m_pConditions != NULL)

7492

{

7493

if (o->m_bSecondShowMol)

7494

mprintf(WHITE,"\n#### Condition between RM and 1st OM ####\n");

7495

7496

o->m_pConditions->PrintData();

7497

if (o->m_pConditions->m_oaConditionSubGroups.GetSize()==2)

7498

o->m_pConditions->PrintTable();

7499

}

7500

7501

if ((o->m_bSecondShowMol) && (o->m_pConditionsOM2 != NULL))

7502

{

7503

mprintf(WHITE,"\n\n#### Condition between RM and 2nd OM ####\n");

7504

o->m_pConditionsOM2->PrintData();

7505

if (o->m_pConditionsOM2->m_oaConditionSubGroups.GetSize()==2)

7506

o->m_pConditionsOM2->PrintTable();

7507

}

7508

7509

if (g_bAggregation)

7510

{

7511

mprintf(WHITE,"* Aggregation Functions\n");

7512

if ((g_iMaxStep > 0) && (((int)g_iSteps*g_iStride) >= g_iMaxStep))

7513

g_pTempTimestep->CopyFrom(GetTimeStep(0)); // Max. Schrittzahl

7514

else g_pTempTimestep->CopyFrom(GetTimeStep(1)); // End Of File

7515

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

7516

{

7517

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

7518

mprintf(WHITE,"\n > Value Set %d: %s\n",zs+1,dacfsub->m_sName);

7519

7520

o->m_pDACF->FinishDACFSub(g_pTempTimestep,dacfsub);

7521

7522

sprintf(buf,"cond_%s.txt",dacfsub->m_sName);

7523

dacfsub->m_pCondition->PrintData(buf);

7524

7525

mprintf(WHITE,"Neighbour Count Distribution\n");

7526

mprintf(" %.0f Bin entries have been made.\n",dacfsub->m_pNDF->m_fBinEntries);

7527

sprintf(buf,"ncd_%s%s.csv",dacfsub->m_sName,multibuf);

7528

mprintf(" Writing Neighbor Count Distribution File \"%s\"...\n",buf);

7529

dacfsub->m_pNDF->Write_Int("",buf,"");

7530

7531

if (g_bDDisp)

7532

{

7533

mprintf(WHITE,"\nDimer Displacement Distribution Function\n");

7534

mprintf(" %.0f Bin entries have been made (%.0f skipped, %.0f total).\n",dacfsub->m_pDDisp->m_fBinEntries,dacfsub->m_pDDisp->m_fSkipEntries,dacfsub->m_pDDisp->m_fBinEntries+dacfsub->m_pDDisp->m_fSkipEntries);

7535

sprintf(buf,"ddisp_%s%s.csv",dacfsub->m_sName,multibuf);

7536

mprintf(" Saving DDisp File as \"%s\"...\n",buf);

7537

dacfsub->m_pDDisp->Write("",buf,"",false);

7538

sprintf(buf,"ddisp_%s%s.agr",dacfsub->m_sName,multibuf);

7539

mprintf(" Saving DDisp Agr File as \"%s\"...\n",buf);

7540

dacfsub->m_pDDisp->WriteAgr("",buf,"","",false);

7541

}

7542

7543

if (g_bDACF)

7544

{

7545

mprintf(WHITE,"\nDimer Existence Autocorrelation Function\n");

7546

mprintf(" %.0f Bin entries have been made (%.0f skipped, %.0f total).\n",dacfsub->m_pDACF->m_fBinEntries,dacfsub->m_pDACF->m_fSkipEntries,dacfsub->m_pDACF->m_fBinEntries+dacfsub->m_pDACF->m_fSkipEntries);

7547

7548

if (dacfsub->m_bBorderMode)

7549

{

7550

mprintf(" *** New Border Mode ***\n");

7551

for (z2=0;z2<o->m_pDACF->m_iDACFRes;z2++)

7552

dacfsub->m_pDACF->m_pBin[z2] /= g_iSteps-z2;

7553

} else

7554

{

7555

for (z2=0;z2<o->m_pDACF->m_iDACFRes;z2++)

7556

dacfsub->m_pDACF->m_pBin[z2] /= g_iSteps;

7557

}

7558

7559

if (dacfsub->m_bNewMode)

7560

{

7561

mprintf(" *** New Mode Processing ***\n");

7562

mprintf(WHITE," [");

7563

tfs = ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex.GetSize() * ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize() / 60.0;

7564

ptfa = new CxFloatArray();

7565

ptfa2 = new CxFloatArray();

7566

ac = new CAutoCorrelation();

7567

ac->Init(g_iSteps,o->m_pDACF->m_iDACFRes,true);

7568

7569

ptfa->SetSize(g_iSteps);

7570

ptfa2->SetSize(o->m_pDACF->m_iDACFRes);

7571

7572

for (z2=0;z2<o->m_pDACF->m_iDACFRes;z2++)

7573

dacfsub->m_pDACF->m_pBin[z2] = 0;

7574

7575

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex.GetSize();z2++)

7576

{

7577

for (z3=0;z3<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize();z3++)

7578

{

7579

if (fmod(z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3,tfs) < 1.0)

7580

mprintf(WHITE,"#");

7581

7582

for (z5=0;z5<(int)g_iSteps;z5++)

7583

(*ptfa)[z5] = 0;

7584

7585

for (z4=0;z4<dacfsub->m_piaIntervals[z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3].GetSize();z4+=2)

7586

{

7587

for (z5=dacfsub->m_piaIntervals[z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3].GetAt(z4);z5<=dacfsub->m_piaIntervals[z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3].GetAt(z4+1);z5++)

7588

(*ptfa)[z5-1] = 1;

7589

}

7590

7591

// if (dacfsub->m_piaIntervals[z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3].GetSize() != 0)

7592

// mprintf("\n%d-%d: %d ",z2,z3,dacfsub->m_piaIntervals[z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3].GetSize()/2);

7593

7594

ac->AutoCorrelate(ptfa,ptfa2);

7595

7596

/* if ((z2==0) && (z3==28))

7597

{

7598

FILE *tfia;

7599

7600

sprintf(buf,"condfunc_%d_%d.csv",z2,z3);

7601

tfia = fopen(buf,"wt");

7602

for (z4=0;z4<(int)g_iSteps;z4++)

7603

fprintf(tfia,"%d; %f\n",z4,(*ptfa)[z4]);

7604

fclose(tfia);

7605

7606

sprintf(buf,"condacf_%d_%d.csv",z2,z3);

7607

tfia = fopen(buf,"wt");

7608

for (z4=0;z4<o->m_pDACF->m_iDACFRes;z4++)

7609

fprintf(tfia,"%d; %f\n",z4,(*ptfa2)[z4]);

7610

fclose(tfia);

7611

}*/

7612

7613

for (z4=0;z4<o->m_pDACF->m_iDACFRes;z4++)

7614

dacfsub->m_pDACF->m_pBin[z4] += (*ptfa2)[z4];

7615

}

7616

}

7617

mprintf(WHITE,"]\n");

7618

}

7619

7620

if (dacfsub->m_bCorrectEq)

7621

{

7622

if (dacfsub->m_iRefMol == dacfsub->m_iShowMol)

7623

{

7624

tf = 100.0*dacfsub->m_fEqCounter/g_iSteps/(((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()-1)/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize();

7625

mprintf(" Ensemble Average is %.6f%c.\n",tf,'%');

7626

7627

tf = 1.0/(((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()-1)/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize();

7628

dacfsub->m_pDACF->MultiplyBin(tf);

7629

7630

tf = dacfsub->m_fEqCounter/g_iSteps/(((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()-1)/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize();

7631

tf = tf*tf;

7632

mprintf(" Subtracting squared average value (%G - %G)...\n",dacfsub->m_pDACF->m_pBin[0],tf);

7633

dacfsub->m_pDACF->SubtractBin(tf);

7634

} else

7635

{

7636

tf = 100.0*dacfsub->m_fEqCounter/g_iSteps/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()/((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize();

7637

mprintf(" Ensemble Average is %.6f%c.\n",tf,'%');

7638

7639

tf = 1.0/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()/((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize();

7640

dacfsub->m_pDACF->MultiplyBin(tf);

7641

7642

tf = dacfsub->m_fEqCounter/g_iSteps/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()/((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize();

7643

tf = tf*tf;

7644

mprintf(" Subtracting squared average value (%G - %G)...\n",dacfsub->m_pDACF->m_pBin[0],tf);

7645

dacfsub->m_pDACF->SubtractBin(tf);

7646

}

7647

}

7648

7649

if (dacfsub->m_pDACF->m_pBin[0] != 0)

7650

{

7651

mprintf(" Normalizing DACF with factor 1/%G ...\n",dacfsub->m_pDACF->m_pBin[0]);

7652

dacfsub->m_pDACF->MultiplyBin(1.0/dacfsub->m_pDACF->m_pBin[0]);

7653

} else mprintf(" Not normalizing this DACF, first entry is 0.\n");

7654

7655

if (o->m_pDACF->m_bFitDACF)

7656

{

7657

mprintf("\n");

7658

7659

try { dacfsub->m_pDACF->m_pParameters = new double*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pParameters = NULL; }

7660

if (dacfsub->m_pDACF->m_pParameters == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7661

7662

try { dacfsub->m_pDACF->m_pFitIntegral = new double[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pFitIntegral = NULL; }

7663

if (dacfsub->m_pDACF->m_pFitIntegral == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7664

7665

try { dacfsub->m_pDACF->m_pCorrCoeff = new double[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pCorrCoeff = NULL; }

7666

if (dacfsub->m_pDACF->m_pCorrCoeff == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7667

7668

try { dacfsub->m_pDACF->m_pAdditionalSets = new double*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pAdditionalSets = NULL; }

7669

if (dacfsub->m_pDACF->m_pAdditionalSets == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7670

7671

try { dacfsub->m_pDACF->m_pAdditionalSetLabels = new char*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pAdditionalSetLabels = NULL; }

7672

if (dacfsub->m_pDACF->m_pAdditionalSetLabels == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7673

7674

dacfsub->m_pDACF->m_iAdditionalSets = o->m_pDACF->m_iFitDegreeMax+1;

7675

7676

for (z2=0;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7677

{

7678

dacfsub->m_pDACF->m_pAdditionalSets[z2] = NULL;

7679

dacfsub->m_pDACF->m_pAdditionalSetLabels[z2] = NULL;

7680

}

7681

7682

mprintf(YELLOW," Please note: ");

7683

mprintf("The lifetime is two times the integral value!\n\n");

7684

7685

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7686

dacfsub->m_pDACF->Fit_PolyExp(z2,5000);

7687

7688

if (o->m_pDACF->m_iFitDegreeMin != o->m_pDACF->m_iFitDegreeMax)

7689

{

7690

mprintf(YELLOW," DACF fit integral overview:\n");

7691

mprintf(" (use the row with the highest R value)\n\n");

7692

mprintf(WHITE," Degree R Integral [ps] Lifetime [ps]\n");

7693

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7694

{

7695

if (dacfsub->m_pDACF->m_pFitIntegral[z2] >= 0)

7696

mprintf(" %d %10.8f %-10G %-10G\n",z2,dacfsub->m_pDACF->m_pCorrCoeff[z2],dacfsub->m_pDACF->m_pFitIntegral[z2],dacfsub->m_pDACF->m_pFitIntegral[z2]*2.0);

7697

else mprintf(" %d %10.8f - -\n",z2,dacfsub->m_pDACF->m_pCorrCoeff[z2]);

7698

}

7699

mprintf("\n");

7700

}

7701

}

7702

sprintf(buf,"dacf_%s%s.csv",dacfsub->m_sName,multibuf);

7703

mprintf(" Saving DACF File as \"%s\"...\n",buf);

7704

dacfsub->m_pDACF->Write("",buf,"",false);

7705

sprintf(buf,"dacf_%s%s.agr",dacfsub->m_sName,multibuf);

7706

mprintf(" Saving DACF Agr File as \"%s\"...\n",buf);

7707

dacfsub->m_pDACF->WriteAgr("",buf,"","",false);

7708

7709

if (o->m_pDACF->m_bLifetimeSpectrum)

7710

{

7711

for (z2=0;z2<o->m_pDACF->m_oaLTSpectra.GetSize();z2++)

7712

{

7713

mprintf(WHITE,"\n * Lifetime Spectrum %d\n\n",z2+1);

7714

((CLTSpec*)o->m_pDACF->m_oaLTSpectra[z2])->ComputeSpectrum("dacf",dacfsub->m_sName,multibuf,"",dacfsub->m_pDACF);

7715

}

7716

/* sprintf(buf,"dacf_lspectrum_N%d_P%d_I%d_%s%s.csv",o->m_pDACF->m_iLSpecData,o->m_pDACF->m_iLSpecPoints,o->m_pDACF->m_iMaxLMIter,dacfsub->m_sName,multibuf);

7717

mprintf(" Saving DACF lifetime spectrum as \"%s\"...\n",buf);

7718

dacfsub->m_pDACF->Fit_ExpSpectrum(o->m_pDACF->m_iLSpecPoints,o->m_pDACF->m_fLSpecMinExp,o->m_pDACF->m_fLSpecMaxExp,buf,o->m_pDACF->m_iLSpecData,o->m_pDACF->m_iMaxLMIter,false,true);

7719

7720

sprintf(buf,"dacf_lsfit_N%d_P%d_I%d_%s%s.csv",o->m_pDACF->m_iLSpecData,o->m_pDACF->m_iLSpecPoints,o->m_pDACF->m_iMaxLMIter,dacfsub->m_sName,multibuf);

7721

mprintf(" Saving DACF lifetime spectrum fit as \"%s\"...\n",buf);

7722

dacfsub->m_pDACF->Write("",buf,"",false);*/

7723

}

7724

}

7725

7726

if (g_bDLDF)

7727

{

7728

mprintf(WHITE,"\nDimer Lifetime Distribution Function\n");

7729

mprintf(" %.0f Bin entries have been made (%.0f skipped, %.0f total).\n",dacfsub->m_pDLDF->m_fBinEntries,dacfsub->m_pDLDF->m_fSkipEntries,dacfsub->m_pDLDF->m_fBinEntries+dacfsub->m_pDLDF->m_fSkipEntries);

7730

sprintf(buf,"dldf_%s%s.csv",dacfsub->m_sName,multibuf);

7731

mprintf(" Saving DLDF File as \"%s\"...\n",buf);

7732

dacfsub->m_pDLDF->Write("",buf,"",false);

7733

sprintf(buf,"dldf_%s%s.agr",dacfsub->m_sName,multibuf);

7734

mprintf(" Saving DLDF Agr File as \"%s\"...\n",buf);

7735

dacfsub->m_pDLDF->WriteAgr("",buf,"","",false);

7736

}

7737

7738

if (g_bDLDisp)

7739

{

7740

mprintf(WHITE,"\nDimer Lifetime Displacement Distribution Function\n");

7741

mprintf(" %.0f Bin entries have been made (%.0f skipped, %.0f total).\n",dacfsub->m_pDLDisp->m_fBinEntries,dacfsub->m_pDLDisp->m_fSkipEntries,dacfsub->m_pDLDisp->m_fBinEntries+dacfsub->m_pDLDisp->m_fSkipEntries);

7742

mprintf(" Normalizing bin integral to 1000000...\n");

7743

dacfsub->m_pDLDisp->NormalizeBinIntegral(1000000.0);

7744

sprintf(buf,"dldisp_%s%s",dacfsub->m_sName,multibuf);

7745

mprintf(" Saving DLDisp triples as \"%s_triples.csv\"...\n",buf);

7746

dacfsub->m_pDLDisp->Write("",buf,"_triples.csv");

7747

mprintf(" Saving DLDisp matrix as \"%s_matrix.csv\"...\n",buf);

7748

dacfsub->m_pDLDisp->WriteCSV("",buf,"_matrix.csv");

7749

mprintf(" Saving DLDisp Mathematica Notebook \"%s.nb\"...\n",buf);

7750

dacfsub->m_pDLDisp->WriteMathematicaNb("",buf,".nb",false);

7751

mprintf(" Saving DLDisp Gnuplot Input \"%s.gp\"...\n",buf);

7752

dacfsub->m_pDLDisp->WriteGnuplotInput("",buf,"",false);

7753

}

7754

7755

if (g_bPairMSD)

7756

{

7757

mprintf(WHITE,"\nPair Mean Square Displacement\n");

7758

mprintf(" %.0f Bin entries have been made.\n",dacfsub->m_pPairMSD->m_fBinEntries);

7759

mprintf(" Calculating average values...\n");

7760

dacfsub->m_pPairMSD->BuildAverage();

7761

sprintf(buf,"pairmsd_%s%s",dacfsub->m_sName,multibuf);

7762

mprintf(" Saving Pair MSD as \"%s.csv\"...\n",buf);

7763

dacfsub->m_pPairMSD->Write("",buf,".csv");

7764

}

7765

}

7766

if (o->m_pDACF->m_bDACFGrid && o->m_pDACF->m_bFitDACF)

7767

{

7768

mprintf(WHITE,"\n*** Condition Grid fitting overview:\n\n");

7769

mprintf(" Degree R(min) R(avg) R(max)\n");

7770

o->m_pDACF->CalcGridFitParms();

7771

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7772

mprintf(" %d %10.8f %10.8f %10.8f\n",z2,o->m_pDACF->m_pFitRMin[z2],o->m_pDACF->m_pFitRAvg[z2],o->m_pDACF->m_pFitRMax[z2]);

7773

mprintf("\n");

7774

7775

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7776

{

7777

if ((o->m_pDACF->m_iGridMode == 3) || (o->m_pDACF->m_iGridMode == 5))

7778

{

7779

if (o->m_pDACF->m_bGridCon)

7780

{

7781

try { temp2df = new C2DF(); } catch(...) { temp2df = NULL; }

7782

if (temp2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7783

7784

o->m_pDACF->CreateGridFit2DF(temp2df,z2,false);

7785

sprintf(buf,"dacf_gridint_%s%s_%dexp",o->m_pDACF->m_sName,multibuf,z2);

7786

mprintf(" Saving Grid Integral triples as \"%s_triples.csv\"...\n",buf);

7787

temp2df->Write("",buf,"_triples.csv");

7788

mprintf(" Saving Grid Integral matrix as \"%s_matrix.csv\"...\n",buf);

7789

temp2df->WriteCSV("",buf,"_matrix.csv");

7790

mprintf(" Saving Grid Integral Mathematica Notebook \"%s.nb\"...\n",buf);

7791

temp2df->WriteMathematicaNb("",buf,".nb",false);

7792

mprintf(" Saving Grid Integral Gnuplot Input \"%s.gp\"...\n",buf);

7793

temp2df->WriteGnuplotInput("",buf,"",false);

7794

delete temp2df;

7795

}

7796

if (o->m_pDACF->m_bGridInt)

7797

{

7798

try { temp2df = new C2DF(); } catch(...) { temp2df = NULL; }

7799

if (temp2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7800

7801

o->m_pDACF->CreateGridFit2DF(temp2df,z2,true);

7802

sprintf(buf,"dacf_gridint_%s%s_%dexp_int%.2f",o->m_pDACF->m_sName,multibuf,z2,o->m_pDACF->m_fGridIntGap);

7803

mprintf(" Saving Grid Integral triples as \"%s_triples.csv\"...\n",buf);

7804

temp2df->Write("",buf,"_triples.csv");

7805

mprintf(" Saving Grid Integral matrix as \"%s_matrix.csv\"...\n",buf);

7806

temp2df->WriteCSV("",buf,"_matrix.csv");

7807

mprintf(" Saving Grid Integral Mathematica Notebook \"%s.nb\"...\n",buf);

7808

temp2df->WriteMathematicaNb("",buf,".nb",false);

7809

mprintf(" Saving Grid Integral Gnuplot Input \"%s.gp\"...\n",buf);

7810

temp2df->WriteGnuplotInput("",buf,"",false);

7811

delete temp2df;

7812

}

7813

} else

7814

{

7815

if (o->m_pDACF->m_bGridCon)

7816

{

7817

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

7818

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7819

7820

// o->m_pDACF->CreateGridFitDF(tdf,z2,false);

7821

abort();

7822

delete tdf;

7823

}

7824

}

7825

}

7826

}

7827

} // END IF AGGREGATION

7828

7829

if (g_bDens)

7830

{

7831

mprintf(WHITE,"* Density Distribution Function\n");

7832

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pDensityDF->m_pDensDF->m_fBinEntries,o->m_pDensityDF->m_pDensDF->m_fSkipEntries,ZeroDivide(o->m_pDensityDF->m_pDensDF->m_fSkipEntries,o->m_pDensityDF->m_pDensDF->m_fBinEntries+o->m_pDensityDF->m_pDensDF->m_fSkipEntries)*100.0);

7833

7834

mprintf(" Correcting radial distribution...\n");

7835

o->m_pDensityDF->m_pDensDF->CorrectRadialDist();

7836

7837

mprintf(" Scaling values to match final density...\n");

7838

7839

if (o->m_pDensityDF->m_bDensityMass)

7840

{

7841

o->m_pDensityDF->m_pDensDF->Integrate(true,1.0 / g_iSteps / (double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

7842

o->m_pDensityDF->m_pDensDF->MultiplyBin(1.66054e6 / (4.0/3.0*Pi) / g_iSteps / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

7843

} else

7844

{

7845

o->m_pDensityDF->m_pDensDF->Integrate(true,1.0 / g_iSteps / (double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

7846

o->m_pDensityDF->m_pDensDF->MultiplyBin(1.0e9 / (4.0/3.0*Pi) / g_iSteps / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

7847

}

7848

7849

/* if (g_bDoubleBox)

7850

{

7851

o->m_pDensityDF->m_pDensDF->MultiplyBin(g_iDoubleBoxFactor);

7852

o->m_pDensityDF->m_pDensDF->MultiplyIntegral(g_iDoubleBoxFactor);

7853

}*/

7854

7855

sprintf(buf,"density_df_%s%s.csv",o->m_pDensityDF->m_sName,multibuf);

7856

mprintf(" Saving Density DF as \"%s\"...\n",buf);

7857

o->m_pDensityDF->m_pDensDF->Write("",buf,"",true);

7858

sprintf(buf,"density_df_%s%s.agr",o->m_pDensityDF->m_sName,multibuf);

7859

mprintf(" Saving Density DF AGR file as \"%s\"...\n",buf);

7860

o->m_pDensityDF->m_pDensDF->WriteAgr("",buf,"",o->m_pDensityDF->m_sName,true);

7861

if (o->m_pDensityDF->m_iHistogramRes != 0)

7862

{

7863

mprintf(" Calculating Histogram...\n");

7864

o->m_pDensityDF->m_pDensDF->CalcHistogram();

7865

sprintf(buf,"his_density_df_%s%s.csv",o->m_pDensityDF->m_sName,multibuf);

7866

mprintf(" Saving Histogram as \"%s\"...\n",buf);

7867

o->m_pDensityDF->m_pDensDF->WriteHistogram("",buf,"");

7868

}

7869

} // END IF g_bDens

7870

7871

if (g_bRDyn)

7872

{

7873

mprintf(WHITE,"* Vector Reorientation Dynamics\n");

7874

o->m_pRDyn->Finish(multibuf);

7875

}

7876

7877

if (g_bIRSpec)

7878

{

7879

mprintf(WHITE,"* IR Spectrum\n");

7880

o->m_pIRSpec->Finish(multibuf);

7881

}

7882

7883

if (g_bVACF)

7884

{

7885

mprintf(WHITE,"* Velocity Autocorrelation Function\n");

7886

if (o->m_pVACF->m_bDerivative)

7887

{

7888

mprintf(" Deriving velocities...\n");

7889

mprintf(WHITE," [");

7890

tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes)/60.0;

7891

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

7892

{

7893

if (fmod(z2,tfs) < 1)

7894

mprintf(WHITE,"#");

7895

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[z2];

7896

7897

for (z3=0;z3<(int)g_iSteps*3-3;z3++)

7898

(*ptfa)[z3] = (*ptfa)[z3+3] - (*ptfa)[z3];

7899

}

7900

mprintf(WHITE,"]\n");

7901

}

7902

if (g_bVACFCacheMode)

7903

{

7904

mprintf(" Autocorrelating cached vectors...\n");

7905

mprintf(WHITE," [");

7906

tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes)/60.0;

7907

7908

try { ptfa2 = new CxFloatArray("main():ptfa2"); } catch(...) { ptfa2 = NULL; }

7909

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7910

7911

ptfa2->SetSize(g_iSteps);

7912

7913

try { ptfa3 = new CxFloatArray("main():ptfa3"); } catch(...) { ptfa3 = NULL; }

7914

if (ptfa3 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7915

7916

ptfa3->SetSize(g_iSteps);

7917

7918

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

7919

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7920

7921

ac->Init(g_iSteps,o->m_pVACF->m_iSize,g_bACFFFT);

7922

ti = 0;

7923

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

7924

{

7925

for (z3=0;z3<o->m_pVACF->m_oAtoms.m_baAtomType.GetSize();z3++)

7926

{

7927

if (o->m_pVACF->m_bMassWeight)

7928

tf = ((CAtom*)g_oaAtoms[o->m_pVACF->m_oAtoms.m_baRealAtomType[z3]])->m_pElement->m_fMass;

7929

else tf = 1.0;

7930

for (z4=0;z4<((CxIntArray*)o->m_pVACF->m_oAtoms.m_oaAtoms[z3])->GetSize();z4++)

7931

{

7932

if (fmod(ti,tfs) < 1)

7933

mprintf(WHITE,"#");

7934

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[ti];

7935

7936

/* X */

7937

for (z5=0;z5<(int)g_iSteps;z5++)

7938

(*ptfa2)[z5] = (*ptfa)[z5*3];

7939

ac->AutoCorrelate(ptfa2,ptfa3);

7940

// mprintf("Lokal Atom %d X: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

7941

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

7942

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

7943

7944

/* Y */

7945

for (z5=0;z5<(int)g_iSteps;z5++)

7946

(*ptfa2)[z5] = (*ptfa)[z5*3+1];

7947

ac->AutoCorrelate(ptfa2,ptfa3);

7948

// mprintf("Lokal Atom %d Y: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

7949

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

7950

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

7951

7952

/* Z */

7953

for (z5=0;z5<(int)g_iSteps;z5++)

7954

(*ptfa2)[z5] = (*ptfa)[z5*3+2];

7955

ac->AutoCorrelate(ptfa2,ptfa3);

7956

// mprintf("Lokal Atom %d Z: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

7957

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

7958

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

7959

7960

ti++;

7961

}

7962

}

7963

}

7964

delete ac;

7965

delete ptfa2;

7966

delete ptfa3;

7967

7968

/* } else

7969

{

7970

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

7971

{

7972

if (fmod(z2,tfs) < 1)

7973

mprintf(WHITE,"#");

7974

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[z2];

7975

for (z3=0;z3<o->m_pVACF->m_iSize;z3+=o->m_pVACF->m_iStride) // Das ist das Tau

7976

{

7977

tf = 0;

7978

for (z4=0;z4<(int)g_iSteps-z3;z4++) // Das ist der Startpunkt

7979

tf += (*ptfa)[z4*3]*(*ptfa)[(z4+z3)*3] + (*ptfa)[z4*3+1]*(*ptfa)[(z4+z3)*3+1] + (*ptfa)[z4*3+2]*(*ptfa)[(z4+z3)*3+2];

7980

o->m_pVACF->m_pData[z3/o->m_pVACF->m_iStride] += tf/(g_iSteps-z3);

7981

}

7982

}

7983

}*/

7984

mprintf(WHITE,"]\n");

7985

// mprintf(" %d atoms, %d time steps and %d correlation depths processed.\n",g_pGlobalVACF->m_oaCache.GetSize(),g_iSteps,g_pGlobalVACF->m_iSize);

7986

mprintf(" %d atoms, %d time steps and %d correlation depths processed.\n",ti,g_iSteps,o->m_pVACF->m_iSize);

7987

o->m_pVACF->MultiplyCached(1.0/g_iGesAtomCount);

7988

} else o->m_pVACF->Multiply(1.0/g_iGesAtomCount);

7989

/* sprintf(buf,"acf_%s%s.csv",o->m_pVACF->m_sName,multibuf);

7990

mprintf(" Saving ACF as %s ...\n",buf);

7991

o->m_pVACF->WriteACF("",buf,"");*/

7992

7993

sprintf(buf,"acf_%s%s.csv",o->m_pVACF->m_sName,multibuf);

7994

mprintf(" Saving ACF as %s ...\n",buf);

7995

o->m_pVACF->WriteACF("",buf,"");

7996

7997

if (o->m_pVACF->m_iMirror != 0)

7998

{

7999

mprintf(" Mirroring ACF...\n");

8000

o->m_pVACF->Mirror(o->m_pVACF->m_iMirror);

8001

sprintf(buf,"acf_%s%s.m.csv",o->m_pVACF->m_sName,multibuf);

8002

mprintf(" Saving mirrored ACF as %s ...\n",buf);

8003

o->m_pVACF->WriteACF("",buf,"");

8004

}

8005

8006

if (o->m_pVACF->m_bWindowFunction)

8007

{

8008

mprintf(" Applying window function to ACF...\n");

8009

o->m_pVACF->Window();

8010

sprintf(buf,"acf_%s%s.w.csv",o->m_pVACF->m_sName,multibuf);

8011

mprintf(" Saving windowed ACF as %s ...\n",buf);

8012

o->m_pVACF->WriteACF("",buf,"");

8013

}

8014

8015

if (o->m_pVACF->m_bSpectrum)

8016

{

8017

mprintf(" Performing fourier transformation...\n");

8018

8019

try { g_pFFT = new CFFT(); } catch(...) { g_pFFT = NULL; }

8020

if (g_pFFT == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8021

8022

/* if (o->m_pVACF->m_bMirror)

8023

g_pFFT->PrepareFFT_C2C((o->m_pVACF->m_iSize+o->m_pVACF->m_iZeroPadding)*2);

8024

else */g_pFFT->PrepareFFT_C2C(o->m_pVACF->m_iSize+o->m_pVACF->m_iZeroPadding);

8025

o->m_pVACF->Transform(g_pFFT);

8026

delete g_pFFT;

8027

o->m_pVACF->m_pSpectrum->SetMaxRWL(1E7f/299.792f/g_fTimestepLength/g_iStride);

8028

if (o->m_pVACF->m_bACF_DB)

8029

{

8030

mprintf(" Normalising spectrum to decibel...\n");

8031

o->m_pVACF->m_pSpectrum->MakeDB();

8032

}/* else

8033

{

8034

mprintf(" Normalising integral of spectrum...\n");

8035

o->m_pVACF->m_pSpectrum->SetIntegral(1000000.0f);

8036

}*/

8037

/* if (o->m_pVACF->m_bWindowFunction)

8038

{

8039

sprintf(buf,"power_%s_w%s.csv",o->m_pVACF->m_sName,multibuf);

8040

mprintf(" Saving spectrum as %s ...\n",buf);

8041

o->m_pVACF->m_pSpectrum->Write("",buf,"");

8042

} else

8043

{*/

8044

sprintf(buf,"power_%s%s.csv",o->m_pVACF->m_sName,multibuf);

8045

mprintf(" Saving spectrum as %s ...\n",buf);

8046

o->m_pVACF->m_pSpectrum->Write("",buf,"");

8047

// }

8048

}

8049

} // End IF VACF

8050

8051

if (g_bMSD)

8052

{

8053

mprintf(WHITE,"* Mean Square Displacement\n");

8054

if (g_bMSDCacheMode)

8055

{

8056

mprintf(" Autocorrelating cached vectors...\n");

8057

// mprintf(WHITE," [");

8058

// tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms)/60.0;

8059

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

8060

{

8061

// if (fmod(z2,tfs) < 1.0)

8062

// mprintf(WHITE,"#");

8063

mprintf(" %4d/%d: [",z2+1,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms);

8064

tfs = o->m_pMSD->m_iResolution/50.0;

8065

ptfa = (CxFloatArray*)o->m_pMSD->m_oaCache[z2];

8066

for (z3=0;z3<o->m_pMSD->m_iResolution;z3+=o->m_pMSD->m_iStride) // Das ist das Tau

8067

{

8068

if (fmod(z3,tfs) < 1.0)

8069

mprintf(WHITE,"#");

8070

tf = 0;

8071

8072

if (o->m_pMSD->m_bTakeX && o->m_pMSD->m_bTakeY && o->m_pMSD->m_bTakeZ)

8073

{

8074

for (z4=0;z4<(int)g_iSteps/g_iStride-z3-1;z4+=o->m_pMSD->m_iStride2) // Das ist der Startpunkt

8075

tf += pow((*ptfa)[(z3+z4)*3]-(*ptfa)[z4*3],2) + pow((*ptfa)[(z3+z4)*3+1]-(*ptfa)[z4*3+1],2) + pow((*ptfa)[(z3+z4)*3+2]-(*ptfa)[z4*3+2],2);

8076

} else

8077

{

8078

for (z4=0;z4<(int)g_iSteps/g_iStride-z3-1;z4+=o->m_pMSD->m_iStride2) // Das ist der Startpunkt

8079

{

8080

if (o->m_pMSD->m_bTakeX)

8081

tf += pow((*ptfa)[(z3+z4)*3]-(*ptfa)[z4*3],2);

8082

if (o->m_pMSD->m_bTakeY)

8083

tf += pow((*ptfa)[(z3+z4)*3+1]-(*ptfa)[z4*3+1],2);

8084

if (o->m_pMSD->m_bTakeZ)

8085

tf += pow((*ptfa)[(z3+z4)*3+2]-(*ptfa)[z4*3+2],2);

8086

}

8087

}

8088

8089

o->m_pMSD->m_pMSD->AddToBin_Index(z3/o->m_pMSD->m_iStride,tf/(g_iSteps/g_iStride-z3-1)*o->m_pMSD->m_iStride2);

8090

o->m_pMSD->m_pMSD->m_fBinEntries += (g_iSteps/g_iStride-z3-1)/o->m_pMSD->m_iStride2;

8091

if (o->m_pMSD->m_bSplit)

8092

{

8093

o->m_pMSD->m_pSplitMSD[z2]->AddToBin_Index(z3/o->m_pMSD->m_iStride,tf/(g_iSteps/g_iStride-z3-1)*o->m_pMSD->m_iStride2);

8094

o->m_pMSD->m_pSplitMSD[z2]->m_fBinEntries += (g_iSteps/g_iStride-z3-1)/o->m_pMSD->m_iStride2;

8095

}

8096

}

8097

mprintf("]\n");

8098

}

8099

for (z3=0;z3<o->m_pMSD->m_iResolution;z3+=o->m_pMSD->m_iStride) // Das ist das Tau

8100

o->m_pMSD->m_pMSD->m_pBin[z3/o->m_pMSD->m_iStride] /= ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;

8101

// mprintf(WHITE,"]\n");

8102

} else

8103

{

8104

o->m_pMSD->m_pMSD->BuildAverage();

8105

}

8106

mprintf(" %.0f bin entries.\n",o->m_pMSD->m_pMSD->m_fBinEntries);

8107

o->m_pMSD->m_pMSD->CalcDeriv(1.0f);

8108

sprintf(buf,"msd_%s%s.csv",o->m_pMSD->m_sName,multibuf);

8109

mprintf(" Saving result as %s ...\n",buf);

8110

if (o->m_pMSD->m_bSplit)

8111

{

8112

o->m_pMSD->WriteSplit(buf);

8113

} else o->m_pMSD->m_pMSD->Write("",buf,"");

8114

mprintf(WHITE,"\n Performing linear regression on interval %.2f - %.2f ps...\n",o->m_pMSD->m_pMSD->m_fMinVal+0.5*(o->m_pMSD->m_pMSD->m_fMaxVal-o->m_pMSD->m_pMSD->m_fMinVal),o->m_pMSD->m_pMSD->m_fMaxVal);

8115

o->m_pMSD->m_pMSD->LinReg(o->m_pMSD->m_pMSD->m_iResolution/2,o->m_pMSD->m_pMSD->m_iResolution-1,&c0,&c1,&r);

8116

mprintf(" MSD(t) = %.6f + %.6f * t (units: [MSD] = pm^2, [t] = ps).\n",c0,c1);

8117

mprintf(" R = %.6f\n",r);

8118

ti = 0;

8119

if (o->m_pMSD->m_bTakeX)

8120

ti++;

8121

if (o->m_pMSD->m_bTakeY)

8122

ti++;

8123

if (o->m_pMSD->m_bTakeZ)

8124

ti++;

8125

if (ti != 3)

8126

mprintf(" Please note: Dimensionality of the system is %d here.\n",ti);

8127

mprintf(" Diffusion coefficient D = %.6f pm^2/ps = %G m^2/s.\n",c1/2.0/ti,c1/2.0e12/ti);

8128

mprintf(" (assuming <x^2> = %d * D * t)\n\n",2*ti);

8129

} // END IF MSD

8130

8131

if (g_bNbAnalysis)

8132

{

8133

mprintf(WHITE,"* Neighborhood Analysis\n");

8134

mprintf(" %.0f bin entries.\n",o->m_pNbAnalysis->m_fBinEntries);

8135

/* for (z2=0;z2<o->m_pNbAnalysis->m_iMaxNbCount-o->m_pNbAnalysis->m_iMinNbCount;z2++)

8136

mprintf(" - %d: %.0f bin entries, %.0f skipped.\n",z2+1,((CDF*)o->m_pNbAnalysis->m_oaDF[z2])->m_fBinEntries,((CDF*)o->m_pNbAnalysis->m_oaDF[z2])->m_fSkipEntries);

8137

8138

8139

try { pf = new float[o->m_pNbAnalysis->m_iNbCount]; } catch(...) { pf = NULL; }

8140

if (pf == NULL) NewException((double)o->m_pNbAnalysis->m_iNbCount*sizeof(float),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8141

8142

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8143

pf[z3] = (float)((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->NormBinIntegral();

8144

8145

sprintf(buf,"nbh_ncf_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8146

mprintf(" Saving neighbor count function as %s ...\n",buf);

8147

a = OpenFileWrite(buf,true);

8148

mfprintf(a,"# distance [pm]; ");

8149

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount+1;z3++)

8150

{

8151

mfprintf(a,"%d neighbors",z3);

8152

if (z3 < o->m_pNbAnalysis->m_iNbCount)

8153

mfprintf(a,"; ");

8154

}

8155

mfprintf(a,"\n");

8156

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8157

{

8158

mfprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

8159

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount+1;z3++)

8160

{

8161

mfprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaNPF[z3])->m_pBin[z2]/o->m_pNbAnalysis->m_pNPFCount->m_pBin[z2]*100.0f);

8162

if (z3 < o->m_pNbAnalysis->m_iNbCount)

8163

mfprintf(a,"; ");

8164

}

8165

mfprintf(a,"\n");

8166

}

8167

fclose(a);

8168

8169

sprintf(buf,"nbh_dist_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8170

mprintf(" Calculating mean values and standard deviation...\n");

8171

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8172

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->CalcMeanSD();

8173

mprintf(" Saving neighborhood distribution as %s ...\n",buf);

8174

a = OpenFileWrite(buf,true);

8175

mfprintf(a,"# distance [pm]; ");

8176

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8177

{

8178

mfprintf(a,"%d. neighbor",z3+1);

8179

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8180

mfprintf(a,"; ");

8181

}

8182

mfprintf(a,"\n");

8183

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8184

{

8185

mfprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

8186

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8187

{

8188

mfprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

8189

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8190

mfprintf(a,"; ");

8191

}

8192

mfprintf(a,"\n");

8193

}

8194

fclose(a);

8195

8196

sprintf(buf,"nbh_minmaxavgsd_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8197

mprintf(" Saving neighborhood min/max/avg/sd as %s ...\n",buf);

8198

a = OpenFileWrite(buf,true);

8199

mfprintf(a,"# n-th neighbor; min. dist [pm]; max. dist [pm]; avg. dist [pm]; standard deviation [pm]\n");

8200

for (z2=0;z2<o->m_pNbAnalysis->m_iNbCount;z2++)

8201

{

8202

mfprintf(a,"%d; %.4f; %.4f; %.4f; %.4f",z2+1,o->m_pNbAnalysis->m_pDistMin[z2],o->m_pNbAnalysis->m_pDistMax[z2],((CDF*)o->m_pNbAnalysis->m_oaDF[z2])->m_fMean,((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_fSD);

8203

mfprintf(a,"\n");

8204

}

8205

fclose(a);

8206

8207

sprintf(buf,"nbh_rdf_decomp_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8208

mprintf(" Saving neighborhood RDF decomposition as %s ...\n",buf);

8209

a = OpenFileWrite(buf,true);

8210

mfprintf(a,"# distance [pm]; ");

8211

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8212

{

8213

mfprintf(a,"%d. neighbor",z3+1);

8214

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8215

mfprintf(a,"; ");

8216

}

8217

mfprintf(a,"\n");

8218

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8219

{

8220

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->MultiplyBin(pf[z3]);

8221

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->CorrectRadialDist();

8222

}

8223

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8224

{

8225

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

8226

if (g_bDoubleBox)

8227

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->MultiplyBin(g_iDoubleBoxFactor);

8228

}

8229

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8230

{

8231

mfprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

8232

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8233

{

8234

mfprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

8235

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8236

mfprintf(a,"; ");

8237

}

8238

mfprintf(a,"\n");

8239

}

8240

fclose(a);

8241

8242

sprintf(buf,"nbh_rdf_decomp_cumulative_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8243

mprintf(" Saving cumulative neighborhood RDF decomposition as %s ...\n",buf);

8244

a = OpenFileWrite(buf,true);

8245

mfprintf(a,"# distance [pm]; ");

8246

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8247

{

8248

mfprintf(a,"%d. neighbor",z3+1);

8249

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8250

mfprintf(a,"; ");

8251

}

8252

mfprintf(a,"\n");

8253

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8254

for (z3=1;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8255

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2] += ((CDF*)o->m_pNbAnalysis->m_oaDF[z3-1])->m_pBin[z2];

8256

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8257

{

8258

mfprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

8259

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8260

{

8261

mfprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

8262

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8263

mfprintf(a,"; ");

8264

}

8265

mfprintf(a,"\n");

8266

}

8267

fclose(a);

8268

delete[] pf;

8269

}

8270

8271

if (g_bDipDF)

8272

{

8273

for (zr=0;zr<g_iCDFChannels;zr++)

8274

{

8275

if (o->m_pDipDF[zr] == NULL)

8276

continue;

8277

mprintf(WHITE,"* Dipole Distribution Function\n");

8278

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pDipDF[zr]->m_pDipoleDF->m_fBinEntries,o->m_pDipDF[zr]->m_pDipoleDF->m_fSkipEntries,ZeroDivide(o->m_pDipDF[zr]->m_pDipoleDF->m_fSkipEntries,o->m_pDipDF[zr]->m_pDipoleDF->m_fSkipEntries+o->m_pDipDF[zr]->m_pDipoleDF->m_fBinEntries)*100.0);

8279

o->m_pDipDF[zr]->m_pDipoleDF->CalcMeanSD();

8280

mprintf(" Mean value: %10G Debye Standard deviation: %10G Debye\n",o->m_pDipDF[zr]->m_pDipoleDF->m_fMean,o->m_pDipDF[zr]->m_pDipoleDF->m_fSD);

8281

mprintf(" Min. value: %10G Debye Max. value: %10G Debye\n",o->m_pDipDF[zr]->m_pDipoleDF->m_fMinInput,o->m_pDipDF[zr]->m_pDipoleDF->m_fMaxInput);

8282

o->m_pDipDF[zr]->m_pDipoleDF->NormBinIntegral();

8283

sprintf(buf,"dipole_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

8284

mprintf(" Saving dipole distribution as %s ...\n",buf);

8285

o->m_pDipDF[zr]->m_pDipoleDF->Write("",buf,"",false);

8286

sprintf(buf,"dipole_%s%s.agr",o->m_pDipDF[zr]->m_sName,multibuf);

8287

mprintf(" Saving dipole distribution AGR file as \"%s\"...\n",buf);

8288

o->m_pDipDF[zr]->m_pDipoleDF->WriteAgr("",buf,"",o->m_pDipDF[zr]->m_sName,false);

8289

if (o->m_pDipDF[zr]->m_iHistogramRes != 0)

8290

{

8291

mprintf(" Calculating Histogram...\n");

8292

o->m_pDipDF[zr]->m_pDipoleDF->CalcHistogram();

8293

sprintf(buf,"his_dipdf_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

8294

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8295

o->m_pDipDF[zr]->m_pDipoleDF->WriteHistogram("",buf,"");

8296

}

8297

if (o->m_bTimeDev)

8298

{

8299

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8300

{

8301

fclose(o->m_pDipDF[zr]->m_fDipole[0]);

8302

mprintf(" Saving temporal development as dipole_timedev_%s%s.csv\n",o->m_pDipDF[zr]->m_sName,multibuf);

8303

} else

8304

{

8305

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8306

{

8307

fclose(o->m_pDipDF[zr]->m_fDipole[z2]);

8308

mprintf(" Saving temporal development as dipole_timedev_%s_ref%d%s.csv\n",o->m_pDipDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8309

}

8310

}

8311

if (o->m_bCombinedPlot)

8312

{

8313

sprintf(buf,"combined_%s%s.agr",o->m_pDipDF[zr]->m_sName,multibuf);

8314

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8315

o->m_pDipDF[zr]->m_pDipoleDF->CreateCombinedPlot(false);

8316

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->WriteAgr(buf,false);

8317

}

8318

} // END IF TIMEDEV

8319

8320

if (o->m_bObsCertain && o->m_bDecompDist)

8321

{

8322

sprintf(buf,"dipdf_decomp_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

8323

mprintf(" Saving DipDF decomposition as \"%s\"...\n",buf);

8324

o->m_pDipDF[zr]->m_pDipoleDF->WriteMulti("",buf,"");

8325

sprintf(buf,"dipdf_decomp_%s%s_cumulative.csv",o->m_pDipDF[zr]->m_sName,multibuf);

8326

mprintf(" Saving cumulative DipoleDF decomposition as \"%s\"...\n",buf);

8327

o->m_pDipDF[zr]->m_pDipoleDF->WriteMulti_Cumulative("",buf,"");

8328

}

8329

8330

if (o->m_bTimeDiff)

8331

o->WriteTimeDiff(o->m_pDipDF[zr]->m_pDipoleDF,"DipDF","dipdf",o->m_pDipDF[zr]->m_sName,multibuf,false);

8332

}

8333

} // END IF DIPOLE

8334

8335

if (g_bVDF)

8336

{

8337

for (zr=0;zr<g_iCDFChannels;zr++)

8338

{

8339

if (o->m_pVDF[zr] == NULL)

8340

continue;

8341

mprintf(WHITE,"* Velocity Distribution Function\n");

8342

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pVDF[zr]->m_pVDF->m_fBinEntries,o->m_pVDF[zr]->m_pVDF->m_fSkipEntries,ZeroDivide(o->m_pVDF[zr]->m_pVDF->m_fSkipEntries,o->m_pVDF[zr]->m_pVDF->m_fBinEntries+o->m_pVDF[zr]->m_pVDF->m_fSkipEntries)*100.0);

8343

o->m_pVDF[zr]->m_pVDF->CalcMeanSD();

8344

mprintf(" Mean value: %10G pm/ps Standard deviation: %10G pm/ps\n",o->m_pVDF[zr]->m_pVDF->m_fMean,o->m_pVDF[zr]->m_pVDF->m_fSD);

8345

mprintf(" Min. value: %10G pm/ps Max. value: %10G pm/ps\n",o->m_pVDF[zr]->m_pVDF->m_fMinInput,o->m_pVDF[zr]->m_pVDF->m_fMaxInput);

8346

o->m_pVDF[zr]->m_pVDF->NormBinIntegral();

8347

sprintf(buf,"vdf_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

8348

mprintf(" Saving velocity distribution as %s ...\n",buf);

8349

o->m_pVDF[zr]->m_pVDF->Write("",buf,"",false);

8350

sprintf(buf,"vdf_%s%s.agr",o->m_pVDF[zr]->m_sName,multibuf);

8351

mprintf(" Saving velocity distribution AGR file as \"%s\"...\n",buf);

8352

o->m_pVDF[zr]->m_pVDF->WriteAgr("",buf,"",o->m_pVDF[zr]->m_sName,false);

8353

if (o->m_pVDF[zr]->m_iHistogramRes != 0)

8354

{

8355

mprintf(" Calculating Histogram...\n");

8356

o->m_pVDF[zr]->m_pVDF->CalcHistogram();

8357

sprintf(buf,"his_vdf_%s%s.agr",o->m_pVDF[zr]->m_sName,multibuf);

8358

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8359

o->m_pVDF[zr]->m_pVDF->WriteHistogram("",buf,"");

8360

}

8361

if (o->m_bTimeDev)

8362

{

8363

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8364

{

8365

fclose(o->m_pVDF[zr]->m_fSpeed[0]);

8366

mprintf(" Saving temporal development as vdf_timedev_%s%s.csv\n",o->m_pVDF[zr]->m_sName,multibuf);

8367

} else

8368

{

8369

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8370

{

8371

fclose(o->m_pVDF[zr]->m_fSpeed[z2]);

8372

mprintf(" Saving temporal development as vdf_timedev_%s_ref%d%s.csv\n",o->m_pVDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8373

}

8374

}

8375

if (o->m_bCombinedPlot)

8376

{

8377

sprintf(buf,"combined_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

8378

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8379

o->m_pVDF[zr]->m_pVDF->CreateCombinedPlot(false);

8380

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->WriteAgr(buf,false);

8381

}

8382

} // END IF TIMEDEV

8383

8384

if (o->m_bObsCertain && o->m_bDecompDist)

8385

{

8386

sprintf(buf,"vdf_decomp_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

8387

mprintf(" Saving VDF decomposition as \"%s\"...\n",buf);

8388

o->m_pVDF[zr]->m_pVDF->WriteMulti("",buf,"");

8389

sprintf(buf,"vdf_decomp_%s%s_cumulative.csv",o->m_pVDF[zr]->m_sName,multibuf);

8390

mprintf(" Saving cumulative VDF decomposition as \"%s\"...\n",buf);

8391

o->m_pVDF[zr]->m_pVDF->WriteMulti_Cumulative("",buf,"");

8392

}

8393

8394

if (o->m_bTimeDiff)

8395

o->WriteTimeDiff(o->m_pVDF[zr]->m_pVDF,"VDF","vdf",o->m_pVDF[zr]->m_sName,multibuf,false);

8396

}

8397

} // END IF VDF

8398

8399

if (g_bPlDF)

8400

{

8401

for (zr=0;zr<g_iCDFChannels;zr++)

8402

{

8403

if (o->m_pPlDF[zr] == NULL)

8404

continue;

8405

mprintf(WHITE,"* Plane Distance Distribution Function\n");

8406

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pPlDF[zr]->m_pPlDF->m_fBinEntries,o->m_pPlDF[zr]->m_pPlDF->m_fSkipEntries,ZeroDivide(o->m_pPlDF[zr]->m_pPlDF->m_fSkipEntries,o->m_pPlDF[zr]->m_pPlDF->m_fBinEntries+o->m_pPlDF[zr]->m_pPlDF->m_fSkipEntries)*100.0);

8407

o->m_pPlDF[zr]->m_pPlDF->CalcMeanSD();

8408

mprintf(" Mean value: %10G pm/ps Standard deviation: %10G pm/ps\n",o->m_pPlDF[zr]->m_pPlDF->m_fMean,o->m_pPlDF[zr]->m_pPlDF->m_fSD);

8409

mprintf(" Min. value: %10G pm/ps Max. value: %10G pm/ps\n",o->m_pPlDF[zr]->m_pPlDF->m_fMinInput,o->m_pPlDF[zr]->m_pPlDF->m_fMaxInput);

8410

o->m_pPlDF[zr]->m_pPlDF->NormBinIntegral();

8411

sprintf(buf,"pldf_%s%s.csv",o->m_pPlDF[zr]->m_sName,multibuf);

8412

mprintf(" Saving plane distance distribution as %s ...\n",buf);

8413

o->m_pPlDF[zr]->m_pPlDF->Write("",buf,"",false);

8414

sprintf(buf,"pldf_%s%s.agr",o->m_pPlDF[zr]->m_sName,multibuf);

8415

mprintf(" Saving plane distance distribution AGR file as \"%s\"...\n",buf);

8416

o->m_pPlDF[zr]->m_pPlDF->WriteAgr("",buf,"",o->m_pPlDF[zr]->m_sName,false);

8417

if (o->m_pPlDF[zr]->m_iHistogramRes != 0)

8418

{

8419

mprintf(" Calculating Histogram...\n");

8420

o->m_pPlDF[zr]->m_pPlDF->CalcHistogram();

8421

sprintf(buf,"his_pldf_%s%s.agr",o->m_pPlDF[zr]->m_sName,multibuf);

8422

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8423

o->m_pPlDF[zr]->m_pPlDF->WriteHistogram("",buf,"");

8424

}

8425

}

8426

} // END IF PlDF

8427

8428

if (g_bLiDF)

8429

{

8430

for (zr=0;zr<g_iCDFChannels;zr++)

8431

{

8432

if (o->m_pLiDF[zr] == NULL)

8433

continue;

8434

mprintf(WHITE,"* Line Distance Distribution Function\n");

8435

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pLiDF[zr]->m_pLiDF->m_fBinEntries,o->m_pLiDF[zr]->m_pLiDF->m_fSkipEntries,ZeroDivide(o->m_pLiDF[zr]->m_pLiDF->m_fSkipEntries,o->m_pLiDF[zr]->m_pLiDF->m_fBinEntries+o->m_pLiDF[zr]->m_pLiDF->m_fSkipEntries)*100.0);

8436

o->m_pLiDF[zr]->m_pLiDF->CalcMeanSD();

8437

mprintf(" Mean value: %10G pm/ps Standard deviation: %10G pm/ps\n",o->m_pLiDF[zr]->m_pLiDF->m_fMean,o->m_pLiDF[zr]->m_pLiDF->m_fSD);

8438

mprintf(" Min. value: %10G pm/ps Max. value: %10G pm/ps\n",o->m_pLiDF[zr]->m_pLiDF->m_fMinInput,o->m_pLiDF[zr]->m_pLiDF->m_fMaxInput);

8439

8440

if (o->m_pLiDF[zr]->m_bRadialCorrect)

8441

{

8442

mprintf(" Correcting radial distribution...\n");

8443

o->m_pLiDF[zr]->m_pLiDF->CorrectLiRadialDist();

8444

}

8445

if (o->m_bOthers && o->m_pLiDF[zr]->m_bRadialCorrect)

8446

{

8447

mprintf(" Scaling LiDF to uniform density...\n");

8448

if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)

8449

{

8450

if (o->m_bObsCertain)

8451

{

8452

o->m_pLiDF[zr]->m_pLiDF->Integrate(true,1.0 / g_iSteps / o->m_waObsRefList.GetSize());

8453

o->m_pLiDF[zr]->m_pLiDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / g_iSteps / o->m_waObsRefList.GetSize() / o->m_pLiDF[zr]->m_iShowAtomGes / o->m_waObsShowList.GetSize() / o->m_pLiDF[zr]->m_iRefAtomGes);

8454

} else

8455

{

8456

o->m_pLiDF[zr]->m_pLiDF->Integrate(true,1.0 / g_iSteps / (double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

8457

o->m_pLiDF[zr]->m_pLiDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pLiDF[zr]->m_iShowAtomGes / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() / o->m_pLiDF[zr]->m_iRefAtomGes);

8458

}

8459

if (g_bDoubleBox)

8460

{

8461

o->m_pLiDF[zr]->m_pLiDF->MultiplyBin(g_iDoubleBoxFactor);

8462

o->m_pLiDF[zr]->m_pLiDF->MultiplyIntegral(g_iDoubleBoxFactor);

8463

}

8464

} else

8465

{

8466

eprintf(" Uniform density not defined if box is not XYZ-periodic!\n");

8467

goto _lidfint1;

8468

}

8469

} else

8470

{

8471

_lidfint1:

8472

mprintf(" Scaling LiDF to integral value 1000 ...\n");

8473

o->m_pLiDF[zr]->m_pLiDF->NormBinIntegral(1000.0);

8474

o->m_pLiDF[zr]->m_pLiDF->Integrate(false,1000.0);

8475

}

8476

8477

8478

o->m_pLiDF[zr]->m_pLiDF->NormBinIntegral();

8479

sprintf(buf,"lidf_%s%s.csv",o->m_pLiDF[zr]->m_sName,multibuf);

8480

mprintf(" Saving line distance distribution as %s ...\n",buf);

8481

o->m_pLiDF[zr]->m_pLiDF->Write("",buf,"",false);

8482

sprintf(buf,"lidf_%s%s.agr",o->m_pLiDF[zr]->m_sName,multibuf);

8483

mprintf(" Saving line distance distribution AGR file as \"%s\"...\n",buf);

8484

o->m_pLiDF[zr]->m_pLiDF->WriteAgr("",buf,"",o->m_pLiDF[zr]->m_sName,false);

8485

if (o->m_pLiDF[zr]->m_iHistogramRes != 0)

8486

{

8487

mprintf(" Calculating Histogram...\n");

8488

o->m_pLiDF[zr]->m_pLiDF->CalcHistogram();

8489

sprintf(buf,"his_lidf_%s%s.agr",o->m_pLiDF[zr]->m_sName,multibuf);

8490

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8491

o->m_pLiDF[zr]->m_pLiDF->WriteHistogram("",buf,"");

8492

}

8493

}

8494

} // END IF LiDF

8495

8496

if (g_bADF)

8497

{

8498

for (zr=0;zr<g_iCDFChannels;zr++)

8499

{

8500

if (o->m_pADF[zr] == NULL)

8501

continue;

8502

mprintf(WHITE,"* Angular Distribution Function\n");

8503

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pADF[zr]->m_pADF->m_fBinEntries,o->m_pADF[zr]->m_pADF->m_fSkipEntries,ZeroDivide(o->m_pADF[zr]->m_pADF->m_fSkipEntries,o->m_pADF[zr]->m_pADF->m_fBinEntries+o->m_pADF[zr]->m_pADF->m_fSkipEntries)*100.0);

8504

o->m_pADF[zr]->m_pADF->CalcMeanSD();

8505

if (o->m_pADF[zr]->m_bCosine)

8506

{

8507

mprintf(" Mean value: %10G Standard deviation: %10G\n",o->m_pADF[zr]->m_pADF->m_fMean,o->m_pADF[zr]->m_pADF->m_fSD);

8508

mprintf(" Min. value: %10G Max. value: %10G\n",o->m_pADF[zr]->m_pADF->m_fMinInput,o->m_pADF[zr]->m_pADF->m_fMaxInput);

8509

} else

8510

{

8511

mprintf(" Mean value: %10G degree Standard deviation: %10G degree\n",o->m_pADF[zr]->m_pADF->m_fMean,o->m_pADF[zr]->m_pADF->m_fSD);

8512

mprintf(" Min. value: %10G degree Max. value: %10G degree\n",o->m_pADF[zr]->m_pADF->m_fMinInput,o->m_pADF[zr]->m_pADF->m_fMaxInput);

8513

}

8514

if (o->m_pADF[zr]->m_bStat)

8515

{

8516

mprintf(" Applying cone correction...\n");

8517

o->m_pADF[zr]->m_pADF->AngleCorrect();

8518

}

8519

/* if (o->m_pADF[zr]->m_bMirror)

8520

{

8521

mprintf(" Making ADF mirror-symmetric...\n");

8522

if (o->m_pADF[zr]->m_bCosine)

8523

o->m_pADF[zr]->m_pADF->Mirror(0.0f);

8524

else o->m_pADF[zr]->m_pADF->Mirror(90.0f);

8525

}*/

8526

o->m_pADF[zr]->m_pADF->NormBinIntegral();

8527

if (o->m_bTimeDev)

8528

{

8529

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8530

{

8531

fclose(o->m_pADF[zr]->m_fAngle[0]);

8532

mprintf(" Saving temporal development as adf_timedev_%s%s.csv\n",o->m_pADF[zr]->m_sName,multibuf);

8533

} else

8534

{

8535

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8536

{

8537

fclose(o->m_pADF[zr]->m_fAngle[z2]);

8538

sprintf(buf,"adf_timedev_%s_ref%d%s.csv",o->m_pADF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8539

mprintf(" Saving temporal development as %s\n",buf);

8540

}

8541

}

8542

// mprintf(" Speichere Winkel-Statistik als %s_angle_stat.txt\n",o->m_pADF->m_sName);

8543

// FreeFileName("",o->m_pADF->m_sName,"_angle_stat.txt");

8544

// o->m_pADF->m_pAngleStat->Evaluate();

8545

// o->m_pADF->m_pAngleStat->Write("",o->m_pADF->m_sName,"_angle_stat.txt");

8546

// delete o->m_pAngleStat;

8547

delete[] o->m_pADF[zr]->m_fAngle;

8548

o->m_pADF[zr]->m_fAngle = NULL;

8549

if (o->m_bCombinedPlot)

8550

{

8551

sprintf(buf,"combined_%s%s.agr",o->m_pADF[zr]->m_sName,multibuf);

8552

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8553

o->m_pADF[zr]->m_pADF->CreateCombinedPlot(false);

8554

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->WriteAgr(buf,false);

8555

}

8556

} // END IF TIMEDEV

8557

sprintf(buf,"adf_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

8558

mprintf(" Saving ADF as %s ...\n",buf);

8559

o->m_pADF[zr]->m_pADF->NormBinIntegral();

8560

o->m_pADF[zr]->m_pADF->Write("",buf,"",false);

8561

sprintf(buf,"adf_%s%s.agr",o->m_pADF[zr]->m_sName,multibuf);

8562

mprintf(" Saving ADF AGR file as \"%s\"...\n",buf);

8563

if (o->m_pADF[zr]->m_bCosine)

8564

o->m_pADF[zr]->m_pADF->WriteAgr("",buf,"",o->m_pADF[zr]->m_sName,false);

8565

else o->m_pADF[zr]->m_pADF->WriteAgr("",buf,"",o->m_pADF[zr]->m_sName,false);

8566

if (o->m_pADF[zr]->m_iHistogramRes != 0)

8567

{

8568

mprintf(" Calculating Histogram...\n");

8569

o->m_pADF[zr]->m_pADF->CalcHistogram();

8570

sprintf(buf,"his_adf_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

8571

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8572

o->m_pADF[zr]->m_pADF->WriteHistogram("",buf,"");

8573

}

8574

8575

if (o->m_bObsCertain && o->m_bDecompDist)

8576

{

8577

sprintf(buf,"adf_decomp_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

8578

mprintf(" Saving ADF decomposition as \"%s\"...\n",buf);

8579

o->m_pADF[zr]->m_pADF->WriteMulti("",buf,"");

8580

sprintf(buf,"adf_decomp_%s%s_cumulative.csv",o->m_pADF[zr]->m_sName,multibuf);

8581

mprintf(" Saving cumulative ADF decomposition as \"%s\"...\n",buf);

8582

o->m_pADF[zr]->m_pADF->WriteMulti_Cumulative("",buf,"");

8583

}

8584

8585

if (o->m_bTimeDiff)

8586

o->WriteTimeDiff(o->m_pADF[zr]->m_pADF,"ADF","adf",o->m_pADF[zr]->m_sName,multibuf,false);

8587

}

8588

} // END IF ADF

8589

8590

if (g_bDDF)

8591

{

8592

for (zr=0;zr<g_iCDFChannels;zr++)

8593

{

8594

if (o->m_pDDF[zr] == NULL)

8595

continue;

8596

mprintf(WHITE,"* Dihedral Distribution Function\n");

8597

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pDDF[zr]->m_pDDF->m_fBinEntries,o->m_pDDF[zr]->m_pDDF->m_fSkipEntries,ZeroDivide(o->m_pDDF[zr]->m_pDDF->m_fSkipEntries,o->m_pDDF[zr]->m_pDDF->m_fBinEntries+o->m_pDDF[zr]->m_pDDF->m_fSkipEntries)*100.0);

8598

o->m_pDDF[zr]->m_pDDF->CalcMeanSD();

8599

if (o->m_pDDF[zr]->m_bCosine)

8600

{

8601

mprintf(" Mean value: %10G Standard deviation: %10G\n",o->m_pDDF[zr]->m_pDDF->m_fMean,o->m_pDDF[zr]->m_pDDF->m_fSD);

8602

mprintf(" Min. value: %10G Max.value: %10G\n",o->m_pDDF[zr]->m_pDDF->m_fMinInput,o->m_pDDF[zr]->m_pDDF->m_fMaxInput);

8603

} else

8604

{

8605

mprintf(" Mean value: %10G degree Standard deviation: %10G degree\n",o->m_pDDF[zr]->m_pDDF->m_fMean,o->m_pDDF[zr]->m_pDDF->m_fSD);

8606

mprintf(" Min. value: %10G degree Max.value: %10G degree\n",o->m_pDDF[zr]->m_pDDF->m_fMinInput,o->m_pDDF[zr]->m_pDDF->m_fMaxInput);

8607

}

8608

if (o->m_bTimeDev)

8609

{

8610

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8611

{

8612

fclose(o->m_pDDF[zr]->m_fAngle[0]);

8613

mprintf(" Saving temporal development as ddf_timedev_%s%s.csv\n",o->m_pDDF[zr]->m_sName,multibuf);

8614

} else

8615

{

8616

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8617

{

8618

fclose(o->m_pDDF[zr]->m_fAngle[z2]);

8619

sprintf(buf,"ddf_timedev_%s_ref%d%s.csv",o->m_pDDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8620

mprintf(" Saving temporal development as %s\n",buf);

8621

}

8622

}

8623

/* mprintf(" Speichere Winkel-Statistik als %s_angle_stat.txt\n",o->m_sName);

8624

FreeFileName("",o->m_sName,"_angle_stat.txt");

8625

o->m_pAngleStat->Evaluate();

8626

o->m_pAngleStat->Write("",o->m_sName,"_angle_stat.txt");

8627

// delete o->m_pAngleStat;*/

8628

delete[] o->m_pDDF[zr]->m_fAngle;

8629

o->m_pDDF[zr]->m_fAngle = NULL;

8630

if (o->m_bCombinedPlot)

8631

{

8632

sprintf(buf,"combined_%s%s.agr",o->m_pDDF[zr]->m_sName,multibuf);

8633

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8634

o->m_pDDF[zr]->m_pDDF->CreateCombinedPlot(false);

8635

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->WriteAgr(buf,false);

8636

}

8637

} // END IF TIMEDEV

8638

/* if (o->m_pDDF->m_iStat != 0)

8639

{

8640

mprintf(" Korrigiere statistische Verteilung...\n");

8641

o->m_pDDF->m_pDDF->AngleCorrect();

8642

}*/

8643

sprintf(buf,"ddf_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

8644

mprintf(" Saving DDF as %s ...\n",buf);

8645

o->m_pDDF[zr]->m_pDDF->NormBinIntegral();

8646

o->m_pDDF[zr]->m_pDDF->Write("",buf,"",false);

8647

sprintf(buf,"ddf_%s%s.agr",o->m_pDDF[zr]->m_sName,multibuf);

8648

mprintf(" Saving DDF AGR file as \"%s\"...\n",buf);

8649

if (o->m_pDDF[zr]->m_bCosine)

8650

o->m_pDDF[zr]->m_pDDF->WriteAgr("",buf,"",o->m_pDDF[zr]->m_sName,false);

8651

else o->m_pDDF[zr]->m_pDDF->WriteAgr("",buf,"",o->m_pDDF[zr]->m_sName,false);

8652

if (o->m_pDDF[zr]->m_iHistogramRes != 0)

8653

{

8654

mprintf(" Calculating Histogram...\n");

8655

o->m_pDDF[zr]->m_pDDF->CalcHistogram();

8656

sprintf(buf,"his_ddf_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

8657

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8658

o->m_pDDF[zr]->m_pDDF->WriteHistogram("",buf,"");

8659

}

8660

8661

if (o->m_bObsCertain && o->m_bDecompDist)

8662

{

8663

sprintf(buf,"ddf_decomp_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

8664

mprintf(" Saving DDF decomposition as \"%s\"...\n",buf);

8665

o->m_pDDF[zr]->m_pDDF->WriteMulti("",buf,"");

8666

sprintf(buf,"ddf_decomp_%s%s_cumulative.csv",o->m_pDDF[zr]->m_sName,multibuf);

8667

mprintf(" Saving cumulative DDF decomposition as \"%s\"...\n",buf);

8668

o->m_pDDF[zr]->m_pDDF->WriteMulti_Cumulative("",buf,"");

8669

}

8670

8671

if (o->m_bTimeDiff)

8672

o->WriteTimeDiff(o->m_pDDF[zr]->m_pDDF,"DDF","ddf",o->m_pDDF[zr]->m_sName,multibuf,true);

8673

}

8674

} // END IF DDF

8675

8676

if (g_bSDF)

6009

o->m_pPlProj->m_vaData[z3].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

6010

} // Ende IF PlProj

6011

6012

if (g_bRevSDF)

6013

{

6014

o->m_pRevSDF->BuildAtomList(smfix,sm,&templa);

6015

for (z4=0;z4<templa.GetSize();z4++)

6016

o->m_pRevSDF->m_vaData[z3].Add(g_pTempTimestep->m_vaCoords[templa[z4]]);

6017

} // Ende IF RevSDF

6018

6019

} // Ende FOR Alle anderen Molekuele durchgehen

6020

if (o->m_bSecondShowMol && (!secondmolrun))

6021

{

6022

secondmolrun = true;

6023

goto _secondmolstart;

6024

}

6025

} // Ende IF m_bOthers

6026

6027

if (g_bSDF)

6028

{

6029

if (o->m_pSDF->m_bSDFMirrorBisect)

6030

{

6031

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

6032

vec3 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])];

6033

vec1 = CrossP(vec2,vec3);

6034

vec2 += vec3;

6035

}

6036

6037

if (o->m_pSDF->m_bCutPlane)

6038

{

6039

o->m_pSDF->m_fAtom2PosX += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])][0];

6040

o->m_pSDF->m_fAtom3PosX += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])][0];

6041

o->m_pSDF->m_fAtom3PosY += g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[2]])->GetAt(g_iFixAtom[2])][1];

6042

o->m_pSDF->m_fPosCounter++;

6043

}

6044

6045

if (o->m_bSelf)

6046

{

6047

for (z5=0;z5<o->m_pSDF->m_vaData[0].GetSize();z5++)

6048

{

6049

vec0 = o->m_pSDF->m_vaData[0][z5];

6050

6051

if (o->m_pSDF->m_bVdWSpheres)

6052

o->m_pSDF->m_pSDF->AddToBin_Sphere(vec0,o->m_pSDF->m_faRadius[0][z5]);

6053

else o->m_pSDF->m_pSDF->AddToBin(vec0);

6054

6055

if (o->m_pSDF->m_bSDFMirrorXY)

6056

{

6057

vec0[2] = -vec0[2];

6058

o->m_pSDF->m_pSDF->AddToBin(vec0);

6059

}

6060

6061

if (o->m_pSDF->m_bSDFMirrorBisect)

6062

{

6063

vec3.PointRoot(vec1,vec2,vec0);

6064

vec3 -= vec0;

6065

vec3 *= 2.0f;

6066

vec0 += vec3;

6067

o->m_pSDF->m_pSDF->AddToBin(vec0);

6068

if (o->m_pSDF->m_bSDFMirrorXY)

6069

{

6070

vec0[2] = -vec0[2];

6071

o->m_pSDF->m_pSDF->AddToBin(vec0);

6072

}

6073

}

6074

}

6075

} else

6076

{

6077

for (z4=0;z4<o->m_iShowMolCount;z4++)

6078

{

6079

for (z5=0;z5<o->m_pSDF->m_vaData[z4].GetSize();z5++)

6080

{

6081

vec0 = o->m_pSDF->m_vaData[z4][z5];

6082

6083

if (o->m_pSDF->m_bVdWSpheres)

6084

o->m_pSDF->m_pSDF->AddToBin_Sphere(vec0,o->m_pSDF->m_faRadius[z4][z5]);

6085

else o->m_pSDF->m_pSDF->AddToBin(vec0);

6086

6087

if (o->m_pSDF->m_bSDFMirrorXY)

6088

{

6089

vec0[2] = -vec0[2];

6090

o->m_pSDF->m_pSDF->AddToBin(vec0);

6091

}

6092

6093

if (o->m_pSDF->m_bSDFMirrorBisect)

6094

{

6095

vec3.PointRoot(vec1,vec2,vec0);

6096

vec3 -= vec0;

6097

vec3 *= 2.0f;

6098

vec0 += vec3;

6099

o->m_pSDF->m_pSDF->AddToBin(vec0);

6100

if (o->m_pSDF->m_bSDFMirrorXY)

6101

{

6102

vec0[2] = -vec0[2];

6103

o->m_pSDF->m_pSDF->AddToBin(vec0);

6104

}

6105

}

6106

}

6107

}

6108

}

6109

} // END IF SDF

6110

6111

if (g_bPlProj)

6112

{

6113

if (o->m_bSelf)

6114

{

6115

for (z5=0;z5<o->m_pPlProj->m_vaData[0].GetSize();z5++)

6116

{

6117

vec0 = o->m_pPlProj->m_vaData[0][z5];

6118

6119

if ((vec0[2] >= o->m_pPlProj->m_fSliceBorder[0]) && (vec0[2] <= o->m_pPlProj->m_fSliceBorder[1]))

6120

o->m_pPlProj->m_p2DF->AddToBin(vec0[0],vec0[1]);

6121

}

6122

} else

6123

{

6124

for (z4=0;z4<o->m_iShowMolCount;z4++)

6125

{

6126

for (z5=0;z5<o->m_pPlProj->m_vaData[z4].GetSize();z5++)

6127

{

6128

vec0 = o->m_pPlProj->m_vaData[z4][z5];

6129

6130

if ((vec0[2] >= o->m_pPlProj->m_fSliceBorder[0]) && (vec0[2] <= o->m_pPlProj->m_fSliceBorder[1]))

6131

o->m_pPlProj->m_p2DF->AddToBin(vec0[0],vec0[1]);

6132

}

6133

}

6134

}

6135

} // END IF PlProj

6136

6137

if (g_bRevSDF)

6138

{

6139

vec2 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])];

6140

tf4 = g_pTempTimestep->m_vaCoords[((CxIntArray*)smfix->m_oaAtomOffset[g_iFixAtomType[1]])->GetAt(g_iFixAtom[1])].GetLength();

6141

o->m_pRevSDF->m_fSecondAtomPosX += tf4;

6142

o->m_pRevSDF->m_fSecondAtomCount++;

6143

if (o->m_bSelf)

6144

{

6145

for (z5=0;z5<o->m_pRevSDF->m_vaData[0].GetSize();z5++)

6146

{

6147

vec0 = o->m_pRevSDF->m_vaData[0][z5];

6148

tf = fabs(Angle(vec2,vec0));

6149

tf2 = vec0.GetLength();

6150

tf3 = 1.0;

6151

if (o->m_pRevSDF->m_bCorrectAngle)

6152

{

6153

if ((tf < 0.001) || (tf > Pi-0.001))

6154

tf3 /= 0.001;

6155

else tf3 /= sin(tf);

6156

}

6157

if (o->m_pRevSDF->m_bCorrectRadial)

6158

tf3 /= tf2; // Erste Potenz, da 2D-Grid (SDF hat "nullte Potenz" ^^)

6159

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,cos(tf)*tf2,tf3);

6160

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,cos(tf)*tf2,tf3);

6161

if (o->m_pRevSDF->m_bMirrorY)

6162

{

6163

if (o->m_pRevSDF->m_bMirrorBond)

6164

{

6165

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

6166

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

6167

} else

6168

{

6169

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,-cos(tf)*tf2,tf3);

6170

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,-cos(tf)*tf2,tf3);

6171

}

6172

}

6173

}

6174

} else

6175

{

6176

for (z4=0;z4<o->m_iShowMolCount;z4++)

6177

{

6178

for (z5=0;z5<o->m_pRevSDF->m_vaData[z4].GetSize();z5++)

6179

{

6180

vec0 = o->m_pRevSDF->m_vaData[z4][z5];

6181

tf = fabs(Angle(vec2,vec0));

6182

tf2 = vec0.GetLength();

6183

tf3 = 1.0;

6184

if (o->m_pRevSDF->m_bCorrectAngle)

6185

{

6186

if ((tf < 0.001) || (tf > Pi-0.001))

6187

tf3 /= 0.001;

6188

else tf3 /= sin(tf);

6189

}

6190

if (o->m_pRevSDF->m_bCorrectRadial)

6191

tf3 /= tf2; // Erste Potenz, da 2D-Grid (SDF hat "nullte Potenz" ^^)

6192

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,cos(tf)*tf2,tf3);

6193

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,cos(tf)*tf2,tf3);

6194

if (o->m_pRevSDF->m_bMirrorY)

6195

{

6196

if (o->m_pRevSDF->m_bMirrorBond)

6197

{

6198

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

6199

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,tf4-cos(tf)*tf2,tf3);

6200

} else

6201

{

6202

o->m_pRevSDF->m_p2DF->AddToBin(sin(tf)*tf2,-cos(tf)*tf2,tf3);

6203

o->m_pRevSDF->m_p2DF->AddToBin(-sin(tf)*tf2,-cos(tf)*tf2,tf3);

6204

}

6205

}

6206

}

6207

}

6208

}

6209

} // END IF REVSDF

6210

6211

if (g_bCDF && (!g_bDeriv || (g_iSteps > 2)))

6212

{

6213

if (o->m_bSecondShowMol)

6214

{

6215

for (zr=0;zr<g_iCDFChannels;zr++)

6216

{

6217

switch(g_iObsChannel[zr])

6218

{

6219

case 0:

6220

apfa[zr] = o->m_pRDF[zr]->m_faData;

6221

apba[zr] = o->m_pRDF[zr]->m_baDataEnabled;

6222

break;

6223

case 1:

6224

apfa[zr] = o->m_pADF[zr]->m_faData;

6225

apba[zr] = o->m_pADF[zr]->m_baDataEnabled;

6226

break;

6227

case 2:

6228

apfa[zr] = o->m_pDDF[zr]->m_faData;

6229

apba[zr] = o->m_pDDF[zr]->m_baDataEnabled;

6230

break;

6231

case 3:

6232

apfa[zr] = o->m_pDipDF[zr]->m_faData;

6233

apba[zr] = o->m_pDipDF[zr]->m_baDataEnabled;

6234

break;

6235

case 4:

6236

apfa[zr] = o->m_pVDF[zr]->m_faData;

6237

apba[zr] = o->m_pVDF[zr]->m_baDataEnabled;

6238

break;

6239

case 5:

6240

apfa[zr] = o->m_pPlDF[zr]->m_faData;

6241

apba[zr] = o->m_pPlDF[zr]->m_baDataEnabled;

6242

break;

6243

case 6:

6244

apfa[zr] = o->m_pLiDF[zr]->m_faData;

6245

apba[zr] = o->m_pLiDF[zr]->m_baDataEnabled;

6246

break;

6247

}

6248

}

6249

6250

if (g_iCDFChannels == 2)

6251

{

6252

for (z4=0;z4<o->m_iShowMolCount;z4++)

6253

{

6254

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

6255

{

6256

for (z8=0;z8<o->m_iShowMol2Count;z8++)

6257

{

6258

if (o->m_bExclude1eq2 && (z4 == z8))

6259

continue;

6260

6261

for (z7=0;z7<apfa[1][z8].GetSize();z7++)

6262

{

6263

if (o->m_bBinOnlyPassedAtoms)

6264

{

6265

if ((apba[0][z4][z5] == 0) || (apba[1][z8][z7] == 0))

6266

goto _nocdfbin2;

6267

}

6268

if (o->m_bBinOnlyNotPassedAtoms)

6269

{

6270

if ((apba[0][z4][z5] != 0) && (apba[1][z8][z7] != 0))

6271

goto _nocdfbin2;

6272

}

6273

6274

o->m_pCDF->m_p2DF->AddToBin(apfa[0][z4][z5],apfa[1][z8][z7]);

6275

_nocdfbin2:

6276

6277

if (o->m_pCDF->m_bDumpDat)

6278

mfprintf(o->m_pCDF->m_fDump,"%d; %d; %d; %d; %10.3f; %10.3f\n",(int)g_iSteps,z2+1,z4+1,z5+1,apfa[0][z4][z5],apfa[1][z8][z7]);

6279

}

6280

}

6281

}

6282

}

6283

}

6284

} else // IF NOT SECOND_OM

6285

{

6286

for (zr=0;zr<g_iCDFChannels;zr++)

6287

{

6288

switch(g_iObsChannel[zr])

6289

{

6290

case 0:

6291

apfa[zr] = o->m_pRDF[zr]->m_faData;

6292

apba[zr] = o->m_pRDF[zr]->m_baDataEnabled;

6293

break;

6294

case 1:

6295

apfa[zr] = o->m_pADF[zr]->m_faData;

6296

apba[zr] = o->m_pADF[zr]->m_baDataEnabled;

6297

break;

6298

case 2:

6299

apfa[zr] = o->m_pDDF[zr]->m_faData;

6300

apba[zr] = o->m_pDDF[zr]->m_baDataEnabled;

6301

break;

6302

case 3:

6303

apfa[zr] = o->m_pDipDF[zr]->m_faData;

6304

apba[zr] = o->m_pDipDF[zr]->m_baDataEnabled;

6305

break;

6306

case 4:

6307

apfa[zr] = o->m_pVDF[zr]->m_faData;

6308

apba[zr] = o->m_pVDF[zr]->m_baDataEnabled;

6309

break;

6310

case 5:

6311

apfa[zr] = o->m_pPlDF[zr]->m_faData;

6312

apba[zr] = o->m_pPlDF[zr]->m_baDataEnabled;

6313

break;

6314

case 6:

6315

apfa[zr] = o->m_pLiDF[zr]->m_faData;

6316

apba[zr] = o->m_pLiDF[zr]->m_baDataEnabled;

6317

break;

6318

}

6319

}

6320

6321

if (g_iCDFChannels == 2)

6322

{

6323

for (z4=0;z4<o->m_iShowMolCount;z4++)

6324

{

6325

ticomb = 0;

6326

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

6327

{

6328

for (z7=0;z7<apfa[1][z4].GetSize();z7++)

6329

{

6330

6331

/* Workaround for symmetrical DDFs (double data amount) */

6332

if (g_iObsChannel[0] == 2)

6333

{

6334

if (o->m_pDDF[0]->m_bSymm)

6335

{

6336

if (g_iObsChannel[1] == 2)

6337

{

6338

if (o->m_pDDF[1]->m_bSymm)

6339

{

6340

if (o->m_pCDF->m_pCombineList[(z5/2)*o->m_pCDF->m_iCombinations[1]+(z7/2)] == 0)

6341

continue;

6342

goto _ddfsymmdone;

6343

}

6344

}

6345

}

6346

if (o->m_pCDF->m_pCombineList[(z5/2)*o->m_pCDF->m_iCombinations[1]+z7] == 0)

6347

continue;

6348

} else

6349

{

6350

if (g_iObsChannel[1] == 2)

6351

{

6352

if (o->m_pDDF[1]->m_bSymm)

6353

{

6354

if (o->m_pCDF->m_pCombineList[z5*o->m_pCDF->m_iCombinations[1]+(z7/2)] == 0)

6355

continue;

6356

goto _ddfsymmdone;

6357

}

6358

}

6359

if (o->m_pCDF->m_pCombineList[z5*o->m_pCDF->m_iCombinations[1]+z7] == 0)

6360

continue;

6361

}

6362

_ddfsymmdone:

6363

6364

if (o->m_bBinOnlyPassedAtoms)

6365

{

6366

if ((apba[0][z4][z5] == 0) || (apba[1][z4][z7] == 0))

6367

goto _nocdfbin;

6368

}

6369

if (o->m_bBinOnlyNotPassedAtoms)

6370

{

6371

if ((apba[0][z4][z5] != 0) && (apba[1][z4][z7] != 0))

6372

goto _nocdfbin;

6373

}

6374

o->m_pCDF->m_p2DF->AddToBin(apfa[0][z4][z5],apfa[1][z4][z7]);

6375

_nocdfbin:;

6376

if (o->m_pCDF->m_bDumpDat)

6377

mfprintf(o->m_pCDF->m_fDump,"%d; %d; %d; ; %10.3f; %10.3f\n",(int)g_iSteps,z2+1,z4+1,apfa[0][z4][z5],apfa[1][z4][z7]);

6378

if (o->m_bTimeDev)

6379

{

6380

ti = o->m_waSaveShowList.GetPosition(z4);

6381

if ((ti2 != -1) && (ti != -1))

6382

{

6383

if (o->m_bSaveSeparateFiles)

6384

mfprintf(o->m_pCDF->m_fTimeDev[ti2],"; %10.3f; %10.3f",apfa[0][z4][z5],apfa[1][z4][z7]);

6385

else mfprintf(o->m_pCDF->m_fTimeDev[0],"; %10.3f; %10.3f",apfa[0][z4][z5],apfa[1][z4][z7]);

6386

if (o->m_pCDF->m_bTDAnimation)

6387

o->m_pCDF->m_pTDAPlot->AddXYTupel((ti2*o->m_waSaveShowList.GetSize()+ti)*o->m_pCDF->m_iCombinationsEnabled+ticomb,apfa[0][z4][z5],apfa[1][z4][z7]);

6388

}

6389

ticomb++;

6390

}

6391

}

6392

}

6393

}

6394

if (o->m_bTimeDev && (ti2 != -1))

6395

{

6396

if (o->m_bSaveSeparateFiles)

6397

mfprintf(o->m_pCDF->m_fTimeDev[ti2],"\n");

6398

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6399

mfprintf(o->m_pCDF->m_fTimeDev[0],"\n");

6400

}

6401

} // END IF CHANNELS == 2

6402

6403

if (g_iCDFChannels == 3)

6404

{

6405

for (z4=0;z4<o->m_iShowMolCount;z4++)

6406

{

6407

ticomb = 0;

6408

for (z5=0;z5<apfa[0][z4].GetSize();z5++)

6409

{

6410

for (z8=0;z8<apfa[1][z4].GetSize();z8++)

6411

{

6412

for (z7=0;z7<apfa[2][z4].GetSize();z7++)

6413

{

6414

if (o->m_pCDF->m_pCombineList[z5*o->m_pCDF->m_iCombinations[1]*o->m_pCDF->m_iCombinations[2]+z8*o->m_pCDF->m_iCombinations[1]+z7] == 0)

6415

continue;

6416

if (o->m_bBinOnlyPassedAtoms)

6417

{

6418

if ((apba[0][z4][z5] == 0) || (apba[1][z4][z8] == 0) || (apba[2][z4][z7] == 0))

6419

goto _3nocdfbin;

6420

}

6421

if (o->m_bBinOnlyNotPassedAtoms)

6422

{

6423

if ((apba[0][z4][z5] != 0) && (apba[1][z4][z8] != 0) && (apba[2][z4][z7] != 0))

6424

goto _3nocdfbin;

6425

}

6426

o->m_pCDF->m_p3DF->AddToBin(apfa[0][z4][z5],apfa[1][z4][z8],apfa[2][z4][z7]);

6427

6428

o->m_pCDF->m_p3DF->m_p2DF[0]->AddToBin(apfa[0][z4][z5],apfa[1][z4][z8]);

6429

o->m_pCDF->m_p3DF->m_p2DF[1]->AddToBin(apfa[0][z4][z5],apfa[2][z4][z7]);

6430

o->m_pCDF->m_p3DF->m_p2DF[2]->AddToBin(apfa[1][z4][z8],apfa[2][z4][z7]);

6431

_3nocdfbin:;

6432

if (o->m_pCDF->m_bDumpDat)

6433

mfprintf(o->m_pCDF->m_fDump,"%d; %d; %d; ; %10.3f; %10.3f; %10.3f\n",(int)g_iSteps,z2+1,z4+1,apfa[0][z4][z5],apfa[1][z4][z8],apfa[2][z4][z7]);

6434

}

6435

}

6436

}

6437

}

6438

} // END IF CHANNELS == 3

6439

} // IF NOT SECOND_OM

6440

} // IF CDF

6441

6442

for (zr=0;zr<g_iCDFChannels;zr++)

6443

{

6444

if (g_bRDF && !(o->m_bObsCertain && o->m_bDecompDist) && (!o->m_bDecompType) && (o->m_pRDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6445

{

6446

if (o->m_bOthers)

6447

{

6448

if (o->m_bSecondShowMol && (zr == 1))

6449

{

6450

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6451

{

6452

for (z5=0;z5<o->m_pRDF[zr]->m_faData[z4].GetSize();z5++)

6453

{

6454

if (o->m_bBinOnlyPassedAtoms)

6455

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] == 0)

6456

continue;

6457

if (o->m_bBinOnlyNotPassedAtoms)

6458

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] != 0)

6459

continue;

6460

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[z4][z5]);

6461

}

6462

}

6463

} else

6464

{

6465

for (z4=0;z4<o->m_iShowMolCount;z4++)

6466

{

6467

for (z5=0;z5<o->m_pRDF[zr]->m_faData[z4].GetSize();z5++)

6468

{

6469

if (o->m_bBinOnlyPassedAtoms)

6470

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] == 0)

6471

continue;

6472

if (o->m_bBinOnlyNotPassedAtoms)

6473

if (o->m_pRDF[zr]->m_baDataEnabled[z4][z5] != 0)

6474

continue;

6475

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[z4][z5]);

6476

}

6477

}

6478

}

6479

} else

6480

{

6481

for (z5=0;z5<o->m_pRDF[zr]->m_faData[0].GetSize();z5++)

6482

o->m_pRDF[zr]->m_pRDF->AddToBin(o->m_pRDF[zr]->m_faData[0][z5]);

6483

}

6484

if (o->m_bTimeDev && (ti2 != -1))

6485

{

6486

if (o->m_bSaveSeparateFiles)

6487

mfprintf(o->m_pRDF[zr]->m_fDist[ti2],"\n");

6488

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6489

mfprintf(o->m_pRDF[zr]->m_fDist[0],"\n");

6490

}

6491

}

6492

6493

if (g_bVDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pVDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6494

{

6495

if (o->m_bOthers)

6496

{

6497

if (o->m_bSecondShowMol && (zr == 1))

6498

{

6499

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6500

for (z5=0;z5<o->m_pVDF[zr]->m_faData[z4].GetSize();z5++)

6501

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[z4][z5]);

6502

} else

6503

{

6504

for (z4=0;z4<o->m_iShowMolCount;z4++)

6505

{

6506

for (z5=0;z5<o->m_pVDF[zr]->m_faData[z4].GetSize();z5++)

6507

{

6508

if (o->m_bBinOnlyPassedAtoms)

6509

if (o->m_pVDF[zr]->m_baDataEnabled[z4][z5] == 0)

6510

continue;

6511

if (o->m_bBinOnlyNotPassedAtoms)

6512

if (o->m_pVDF[zr]->m_baDataEnabled[z4][z5] != 0)

6513

continue;

6514

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[z4][z5]);

6515

}

6516

}

6517

}

6518

} else

6519

{

6520

for (z5=0;z5<o->m_pVDF[zr]->m_faData[0].GetSize();z5++)

6521

o->m_pVDF[zr]->m_pVDF->AddToBin(o->m_pVDF[zr]->m_faData[0][z5]);

6522

}

6523

if (o->m_bTimeDev && (ti2 != -1))

6524

{

6525

if (o->m_bSaveSeparateFiles)

6526

mfprintf(o->m_pVDF[zr]->m_fSpeed[ti2],"\n");

6527

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6528

mfprintf(o->m_pVDF[zr]->m_fSpeed[0],"\n");

6529

}

6530

}

6531

6532

if (g_bDipDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pDipDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6533

{

6534

if (o->m_bOthers)

6535

{

6536

if (o->m_bSecondShowMol && (zr == 1))

6537

{

6538

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6539

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[z4].GetSize();z5++)

6540

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[z4][z5]);

6541

} else

6542

{

6543

for (z4=0;z4<o->m_iShowMolCount;z4++)

6544

{

6545

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[z4].GetSize();z5++)

6546

{

6547

if (o->m_bBinOnlyPassedAtoms)

6548

if (o->m_pDipDF[zr]->m_baDataEnabled[z4][z5] == 0)

6549

continue;

6550

if (o->m_bBinOnlyNotPassedAtoms)

6551

if (o->m_pDipDF[zr]->m_baDataEnabled[z4][z5] != 0)

6552

continue;

6553

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[z4][z5]);

6554

}

6555

}

6556

}

6557

} else

6558

{

6559

for (z5=0;z5<o->m_pDipDF[zr]->m_faData[0].GetSize();z5++)

6560

o->m_pDipDF[zr]->m_pDipoleDF->AddToBin(o->m_pDipDF[zr]->m_faData[0][z5]);

6561

}

6562

if (o->m_bTimeDev && (ti2 != -1))

6563

{

6564

if (o->m_bSaveSeparateFiles)

6565

mfprintf(o->m_pDipDF[zr]->m_fDipole[ti2],"\n");

6566

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6567

mfprintf(o->m_pDipDF[zr]->m_fDipole[0],"\n");

6568

}

6569

}

6570

6571

if (g_bADF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pADF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6572

{

6573

if (o->m_bOthers)

6574

{

6575

if (o->m_bSecondShowMol && (zr == 1))

6576

{

6577

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6578

for (z5=0;z5<o->m_pADF[zr]->m_faData[z4].GetSize();z5++)

6579

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[z4][z5]);

6580

} else

6581

{

6582

for (z4=0;z4<o->m_iShowMolCount;z4++)

6583

{

6584

for (z5=0;z5<o->m_pADF[zr]->m_faData[z4].GetSize();z5++)

6585

{

6586

if (o->m_bBinOnlyPassedAtoms)

6587

if (o->m_pADF[zr]->m_baDataEnabled[z4][z5] == 0)

6588

continue;

6589

if (o->m_bBinOnlyNotPassedAtoms)

6590

if (o->m_pADF[zr]->m_baDataEnabled[z4][z5] != 0)

6591

continue;

6592

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[z4][z5]);

6593

}

6594

}

6595

}

6596

} else

6597

{

6598

for (z5=0;z5<o->m_pADF[zr]->m_faData[0].GetSize();z5++)

6599

o->m_pADF[zr]->m_pADF->AddToBin(o->m_pADF[zr]->m_faData[0][z5]);

6600

}

6601

if (o->m_bTimeDev && (ti2 != -1))

6602

{

6603

if (o->m_bSaveSeparateFiles)

6604

mfprintf(o->m_pADF[zr]->m_fAngle[ti2],"\n");

6605

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6606

mfprintf(o->m_pADF[zr]->m_fAngle[0],"\n");

6607

}

6608

}

6609

6610

if (g_bDDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pDDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6611

{

6612

if (o->m_bOthers)

6613

{

6614

if (o->m_bSecondShowMol && (zr == 1))

6615

{

6616

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6617

for (z5=0;z5<o->m_pDDF[zr]->m_faData[z4].GetSize();z5++)

6618

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[z4][z5]);

6619

} else

6620

{

6621

for (z4=0;z4<o->m_iShowMolCount;z4++)

6622

{

6623

for (z5=0;z5<o->m_pDDF[zr]->m_faData[z4].GetSize();z5++)

6624

{

6625

if (o->m_bBinOnlyPassedAtoms)

6626

if (o->m_pDDF[zr]->m_baDataEnabled[z4][z5] == 0)

6627

continue;

6628

if (o->m_bBinOnlyNotPassedAtoms)

6629

if (o->m_pDDF[zr]->m_baDataEnabled[z4][z5] != 0)

6630

continue;

6631

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[z4][z5]);

6632

}

6633

}

6634

}

6635

} else

6636

{

6637

for (z5=0;z5<o->m_pDDF[zr]->m_faData[0].GetSize();z5++)

6638

o->m_pDDF[zr]->m_pDDF->AddToBin(o->m_pDDF[zr]->m_faData[0][z5]);

6639

}

6640

if (o->m_bTimeDev && (ti2 != -1))

6641

{

6642

if (o->m_bSaveSeparateFiles)

6643

mfprintf(o->m_pDDF[zr]->m_fAngle[ti2],"\n");

6644

else if (ti2 == (int)o->m_waSaveRefList.GetSize()-1)

6645

mfprintf(o->m_pDDF[zr]->m_fAngle[0],"\n");

6646

}

6647

} // End IF DDF

6648

6649

if (g_bPlDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pPlDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6650

{

6651

if (o->m_bOthers)

6652

{

6653

if (o->m_bSecondShowMol && (zr == 1))

6654

{

6655

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6656

for (z5=0;z5<o->m_pPlDF[zr]->m_faData[z4].GetSize();z5++)

6657

o->m_pPlDF[zr]->m_pPlDF->AddToBin(o->m_pPlDF[zr]->m_faData[z4][z5]);

6658

} else

6659

{

6660

for (z4=0;z4<o->m_iShowMolCount;z4++)

6661

{

6662

for (z5=0;z5<o->m_pPlDF[zr]->m_faData[z4].GetSize();z5++)

6663

{

6664

if (o->m_bBinOnlyPassedAtoms)

6665

if (o->m_pPlDF[zr]->m_baDataEnabled[z4][z5] == 0)

6666

continue;

6667

if (o->m_bBinOnlyNotPassedAtoms)

6668

if (o->m_pPlDF[zr]->m_baDataEnabled[z4][z5] != 0)

6669

continue;

6670

o->m_pPlDF[zr]->m_pPlDF->AddToBin(o->m_pPlDF[zr]->m_faData[z4][z5]);

6671

}

6672

}

6673

}

6674

} else

6675

{

6676

for (z5=0;z5<o->m_pPlDF[zr]->m_faData[0].GetSize();z5++)

6677

o->m_pPlDF[zr]->m_pPlDF->AddToBin(o->m_pPlDF[zr]->m_faData[0][z5]);

6678

}

6679

} // End IF PlDF

6680

6681

if (g_bLiDF && !(o->m_bObsCertain && o->m_bDecompDist) && (o->m_pLiDF[zr] != NULL) && (!g_bDeriv || (g_iSteps > 2)))

6682

{

6683

if (o->m_bOthers)

6684

{

6685

if (o->m_bSecondShowMol && (zr == 1))

6686

{

6687

for (z4=0;z4<o->m_iShowMol2Count;z4++)

6688

for (z5=0;z5<o->m_pLiDF[zr]->m_faData[z4].GetSize();z5++)

6689

o->m_pLiDF[zr]->m_pLiDF->AddToBin(o->m_pLiDF[zr]->m_faData[z4][z5]);

6690

} else

6691

{

6692

for (z4=0;z4<o->m_iShowMolCount;z4++)

6693

{

6694

for (z5=0;z5<o->m_pLiDF[zr]->m_faData[z4].GetSize();z5++)

6695

{

6696

if (o->m_bBinOnlyPassedAtoms)

6697

if (o->m_pLiDF[zr]->m_baDataEnabled[z4][z5] == 0)

6698

continue;

6699

if (o->m_bBinOnlyNotPassedAtoms)

6700

if (o->m_pLiDF[zr]->m_baDataEnabled[z4][z5] != 0)

6701

continue;

6702

o->m_pLiDF[zr]->m_pLiDF->AddToBin(o->m_pLiDF[zr]->m_faData[z4][z5]);

6703

}

6704

}

6705

}

6706

} else

6707

{

6708

for (z5=0;z5<o->m_pLiDF[zr]->m_faData[0].GetSize();z5++)

6709

o->m_pLiDF[zr]->m_pLiDF->AddToBin(o->m_pLiDF[zr]->m_faData[0][z5]);

6710

}

6711

} // End IF LiDF

6712

6713

} // FOR CDFChannels

6714

6715

} // Ende FOR g_oaObserv.GetSize

6716

} // Ende IF [blabla]

6717

6718

if (g_bMiddleAvg) // Referenzmolekuel mitteln

6719

{

6720

cc = 0;

6721

ti2 = (g_iSteps-2)*((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()+z2;

6722

// Jeden Atomtyp des Zielmolekuels durchgehen

6723

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z3++)

6724

{

6725

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z4++)

6726

{

6727

// Atome vertauschen, aber nicht im allerersten Durchgang hier, und nur wenn mehr als 1 Atom dieser Sorte

6728

if ((g_iSwapAtoms) && (ti2 != 0) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3]>1))

6729

{

6730

vec4 = g_pRefMol[cc];

6731

vec4 /= (float)ti2; // der bisherige Mittelwert des Referenzmolekuels

6732

6733

ti3 = -1;

6734

for (z5=z4+1;z5<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z3];z5++) // Alle folgenden Atome dieser Sorte durchgehen

6735

{

6736

tf2 = VecDist(g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z5)],vec4);

6737

if (tf2 < tf) // Das andere Atom ist naeher am Platz im Referenzmolekuel als das eigentlich vorgesehene

6738

{

6739

ti3 = z5;

6740

tf = tf2;

6741

}

6742

}

6743

if (ti3 != -1) // Ein Anderes ist naeher dran als unseres: Vertausche diese beiden

6744

{

6745

6746

pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+(cc-z4+ti3)] += 1;

6747

pSwapMatrix[(cc-z4+ti3)*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc] += 1;

6748

}

6749

} // Ende IF SwapAtoms

6750

g_pRefMol[cc] += g_pTempTimestep->m_vaCoords[((CxIntArray*)((CSingleMolecule*)g_oaSingleMolecules[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex[z2]])->m_oaAtomOffset[z3])->GetAt(z4)];

6751

cc++;

6752

} // Ende FOR Atom des Referenzmolekuels

6753

} // Ende FOR Atomtyp des Referenzmolekuels

6754

} // Ende IF Referenzmolekuel mitteln

6755

} // Ende FOR RefMol (z2)

6756

6757

for (z6=0;z6<g_oaObserv.GetSize();z6++)

6758

{

6759

o = (CObservation*)g_oaObserv[z6];

6760

6761

if (o->m_pConditions != NULL)

6762

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

6763

if (o->m_pConditions->m_iPassCounter[z2] != 0)

6764

o->m_pConditions->m_iOMPassCounter[z2]++;

6765

6766

if (o->m_pConditionsOM2 != NULL)

6767

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

6768

if (o->m_pConditionsOM2->m_iPassCounter[z2] != 0)

6769

o->m_pConditionsOM2->m_iOMPassCounter[z2]++;

6770

6771

if (g_bRDF)

6772

{

6773

for (zr=0;zr<g_iCDFChannels;zr++)

6774

{

6775

if (o->m_pRDF[zr] != NULL)

6776

if (o->m_pRDF[zr]->m_bCalcSD)

6777

o->m_pRDF[zr]->m_pRDF->m_pSDEngine->FinishStep();

6778

}

6779

}

6780

}

6781

6782

6783

//_end:;

6784

_endstep:

6785

_norefmol:

6786

if ((g_iMaxStep > 0) && ((int)g_iSteps >= g_iMaxStep))

6787

{

6788

mprintf("\n\nMaximum step count of %d reached, stopping.",g_iMaxStep);

6789

break;

6790

}

6791

} // Ende while

6792

6793

/*************************************************************************

6794

*************** Ende Hauptschleife ***************************************

6795

*************************************************************************/

6796

6797

// fclose(fff);

6798

6799

_endmainloop:

6800

if (g_bUseVelocities)

6801

g_iSteps -= 2;

6802

6803

mprintf(WHITE,"\n\n########## Analysis finished ##########\n");

6804

6805

if (g_iStride != 1)

6806

mprintf("\n%d time steps processed (every %dth from %d).\n\n",g_iSteps/g_iStride,g_iStride,g_iSteps);

6807

else mprintf("\n%d time steps processed.\n\n",g_iSteps);

6808

6809

fclose(g_fPos);

6810

if (g_fVel != NULL)

6811

fclose(g_fVel);

6812

if (g_fForce != NULL)

6813

fclose(g_fForce);

6814

if ((g_bNPT) && (g_sNPTFile[0] != 0))

6815

fclose(g_fNPTFile);

6816

6817

if (g_bDipole && g_bDumpDipoleVector)

6818

{

6819

fclose(g_fDumpDipole);

6820

mprintf(" Dipole vectors written to file \"dipole_vectors.csv\".\n");

6821

if (g_bDumpDipoleXYZ)

6822

{

6823

fclose(g_fDumpDipoleXYZ);

6824

mprintf(" Dipole XYZ trajectory written to file \"dipole_vectors.xyz\".\n");

6825

}

6826

mprintf("\n");

6827

}

6828

6829

6830

/************ Interface **************/

6831

Interface_AfterAnalysis();

6832

6833

6834

if (g_bVoro)

6835

{

6836

g_pVoroWrapper->Finish();

6837

}

6838

6839

if (g_bVoid)

6840

{

6841

g_pVoroAnalysis->Finish();

6842

}

6843

6844

if (g_bReact)

6845

{

6846

if (!ReactSecondRun)

6847

{

6848

g_pReact->Finish();

6849

g_pReact->DumpMolecules();

6850

g_pReact->CreateOutput();

6851

}

6852

if (g_pReact->m_oaReactTrajectories.GetSize() != 0)

6853

{

6854

if (!ReactSecondRun)

6855

{

6856

mprintf(WHITE,"Starting second pass for Reaction Analysis...\n\n");

6857

ReactSecondRun = true;

6858

goto _beginmain;

6859

} else

6860

{

6861

mprintf(WHITE,"Second pass for Reaction Analysis finished.\n\n");

6862

}

6863

}

6864

}

6865

g_bAbortAnalysis = true;

6866

6867

if (g_bSaveCondSnapshot)

6868

{

6869

fclose(g_fSaveCondFile);

6870

mprintf("%d condition snapshots saved as savecondition.xyz\n\n",g_iSaveCondCount);

6871

}

6872

6873

if (g_bMicroHet)

6874

{

6875

mprintf(WHITE,"*** Microheterogeneity Analysis\n\n");

6876

for (z=0;z<g_pMicroHet->m_oaObservations.GetSize();z++)

6877

{

6878

mho = (CMicroHetObservation*)g_pMicroHet->m_oaObservations[z];

6879

mprintf(WHITE," * Observation %d: %s\n",z+1,mho->m_sName);

6880

6881

if (mho->m_bCSV)

6882

{

6883

/* mprintf(" Creating Microheterogeneity plot...\n");

6884

sprintf(buf,"microhet_df_obs%d%s",z+1,multibuf);

6885

mho->BuildSlices(buf);*/

6886

6887

mprintf(" Creating entry plot...\n");

6888

sprintf(buf,"microhet_entry_obs%d%s",z+1,multibuf);

6889

mho->BuildZeroPlot(buf,true);

6890

}

6891

6892

if (mho->m_bCDF)

6893

{

6894

if (mho->m_bCDF_Dens)

6895

mho->BuildCDF(0,z,multibuf);

6896

6897

if (mho->m_bCDF_Tot)

6898

mho->BuildCDF(1,z,multibuf);

6899

6900

if (mho->m_bCDF_Mode3)

6901

mho->BuildCDF(2,z,multibuf);

6902

}

6903

}

6904

mprintf("\n");

6905

}

6906

6907

if (g_bClusterAnalysis)

6908

{

6909

mprintf(WHITE,"*** Cluster Analysis\n\n");

6910

g_pClusterAnalysis->BuildClusterDistribution();

6911

g_pClusterAnalysis->WriteOutput(multibuf);

6912

}

6913

6914

if (g_bFESA)

6915

{

6916

mprintf(WHITE,"*** FES Analysis\n\n");

6917

g_pFESA->Finish();

6918

}

6919

6920

/* if (g_bSFac)

6921

{

6922

g_pSFac->Finish();

6923

}*/

6924

6925

if (g_bBondACF)

6926

{

6927

mprintf(WHITE,"*** Bond autocorrelation function\n");

6928

if (g_bBondACFDebug)

6929

{

6930

mprintf(" Writing \"bondacf.agr\"...\n");

6931

6932

try { gc = new CGrace(); } catch(...) { gc = NULL; }

6933

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6934

6935

gc->SetRangeX(0,g_iSteps*g_fTimestepLength/1000.0);

6936

gc->SetRangeY(0,250);

6937

gc->MakeTicks();

6938

gc->SetLabelX("Time [ps]");

6939

gc->SetLabelY("Bond length [pm]");

6940

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6941

{

6942

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6943

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

6944

{

6945

bond = (CMolBond*)sm->m_oaBonds[z3];

6946

gc->AddDataset();

6947

for (z4=0;z4<bond->m_faData.GetSize();z4++)

6948

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

6949

}

6950

}

6951

gc->WriteAgr("bondacf.agr",false);

6952

delete gc;

6953

}

6954

mprintf(" Differentiating bond length developments...\n");

6955

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6956

{

6957

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6958

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

6959

{

6960

bond = (CMolBond*)sm->m_oaBonds[z3];

6961

for (z4=0;z4<bond->m_faData.GetSize()-1;z4++)

6962

bond->m_faData[z4] = bond->m_faData[z4+1] - bond->m_faData[z4];

6963

}

6964

}

6965

if (g_bBondACFDebug)

6966

{

6967

mprintf(" Writing \"bondacf_diff.agr\"...\n");

6968

6969

try { gc = new CGrace(); } catch(...) { gc = NULL; }

6970

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

6971

6972

gc->SetRangeX(0,g_iSteps*g_fTimestepLength/1000.0);

6973

gc->SetRangeY(-15,15);

6974

gc->MakeTicks();

6975

gc->SetLabelX("Time [ps]");

6976

gc->SetLabelY("Bond length change rate");

6977

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6978

{

6979

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6980

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

6981

{

6982

bond = (CMolBond*)sm->m_oaBonds[z3];

6983

gc->AddDataset();

6984

for (z4=0;z4<bond->m_faData.GetSize();z4++)

6985

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

6986

}

6987

}

6988

gc->WriteAgr("bondacf_diff.agr",false);

6989

delete gc;

6990

}

6991

mprintf(" Autocorrelating bond length developments...\n");

6992

mprintf(WHITE," [");

6993

tfs = 0;

6994

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

6995

{

6996

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

6997

tfs += sm->m_oaBonds.GetSize();

6998

}

6999

tfs /= 60.0;

7000

ti2 = 0;

7001

/* fft = new CFFT();

7002

fft->PrepareFFT_C2C(g_iSteps*2);

7003

fft2 = new CFFT();

7004

fft2->PrepareInverseFFT_C2C(g_iSteps*2);*/

7005

7006

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

7007

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7008

7009

ac->Init(g_iSteps,g_iBondACFDepth,g_bACFFFT);

7010

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

7011

{

7012

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

7013

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

7014

{

7015

if (fmod(ti2,tfs) < 1.0)

7016

mprintf(WHITE,"#");

7017

bond = (CMolBond*)sm->m_oaBonds[z3];

7018

ac->AutoCorrelate(&bond->m_faData,&tempfa);

7019

bond->m_faData.CopyFrom(&tempfa);

7020

ti2++;

7021

}

7022

}

7023

delete ac;

7024

mprintf(WHITE,"]\n");

7025

if (g_bBondACFDebug)

7026

{

7027

mprintf(" Writing \"bondacf_autocorr.agr\"...\n");

7028

7029

try { gc = new CGrace(); } catch(...) { gc = NULL; }

7030

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7031

7032

gc->SetRangeX(0,g_iBondACFDepth*g_fTimestepLength/1000.0);

7033

gc->SetRangeY(-25,25);

7034

gc->MakeTicks();

7035

gc->SetLabelX("Time [ps]");

7036

gc->SetLabelY("ACF(Bond length change rate)");

7037

for (z2=0;z2<g_oaSingleMolecules.GetSize();z2++)

7038

{

7039

sm = (CSingleMolecule*)g_oaSingleMolecules[z2];

7040

for (z3=0;z3<sm->m_oaBonds.GetSize();z3++)

7041

{

7042

bond = (CMolBond*)sm->m_oaBonds[z3];

7043

gc->AddDataset();

7044

for (z4=0;z4<g_iBondACFDepth;z4++)

7045

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

7046

}

7047

}

7048

gc->WriteAgr("bondacf_autocorr.agr",false);

7049

delete gc;

7050

}

7051

mprintf(" Merging equivalent Bonds...\n");

7052

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7053

{

7054

m = (CMolecule*)g_oaMolecules[z0];

7055

sm2 = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7056

for (z2=0;z2<m->m_laSingleMolIndex.GetSize();z2++)

7057

{

7058

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[z2]];

7059

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7060

{

7061

bg = (CMolBondGroup*)sm->m_oaBondGroups[z3];

7062

for (z4=1;z4<bg->m_oaBonds.GetSize();z4++)

7063

{

7064

bond = (CMolBond*)bg->m_oaBonds[z4];

7065

for (z5=0;z5<g_iBondACFDepth;z5++)

7066

((CMolBond*)((CMolBondGroup*)sm2->m_oaBondGroups[z3])->m_oaBonds[0])->m_faData[z5] += bond->m_faData[z5];

7067

}

7068

}

7069

}

7070

}

7071

if (g_bBondACFSymmetrize)

7072

{

7073

mprintf(" Symmetrizing bond ACFs...\n");

7074

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7075

{

7076

m = (CMolecule*)g_oaMolecules[z0];

7077

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7078

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7079

{

7080

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7081

bond->m_faData.SetSize(2*g_iBondACFDepth);

7082

for (z4=0;z4<g_iBondACFDepth;z4++)

7083

bond->m_faData[z4+g_iBondACFDepth] = bond->m_faData[z4];

7084

for (z4=0;z4<g_iBondACFDepth;z4++)

7085

bond->m_faData[z4] = bond->m_faData[2*g_iBondACFDepth-z4-1];

7086

}

7087

}

7088

g_iBondACFDepth *= 2;

7089

}

7090

if (g_bBondACFWindow)

7091

{

7092

mprintf(" Applying Window Function...\n");

7093

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7094

{

7095

m = (CMolecule*)g_oaMolecules[z0];

7096

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7097

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7098

{

7099

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7100

for (z4=0;z4<g_iBondACFDepth;z4++)

7101

bond->m_faData[z4] *= (float)pow(sin(z4*Pi/(bond->m_faData.GetSize()-1)),2);

7102

}

7103

}

7104

}

7105

if (g_bBondACFNormalize)

7106

{

7107

mprintf(" Normalizing bond ACFs...\n");

7108

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7109

{

7110

m = (CMolecule*)g_oaMolecules[z0];

7111

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7112

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7113

{

7114

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7115

tf = 0;

7116

for (z4=0;z4<g_iBondACFDepth;z4++)

7117

if (tf < bond->m_faData[z4])

7118

tf = bond->m_faData[z4];

7119

for (z4=0;z4<g_iBondACFDepth;z4++)

7120

bond->m_faData[z4] /= (float)tf;

7121

}

7122

}

7123

}

7124

mprintf(" Writing \"bondacf_ac_merged.agr\"...\n");

7125

7126

try { gc = new CGrace(); } catch(...) { gc = NULL; }

7127

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7128

7129

gc->SetRangeX(0,g_iBondACFDepth*g_fTimestepLength/1000.0);

7130

gc->SetRangeY(-200,200);

7131

gc->MakeTicks();

7132

gc->SetLabelX("Time [ps]");

7133

gc->SetLabelY("Sum ACF(Bond length change rate)");

7134

gc->CurrentGraph()->m_bLegend = true;

7135

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7136

{

7137

m = (CMolecule*)g_oaMolecules[z0];

7138

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7139

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7140

{

7141

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7142

gc->AddDataset();

7143

7144

gc->SetDatasetName(buf);

7145

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth*2);

7146

for (z4=0;z4<g_iBondACFDepth;z4++)

7147

gc->AddXYTupel(z4*g_fTimestepLength/1000.0,bond->m_faData[z4]);

7148

}

7149

}

7150

gc->WriteAgr("bondacf_ac_merged.agr",false);

7151

delete gc;

7152

mprintf(" Applying Fourier Transformation...\n");

7153

7154

try { fft = new CFFT(); } catch(...) { fft = NULL; }

7155

if (fft == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7156

7157

fft->PrepareFFT_C2C(g_iBondACFDepth);

7158

tf3 = 0;

7159

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7160

{

7161

m = (CMolecule*)g_oaMolecules[z0];

7162

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7163

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7164

{

7165

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7166

for (z4=0;z4<g_iBondACFDepth;z4++)

7167

{

7168

fft->m_pInput[z4*2] = bond->m_faData[z4];

7169

fft->m_pInput[z4*2+1] = 0;

7170

}

7171

fft->DoFFT();

7172

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7173

{

7174

bond->m_faData[z4] = (float)(pow(fft->m_pOutput[z4*2],2) + pow(fft->m_pOutput[z4*2+1],2)) / g_iBondACFDepth;

7175

if (bond->m_faData[z4] > tf3)

7176

tf3 = bond->m_faData[z4];

7177

}

7178

}

7179

}

7180

delete fft;

7181

mprintf(" Writing \"bond_spectrum.agr\"...\n");

7182

7183

try { gc = new CGrace(); } catch(...) { gc = NULL; }

7184

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7185

7186

gc->SetRangeX(0,4000.0);

7187

gc->SetRangeY(0,tf3*1.1);

7188

gc->MakeTicks();

7189

gc->SetLabelX("Wave number [1/cm]");

7190

gc->SetLabelY("Intensity");

7191

gc->CurrentGraph()->m_bInvertXAxis = true;

7192

gc->CurrentGraph()->m_bLegend = true;

7193

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7194

{

7195

m = (CMolecule*)g_oaMolecules[z0];

7196

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7197

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7198

{

7199

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7200

gc->AddDataset();

7201

7202

gc->SetDatasetName(buf);

7203

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth*2);

7204

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7205

gc->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,bond->m_faData[z4]);

7206

}

7207

}

7208

gc->WriteAgr("bond_spectrum.agr",false);

7209

delete gc;

7210

for (z5=1;z5<5;z5++)

7211

{

7212

mprintf(" Smoothing spectrum, degree %d...\n",z5);

7213

mprintf(" Writing \"bond_spectrum_s%d.agr\"...\n",z5);

7214

7215

try { gc = new CGrace(); } catch(...) { gc = NULL; }

7216

if (gc == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7217

7218

gc->SetRangeX(0,4000.0);

7219

gc->SetRangeY(0,tf3*1.1);

7220

gc->MakeTicks();

7221

gc->SetLabelX("Wave number [1/cm]");

7222

gc->SetLabelY("Intensity");

7223

gc->CurrentGraph()->m_bInvertXAxis = true;

7224

gc->CurrentGraph()->m_bLegend = true;

7225

7226

try { gc2 = new CGrace(); } catch(...) { gc2 = NULL; }

7227

if (gc2 == NULL) NewException((double)sizeof(CGrace),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7228

7229

gc2->SetRangeX(0,4000.0);

7230

gc2->SetRangeY(0,tf3*1.1);

7231

gc2->MakeTicks();

7232

gc2->SetLabelX("Wave number [1/cm]");

7233

gc2->SetLabelY("Intensity");

7234

gc2->CurrentGraph()->m_bInvertXAxis = true;

7235

gc2->CurrentGraph()->m_bLegend = true;

7236

7237

tempfa.SetSize(g_iBondACFDepth/2);

7238

tempfa2.SetSize(g_iBondACFDepth/2);

7239

7240

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7241

tempfa2[z4] = 0;

7242

7243

for (z0=0;z0<g_oaMolecules.GetSize();z0++)

7244

{

7245

m = (CMolecule*)g_oaMolecules[z0];

7246

sm = (CSingleMolecule*)g_oaSingleMolecules[m->m_laSingleMolIndex[0]];

7247

for (z3=0;z3<sm->m_oaBondGroups.GetSize();z3++)

7248

{

7249

bond = (CMolBond*)((CMolBondGroup*)sm->m_oaBondGroups[z3])->m_oaBonds[0];

7250

7251

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7252

{

7253

tf = 0;

7254

tf2 = 0;

7255

for (z6=-z5;z6<=z5;z6++)

7256

{

7257

if ((z4+z6 < 0) || (z4+z6 >= g_iBondACFDepth/2))

7258

continue;

7259

tf += bond->m_faData[z4+z6] / (pow((double)z6,2)+1.0);

7260

tf2 += 1.0 / (pow((double)z6,2)+1.0);

7261

}

7262

tempfa[z4] = (float)(tf / tf2);

7263

tempfa2[z4] += tempfa[z4];

7264

}

7265

7266

gc->AddDataset();

7267

gc2->AddDataset();

7268

7269

gc->SetDatasetName(buf);

7270

gc2->SetDatasetName(buf);

7271

((CGraceDataset*)gc->CurrentGraph()->m_oaDatasets[gc->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth);

7272

((CGraceDataset*)gc2->CurrentGraph()->m_oaDatasets[gc2->CurrentGraph()->m_oaDatasets.GetSize()-1])->m_faValues.SetMaxSize(g_iBondACFDepth);

7273

7274

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7275

gc->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,tempfa[z4]);

7276

7277

for (z4=0;z4<g_iBondACFDepth/2;z4++)

7278

gc2->AddXYTupel(z4*2.0/g_iBondACFDepth*1E7f/299.792f/2.0f/g_fTimestepLength/g_iStride,tempfa2[z4]);

7279

}

7280

}

7281

7282

sprintf(buf,"bond_spectrum_s%d.agr",z5);

7283

gc->WriteAgr(buf,false);

7284

delete gc;

7285

7286

mprintf(" Writing \"bond_spectrum_cumulative_s%d.agr\"...\n",z5);

7287

sprintf(buf,"bond_spectrum_cumulative_s%d.agr",z5);

7288

gc2->WriteAgr(buf,false);

7289

delete gc2;

7290

}

7291

}

7292

7293

if (g_bSaveRefEnv)

7294

{

7295

fclose(g_fRefEnv);

7296

mprintf("\nTrajectory of reference molecule was saved as %s.\n",g_sRefEnv);

7297

if (g_bTDO)

7298

{

7299

#ifdef TARGET_WINDOWS

7300

sprintf(buf,"tdo_pymol_%s_%d%s.bat",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

7301

#else

7302

sprintf(buf,"tdo_pymol_%s_%d%s.sh",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

7303

#endif

7304

mprintf("Saving TDO PyMol script as %s.\n",buf);

7305

tfi = OpenFileWrite(buf,true);

7306

#ifdef TARGET_WINDOWS

7307

mfprintf(tfi,"pymolwin ");

7308

#else

7309

mfprintf(tfi,"pymol ");

7310

#endif

7311

for (z=0;z<g_laTDOSteps.GetSize();z++)

7312

mfprintf(tfi,"tdo_%s_%d_%06d%s.xyz ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,g_laTDOSteps[z],multibuf);

7313

mfprintf(tfi,"-d \"set sphere_scale,0.25\" ");

7314

mfprintf(tfi,"-d \"set stick_radius,0.17\" ");

7315

mfprintf(tfi,"-d \"set ray_trace_mode,1\" ");

7316

mfprintf(tfi,"-d \"set fog,0\" ");

7317

mfprintf(tfi,"-d \"set ray_trace_fog,0\" ");

7318

mfprintf(tfi,"-d \"set bg_rgb,(1,1,1)\" ");

7319

mfprintf(tfi,"-d \"set ray_shadow,0\" ");

7320

mfprintf(tfi,"-d \"set ray_shadows,0\" ");

7321

mfprintf(tfi,"-d \"set ray_interior_shadows,0\" ");

7322

mfprintf(tfi,"-d \"show sticks; show spheres\" ");

7323

7324

for (z=0;z<g_laTDOSteps.GetSize();z++)

7325

{

7326

for (z2=0;z2<g_oaAtoms.GetSize();z2++)

7327

{

7328

if ((z2 == g_iVirtAtomType) && (!g_bSaveVirtAtoms))

7329

continue;

7330

7331

}

7332

}

7333

for (z=0;z<g_laTDOSteps.GetSize();z++)

7334

{

7335

for (z2=0;z2<g_oaAtoms.GetSize();z2++)

7336

{

7337

if ((z2 == g_iVirtAtomType) && (!g_bSaveVirtAtoms))

7338

continue;

7339

7340

}

7341

}

7342

mfprintf(tfi,"\n");

7343

fclose(tfi);

7344

#ifdef TARGET_LINUX

7345

sprintf(buf,"chmod 755 tdo_pymol_%s_%d%s.sh",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,g_iSaveRefMol+1,multibuf);

7346

mprintf("Executing \"%s\"...\n",buf);

7347

system(buf);

7348

#endif

7349

}

7350

}

7351

if (g_bCutCluster)

7352

{

7353

fclose(g_fRefEnv);

7354

mprintf("\nCluster trajectory was saved as %s.\n",g_sRefEnv);

7355

}

7356

7357

if (g_bSaveJustTraj)

7358

{

7359

fclose(g_fSaveJustTraj);

7360

/* strcpy(buf,g_sInputTraj);

7361

p = strrchr(buf,'.');

7362

*p = 0;

7363

strcat(buf,multibuf);

7364

strcat(buf,".out.xyz");*/

7365

// mprintf("\nProcessed output trajectory was saved as traj_out.xyz\n",buf);

7366

}

7367

7368

if (g_bIRSpec && g_bGlobalIR)

7369

{

7370

mprintf(WHITE,"\n*** Global IR Spectrum\n");

7371

g_pGlobalIR->Finish(multibuf);

7372

}

7373

7374

if (g_bVACF && g_bGlobalVACF)

7375

{

7376

mprintf(WHITE,"\n*** Global velocity autocorrelation function\n");

7377

if (g_pGlobalVACF->m_bDerivative)

7378

{

7379

mprintf(" Deriving velocities...\n");

7380

mprintf(WHITE," [");

7381

tfs = g_iGesAtomCount/60.0;

7382

ti = 0;

7383

for (z2=0;z2<g_iGesAtomCount;z2++)

7384

{

7385

if (fmod(z2,tfs) < 1)

7386

mprintf(WHITE,"#");

7387

7388

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z2] > 1000))

7389

continue;

7390

7391

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[ti];

7392

7393

for (z3=0;z3<(int)g_iSteps*3-3;z3++)

7394

(*ptfa)[z3] = (*ptfa)[z3+3] - (*ptfa)[z3];

7395

7396

ti++;

7397

}

7398

mprintf(WHITE,"]\n");

7399

}

7400

if (g_bVACFCacheMode)

7401

{

7402

tfs = g_iGesAtomCount/60.0;

7403

/* if (g_bACFFFT)

7404

{*/

7405

mprintf(" Autocorrelating cached vectors...\n");

7406

mprintf(WHITE," [");

7407

/* fft = new CFFT();

7408

fft->PrepareFFT_C2C(2*g_iSteps);

7409

fft2 = new CFFT();

7410

fft2->PrepareInverseFFT_C2C(2*g_iSteps);*/

7411

7412

try { ptfa2 = new CxFloatArray("main():ptfa2"); } catch(...) { ptfa2 = NULL; }

7413

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7414

7415

ptfa2->SetSize(g_iSteps);

7416

7417

try { ptfa3 = new CxFloatArray("main():ptfa3"); } catch(...) { ptfa3 = NULL; }

7418

if (ptfa3 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7419

7420

ptfa3->SetSize(g_iSteps);

7421

7422

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

7423

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7424

7425

ac->Init(g_iSteps,g_pGlobalVACF->m_iSize,g_bACFFFT);

7426

ti = 0;

7427

for (z2=0;z2<g_iGesAtomCount;z2++)

7428

{

7429

if (fmod(z2,tfs) < 1.0)

7430

mprintf(WHITE,"#");

7431

7432

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z2] > 1000))

7433

continue;

7434

7435

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[ti];

7436

7437

if (g_pGlobalVACF->m_bMassWeight)

7438

tf = ((CAtom*)g_oaAtoms[g_waAtomRealElement[z2]])->m_pElement->m_fMass;

7439

else tf = 1.0f;

7440

7441

/* X */

7442

for (z3=0;z3<(int)g_iSteps;z3++)

7443

(*ptfa2)[z3] = (*ptfa)[z3*3];

7444

ac->AutoCorrelate(ptfa2,ptfa3);

7445

// mprintf("Global Atom %d X: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

7446

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

7447

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

7448

7449

/* Y */

7450

for (z3=0;z3<(int)g_iSteps;z3++)

7451

(*ptfa2)[z3] = (*ptfa)[z3*3+1];

7452

ac->AutoCorrelate(ptfa2,ptfa3);

7453

// mprintf("Global Atom %d Y: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

7454

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

7455

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

7456

7457

/* Z */

7458

for (z3=0;z3<(int)g_iSteps;z3++)

7459

(*ptfa2)[z3] = (*ptfa)[z3*3+2];

7460

ac->AutoCorrelate(ptfa2,ptfa3);

7461

// mprintf("Global Atom %d Z: %f + %f = %f.\n",z2+1,g_pGlobalVACF->m_pData[0],(*ptfa3)[0]*tf,g_pGlobalVACF->m_pData[0]+(*ptfa3)[0]*tf);

7462

for (z3=0;z3<(int)g_pGlobalVACF->m_iSize;z3++)

7463

g_pGlobalVACF->m_pData[z3] += (*ptfa3)[z3] * tf;

7464

7465

ti++;

7466

}

7467

delete ac;

7468

delete ptfa2;

7469

delete ptfa3;

7470

/* delete fft2;

7471

delete fft;*/

7472

/* } else

7473

{

7474

mprintf(" Autocorrelating cached vectors...\n");

7475

mprintf(WHITE," [");

7476

for (z2=0;z2<g_iGesAtomCount;z2++)

7477

{

7478

if (fmod(z2,tfs) < 1.0)

7479

mprintf(WHITE,"#");

7480

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[z2];

7481

for (z3=0;z3<g_pGlobalVACF->m_iSize;z3+=g_pGlobalVACF->m_iStride) // Das ist das Tau

7482

{

7483

tf = 0;

7484

for (z4=0;z4<(int)g_iSteps-z3;z4++) // Das ist der Startpunkt

7485

tf += (*ptfa)[z4*3]*(*ptfa)[(z4+z3)*3] + (*ptfa)[z4*3+1]*(*ptfa)[(z4+z3)*3+1] + (*ptfa)[z4*3+2]*(*ptfa)[(z4+z3)*3+2];

7486

g_pGlobalVACF->m_pData[z3/g_pGlobalVACF->m_iStride] += tf/(g_iSteps-z3);

7487

}

7488

}

7489

}*/

7490

mprintf(WHITE,"]\n");

7491

mprintf(" %d atoms, %d time steps and %d correlation depths processed.\n",g_pGlobalVACF->m_oaCache.GetSize(),g_iSteps,g_pGlobalVACF->m_iSize);

7492

g_pGlobalVACF->MultiplyCached(1.0/g_iGesAtomCount);

7493

7494

if (g_pGlobalVACF->m_bDecomposeModes)

7495

{

7496

tfs = g_iGesAtomCount*g_iGesAtomCount*3/60.0;

7497

7498

mprintf(" Allocating cross-correlation matrix (%s)...\n",FormatBytes((double)sizeof(float)*g_pGlobalVACF->m_iSize*g_pGlobalVACF->m_iParticles*3*g_pGlobalVACF->m_iParticles*3));

7499

7500

g_pGlobalVACF->m_oaCCRMatrix.SetMaxSize(g_pGlobalVACF->m_iParticles*3*g_pGlobalVACF->m_iParticles*3);

7501

for (z2=0;z2<g_pGlobalVACF->m_iParticles*3;z2++)

7502

{

7503

for (z3=0;z3<g_pGlobalVACF->m_iParticles*3;z3++)

7504

{

7505

// mprintf("X: %X\n",g_pGlobalVACF);

7506

// mprintf("%d - %d -->\n",z2,z3);

7507

try { ptfa = new CxFloatArray("main():ptfa"); } catch(...) { ptfa = NULL; }

7508

if (ptfa == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7509

7510

// mprintf("A\n");

7511

ptfa->SetSize(g_pGlobalVACF->m_iSize);

7512

// mprintf("B\n");

7513

// mprintf("X2: %X\n",g_pGlobalVACF);

7514

g_pGlobalVACF->m_oaCCRMatrix.Add(ptfa);

7515

// mprintf("%d - %d <--\n",z2,z3);

7516

}

7517

}

7518

7519

mprintf(" Computing %d cross-correlations...\n",g_pGlobalVACF->m_iParticles*3*g_pGlobalVACF->m_iParticles*3);

7520

mprintf(WHITE," [");

7521

7522

try { ptfa2 = new CxFloatArray("main():ptfa2"); } catch(...) { ptfa2 = NULL; }

7523

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7524

7525

ptfa2->SetSize(g_iSteps);

7526

7527

try { ptfa2b = new CxFloatArray("main():ptfa2b"); } catch(...) { ptfa2b = NULL; }

7528

if (ptfa2b == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7529

7530

ptfa2b->SetSize(g_iSteps);

7531

7532

try { ccr = new CCrossCorrelation(); } catch(...) { ccr = NULL; }

7533

if (ccr == NULL) NewException((double)sizeof(CCrossCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7534

7535

ccr->Init(g_iSteps,g_pGlobalVACF->m_iSize,g_bACFFFT);

7536

7537

ti = 0;

7538

7539

for (z2=0;z2<g_iGesAtomCount;z2++)

7540

{

7541

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z2] > 1000))

7542

continue;

7543

7544

ptfa = (CxFloatArray*)g_pGlobalVACF->m_oaCache[ti];

7545

7546

for (z2b=0;z2b<3;z2b++)

7547

{

7548

ti2 = 0;

7549

for (z3=0;z3<g_iGesAtomCount;z3++)

7550

{

7551

if (fmod(z2*g_iGesAtomCount*3+z2b*g_iGesAtomCount+z3,tfs) < 1.0)

7552

mprintf(WHITE,"#");

7553

7554

if (g_pGlobalVACF->m_bExcludeR0 && (g_waAtomRealElement[z3] > 1000))

7555

continue;

7556

7557

ptfab = (CxFloatArray*)g_pGlobalVACF->m_oaCache[ti2];

7558

7559

if (g_pGlobalVACF->m_bMassWeight)

7560

tf = ((CAtom*)g_oaAtoms[g_waAtomRealElement[z2]])->m_pElement->m_fMass;

7561

else tf = 1.0f;

7562

7563

for (z3b=0;z3b<3;z3b++)

7564

{

7565

for (z4=0;z4<(int)g_iSteps;z4++)

7566

{

7567

(*ptfa2)[z4] = (*ptfa)[z4*3+z2b];

7568

(*ptfa2b)[z4] = (*ptfab)[z4*3+z3b];

7569

}

7570

ccr->CrossCorrelate(ptfa2,ptfa2b,(CxFloatArray*)g_pGlobalVACF->m_oaCCRMatrix[ti*g_pGlobalVACF->m_iParticles*9 + z2b*g_pGlobalVACF->m_iParticles*3 + ti2*3 + z3b]);

7571

// mprintf("z2=%d, z2b=%d, z3=%d, z3b=%d, I=%d\n",z2,z2b,z3,z3b,ti*g_pGlobalVACF->m_iParticles*9 + z2b*g_pGlobalVACF->m_iParticles*3 + ti2*3 + z3b);

7572

}

7573

7574

ti2++;

7575

}

7576

}

7577

ti++;

7578

}

7579

delete ccr;

7580

delete ptfa2;

7581

delete ptfa2b;

7582

7583

mprintf(WHITE,"]\n");

7584

7585

/* for (z2=0;z2<g_pGlobalVACF->m_iParticles*3;z2++)

7586

{

7587

for (z3=0;z3<g_pGlobalVACF->m_iParticles*3;z3++)

7588

mprintf("%6G ",((CxFloatArray*)g_pGlobalVACF->m_oaCCRMatrix[z2*g_pGlobalVACF->m_iParticles*3+z3])->GetAt(0));

7589

mprintf("\n");

7590

}*/

7591

7592

Interface_DecomposeModes(g_pGlobalVACF->m_iParticles*3, &g_pGlobalVACF->m_oaCCRMatrix);

7593

7594

} // END IF m_bDecomposeModes

7595

7596

} else g_pGlobalVACF->Multiply(1.0/g_iGesAtomCount);

7597

7598

mprintf(" Saving global VACF as acf_global%s.csv ...\n",multibuf);

7599

g_pGlobalVACF->WriteACF("acf_global",multibuf,".csv");

7600

7601

if (g_pGlobalVACF->m_iMirror != 0)

7602

{

7603

mprintf(" Mirroring global VACF...\n");

7604

g_pGlobalVACF->Mirror(g_pGlobalVACF->m_iMirror);

7605

mprintf(" Saving mirrored global VACF as acf_global.m%s.csv ...\n",multibuf);

7606

g_pGlobalVACF->WriteACF("acf_global.m",multibuf,".csv");

7607

}

7608

7609

if (g_pGlobalVACF->m_bWindowFunction)

7610

{

7611

mprintf(" Applying window function...\n");

7612

g_pGlobalVACF->Window();

7613

mprintf(" Saving windowed global VACF as acf_global.w%s.csv ...\n",multibuf);

7614

g_pGlobalVACF->WriteACF("acf_global.w",multibuf,".csv");

7615

}

7616

7617

if (g_pGlobalVACF->m_bSpectrum)

7618

{

7619

mprintf(" Performing Fourier transformation...\n");

7620

7621

try { g_pFFT = new CFFT(); } catch(...) { g_pFFT = NULL; }

7622

if (g_pFFT == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7623

7624

g_pFFT->PrepareFFT_C2C(g_pGlobalVACF->m_iSize+g_pGlobalVACF->m_iZeroPadding);

7625

g_pGlobalVACF->Transform(g_pFFT);

7626

delete g_pFFT;

7627

g_pGlobalVACF->m_pSpectrum->SetMaxRWL(1E7f/299.792f/g_fTimestepLength/g_iStride);

7628

if (g_pGlobalVACF->m_bACF_DB)

7629

{

7630

mprintf(" Normalising spectrum to decibel...\n");

7631

g_pGlobalVACF->m_pSpectrum->MakeDB();

7632

}/* else

7633

{

7634

mprintf(" Normalising integral of spectrum...\n");

7635

g_pGlobalVACF->m_pSpectrum->SetIntegral(1000000.0f);

7636

}*/

7637

if (g_pGlobalVACF->m_bWindowFunction)

7638

{

7639

mprintf(" Saving spectrum as power_global_w%s.csv ...\n",multibuf);

7640

g_pGlobalVACF->m_pSpectrum->Write("power_global_w",multibuf,".csv");

7641

} else

7642

{

7643

mprintf(" Saving spectrum as power_global%s.csv ...\n",multibuf);

7644

g_pGlobalVACF->m_pSpectrum->Write("power_global",multibuf,".csv");

7645

}

7646

}

7647

mprintf("\n");

7648

}

7649

7650

if (g_bVFDF)

7651

{

7652

for (z=0;z<g_iVFCorrCount;z++)

7653

fclose(g_fVFCorr[z]);

7654

}

7655

7656

7657

// fclose(ff);

7658

7659

for (z=0;z<g_oaObserv.GetSize();z++)

7660

{

7661

o = (CObservation*)g_oaObserv[z];

7662

mprintf(YELLOW,"\n>>> Observation %d >>>\n",z+1);

7663

7664

if (o->m_pConditions != NULL)

7665

{

7666

if (o->m_bSecondShowMol)

7667

mprintf(WHITE,"\n#### Condition between RM and 1st OM ####\n");

7668

7669

o->m_pConditions->PrintData();

7670

if (o->m_pConditions->m_oaConditionSubGroups.GetSize()==2)

7671

o->m_pConditions->PrintTable();

7672

}

7673

7674

if ((o->m_bSecondShowMol) && (o->m_pConditionsOM2 != NULL))

7675

{

7676

mprintf(WHITE,"\n\n#### Condition between RM and 2nd OM ####\n");

7677

o->m_pConditionsOM2->PrintData();

7678

if (o->m_pConditionsOM2->m_oaConditionSubGroups.GetSize()==2)

7679

o->m_pConditionsOM2->PrintTable();

7680

}

7681

7682

if (g_bAggregation)

7683

{

7684

mprintf(WHITE,"* Aggregation Functions\n");

7685

if ((g_iMaxStep > 0) && (((int)g_iSteps*g_iStride) >= g_iMaxStep))

7686

g_pTempTimestep->CopyFrom(GetTimeStep(0)); // Max. Schrittzahl

7687

else g_pTempTimestep->CopyFrom(GetTimeStep(1)); // End Of File

7688

for (zs=0;zs<o->m_pDACF->m_oaSubDACFs.GetSize();zs++)

7689

{

7690

dacfsub = (CDACFSub*)o->m_pDACF->m_oaSubDACFs[zs];

7691

mprintf(WHITE,"\n > Value Set %d: %s\n",zs+1,dacfsub->m_sName);

7692

7693

o->m_pDACF->FinishDACFSub(g_pTempTimestep,dacfsub);

7694

7695

sprintf(buf,"cond_%s.txt",dacfsub->m_sName);

7696

dacfsub->m_pCondition->PrintData(buf);

7697

7698

mprintf(WHITE,"Neighbour Count Distribution\n");

7699

mprintf(" %.0f Bin entries have been made.\n",dacfsub->m_pNDF->m_fBinEntries);

7700

sprintf(buf,"ncd_%s%s.csv",dacfsub->m_sName,multibuf);

7701

mprintf(" Writing Neighbor Count Distribution File \"%s\"...\n",buf);

7702

dacfsub->m_pNDF->Write_Int("",buf,"");

7703

7704

if (g_bDDisp)

7705

{

7706

mprintf(WHITE,"\nDimer Displacement Distribution Function\n");

7707

7708

sprintf(buf,"ddisp_%s%s.csv",dacfsub->m_sName,multibuf);

7709

mprintf(" Saving DDisp File as \"%s\"...\n",buf);

7710

dacfsub->m_pDDisp->Write("",buf,"",false);

7711

sprintf(buf,"ddisp_%s%s.agr",dacfsub->m_sName,multibuf);

7712

mprintf(" Saving DDisp Agr File as \"%s\"...\n",buf);

7713

dacfsub->m_pDDisp->WriteAgr("",buf,"","",false);

7714

}

7715

7716

if (g_bDACF)

7717

{

7718

mprintf(WHITE,"\nDimer Existence Autocorrelation Function\n");

7719

7720

7721

if (dacfsub->m_bBorderMode)

7722

{

7723

mprintf(" *** New Border Mode ***\n");

7724

for (z2=0;z2<o->m_pDACF->m_iDACFRes;z2++)

7725

dacfsub->m_pDACF->m_pBin[z2] /= g_iSteps-z2;

7726

} else

7727

{

7728

for (z2=0;z2<o->m_pDACF->m_iDACFRes;z2++)

7729

dacfsub->m_pDACF->m_pBin[z2] /= g_iSteps;

7730

}

7731

7732

if (dacfsub->m_bNewMode)

7733

{

7734

mprintf(" *** New Mode Processing ***\n");

7735

mprintf(WHITE," [");

7736

tfs = ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex.GetSize() * ((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize() / 60.0;

7737

ptfa = new CxFloatArray();

7738

ptfa2 = new CxFloatArray();

7739

ac = new CAutoCorrelation();

7740

ac->Init(g_iSteps,o->m_pDACF->m_iDACFRes,true);

7741

7742

ptfa->SetSize(g_iSteps);

7743

ptfa2->SetSize(o->m_pDACF->m_iDACFRes);

7744

7745

for (z2=0;z2<o->m_pDACF->m_iDACFRes;z2++)

7746

dacfsub->m_pDACF->m_pBin[z2] = 0;

7747

7748

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iFirstMol])->m_laSingleMolIndex.GetSize();z2++)

7749

{

7750

for (z3=0;z3<((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize();z3++)

7751

{

7752

if (fmod(z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3,tfs) < 1.0)

7753

mprintf(WHITE,"#");

7754

7755

for (z5=0;z5<(int)g_iSteps;z5++)

7756

(*ptfa)[z5] = 0;

7757

7758

for (z4=0;z4<dacfsub->m_piaIntervals[z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3].GetSize();z4+=2)

7759

{

7760

7761

(*ptfa)[z5-1] = 1;

7762

}

7763

7764

// if (dacfsub->m_piaIntervals[z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3].GetSize() != 0)

7765

// mprintf("\n%d-%d: %d ",z2,z3,dacfsub->m_piaIntervals[z2*((CMolecule*)g_oaMolecules[o->m_pDACF->m_iSecondMol])->m_laSingleMolIndex.GetSize()+z3].GetSize()/2);

7766

7767

ac->AutoCorrelate(ptfa,ptfa2);

7768

7769

/* if ((z2==0) && (z3==28))

7770

{

7771

FILE *tfia;

7772

7773

sprintf(buf,"condfunc_%d_%d.csv",z2,z3);

7774

tfia = fopen(buf,"wt");

7775

for (z4=0;z4<(int)g_iSteps;z4++)

7776

fprintf(tfia,"%d; %f\n",z4,(*ptfa)[z4]);

7777

fclose(tfia);

7778

7779

sprintf(buf,"condacf_%d_%d.csv",z2,z3);

7780

tfia = fopen(buf,"wt");

7781

for (z4=0;z4<o->m_pDACF->m_iDACFRes;z4++)

7782

fprintf(tfia,"%d; %f\n",z4,(*ptfa2)[z4]);

7783

fclose(tfia);

7784

}*/

7785

7786

for (z4=0;z4<o->m_pDACF->m_iDACFRes;z4++)

7787

dacfsub->m_pDACF->m_pBin[z4] += (*ptfa2)[z4];

7788

}

7789

}

7790

mprintf(WHITE,"]\n");

7791

}

7792

7793

if (dacfsub->m_bCorrectEq)

7794

{

7795

if (dacfsub->m_iRefMol == dacfsub->m_iShowMol)

7796

{

7797

7798

mprintf(" Ensemble Average is %.6f%c.\n",tf,'%');

7799

7800

tf = 1.0/(((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()-1)/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize();

7801

dacfsub->m_pDACF->MultiplyBin(tf);

7802

7803

tf = dacfsub->m_fEqCounter/g_iSteps/(((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()-1)/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize();

7804

tf = tf*tf;

7805

mprintf(" Subtracting squared average value (%G - %G)...\n",dacfsub->m_pDACF->m_pBin[0],tf);

7806

dacfsub->m_pDACF->SubtractBin(tf);

7807

} else

7808

{

7809

tf = 100.0*dacfsub->m_fEqCounter/g_iSteps/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()/((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize();

7810

mprintf(" Ensemble Average is %.6f%c.\n",tf,'%');

7811

7812

tf = 1.0/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()/((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize();

7813

dacfsub->m_pDACF->MultiplyBin(tf);

7814

7815

tf = dacfsub->m_fEqCounter/g_iSteps/((CMolecule*)g_oaMolecules[dacfsub->m_iRefMol])->m_laSingleMolIndex.GetSize()/((CMolecule*)g_oaMolecules[dacfsub->m_iShowMol])->m_laSingleMolIndex.GetSize();

7816

tf = tf*tf;

7817

mprintf(" Subtracting squared average value (%G - %G)...\n",dacfsub->m_pDACF->m_pBin[0],tf);

7818

dacfsub->m_pDACF->SubtractBin(tf);

7819

}

7820

}

7821

7822

if (dacfsub->m_pDACF->m_pBin[0] != 0)

7823

{

7824

mprintf(" Normalizing DACF with factor 1/%G ...\n",dacfsub->m_pDACF->m_pBin[0]);

7825

dacfsub->m_pDACF->MultiplyBin(1.0/dacfsub->m_pDACF->m_pBin[0]);

7826

} else mprintf(" Not normalizing this DACF, first entry is 0.\n");

7827

7828

if (o->m_pDACF->m_bFitDACF)

7829

{

7830

mprintf("\n");

7831

7832

try { dacfsub->m_pDACF->m_pParameters = new double*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pParameters = NULL; }

7833

if (dacfsub->m_pDACF->m_pParameters == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7834

7835

try { dacfsub->m_pDACF->m_pFitIntegral = new double[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pFitIntegral = NULL; }

7836

if (dacfsub->m_pDACF->m_pFitIntegral == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7837

7838

try { dacfsub->m_pDACF->m_pCorrCoeff = new double[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pCorrCoeff = NULL; }

7839

if (dacfsub->m_pDACF->m_pCorrCoeff == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7840

7841

try { dacfsub->m_pDACF->m_pAdditionalSets = new double*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pAdditionalSets = NULL; }

7842

if (dacfsub->m_pDACF->m_pAdditionalSets == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(double*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7843

7844

try { dacfsub->m_pDACF->m_pAdditionalSetLabels = new char*[o->m_pDACF->m_iFitDegreeMax+1]; } catch(...) { dacfsub->m_pDACF->m_pAdditionalSetLabels = NULL; }

7845

if (dacfsub->m_pDACF->m_pAdditionalSetLabels == NULL) NewException((double)(o->m_pDACF->m_iFitDegreeMax+1)*sizeof(char*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7846

7847

dacfsub->m_pDACF->m_iAdditionalSets = o->m_pDACF->m_iFitDegreeMax+1;

7848

7849

for (z2=0;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7850

{

7851

dacfsub->m_pDACF->m_pAdditionalSets[z2] = NULL;

7852

dacfsub->m_pDACF->m_pAdditionalSetLabels[z2] = NULL;

7853

}

7854

7855

mprintf(YELLOW," Please note: ");

7856

mprintf("The lifetime is two times the integral value!\n\n");

7857

7858

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7859

dacfsub->m_pDACF->Fit_PolyExp(z2,5000);

7860

7861

if (o->m_pDACF->m_iFitDegreeMin != o->m_pDACF->m_iFitDegreeMax)

7862

{

7863

mprintf(YELLOW," DACF fit integral overview:\n");

7864

mprintf(" (use the row with the highest R value)\n\n");

7865

mprintf(WHITE," Degree R Integral [ps] Lifetime [ps]\n");

7866

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7867

{

7868

if (dacfsub->m_pDACF->m_pFitIntegral[z2] >= 0)

7869

mprintf(" %d %10.8f %-10G %-10G\n",z2,dacfsub->m_pDACF->m_pCorrCoeff[z2],dacfsub->m_pDACF->m_pFitIntegral[z2],dacfsub->m_pDACF->m_pFitIntegral[z2]*2.0);

7870

else mprintf(" %d %10.8f - -\n",z2,dacfsub->m_pDACF->m_pCorrCoeff[z2]);

7871

}

7872

mprintf("\n");

7873

}

7874

}

7875

sprintf(buf,"dacf_%s%s.csv",dacfsub->m_sName,multibuf);

7876

mprintf(" Saving DACF File as \"%s\"...\n",buf);

7877

dacfsub->m_pDACF->Write("",buf,"",false);

7878

sprintf(buf,"dacf_%s%s.agr",dacfsub->m_sName,multibuf);

7879

mprintf(" Saving DACF Agr File as \"%s\"...\n",buf);

7880

dacfsub->m_pDACF->WriteAgr("",buf,"","",false);

7881

7882

if (o->m_pDACF->m_bLifetimeSpectrum)

7883

{

7884

for (z2=0;z2<o->m_pDACF->m_oaLTSpectra.GetSize();z2++)

7885

{

7886

mprintf(WHITE,"\n * Lifetime Spectrum %d\n\n",z2+1);

7887

((CLTSpec*)o->m_pDACF->m_oaLTSpectra[z2])->ComputeSpectrum("dacf",dacfsub->m_sName,multibuf,"",dacfsub->m_pDACF);

7888

}

7889

/* sprintf(buf,"dacf_lspectrum_N%d_P%d_I%d_%s%s.csv",o->m_pDACF->m_iLSpecData,o->m_pDACF->m_iLSpecPoints,o->m_pDACF->m_iMaxLMIter,dacfsub->m_sName,multibuf);

7890

mprintf(" Saving DACF lifetime spectrum as \"%s\"...\n",buf);

7891

dacfsub->m_pDACF->Fit_ExpSpectrum(o->m_pDACF->m_iLSpecPoints,o->m_pDACF->m_fLSpecMinExp,o->m_pDACF->m_fLSpecMaxExp,buf,o->m_pDACF->m_iLSpecData,o->m_pDACF->m_iMaxLMIter,false,true);

7892

7893

sprintf(buf,"dacf_lsfit_N%d_P%d_I%d_%s%s.csv",o->m_pDACF->m_iLSpecData,o->m_pDACF->m_iLSpecPoints,o->m_pDACF->m_iMaxLMIter,dacfsub->m_sName,multibuf);

7894

mprintf(" Saving DACF lifetime spectrum fit as \"%s\"...\n",buf);

7895

dacfsub->m_pDACF->Write("",buf,"",false);*/

7896

}

7897

}

7898

7899

if (g_bDLDF)

7900

{

7901

mprintf(WHITE,"\nDimer Lifetime Distribution Function\n");

7902

7903

sprintf(buf,"dldf_%s%s.csv",dacfsub->m_sName,multibuf);

7904

mprintf(" Saving DLDF File as \"%s\"...\n",buf);

7905

dacfsub->m_pDLDF->Write("",buf,"",false);

7906

sprintf(buf,"dldf_%s%s.agr",dacfsub->m_sName,multibuf);

7907

mprintf(" Saving DLDF Agr File as \"%s\"...\n",buf);

7908

dacfsub->m_pDLDF->WriteAgr("",buf,"","",false);

7909

}

7910

7911

if (g_bDLDisp)

7912

{

7913

mprintf(WHITE,"\nDimer Lifetime Displacement Distribution Function\n");

7914

7915

mprintf(" Normalizing bin integral to 1000000...\n");

7916

dacfsub->m_pDLDisp->NormalizeBinIntegral(1000000.0);

7917

sprintf(buf,"dldisp_%s%s",dacfsub->m_sName,multibuf);

7918

mprintf(" Saving DLDisp triples as \"%s_triples.csv\"...\n",buf);

7919

dacfsub->m_pDLDisp->Write("",buf,"_triples.csv");

7920

mprintf(" Saving DLDisp matrix as \"%s_matrix.csv\"...\n",buf);

7921

dacfsub->m_pDLDisp->WriteCSV("",buf,"_matrix.csv");

7922

mprintf(" Saving DLDisp Mathematica Notebook \"%s.nb\"...\n",buf);

7923

dacfsub->m_pDLDisp->WriteMathematicaNb("",buf,".nb",false);

7924

mprintf(" Saving DLDisp Gnuplot Input \"%s.gp\"...\n",buf);

7925

dacfsub->m_pDLDisp->WriteGnuplotInput("",buf,"",false);

7926

}

7927

7928

if (g_bPairMSD)

7929

{

7930

mprintf(WHITE,"\nPair Mean Square Displacement\n");

7931

mprintf(" %.0f Bin entries have been made.\n",dacfsub->m_pPairMSD->m_fBinEntries);

7932

mprintf(" Calculating average values...\n");

7933

dacfsub->m_pPairMSD->BuildAverage();

7934

sprintf(buf,"pairmsd_%s%s",dacfsub->m_sName,multibuf);

7935

mprintf(" Saving Pair MSD as \"%s.csv\"...\n",buf);

7936

dacfsub->m_pPairMSD->Write("",buf,".csv");

7937

}

7938

}

7939

if (o->m_pDACF->m_bDACFGrid && o->m_pDACF->m_bFitDACF)

7940

{

7941

mprintf(WHITE,"\n*** Condition Grid fitting overview:\n\n");

7942

mprintf(" Degree R(min) R(avg) R(max)\n");

7943

o->m_pDACF->CalcGridFitParms();

7944

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7945

mprintf(" %d %10.8f %10.8f %10.8f\n",z2,o->m_pDACF->m_pFitRMin[z2],o->m_pDACF->m_pFitRAvg[z2],o->m_pDACF->m_pFitRMax[z2]);

7946

mprintf("\n");

7947

7948

for (z2=o->m_pDACF->m_iFitDegreeMin;z2<=o->m_pDACF->m_iFitDegreeMax;z2++)

7949

{

7950

if ((o->m_pDACF->m_iGridMode == 3) || (o->m_pDACF->m_iGridMode == 5))

7951

{

7952

if (o->m_pDACF->m_bGridCon)

7953

{

7954

try { temp2df = new C2DF(); } catch(...) { temp2df = NULL; }

7955

if (temp2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7956

7957

o->m_pDACF->CreateGridFit2DF(temp2df,z2,false);

7958

sprintf(buf,"dacf_gridint_%s%s_%dexp",o->m_pDACF->m_sName,multibuf,z2);

7959

mprintf(" Saving Grid Integral triples as \"%s_triples.csv\"...\n",buf);

7960

temp2df->Write("",buf,"_triples.csv");

7961

mprintf(" Saving Grid Integral matrix as \"%s_matrix.csv\"...\n",buf);

7962

temp2df->WriteCSV("",buf,"_matrix.csv");

7963

mprintf(" Saving Grid Integral Mathematica Notebook \"%s.nb\"...\n",buf);

7964

temp2df->WriteMathematicaNb("",buf,".nb",false);

7965

mprintf(" Saving Grid Integral Gnuplot Input \"%s.gp\"...\n",buf);

7966

temp2df->WriteGnuplotInput("",buf,"",false);

7967

delete temp2df;

7968

}

7969

if (o->m_pDACF->m_bGridInt)

7970

{

7971

try { temp2df = new C2DF(); } catch(...) { temp2df = NULL; }

7972

if (temp2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7973

7974

o->m_pDACF->CreateGridFit2DF(temp2df,z2,true);

7975

sprintf(buf,"dacf_gridint_%s%s_%dexp_int%.2f",o->m_pDACF->m_sName,multibuf,z2,o->m_pDACF->m_fGridIntGap);

7976

mprintf(" Saving Grid Integral triples as \"%s_triples.csv\"...\n",buf);

7977

temp2df->Write("",buf,"_triples.csv");

7978

mprintf(" Saving Grid Integral matrix as \"%s_matrix.csv\"...\n",buf);

7979

temp2df->WriteCSV("",buf,"_matrix.csv");

7980

mprintf(" Saving Grid Integral Mathematica Notebook \"%s.nb\"...\n",buf);

7981

temp2df->WriteMathematicaNb("",buf,".nb",false);

7982

mprintf(" Saving Grid Integral Gnuplot Input \"%s.gp\"...\n",buf);

7983

temp2df->WriteGnuplotInput("",buf,"",false);

7984

delete temp2df;

7985

}

7986

} else

7987

{

7988

if (o->m_pDACF->m_bGridCon)

7989

{

7990

try { tdf = new CDF(); } catch(...) { tdf = NULL; }

7991

if (tdf == NULL) NewException((double)sizeof(CDF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

7992

7993

// o->m_pDACF->CreateGridFitDF(tdf,z2,false);

7994

abort();

7995

delete tdf;

7996

}

7997

}

7998

}

7999

}

8000

} // END IF AGGREGATION

8001

8002

if (g_bDens)

8003

{

8004

mprintf(WHITE,"* Density Distribution Function\n");

8005

8006

8007

mprintf(" Correcting radial distribution...\n");

8008

o->m_pDensityDF->m_pDensDF->CorrectRadialDist();

8009

8010

mprintf(" Scaling values to match final density...\n");

8011

8012

if (o->m_pDensityDF->m_bDensityMass)

8013

{

8014

o->m_pDensityDF->m_pDensDF->Integrate(true,1.0 / g_iSteps / (double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

8015

o->m_pDensityDF->m_pDensDF->MultiplyBin(1.66054e6 / (4.0/3.0*Pi) / g_iSteps / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

8016

} else

8017

{

8018

o->m_pDensityDF->m_pDensDF->Integrate(true,1.0 / g_iSteps / (double)((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

8019

o->m_pDensityDF->m_pDensDF->MultiplyBin(1.0e9 / (4.0/3.0*Pi) / g_iSteps / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize());

8020

}

8021

8022

/* if (g_bDoubleBox)

8023

{

8024

o->m_pDensityDF->m_pDensDF->MultiplyBin(g_iDoubleBoxFactor);

8025

o->m_pDensityDF->m_pDensDF->MultiplyIntegral(g_iDoubleBoxFactor);

8026

}*/

8027

8028

sprintf(buf,"density_df_%s%s.csv",o->m_pDensityDF->m_sName,multibuf);

8029

mprintf(" Saving Density DF as \"%s\"...\n",buf);

8030

o->m_pDensityDF->m_pDensDF->Write("",buf,"",true);

8031

sprintf(buf,"density_df_%s%s.agr",o->m_pDensityDF->m_sName,multibuf);

8032

mprintf(" Saving Density DF AGR file as \"%s\"...\n",buf);

8033

o->m_pDensityDF->m_pDensDF->WriteAgr("",buf,"",o->m_pDensityDF->m_sName,true);

8034

if (o->m_pDensityDF->m_iHistogramRes != 0)

8035

{

8036

mprintf(" Calculating Histogram...\n");

8037

o->m_pDensityDF->m_pDensDF->CalcHistogram();

8038

sprintf(buf,"his_density_df_%s%s.csv",o->m_pDensityDF->m_sName,multibuf);

8039

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8040

o->m_pDensityDF->m_pDensDF->WriteHistogram("",buf,"");

8041

}

8042

} // END IF g_bDens

8043

8044

if (g_bRDyn)

8045

{

8046

mprintf(WHITE,"* Vector Reorientation Dynamics\n");

8047

o->m_pRDyn->Finish(multibuf);

8048

}

8049

8050

if (g_bIRSpec)

8051

{

8052

mprintf(WHITE,"* IR Spectrum\n");

8053

o->m_pIRSpec->Finish(multibuf);

8054

}

8055

8056

if (g_bVACF)

8057

{

8058

mprintf(WHITE,"* Velocity Autocorrelation Function\n");

8059

if (o->m_pVACF->m_bDerivative)

8060

{

8061

mprintf(" Deriving velocities...\n");

8062

mprintf(WHITE," [");

8063

tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes)/60.0;

8064

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

8065

{

8066

if (fmod(z2,tfs) < 1)

8067

mprintf(WHITE,"#");

8068

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[z2];

8069

8070

for (z3=0;z3<(int)g_iSteps*3-3;z3++)

8071

(*ptfa)[z3] = (*ptfa)[z3+3] - (*ptfa)[z3];

8072

}

8073

mprintf(WHITE,"]\n");

8074

}

8075

if (g_bVACFCacheMode)

8076

{

8077

mprintf(" Autocorrelating cached vectors...\n");

8078

mprintf(WHITE," [");

8079

tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes)/60.0;

8080

8081

try { ptfa2 = new CxFloatArray("main():ptfa2"); } catch(...) { ptfa2 = NULL; }

8082

if (ptfa2 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8083

8084

ptfa2->SetSize(g_iSteps);

8085

8086

try { ptfa3 = new CxFloatArray("main():ptfa3"); } catch(...) { ptfa3 = NULL; }

8087

if (ptfa3 == NULL) NewException((double)sizeof(CxFloatArray),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8088

8089

ptfa3->SetSize(g_iSteps);

8090

8091

try { ac = new CAutoCorrelation(); } catch(...) { ac = NULL; }

8092

if (ac == NULL) NewException((double)sizeof(CAutoCorrelation),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8093

8094

ac->Init(g_iSteps,o->m_pVACF->m_iSize,g_bACFFFT);

8095

ti = 0;

8096

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize();z2++)

8097

{

8098

for (z3=0;z3<o->m_pVACF->m_oAtoms.m_baAtomType.GetSize();z3++)

8099

{

8100

if (o->m_pVACF->m_bMassWeight)

8101

tf = ((CAtom*)g_oaAtoms[o->m_pVACF->m_oAtoms.m_baRealAtomType[z3]])->m_pElement->m_fMass;

8102

else tf = 1.0;

8103

for (z4=0;z4<((CxIntArray*)o->m_pVACF->m_oAtoms.m_oaAtoms[z3])->GetSize();z4++)

8104

{

8105

if (fmod(ti,tfs) < 1)

8106

mprintf(WHITE,"#");

8107

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[ti];

8108

8109

/* X */

8110

for (z5=0;z5<(int)g_iSteps;z5++)

8111

(*ptfa2)[z5] = (*ptfa)[z5*3];

8112

ac->AutoCorrelate(ptfa2,ptfa3);

8113

// mprintf("Lokal Atom %d X: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

8114

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

8115

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

8116

8117

/* Y */

8118

for (z5=0;z5<(int)g_iSteps;z5++)

8119

(*ptfa2)[z5] = (*ptfa)[z5*3+1];

8120

ac->AutoCorrelate(ptfa2,ptfa3);

8121

// mprintf("Lokal Atom %d Y: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

8122

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

8123

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

8124

8125

/* Z */

8126

for (z5=0;z5<(int)g_iSteps;z5++)

8127

(*ptfa2)[z5] = (*ptfa)[z5*3+2];

8128

ac->AutoCorrelate(ptfa2,ptfa3);

8129

// mprintf("Lokal Atom %d Z: %f + %f = %f.\n",ti+1,o->m_pVACF->m_pData[0],(*ptfa3)[0]*tf,o->m_pVACF->m_pData[0]+(*ptfa3)[0]*tf);

8130

for (z5=0;z5<(int)o->m_pVACF->m_iSize;z5++)

8131

o->m_pVACF->m_pData[z5] += (*ptfa3)[z5]*tf;

8132

8133

ti++;

8134

}

8135

}

8136

}

8137

delete ac;

8138

delete ptfa2;

8139

delete ptfa3;

8140

8141

/* } else

8142

{

8143

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pVACF->m_iShowAtomGes;z2++)

8144

{

8145

if (fmod(z2,tfs) < 1)

8146

mprintf(WHITE,"#");

8147

ptfa = (CxFloatArray*)o->m_pVACF->m_oaCache[z2];

8148

for (z3=0;z3<o->m_pVACF->m_iSize;z3+=o->m_pVACF->m_iStride) // Das ist das Tau

8149

{

8150

tf = 0;

8151

for (z4=0;z4<(int)g_iSteps-z3;z4++) // Das ist der Startpunkt

8152

tf += (*ptfa)[z4*3]*(*ptfa)[(z4+z3)*3] + (*ptfa)[z4*3+1]*(*ptfa)[(z4+z3)*3+1] + (*ptfa)[z4*3+2]*(*ptfa)[(z4+z3)*3+2];

8153

o->m_pVACF->m_pData[z3/o->m_pVACF->m_iStride] += tf/(g_iSteps-z3);

8154

}

8155

}

8156

}*/

8157

mprintf(WHITE,"]\n");

8158

// mprintf(" %d atoms, %d time steps and %d correlation depths processed.\n",g_pGlobalVACF->m_oaCache.GetSize(),g_iSteps,g_pGlobalVACF->m_iSize);

8159

mprintf(" %d atoms, %d time steps and %d correlation depths processed.\n",ti,g_iSteps,o->m_pVACF->m_iSize);

8160

o->m_pVACF->MultiplyCached(1.0/g_iGesAtomCount);

8161

} else o->m_pVACF->Multiply(1.0/g_iGesAtomCount);

8162

/* sprintf(buf,"acf_%s%s.csv",o->m_pVACF->m_sName,multibuf);

8163

mprintf(" Saving ACF as %s ...\n",buf);

8164

o->m_pVACF->WriteACF("",buf,"");*/

8165

8166

sprintf(buf,"acf_%s%s.csv",o->m_pVACF->m_sName,multibuf);

8167

mprintf(" Saving ACF as %s ...\n",buf);

8168

o->m_pVACF->WriteACF("",buf,"");

8169

8170

if (o->m_pVACF->m_iMirror != 0)

8171

{

8172

mprintf(" Mirroring ACF...\n");

8173

o->m_pVACF->Mirror(o->m_pVACF->m_iMirror);

8174

sprintf(buf,"acf_%s%s.m.csv",o->m_pVACF->m_sName,multibuf);

8175

mprintf(" Saving mirrored ACF as %s ...\n",buf);

8176

o->m_pVACF->WriteACF("",buf,"");

8177

}

8178

8179

if (o->m_pVACF->m_bWindowFunction)

8180

{

8181

mprintf(" Applying window function to ACF...\n");

8182

o->m_pVACF->Window();

8183

sprintf(buf,"acf_%s%s.w.csv",o->m_pVACF->m_sName,multibuf);

8184

mprintf(" Saving windowed ACF as %s ...\n",buf);

8185

o->m_pVACF->WriteACF("",buf,"");

8186

}

8187

8188

if (o->m_pVACF->m_bSpectrum)

8189

{

8190

mprintf(" Performing fourier transformation...\n");

8191

8192

try { g_pFFT = new CFFT(); } catch(...) { g_pFFT = NULL; }

8193

if (g_pFFT == NULL) NewException((double)sizeof(CFFT),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8194

8195

/* if (o->m_pVACF->m_bMirror)

8196

g_pFFT->PrepareFFT_C2C((o->m_pVACF->m_iSize+o->m_pVACF->m_iZeroPadding)*2);

8197

else */g_pFFT->PrepareFFT_C2C(o->m_pVACF->m_iSize+o->m_pVACF->m_iZeroPadding);

8198

o->m_pVACF->Transform(g_pFFT);

8199

delete g_pFFT;

8200

o->m_pVACF->m_pSpectrum->SetMaxRWL(1E7f/299.792f/g_fTimestepLength/g_iStride);

8201

if (o->m_pVACF->m_bACF_DB)

8202

{

8203

mprintf(" Normalising spectrum to decibel...\n");

8204

o->m_pVACF->m_pSpectrum->MakeDB();

8205

}/* else

8206

{

8207

mprintf(" Normalising integral of spectrum...\n");

8208

o->m_pVACF->m_pSpectrum->SetIntegral(1000000.0f);

8209

}*/

8210

/* if (o->m_pVACF->m_bWindowFunction)

8211

{

8212

sprintf(buf,"power_%s_w%s.csv",o->m_pVACF->m_sName,multibuf);

8213

mprintf(" Saving spectrum as %s ...\n",buf);

8214

o->m_pVACF->m_pSpectrum->Write("",buf,"");

8215

} else

8216

{*/

8217

sprintf(buf,"power_%s%s.csv",o->m_pVACF->m_sName,multibuf);

8218

mprintf(" Saving spectrum as %s ...\n",buf);

8219

o->m_pVACF->m_pSpectrum->Write("",buf,"");

8220

// }

8221

}

8222

} // End IF VACF

8223

8224

if (g_bMSD)

8225

{

8226

mprintf(WHITE,"* Mean Square Displacement\n");

8227

if (g_bMSDCacheMode)

8228

{

8229

mprintf(" Autocorrelating cached vectors...\n");

8230

// mprintf(WHITE," [");

8231

// tfs = (((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms)/60.0;

8232

for (z2=0;z2<((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;z2++)

8233

{

8234

// if (fmod(z2,tfs) < 1.0)

8235

// mprintf(WHITE,"#");

8236

mprintf(" %4d/%d: [",z2+1,((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms);

8237

tfs = o->m_pMSD->m_iResolution/50.0;

8238

ptfa = (CxFloatArray*)o->m_pMSD->m_oaCache[z2];

8239

for (z3=0;z3<o->m_pMSD->m_iResolution;z3+=o->m_pMSD->m_iStride) // Das ist das Tau

8240

{

8241

if (fmod(z3,tfs) < 1.0)

8242

mprintf(WHITE,"#");

8243

tf = 0;

8244

8245

if (o->m_pMSD->m_bTakeX && o->m_pMSD->m_bTakeY && o->m_pMSD->m_bTakeZ)

8246

{

8247

for (z4=0;z4<(int)g_iSteps/g_iStride-z3-1;z4+=o->m_pMSD->m_iStride2) // Das ist der Startpunkt

8248

tf += pow((*ptfa)[(z3+z4)*3]-(*ptfa)[z4*3],2) + pow((*ptfa)[(z3+z4)*3+1]-(*ptfa)[z4*3+1],2) + pow((*ptfa)[(z3+z4)*3+2]-(*ptfa)[z4*3+2],2);

8249

} else

8250

{

8251

for (z4=0;z4<(int)g_iSteps/g_iStride-z3-1;z4+=o->m_pMSD->m_iStride2) // Das ist der Startpunkt

8252

{

8253

if (o->m_pMSD->m_bTakeX)

8254

tf += pow((*ptfa)[(z3+z4)*3]-(*ptfa)[z4*3],2);

8255

if (o->m_pMSD->m_bTakeY)

8256

tf += pow((*ptfa)[(z3+z4)*3+1]-(*ptfa)[z4*3+1],2);

8257

if (o->m_pMSD->m_bTakeZ)

8258

tf += pow((*ptfa)[(z3+z4)*3+2]-(*ptfa)[z4*3+2],2);

8259

}

8260

}

8261

8262

o->m_pMSD->m_pMSD->AddToBin_Index(z3/o->m_pMSD->m_iStride,tf/(g_iSteps/g_iStride-z3-1)*o->m_pMSD->m_iStride2);

8263

o->m_pMSD->m_pMSD->m_fBinEntries += (g_iSteps/g_iStride-z3-1)/o->m_pMSD->m_iStride2;

8264

if (o->m_pMSD->m_bSplit)

8265

{

8266

o->m_pMSD->m_pSplitMSD[z2]->AddToBin_Index(z3/o->m_pMSD->m_iStride,tf/(g_iSteps/g_iStride-z3-1)*o->m_pMSD->m_iStride2);

8267

o->m_pMSD->m_pSplitMSD[z2]->m_fBinEntries += (g_iSteps/g_iStride-z3-1)/o->m_pMSD->m_iStride2;

8268

}

8269

}

8270

mprintf("]\n");

8271

}

8272

for (z3=0;z3<o->m_pMSD->m_iResolution;z3+=o->m_pMSD->m_iStride) // Das ist das Tau

8273

o->m_pMSD->m_pMSD->m_pBin[z3/o->m_pMSD->m_iStride] /= ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()*o->m_pMSD->m_iShowAtoms;

8274

// mprintf(WHITE,"]\n");

8275

} else

8276

{

8277

o->m_pMSD->m_pMSD->BuildAverage();

8278

}

8279

mprintf(" %.0f bin entries.\n",o->m_pMSD->m_pMSD->m_fBinEntries);

8280

o->m_pMSD->m_pMSD->CalcDeriv(1.0f);

8281

sprintf(buf,"msd_%s%s.csv",o->m_pMSD->m_sName,multibuf);

8282

mprintf(" Saving result as %s ...\n",buf);

8283

if (o->m_pMSD->m_bSplit)

8284

{

8285

o->m_pMSD->WriteSplit(buf);

8286

} else o->m_pMSD->m_pMSD->Write("",buf,"");

8287

8288

o->m_pMSD->m_pMSD->LinReg(o->m_pMSD->m_pMSD->m_iResolution/2,o->m_pMSD->m_pMSD->m_iResolution-1,&c0,&c1,&r);

8289

mprintf(" MSD(t) = %.6f + %.6f * t (units: [MSD] = pm^2, [t] = ps).\n",c0,c1);

8290

mprintf(" R = %.6f\n",r);

8291

ti = 0;

8292

if (o->m_pMSD->m_bTakeX)

8293

ti++;

8294

if (o->m_pMSD->m_bTakeY)

8295

ti++;

8296

if (o->m_pMSD->m_bTakeZ)

8297

ti++;

8298

if (ti != 3)

8299

mprintf(" Please note: Dimensionality of the system is %d here.\n",ti);

8300

mprintf(" Diffusion coefficient D = %.6f pm^2/ps = %G m^2/s.\n",c1/2.0/ti,c1/2.0e12/ti);

8301

mprintf(" (assuming <x^2> = %d * D * t)\n\n",2*ti);

8302

} // END IF MSD

8303

8304

if (g_bNbAnalysis)

8305

{

8306

mprintf(WHITE,"* Neighborhood Analysis\n");

8307

mprintf(" %.0f bin entries.\n",o->m_pNbAnalysis->m_fBinEntries);

8308

/* for (z2=0;z2<o->m_pNbAnalysis->m_iMaxNbCount-o->m_pNbAnalysis->m_iMinNbCount;z2++)

8309

mprintf(" - %d: %.0f bin entries, %.0f skipped.\n",z2+1,((CDF*)o->m_pNbAnalysis->m_oaDF[z2])->m_fBinEntries,((CDF*)o->m_pNbAnalysis->m_oaDF[z2])->m_fSkipEntries);

8310

8311

8312

try { pf = new float[o->m_pNbAnalysis->m_iNbCount]; } catch(...) { pf = NULL; }

8313

if (pf == NULL) NewException((double)o->m_pNbAnalysis->m_iNbCount*sizeof(float),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8314

8315

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8316

pf[z3] = (float)((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->NormBinIntegral();

8317

8318

sprintf(buf,"nbh_ncf_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8319

mprintf(" Saving neighbor count function as %s ...\n",buf);

8320

a = OpenFileWrite(buf,true);

8321

mfprintf(a,"# distance [pm]; ");

8322

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount+1;z3++)

8323

{

8324

mfprintf(a,"%d neighbors",z3);

8325

if (z3 < o->m_pNbAnalysis->m_iNbCount)

8326

mfprintf(a,"; ");

8327

}

8328

mfprintf(a,"\n");

8329

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8330

{

8331

mfprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

8332

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount+1;z3++)

8333

{

8334

mfprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaNPF[z3])->m_pBin[z2]/o->m_pNbAnalysis->m_pNPFCount->m_pBin[z2]*100.0f);

8335

if (z3 < o->m_pNbAnalysis->m_iNbCount)

8336

mfprintf(a,"; ");

8337

}

8338

mfprintf(a,"\n");

8339

}

8340

fclose(a);

8341

8342

sprintf(buf,"nbh_dist_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8343

mprintf(" Calculating mean values and standard deviation...\n");

8344

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8345

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->CalcMeanSD();

8346

mprintf(" Saving neighborhood distribution as %s ...\n",buf);

8347

a = OpenFileWrite(buf,true);

8348

mfprintf(a,"# distance [pm]; ");

8349

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8350

{

8351

mfprintf(a,"%d. neighbor",z3+1);

8352

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8353

mfprintf(a,"; ");

8354

}

8355

mfprintf(a,"\n");

8356

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8357

{

8358

mfprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

8359

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8360

{

8361

mfprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

8362

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8363

mfprintf(a,"; ");

8364

}

8365

mfprintf(a,"\n");

8366

}

8367

fclose(a);

8368

8369

sprintf(buf,"nbh_minmaxavgsd_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8370

mprintf(" Saving neighborhood min/max/avg/sd as %s ...\n",buf);

8371

a = OpenFileWrite(buf,true);

8372

mfprintf(a,"# n-th neighbor; min. dist [pm]; max. dist [pm]; avg. dist [pm]; standard deviation [pm]\n");

8373

for (z2=0;z2<o->m_pNbAnalysis->m_iNbCount;z2++)

8374

{

8375

8376

mfprintf(a,"\n");

8377

}

8378

fclose(a);

8379

8380

sprintf(buf,"nbh_rdf_decomp_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8381

mprintf(" Saving neighborhood RDF decomposition as %s ...\n",buf);

8382

a = OpenFileWrite(buf,true);

8383

mfprintf(a,"# distance [pm]; ");

8384

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8385

{

8386

mfprintf(a,"%d. neighbor",z3+1);

8387

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8388

mfprintf(a,"; ");

8389

}

8390

mfprintf(a,"\n");

8391

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8392

{

8393

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->MultiplyBin(pf[z3]);

8394

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->CorrectRadialDist();

8395

}

8396

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8397

{

8398

8399

if (g_bDoubleBox)

8400

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->MultiplyBin(g_iDoubleBoxFactor);

8401

}

8402

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8403

{

8404

mfprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

8405

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8406

{

8407

mfprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

8408

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8409

mfprintf(a,"; ");

8410

}

8411

mfprintf(a,"\n");

8412

}

8413

fclose(a);

8414

8415

sprintf(buf,"nbh_rdf_decomp_cumulative_%s%s.csv",o->m_pNbAnalysis->m_sName,multibuf);

8416

mprintf(" Saving cumulative neighborhood RDF decomposition as %s ...\n",buf);

8417

a = OpenFileWrite(buf,true);

8418

mfprintf(a,"# distance [pm]; ");

8419

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8420

{

8421

mfprintf(a,"%d. neighbor",z3+1);

8422

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8423

mfprintf(a,"; ");

8424

}

8425

mfprintf(a,"\n");

8426

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8427

for (z3=1;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8428

((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2] += ((CDF*)o->m_pNbAnalysis->m_oaDF[z3-1])->m_pBin[z2];

8429

for (z2=0;z2<o->m_pNbAnalysis->m_iResolution;z2++)

8430

{

8431

mfprintf(a,"%.4f; ",o->m_pNbAnalysis->m_fMinDist+(z2+0.5)*(o->m_pNbAnalysis->m_fMaxDist-o->m_pNbAnalysis->m_fMinDist)/o->m_pNbAnalysis->m_iResolution);

8432

for (z3=0;z3<o->m_pNbAnalysis->m_iNbCount;z3++)

8433

{

8434

mfprintf(a,"%.6f",((CDF*)o->m_pNbAnalysis->m_oaDF[z3])->m_pBin[z2]);

8435

if (z3 < o->m_pNbAnalysis->m_iNbCount-1)

8436

mfprintf(a,"; ");

8437

}

8438

mfprintf(a,"\n");

8439

}

8440

fclose(a);

8441

delete[] pf;

8442

}

8443

8444

if (g_bDipDF)

8445

{

8446

for (zr=0;zr<g_iCDFChannels;zr++)

8447

{

8448

if (o->m_pDipDF[zr] == NULL)

8449

continue;

8450

mprintf(WHITE,"* Dipole Distribution Function\n");

8451

8452

o->m_pDipDF[zr]->m_pDipoleDF->CalcMeanSD();

8453

mprintf(" Mean value: %10G Debye Standard deviation: %10G Debye\n",o->m_pDipDF[zr]->m_pDipoleDF->m_fMean,o->m_pDipDF[zr]->m_pDipoleDF->m_fSD);

8454

mprintf(" Min. value: %10G Debye Max. value: %10G Debye\n",o->m_pDipDF[zr]->m_pDipoleDF->m_fMinInput,o->m_pDipDF[zr]->m_pDipoleDF->m_fMaxInput);

8455

o->m_pDipDF[zr]->m_pDipoleDF->NormBinIntegral();

8456

sprintf(buf,"dipole_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

8457

mprintf(" Saving dipole distribution as %s ...\n",buf);

8458

o->m_pDipDF[zr]->m_pDipoleDF->Write("",buf,"",false);

8459

sprintf(buf,"dipole_%s%s.agr",o->m_pDipDF[zr]->m_sName,multibuf);

8460

mprintf(" Saving dipole distribution AGR file as \"%s\"...\n",buf);

8461

o->m_pDipDF[zr]->m_pDipoleDF->WriteAgr("",buf,"",o->m_pDipDF[zr]->m_sName,false);

8462

if (o->m_pDipDF[zr]->m_iHistogramRes != 0)

8463

{

8464

mprintf(" Calculating Histogram...\n");

8465

o->m_pDipDF[zr]->m_pDipoleDF->CalcHistogram();

8466

sprintf(buf,"his_dipdf_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

8467

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8468

o->m_pDipDF[zr]->m_pDipoleDF->WriteHistogram("",buf,"");

8469

}

8470

if (o->m_bTimeDev)

8471

{

8472

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8473

{

8474

fclose(o->m_pDipDF[zr]->m_fDipole[0]);

8475

mprintf(" Saving temporal development as dipole_timedev_%s%s.csv\n",o->m_pDipDF[zr]->m_sName,multibuf);

8476

} else

8477

{

8478

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8479

{

8480

fclose(o->m_pDipDF[zr]->m_fDipole[z2]);

8481

mprintf(" Saving temporal development as dipole_timedev_%s_ref%d%s.csv\n",o->m_pDipDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8482

}

8483

}

8484

if (o->m_bCombinedPlot)

8485

{

8486

sprintf(buf,"combined_%s%s.agr",o->m_pDipDF[zr]->m_sName,multibuf);

8487

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8488

o->m_pDipDF[zr]->m_pDipoleDF->CreateCombinedPlot(false);

8489

o->m_pDipDF[zr]->m_pDipoleDF->m_pCombinedPlot->WriteAgr(buf,false);

8490

}

8491

} // END IF TIMEDEV

8492

8493

if (o->m_bObsCertain && o->m_bDecompDist)

8494

{

8495

sprintf(buf,"dipdf_decomp_%s%s.csv",o->m_pDipDF[zr]->m_sName,multibuf);

8496

mprintf(" Saving DipDF decomposition as \"%s\"...\n",buf);

8497

o->m_pDipDF[zr]->m_pDipoleDF->WriteMulti("",buf,"");

8498

sprintf(buf,"dipdf_decomp_%s%s_cumulative.csv",o->m_pDipDF[zr]->m_sName,multibuf);

8499

mprintf(" Saving cumulative DipoleDF decomposition as \"%s\"...\n",buf);

8500

o->m_pDipDF[zr]->m_pDipoleDF->WriteMulti_Cumulative("",buf,"");

8501

}

8502

8503

if (o->m_bTimeDiff)

8504

o->WriteTimeDiff(o->m_pDipDF[zr]->m_pDipoleDF,"DipDF","dipdf",o->m_pDipDF[zr]->m_sName,multibuf,false);

8505

}

8506

} // END IF DIPOLE

8507

8508

if (g_bVDF)

8509

{

8510

for (zr=0;zr<g_iCDFChannels;zr++)

8511

{

8512

if (o->m_pVDF[zr] == NULL)

8513

continue;

8514

mprintf(WHITE,"* Velocity Distribution Function\n");

8515

8516

o->m_pVDF[zr]->m_pVDF->CalcMeanSD();

8517

mprintf(" Mean value: %10G pm/ps Standard deviation: %10G pm/ps\n",o->m_pVDF[zr]->m_pVDF->m_fMean,o->m_pVDF[zr]->m_pVDF->m_fSD);

8518

mprintf(" Min. value: %10G pm/ps Max. value: %10G pm/ps\n",o->m_pVDF[zr]->m_pVDF->m_fMinInput,o->m_pVDF[zr]->m_pVDF->m_fMaxInput);

8519

o->m_pVDF[zr]->m_pVDF->NormBinIntegral();

8520

sprintf(buf,"vdf_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

8521

mprintf(" Saving velocity distribution as %s ...\n",buf);

8522

o->m_pVDF[zr]->m_pVDF->Write("",buf,"",false);

8523

sprintf(buf,"vdf_%s%s.agr",o->m_pVDF[zr]->m_sName,multibuf);

8524

mprintf(" Saving velocity distribution AGR file as \"%s\"...\n",buf);

8525

o->m_pVDF[zr]->m_pVDF->WriteAgr("",buf,"",o->m_pVDF[zr]->m_sName,false);

8526

if (o->m_pVDF[zr]->m_iHistogramRes != 0)

8527

{

8528

mprintf(" Calculating Histogram...\n");

8529

o->m_pVDF[zr]->m_pVDF->CalcHistogram();

8530

sprintf(buf,"his_vdf_%s%s.agr",o->m_pVDF[zr]->m_sName,multibuf);

8531

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8532

o->m_pVDF[zr]->m_pVDF->WriteHistogram("",buf,"");

8533

}

8534

if (o->m_bTimeDev)

8535

{

8536

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8537

{

8538

fclose(o->m_pVDF[zr]->m_fSpeed[0]);

8539

mprintf(" Saving temporal development as vdf_timedev_%s%s.csv\n",o->m_pVDF[zr]->m_sName,multibuf);

8540

} else

8541

{

8542

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8543

{

8544

fclose(o->m_pVDF[zr]->m_fSpeed[z2]);

8545

mprintf(" Saving temporal development as vdf_timedev_%s_ref%d%s.csv\n",o->m_pVDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8546

}

8547

}

8548

if (o->m_bCombinedPlot)

8549

{

8550

sprintf(buf,"combined_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

8551

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8552

o->m_pVDF[zr]->m_pVDF->CreateCombinedPlot(false);

8553

o->m_pVDF[zr]->m_pVDF->m_pCombinedPlot->WriteAgr(buf,false);

8554

}

8555

} // END IF TIMEDEV

8556

8557

if (o->m_bObsCertain && o->m_bDecompDist)

8558

{

8559

sprintf(buf,"vdf_decomp_%s%s.csv",o->m_pVDF[zr]->m_sName,multibuf);

8560

mprintf(" Saving VDF decomposition as \"%s\"...\n",buf);

8561

o->m_pVDF[zr]->m_pVDF->WriteMulti("",buf,"");

8562

sprintf(buf,"vdf_decomp_%s%s_cumulative.csv",o->m_pVDF[zr]->m_sName,multibuf);

8563

mprintf(" Saving cumulative VDF decomposition as \"%s\"...\n",buf);

8564

o->m_pVDF[zr]->m_pVDF->WriteMulti_Cumulative("",buf,"");

8565

}

8566

8567

if (o->m_bTimeDiff)

8568

o->WriteTimeDiff(o->m_pVDF[zr]->m_pVDF,"VDF","vdf",o->m_pVDF[zr]->m_sName,multibuf,false);

8569

}

8570

} // END IF VDF

8571

8572

if (g_bPlDF)

8573

{

8574

for (zr=0;zr<g_iCDFChannels;zr++)

8575

{

8576

if (o->m_pPlDF[zr] == NULL)

8577

continue;

8578

mprintf(WHITE,"* Plane Distance Distribution Function\n");

8579

8580

o->m_pPlDF[zr]->m_pPlDF->CalcMeanSD();

8581

mprintf(" Mean value: %10G pm/ps Standard deviation: %10G pm/ps\n",o->m_pPlDF[zr]->m_pPlDF->m_fMean,o->m_pPlDF[zr]->m_pPlDF->m_fSD);

8582

mprintf(" Min. value: %10G pm/ps Max. value: %10G pm/ps\n",o->m_pPlDF[zr]->m_pPlDF->m_fMinInput,o->m_pPlDF[zr]->m_pPlDF->m_fMaxInput);

8583

o->m_pPlDF[zr]->m_pPlDF->NormBinIntegral();

8584

sprintf(buf,"pldf_%s%s.csv",o->m_pPlDF[zr]->m_sName,multibuf);

8585

mprintf(" Saving plane distance distribution as %s ...\n",buf);

8586

o->m_pPlDF[zr]->m_pPlDF->Write("",buf,"",false);

8587

sprintf(buf,"pldf_%s%s.agr",o->m_pPlDF[zr]->m_sName,multibuf);

8588

mprintf(" Saving plane distance distribution AGR file as \"%s\"...\n",buf);

8589

o->m_pPlDF[zr]->m_pPlDF->WriteAgr("",buf,"",o->m_pPlDF[zr]->m_sName,false);

8590

if (o->m_pPlDF[zr]->m_iHistogramRes != 0)

8591

{

8592

mprintf(" Calculating Histogram...\n");

8593

o->m_pPlDF[zr]->m_pPlDF->CalcHistogram();

8594

sprintf(buf,"his_pldf_%s%s.agr",o->m_pPlDF[zr]->m_sName,multibuf);

8595

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8596

o->m_pPlDF[zr]->m_pPlDF->WriteHistogram("",buf,"");

8597

}

8598

}

8599

} // END IF PlDF

8600

8601

if (g_bLiDF)

8602

{

8603

for (zr=0;zr<g_iCDFChannels;zr++)

8604

{

8605

if (o->m_pLiDF[zr] == NULL)

8606

continue;

8607

mprintf(WHITE,"* Line Distance Distribution Function\n");

8608

8609

o->m_pLiDF[zr]->m_pLiDF->CalcMeanSD();

8610

mprintf(" Mean value: %10G pm/ps Standard deviation: %10G pm/ps\n",o->m_pLiDF[zr]->m_pLiDF->m_fMean,o->m_pLiDF[zr]->m_pLiDF->m_fSD);

8611

mprintf(" Min. value: %10G pm/ps Max. value: %10G pm/ps\n",o->m_pLiDF[zr]->m_pLiDF->m_fMinInput,o->m_pLiDF[zr]->m_pLiDF->m_fMaxInput);

8612

8613

if (o->m_pLiDF[zr]->m_bRadialCorrect)

8614

{

8615

mprintf(" Correcting radial distribution...\n");

8616

o->m_pLiDF[zr]->m_pLiDF->CorrectLiRadialDist();

8617

}

8618

if (o->m_bOthers && o->m_pLiDF[zr]->m_bRadialCorrect)

8619

{

8620

mprintf(" Scaling LiDF to uniform density...\n");

8621

if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)

8622

{

8623

if (o->m_bObsCertain)

8624

{

8625

o->m_pLiDF[zr]->m_pLiDF->Integrate(true,1.0 / g_iSteps / o->m_waObsRefList.GetSize());

8626

8627

} else

8628

{

8629

o->m_pLiDF[zr]->m_pLiDF->Integrate(true,1.0 / g_iSteps / (double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

8630

8631

}

8632

if (g_bDoubleBox)

8633

{

8634

o->m_pLiDF[zr]->m_pLiDF->MultiplyBin(g_iDoubleBoxFactor);

8635

o->m_pLiDF[zr]->m_pLiDF->MultiplyIntegral(g_iDoubleBoxFactor);

8636

}

8637

} else

8638

{

8639

eprintf(" Uniform density not defined if box is not XYZ-periodic!\n");

8640

goto _lidfint1;

8641

}

8642

} else

8643

{

8644

_lidfint1:

8645

mprintf(" Scaling LiDF to integral value 1000 ...\n");

8646

o->m_pLiDF[zr]->m_pLiDF->NormBinIntegral(1000.0);

8647

o->m_pLiDF[zr]->m_pLiDF->Integrate(false,1000.0);

8648

}

8649

8650

8651

o->m_pLiDF[zr]->m_pLiDF->NormBinIntegral();

8652

sprintf(buf,"lidf_%s%s.csv",o->m_pLiDF[zr]->m_sName,multibuf);

8653

mprintf(" Saving line distance distribution as %s ...\n",buf);

8654

o->m_pLiDF[zr]->m_pLiDF->Write("",buf,"",false);

8655

sprintf(buf,"lidf_%s%s.agr",o->m_pLiDF[zr]->m_sName,multibuf);

8656

mprintf(" Saving line distance distribution AGR file as \"%s\"...\n",buf);

8657

o->m_pLiDF[zr]->m_pLiDF->WriteAgr("",buf,"",o->m_pLiDF[zr]->m_sName,false);

8658

if (o->m_pLiDF[zr]->m_iHistogramRes != 0)

8659

{

8660

mprintf(" Calculating Histogram...\n");

8661

o->m_pLiDF[zr]->m_pLiDF->CalcHistogram();

8662

sprintf(buf,"his_lidf_%s%s.agr",o->m_pLiDF[zr]->m_sName,multibuf);

8663

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8664

o->m_pLiDF[zr]->m_pLiDF->WriteHistogram("",buf,"");

8665

}

8666

}

8667

} // END IF LiDF

8668

8669

if (g_bADF)

8670

{

8671

for (zr=0;zr<g_iCDFChannels;zr++)

8672

{

8673

if (o->m_pADF[zr] == NULL)

8674

continue;

8675

mprintf(WHITE,"* Angular Distribution Function\n");

8676

8677

o->m_pADF[zr]->m_pADF->CalcMeanSD();

8678

if (o->m_pADF[zr]->m_bCosine)

8679

{

8680

mprintf(" Mean value: %10G Standard deviation: %10G\n",o->m_pADF[zr]->m_pADF->m_fMean,o->m_pADF[zr]->m_pADF->m_fSD);

8681

mprintf(" Min. value: %10G Max. value: %10G\n",o->m_pADF[zr]->m_pADF->m_fMinInput,o->m_pADF[zr]->m_pADF->m_fMaxInput);

8682

} else

8683

{

8684

mprintf(" Mean value: %10G degree Standard deviation: %10G degree\n",o->m_pADF[zr]->m_pADF->m_fMean,o->m_pADF[zr]->m_pADF->m_fSD);

8685

mprintf(" Min. value: %10G degree Max. value: %10G degree\n",o->m_pADF[zr]->m_pADF->m_fMinInput,o->m_pADF[zr]->m_pADF->m_fMaxInput);

8686

}

8687

if (o->m_pADF[zr]->m_bStat)

8688

{

8689

mprintf(" Applying cone correction...\n");

8690

o->m_pADF[zr]->m_pADF->AngleCorrect();

8691

}

8692

/* if (o->m_pADF[zr]->m_bMirror)

8693

{

8694

mprintf(" Making ADF mirror-symmetric...\n");

8695

if (o->m_pADF[zr]->m_bCosine)

8696

o->m_pADF[zr]->m_pADF->Mirror(0.0f);

8697

else o->m_pADF[zr]->m_pADF->Mirror(90.0f);

8698

}*/

8699

o->m_pADF[zr]->m_pADF->NormBinIntegral();

8700

if (o->m_bTimeDev)

8701

{

8702

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8703

{

8704

fclose(o->m_pADF[zr]->m_fAngle[0]);

8705

mprintf(" Saving temporal development as adf_timedev_%s%s.csv\n",o->m_pADF[zr]->m_sName,multibuf);

8706

} else

8707

{

8708

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8709

{

8710

fclose(o->m_pADF[zr]->m_fAngle[z2]);

8711

sprintf(buf,"adf_timedev_%s_ref%d%s.csv",o->m_pADF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8712

mprintf(" Saving temporal development as %s\n",buf);

8713

}

8714

}

8715

// mprintf(" Speichere Winkel-Statistik als %s_angle_stat.txt\n",o->m_pADF->m_sName);

8716

// FreeFileName("",o->m_pADF->m_sName,"_angle_stat.txt");

8717

// o->m_pADF->m_pAngleStat->Evaluate();

8718

// o->m_pADF->m_pAngleStat->Write("",o->m_pADF->m_sName,"_angle_stat.txt");

8719

// delete o->m_pAngleStat;

8720

delete[] o->m_pADF[zr]->m_fAngle;

8721

o->m_pADF[zr]->m_fAngle = NULL;

8722

if (o->m_bCombinedPlot)

8723

{

8724

sprintf(buf,"combined_%s%s.agr",o->m_pADF[zr]->m_sName,multibuf);

8725

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8726

o->m_pADF[zr]->m_pADF->CreateCombinedPlot(false);

8727

o->m_pADF[zr]->m_pADF->m_pCombinedPlot->WriteAgr(buf,false);

8728

}

8729

} // END IF TIMEDEV

8730

sprintf(buf,"adf_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

8731

mprintf(" Saving ADF as %s ...\n",buf);

8732

o->m_pADF[zr]->m_pADF->NormBinIntegral();

8733

o->m_pADF[zr]->m_pADF->Write("",buf,"",false);

8734

sprintf(buf,"adf_%s%s.agr",o->m_pADF[zr]->m_sName,multibuf);

8735

mprintf(" Saving ADF AGR file as \"%s\"...\n",buf);

8736

if (o->m_pADF[zr]->m_bCosine)

8737

o->m_pADF[zr]->m_pADF->WriteAgr("",buf,"",o->m_pADF[zr]->m_sName,false);

8738

else o->m_pADF[zr]->m_pADF->WriteAgr("",buf,"",o->m_pADF[zr]->m_sName,false);

8739

if (o->m_pADF[zr]->m_iHistogramRes != 0)

8740

{

8741

mprintf(" Calculating Histogram...\n");

8742

o->m_pADF[zr]->m_pADF->CalcHistogram();

8743

sprintf(buf,"his_adf_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

8744

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8745

o->m_pADF[zr]->m_pADF->WriteHistogram("",buf,"");

8746

}

8747

8748

if (o->m_bObsCertain && o->m_bDecompDist)

8749

{

8750

sprintf(buf,"adf_decomp_%s%s.csv",o->m_pADF[zr]->m_sName,multibuf);

8751

mprintf(" Saving ADF decomposition as \"%s\"...\n",buf);

8752

o->m_pADF[zr]->m_pADF->WriteMulti("",buf,"");

8753

sprintf(buf,"adf_decomp_%s%s_cumulative.csv",o->m_pADF[zr]->m_sName,multibuf);

8754

mprintf(" Saving cumulative ADF decomposition as \"%s\"...\n",buf);

8755

o->m_pADF[zr]->m_pADF->WriteMulti_Cumulative("",buf,"");

8756

}

8757

8758

if (o->m_bTimeDiff)

8759

o->WriteTimeDiff(o->m_pADF[zr]->m_pADF,"ADF","adf",o->m_pADF[zr]->m_sName,multibuf,false);

8760

}

8761

} // END IF ADF

8762

8763

if (g_bDDF)

8764

{

8765

for (zr=0;zr<g_iCDFChannels;zr++)

8766

{

8767

if (o->m_pDDF[zr] == NULL)

8768

continue;

8769

mprintf(WHITE,"* Dihedral Distribution Function\n");

8770

8771

o->m_pDDF[zr]->m_pDDF->CalcMeanSD();

8772

if (o->m_pDDF[zr]->m_bCosine)

8773

{

8774

mprintf(" Mean value: %10G Standard deviation: %10G\n",o->m_pDDF[zr]->m_pDDF->m_fMean,o->m_pDDF[zr]->m_pDDF->m_fSD);

8775

mprintf(" Min. value: %10G Max.value: %10G\n",o->m_pDDF[zr]->m_pDDF->m_fMinInput,o->m_pDDF[zr]->m_pDDF->m_fMaxInput);

8776

} else

8777

{

8778

mprintf(" Mean value: %10G degree Standard deviation: %10G degree\n",o->m_pDDF[zr]->m_pDDF->m_fMean,o->m_pDDF[zr]->m_pDDF->m_fSD);

8779

mprintf(" Min. value: %10G degree Max.value: %10G degree\n",o->m_pDDF[zr]->m_pDDF->m_fMinInput,o->m_pDDF[zr]->m_pDDF->m_fMaxInput);

8780

}

8781

if (o->m_bTimeDev)

8782

{

8783

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8784

{

8785

fclose(o->m_pDDF[zr]->m_fAngle[0]);

8786

mprintf(" Saving temporal development as ddf_timedev_%s%s.csv\n",o->m_pDDF[zr]->m_sName,multibuf);

8787

} else

8788

{

8789

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8790

{

8791

fclose(o->m_pDDF[zr]->m_fAngle[z2]);

8792

sprintf(buf,"ddf_timedev_%s_ref%d%s.csv",o->m_pDDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8793

mprintf(" Saving temporal development as %s\n",buf);

8794

}

8795

}

8796

/* mprintf(" Speichere Winkel-Statistik als %s_angle_stat.txt\n",o->m_sName);

8797

FreeFileName("",o->m_sName,"_angle_stat.txt");

8798

o->m_pAngleStat->Evaluate();

8799

o->m_pAngleStat->Write("",o->m_sName,"_angle_stat.txt");

8800

// delete o->m_pAngleStat;*/

8801

delete[] o->m_pDDF[zr]->m_fAngle;

8802

o->m_pDDF[zr]->m_fAngle = NULL;

8803

if (o->m_bCombinedPlot)

8804

{

8805

sprintf(buf,"combined_%s%s.agr",o->m_pDDF[zr]->m_sName,multibuf);

8806

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8807

o->m_pDDF[zr]->m_pDDF->CreateCombinedPlot(false);

8808

o->m_pDDF[zr]->m_pDDF->m_pCombinedPlot->WriteAgr(buf,false);

8809

}

8810

} // END IF TIMEDEV

8811

/* if (o->m_pDDF->m_iStat != 0)

8812

{

8813

mprintf(" Korrigiere statistische Verteilung...\n");

8814

o->m_pDDF->m_pDDF->AngleCorrect();

8815

}*/

8816

sprintf(buf,"ddf_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

8817

mprintf(" Saving DDF as %s ...\n",buf);

8818

o->m_pDDF[zr]->m_pDDF->NormBinIntegral();

8819

o->m_pDDF[zr]->m_pDDF->Write("",buf,"",false);

8820

sprintf(buf,"ddf_%s%s.agr",o->m_pDDF[zr]->m_sName,multibuf);

8821

mprintf(" Saving DDF AGR file as \"%s\"...\n",buf);

8822

if (o->m_pDDF[zr]->m_bCosine)

8823

o->m_pDDF[zr]->m_pDDF->WriteAgr("",buf,"",o->m_pDDF[zr]->m_sName,false);

8824

else o->m_pDDF[zr]->m_pDDF->WriteAgr("",buf,"",o->m_pDDF[zr]->m_sName,false);

8825

if (o->m_pDDF[zr]->m_iHistogramRes != 0)

8826

{

8827

mprintf(" Calculating Histogram...\n");

8828

o->m_pDDF[zr]->m_pDDF->CalcHistogram();

8829

sprintf(buf,"his_ddf_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

8830

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8831

o->m_pDDF[zr]->m_pDDF->WriteHistogram("",buf,"");

8832

}

8833

8834

if (o->m_bObsCertain && o->m_bDecompDist)

8835

{

8836

sprintf(buf,"ddf_decomp_%s%s.csv",o->m_pDDF[zr]->m_sName,multibuf);

8837

mprintf(" Saving DDF decomposition as \"%s\"...\n",buf);

8838

o->m_pDDF[zr]->m_pDDF->WriteMulti("",buf,"");

8839

sprintf(buf,"ddf_decomp_%s%s_cumulative.csv",o->m_pDDF[zr]->m_sName,multibuf);

8840

mprintf(" Saving cumulative DDF decomposition as \"%s\"...\n",buf);

8841

o->m_pDDF[zr]->m_pDDF->WriteMulti_Cumulative("",buf,"");

8842

}

8843

8844

if (o->m_bTimeDiff)

8845

o->WriteTimeDiff(o->m_pDDF[zr]->m_pDDF,"DDF","ddf",o->m_pDDF[zr]->m_sName,multibuf,true);

8846

}

8847

} // END IF DDF

8848

8849

if (g_bSDF)

8850

{

8851

mprintf(WHITE,"* Spatial Distribution Function\n");

8852

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pSDF->m_pSDF->m_fBinEntries,o->m_pSDF->m_pSDF->m_fSkipEntries,ZeroDivide(o->m_pSDF->m_pSDF->m_fSkipEntries,o->m_pSDF->m_pSDF->m_fBinEntries+o->m_pSDF->m_pSDF->m_fSkipEntries)*100.0);

8853

o->m_pSDF->m_pSDF->CalcMaxEntry();

8854

mprintf(" Raw data range from %.0f to %.0f hits.\n",o->m_pSDF->m_pSDF->m_fMinEntry,o->m_pSDF->m_pSDF->m_fMaxEntry);

8855

mprintf(" The volume of one bin is %.3f pm^3.\n",pow(o->m_pSDF->m_fRadius*2.0/o->m_pSDF->m_iResolution,3));

8856

if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)

8857

mprintf(" The uniform particle density of this observation is %.6f nm^-3.\n",o->m_pSDF->m_fParticleDensity);

8858

else mprintf(" The uniform particle density of non-periodic boxes is not defined.\n");

8859

/* switch(g_iSDFScale)

8860

{

8861

case 0:

8862

mprintf(" Scaling values to ppm...\n");

8863

o->m_pSDF->m_pSDF->MultiplyBin(1000000.0 / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

8864

break;

8865

case 1:

8866

mprintf(" Scaling values to pm^-3...\n");

8867

o->m_pSDF->m_pSDF->MultiplyBin(pow(o->m_pSDF->m_iResolution/o->m_pSDF->m_fRadius,3) / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

8868

break;

8869

case 2:

8870

mprintf(" Scaling values to nm^-3...\n");*/

8871

/* break;

8872

case 3:

8873

mprintf(" Scaling values relative to average particle density...\n");

8874

o->m_pSDF->m_pSDF->MultiplyBin(pow(o->m_pSDF->m_iResolution/o->m_pSDF->m_fRadius*1000.0,3) / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes / o->m_pSDF->m_fParticleDensity * (g_bDoubleBox?g_iDoubleBoxFactor:1));

8875

break;

8876

}*/

8877

8878

o->m_pSDF->m_pSDF->MultiplyBin(pow(o->m_pSDF->m_iResolution/o->m_pSDF->m_fRadius/2.0*1000.0,3) / (double)g_iSteps * g_iStride / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

8879

8880

if (g_bSDFUniform)

8881

{

8882

if ((!g_bPeriodicX) || (!g_bPeriodicY) || (!g_bPeriodicZ))

8883

goto _sdf_nm;

8884

o->m_pSDF->m_pSDF->MultiplyBin(1.0/o->m_pSDF->m_fParticleDensity);

8885

mprintf(WHITE," Bin values are given relative to this uniform particle density.\n");

8886

} else

8887

{

8888

_sdf_nm:

8889

mprintf(WHITE," Bin values are given in nm^-3 (particle density).\n");

8890

}

8891

o->m_pSDF->m_pSDF->CalcMaxEntry();

8892

mprintf(" Data range from %.6f to %.6f%s.\n",o->m_pSDF->m_pSDF->m_fMinEntry,o->m_pSDF->m_pSDF->m_fMaxEntry,g_bSDFUniform?"":" nm^-3");

8893

8894

if (o->m_pSDF->m_bInvert)

8895

{

8896

mprintf(" Inverting SDF...\n");

8897

o->m_pSDF->m_pSDF->Invert();

8898

}

8899

if (o->m_pSDF->m_bCutPlane)

8900

{

8901

mprintf(" Creating Cut Plane...\n");

8902

o->m_pSDF->CreateCutPlane();

8903

sprintf(buf,"sdf_cut_%s%s",o->m_pSDF->m_sName,multibuf);

8904

mprintf(" Saving SDF Cut Plane triples as \"%s_triples.csv\"...\n",buf);

8905

o->m_pSDF->m_pCutPlane->Write("",buf,"_triples.csv");

8906

mprintf(" Saving SDF Cut Plane matrix as \"%s_matrix.csv\"...\n",buf);

8907

o->m_pSDF->m_pCutPlane->WriteCSV("",buf,"_matrix.csv");

8908

mprintf(" Saving CDF Mathematica Notebook as \"%s.nb\"...\n",buf);

8909

o->m_pSDF->m_pCutPlane->WriteMathematicaNb("",buf,".nb",false);

8910

mprintf(" Saving CDF Gnuplot Input as \"%s.gp\"...\n",buf);

8911

o->m_pSDF->m_pCutPlane->WriteGnuplotInput("",buf,"",false);

8912

}

8913

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

8914

{

8915

try { tempSDF = new C3DF(); } catch(...) { tempSDF = NULL; }

8916

if (tempSDF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8917

8918

tempSDF->CopyFrom(o->m_pSDF->m_pSDF);

8919

8920

if (z2 != 0)

8921

tempSDF->Smooth(z2);

8922

8923

tempSDF->CalcMaxEntry();

8924

mprintf(" Data range from %.6f to %.6f%s.\n",tempSDF->m_fMinEntry,tempSDF->m_fMaxEntry,g_bSDFUniform?"":" nm^-3");

8925

if (o->m_pSDF->m_bClipPlane)

8926

{

8927

mprintf(" Creating Clip Plane in %c direction with value %.3f...\n",(o->m_pSDF->m_iClipDirection==0)?'X':((o->m_pSDF->m_iClipDirection==1)?'Y':'Z'),o->m_pSDF->m_fClipValue);

8928

o->m_pSDF->m_pSDF->ClipPlane(o->m_pSDF->m_iClipDirection,o->m_pSDF->m_fClipValue);

8929

}

8930

8931

if (g_pDatabase->GetBool("/PLOT3D/FORMATS/WRITE_PLT"))

8932

{

8933

if (z2 != 0)

8934

sprintf(buf,".s%d%s.plt",z2,multibuf);

8935

else sprintf(buf,"%s.plt",multibuf);

8936

mprintf(" Saving SDF as \"sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

8937

tempSDF->WritePLT("sdf_",o->m_pSDF->m_sName,buf,true);

8938

}

8939

8940

if (g_pDatabase->GetBool("/PLOT3D/FORMATS/WRITE_CUBE"))

8941

{

8942

if (z2 != 0)

8943

sprintf(buf,".s%d%s.cube",z2,multibuf);

8944

else sprintf(buf,"%s.cube",multibuf);

8945

mprintf(" Saving SDF as \"sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

8946

tempSDF->WriteCube("sdf_",o->m_pSDF->m_sName,buf,true);

8947

}

8948

8949

if (o->m_pSDF->m_iHistogramRes != 0)

8950

{

8951

if (z2 != 0)

8952

sprintf(buf,".s%d%s.csv",z2,multibuf);

8953

else sprintf(buf,"%s.csv",multibuf);

8954

mprintf(" Saving SDF Histogram as \"his_sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

8955

tempSDF->CalcHistogram();

8956

tempSDF->WriteHistogram("his_sdf_",o->m_pSDF->m_sName,buf);

8957

}

8958

}

8959

mprintf(YELLOW,"\n Important: ");

8960

mprintf(WHITE,"The PLT/CUBE files only contain the volumetric data.\n");

8961

mprintf(WHITE," The atoms of the reference molecule are saved in the ref_*.xyz file!\n");

8962

mprintf(WHITE," You need to load *both files* into the visualization program (e.g. VMD).\n");

8963

} // END IF SDF

8964

8965

if (g_bPlProj)

8677

8966

{

8678

mprintf(WHITE,"* Spatial Distribution Function\n");

8679

8680

o->m_pSDF->m_pSDF->CalcMaxEntry();

8681

mprintf(" Raw data range from %.0f to %.0f hits.\n",o->m_pSDF->m_pSDF->m_fMinEntry,o->m_pSDF->m_pSDF->m_fMaxEntry);

8682

mprintf(" The volume of one bin is %.3f pm^3.\n",pow(o->m_pSDF->m_fRadius*2.0/o->m_pSDF->m_iResolution,3));

8683

if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)

8684

mprintf(" The uniform particle density of this observation is %.6f nm^-3.\n",o->m_pSDF->m_fParticleDensity);

8685

mprintf(" The uniform particle density of non-periodic boxes is not defined.\n");

8686

/* switch(g_iSDFScale)

8687

{

8688

case 0:

8689

mprintf(" Scaling values to ppm...\n");

8690

o->m_pSDF->m_pSDF->MultiplyBin(1000000.0 / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

8691

break;

8692

case 1:

8693

mprintf(" Scaling values to pm^-3...\n");

8694

8695

break;

8696

case 2:

8697

mprintf(" Scaling values to nm^-3...\n");*/

8698

/* break;

8699

case 3:

8700

mprintf(" Scaling values relative to average particle density...\n");

8701

8702

break;

8703

}*/

8704

8705

o->m_pSDF->m_pSDF->MultiplyBin(pow(o->m_pSDF->m_iResolution/o->m_pSDF->m_fRadius/2.0*1000.0,3) / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pSDF->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

8706

8707

if (g_bSDFUniform)

8708

{

8709

if ((!g_bPeriodicX) || (!g_bPeriodicY) || (!g_bPeriodicZ))

8710

goto _sdf_nm;

8711

o->m_pSDF->m_pSDF->MultiplyBin(1.0/o->m_pSDF->m_fParticleDensity);

8712

mprintf(WHITE," Bin values are given relative to this uniform particle density.\n");

8713

} else

8714

{

8715

_sdf_nm:

8716

mprintf(WHITE," Bin values are given in nm^-3 (particle density).\n");

8717

}

8718

o->m_pSDF->m_pSDF->CalcMaxEntry();

8719

mprintf(" Data range from %.6f to %.6f%s.\n",o->m_pSDF->m_pSDF->m_fMinEntry,o->m_pSDF->m_pSDF->m_fMaxEntry,g_bSDFUniform?"":" nm^-3");

8720

8721

if (o->m_pSDF->m_bInvert)

8722

{

8723

mprintf(" Inverting SDF...\n");

8724

o->m_pSDF->m_pSDF->Invert();

8725

}

8726

if (o->m_pSDF->m_bCutPlane)

8727

{

8728

mprintf(" Creating Cut Plane...\n");

8729

o->m_pSDF->CreateCutPlane();

8730

sprintf(buf,"sdf_cut_%s%s",o->m_pSDF->m_sName,multibuf);

8731

mprintf(" Saving SDF Cut Plane triples as \"%s_triples.csv\"...\n",buf);

8732

o->m_pSDF->m_pCutPlane->Write("",buf,"_triples.csv");

8733

mprintf(" Saving SDF Cut Plane matrix as \"%s_matrix.csv\"...\n",buf);

8734

o->m_pSDF->m_pCutPlane->WriteCSV("",buf,"_matrix.csv");

8735

mprintf(" Saving CDF Mathematica Notebook as \"%s.nb\"...\n",buf);

8736

o->m_pSDF->m_pCutPlane->WriteMathematicaNb("",buf,".nb",false);

8737

mprintf(" Saving CDF Gnuplot Input as \"%s.gp\"...\n",buf);

8738

o->m_pSDF->m_pCutPlane->WriteGnuplotInput("",buf,"",false);

8739

}

8740

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

8741

{

8742

try { tempSDF = new C3DF(); } catch(...) { tempSDF = NULL; }

8743

if (tempSDF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

8744

8745

tempSDF->CopyFrom(o->m_pSDF->m_pSDF);

8746

8747

if (z2 != 0)

8748

tempSDF->Smooth(z2);

8749

8750

tempSDF->CalcMaxEntry();

8751

mprintf(" Data range from %.6f to %.6f%s.\n",tempSDF->m_fMinEntry,tempSDF->m_fMaxEntry,g_bSDFUniform?"":" nm^-3");

8752

if (o->m_pSDF->m_bClipPlane)

8753

{

8754

mprintf(" Creating Clip Plane in %c direction with value %.3f...\n",(o->m_pSDF->m_iClipDirection==0)?'X':((o->m_pSDF->m_iClipDirection==1)?'Y':'Z'),o->m_pSDF->m_fClipValue);

8755

o->m_pSDF->m_pSDF->ClipPlane(o->m_pSDF->m_iClipDirection,o->m_pSDF->m_fClipValue);

8756

}

8757

8758

if (g_pDatabase->GetBool("/PLOT3D/FORMATS/WRITE_PLT"))

8759

{

8760

if (z2 != 0)

8761

sprintf(buf,".s%d%s.plt",z2,multibuf);

8762

else sprintf(buf,"%s.plt",multibuf);

8763

mprintf(" Saving SDF as \"sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

8764

tempSDF->WritePLT("sdf_",o->m_pSDF->m_sName,buf,true);

8765

}

8766

8767

if (g_pDatabase->GetBool("/PLOT3D/FORMATS/WRITE_CUBE"))

8768

{

8769

if (z2 != 0)

8770

sprintf(buf,".s%d%s.cube",z2,multibuf);

8771

else sprintf(buf,"%s.cube",multibuf);

8772

mprintf(" Saving SDF as \"sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

8773

tempSDF->WriteCube("sdf_",o->m_pSDF->m_sName,buf,true);

8774

}

8775

8776

if (o->m_pSDF->m_iHistogramRes != 0)

8777

{

8778

if (z2 != 0)

8779

sprintf(buf,".s%d%s.csv",z2,multibuf);

8780

else sprintf(buf,"%s.csv",multibuf);

8781

mprintf(" Saving SDF Histogram as \"his_sdf_%s%s\"...\n",o->m_pSDF->m_sName,buf);

8782

tempSDF->CalcHistogram();

8783

tempSDF->WriteHistogram("his_sdf_",o->m_pSDF->m_sName,buf);

8784

}

8785

}

8786

mprintf(YELLOW,"\n Important: ");

8787

mprintf(WHITE,"The PLT/CUBE files only contain the volumetric data.\n");

8788

mprintf(WHITE," The atoms of the reference molecule are saved in the ref_*.xyz file!\n");

8789

mprintf(WHITE," You need to load *both files* into the visualization program (e.g. VMD).\n");

8790

} // END IF SDF

8791

8792

if (g_bRDF)

8793

{

8794

for (zr=0;zr<g_iCDFChannels;zr++)

8795

{

8796

if (o->m_pRDF[zr] == NULL)

8797

continue;

8798

mprintf(WHITE,"* Radial Distribution Function\n");

8799

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pRDF[zr]->m_pRDF->m_fBinEntries,o->m_pRDF[zr]->m_pRDF->m_fSkipEntries,ZeroDivide(o->m_pRDF[zr]->m_pRDF->m_fSkipEntries,o->m_pRDF[zr]->m_pRDF->m_fBinEntries+o->m_pRDF[zr]->m_pRDF->m_fSkipEntries)*100.0);

8800

o->m_pRDF[zr]->m_pRDF->CalcMeanSD();

8801

mprintf(" Mean value: %10G pm Standard deviation: %10G pm\n",o->m_pRDF[zr]->m_pRDF->m_fMean,o->m_pRDF[zr]->m_pRDF->m_fSD);

8802

mprintf(" Min. value: %10G pm Max.value: %10G pm\n",o->m_pRDF[zr]->m_pRDF->m_fMinInput,o->m_pRDF[zr]->m_pRDF->m_fMaxInput);

8803

8804

o->m_pRDF[zr]->m_pRDF->MultiplyBin(1.0 / g_iSteps);

8805

8806

if (o->m_pRDF[zr]->m_bCalcSD)

8807

{

8808

mprintf(GREEN,"\n>>> Standard Deviation Engine >>>\n\n");

8809

o->m_pRDF[zr]->m_pRDF->m_pSDEngine->FinishAnalysis();

8810

o->m_pRDF[zr]->m_pRDF->m_pSDEngine->DumpData(o->m_pRDF[zr]->m_pRDF,o->m_pRDF[zr]->m_fSDTimesSigma,o->m_pRDF[zr]->m_bSDVerbose);

8811

mprintf(GREEN,"\n<<< Standard Deviation Engine <<<\n\n");

8812

}

8813

if (o->m_pRDF[zr]->m_bAdaptive)

8814

{

8815

// o->m_pRDF[zr]->m_pRDF->WriteHenry("rdf_",o->m_pRDF[zr]->m_sName,".csv");

8816

o->m_pRDF[zr]->m_pRDF->PrepareAdapt();

8817

o->m_pRDF[zr]->m_pRDF->BinTree_RadialDist();

8818

if (o->m_iShowMol == g_iFixMol)

8819

o->m_pRDF[zr]->m_pRDF->BinTree_MultiplyBin(3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/(((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()-1.0f)/o->m_pRDF[zr]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[zr]->m_iRefAtomGes);

8820

else o->m_pRDF[zr]->m_pRDF->BinTree_MultiplyBin(3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() /o->m_pRDF[zr]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[zr]->m_iRefAtomGes);

8821

8822

mprintf(" Saving RDF as \"rdf_%s.csv\"...\n",o->m_pRDF[zr]->m_sName);

8823

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".001.csv",5,10,0.001,true);

8824

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".002.csv",5,10,0.002,true);

8825

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".005.csv",5,10,0.005,true);

8826

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".010.csv",5,10,0.01,true);

8827

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".020.csv",5,10,0.02,true);

8828

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".050.csv",5,10,0.05,true);

8829

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".100.csv",5,10,0.1,true);

8830

8831

/* o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".50.csv",16,0,50,true);

8832

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".100.csv",16,0,100,true);

8833

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".500.csv",16,0,500,true);

8834

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".1000.csv",16,0,1000,true);*/

8835

} else

8836

{

8837

if (o->m_pRDF[zr]->m_bRadialCorrect)

8838

{

8839

mprintf(" Correcting radial distribution...\n");

8840

o->m_pRDF[zr]->m_pRDF->CorrectRadialDist();

8841

}

8842

if (o->m_bOthers && o->m_pRDF[zr]->m_bRadialCorrect)

8843

{

8844

if (o->m_pRDF[zr]->m_bProbDens)

8845

{

8846

mprintf(" Scaling RDF to nm^(-3) ...\n");

8847

if (o->m_bObsCertain)

8848

{

8849

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / o->m_waObsRefList.GetSize());

8850

o->m_pRDF[zr]->m_pRDF->MultiplyBin(1e9 / (4.0/3.0*Pi) / o->m_waObsRefList.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

8851

} else

8852

{

8853

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / (double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

8854

o->m_pRDF[zr]->m_pRDF->MultiplyBin(1e9 / (4.0/3.0*Pi) / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

8855

}

8856

if (g_bDoubleBox)

8857

{

8858

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_iDoubleBoxFactor);

8859

o->m_pRDF[zr]->m_pRDF->MultiplyIntegral(g_iDoubleBoxFactor);

8860

}

8861

} else

8862

{

8863

mprintf(" Scaling RDF to uniform density ...\n");

8864

if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)

8865

{

8866

if (o->m_bObsCertain)

8867

{

8868

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / o->m_waObsRefList.GetSize());

8869

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / o->m_waObsRefList.GetSize() / o->m_pRDF[zr]->m_iShowAtomGes / o->m_waObsShowList.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

8870

} else

8871

{

8872

if (g_bRegionAnalysis)

8873

{

8874

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 * g_iSteps / (o->m_pRDF[zr]->m_pRDF->m_fBinEntries + o->m_pRDF[zr]->m_pRDF-> m_fSkipEntries) * o->m_pRDF[zr]->m_iShowAtomGes * ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() * o->m_pRDF[zr]->m_iRefAtomGes);

8875

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ * g_iSteps / (4.0/3.0*Pi) / (o->m_pRDF[zr]->m_pRDF->m_fBinEntries + o->m_pRDF[zr]->m_pRDF-> m_fSkipEntries) );

8876

} else

8877

{

8878

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / (double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

8879

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pRDF[zr]->m_iShowAtomGes / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

8880

}

8881

}

8882

if (g_bDoubleBox)

8883

{

8884

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_iDoubleBoxFactor);

8885

o->m_pRDF[zr]->m_pRDF->MultiplyIntegral(g_iDoubleBoxFactor);

8886

}

8887

} else

8888

{

8889

eprintf(" Uniform density not defined if box is not XYZ-periodic!\n");

8890

goto _rdfint1;

8891

}

8892

}

8893

} else

8894

{

8895

_rdfint1:

8896

mprintf(" Scaling RDF to integral value 1000 ...\n");

8897

o->m_pRDF[zr]->m_pRDF->NormBinIntegral(1000.0);

8898

o->m_pRDF[zr]->m_pRDF->Integrate(false,1000.0);

8899

}

8900

sprintf(buf,"rdf_%s%s.csv",o->m_pRDF[zr]->m_sName,multibuf);

8901

mprintf(" Saving RDF as \"%s\"...\n",buf);

8902

o->m_pRDF[zr]->m_pRDF->Write("",buf,"",true);

8903

sprintf(buf,"rdf_%s%s.agr",o->m_pRDF[zr]->m_sName,multibuf);

8904

mprintf(" Saving RDF AGR file as \"%s\"...\n",buf);

8905

o->m_pRDF[zr]->m_pRDF->WriteAgr("",buf,"",o->m_pRDF[zr]->m_sName,true);

8906

if (o->m_pRDF[zr]->m_iHistogramRes != 0)

8907

{

8908

mprintf(" Calculating Histogram...\n");

8909

o->m_pRDF[zr]->m_pRDF->CalcHistogram();

8910

sprintf(buf,"his_rdf_%s%s.csv",o->m_pRDF[zr]->m_sName,multibuf);

8911

mprintf(" Saving Histogram as \"%s\"...\n",buf);

8912

o->m_pRDF[zr]->m_pRDF->WriteHistogram("",buf,"");

8913

}

8914

if (o->m_bObsCertain && o->m_bDecompDist)

8915

{

8916

sprintf(buf,"rdf_decomp_mol_%s%s",o->m_pRDF[zr]->m_sName,multibuf);

8917

mprintf(" Saving RDF molecule decomposition as \"%s.csv\"...\n",buf);

8918

o->m_pRDF[zr]->m_pRDF->WriteMulti("",buf,".csv");

8919

mprintf(" Saving RDF molecule decomposition as \"%s.agr\"...\n",buf);

8920

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr("",buf,".agr",buf,true);

8921

8922

sprintf(buf,"rdf_decomp_nb_%s%s_cumulative",o->m_pRDF[zr]->m_sName,multibuf);

8923

mprintf(" Saving cumulative RDF molecule decomposition as \"%s.csv\"...\n",buf);

8924

o->m_pRDF[zr]->m_pRDF->WriteMulti_Cumulative("",buf,".csv");

8925

mprintf(" Saving cumulative RDF molecule decomposition as \"%s.agr\"...\n",buf);

8926

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr_Cumulative("",buf,".agr",buf,true);

8927

}

8928

if (o->m_bDecompType)

8929

{

8930

sprintf(buf,"rdf_decomp_type_%s%s",o->m_pRDF[zr]->m_sName,multibuf);

8931

mprintf(" Saving RDF type decomposition as \"%s.csv\"...\n",buf);

8932

o->m_pRDF[zr]->m_pRDF->WriteMulti("",buf,".csv");

8933

mprintf(" Saving RDF type decomposition as \"%s.agr\"...\n",buf);

8934

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr("",buf,".agr",buf,true);

8935

8936

sprintf(buf,"rdf_decomp_type_%s%s_cumulative",o->m_pRDF[zr]->m_sName,multibuf);

8937

mprintf(" Saving cumulative RDF type decomposition as \"%s.csv\"...\n",buf);

8938

o->m_pRDF[zr]->m_pRDF->WriteMulti_Cumulative("",buf,".csv");

8939

mprintf(" Saving cumulative RDF type decomposition as \"%s.agr\"...\n",buf);

8940

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr_Cumulative("",buf,".agr",buf,true);

8941

}

8942

8943

if (o->m_bTimeDiff)

8944

o->WriteTimeDiff(o->m_pRDF[zr]->m_pRDF,"RDF","rdf",o->m_pRDF[zr]->m_sName,multibuf,false);

8945

8946

if (o->m_pRDF[zr]->m_bACF)

8947

{

8948

o->m_pRDF[zr]->Autocorrelate();

8949

}

8950

}

8951

if (o->m_bTimeDev)

8952

{

8953

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

8954

{

8955

fclose(o->m_pRDF[zr]->m_fDist[0]);

8956

mprintf(" Saving temporal development as \"rdf_timedev_%s%s.csv\"...\n",o->m_pRDF[zr]->m_sName,multibuf);

8957

} else

8958

{

8959

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

8960

{

8961

fclose(o->m_pRDF[zr]->m_fDist[z2]);

8962

sprintf(buf,"rdf_timedev_%s_ref%d%s.csv",o->m_pRDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

8963

mprintf(" Saving temporal development as \"%s\"...\n",buf);

8964

}

8965

}

8966

delete[] o->m_pRDF[zr]->m_fDist;

8967

o->m_pRDF[zr]->m_fDist = NULL;

8968

if (o->m_bCombinedPlot)

8969

{

8970

sprintf(buf,"combined_%s%s.agr",o->m_pRDF[zr]->m_sName,multibuf);

8971

mprintf(" Saving combined plot as \"%s\"...\n",buf);

8972

o->m_pRDF[zr]->m_pRDF->CreateCombinedPlot(true);

8973

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->WriteAgr(buf,false);

8974

}

8975

}

8976

}

8977

} // END IF RDF

8978

8979

if (g_bVHDF)

8980

{

8981

mprintf(WHITE,"* Van Hove Correlation Function\n");

8982

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pVHDF->m_pVHDF->m_fBinEntries,o->m_pVHDF->m_pVHDF->m_fSkipEntries,ZeroDivide(o->m_pVHDF->m_pVHDF->m_fSkipEntries,o->m_pVHDF->m_pVHDF->m_fBinEntries+o->m_pVHDF->m_pVHDF->m_fSkipEntries)*100.0);

8983

o->m_pVHDF->CorrectCount();

8984

if (o->m_pVHDF->m_bRadialCorrect)

8985

{

8986

mprintf(" Correcting radial distribution...\n");

8987

o->m_pVHDF->m_pVHDF->CorrectRadialDist(1);

8988

if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)

8989

{

8990

mprintf(" Normalizing bin to uniform density...\n");

8991

o->m_pVHDF->m_pVHDF->MultiplyBin(3.0f/4.0f/Pi*g_fBoxX*g_fBoxY*g_fBoxZ);

8992

}

8993

if (g_bDoubleBox)

8994

o->m_pVHDF->m_pVHDF->MultiplyBin(g_iDoubleBoxFactor);

8995

} else

8996

{

8997

mprintf(" Normalizing bin integral to 1000000...\n");

8998

o->m_pVHDF->m_pVHDF->NormalizeBinIntegral(1000000.0);

8999

}

9000

9001

sprintf(buf,"vhcf_%s%s",o->m_pVHDF->m_sName,multibuf);

9002

9003

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_TRIPLES"))

9004

{

9005

mprintf(" Saving VHCF triples as \"%s_triples.csv\"...\n",buf);

9006

o->m_pVHDF->m_pVHDF->Write("",buf,"_triples.csv");

9007

}

9008

9009

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_MATRIX"))

9010

{

9011

mprintf(" Saving VHCF matrix as \"%s_matrix.csv\"...\n",buf);

9012

o->m_pVHDF->m_pVHDF->WriteCSV("",buf,"_matrix.csv");

9013

}

9014

9015

if (o->m_pVHDF->m_iGraceBunchDist > 0)

9016

{

9017

sprintf(buf,"vhcf_dist_%s%s.agr",o->m_pVHDF->m_sName,multibuf);

9018

mprintf(" Saving VHCF distance Grace Stack as \"%s\"...\n",buf);

9019

o->m_pVHDF->m_pVHDF->WriteGraceBunch(0,o->m_pVHDF->m_iGraceBunchDist,1.0f,"",buf,"");

9020

}

9021

9022

if (o->m_pVHDF->m_iGraceBunchTime > 0)

9023

{

9024

sprintf(buf,"vhcf_time_%s%s.agr",o->m_pVHDF->m_sName,multibuf);

9025

mprintf(" Saving VHCF time Grace Stack as \"%s\"...\n",buf);

9026

o->m_pVHDF->m_pVHDF->WriteGraceBunch(1,o->m_pVHDF->m_iGraceBunchTime,1.0f,"",buf,"");

9027

}

9028

9029

if (o->m_pVHDF->m_bSwapAxes)

9030

o->m_pVHDF->m_pVHDF->SwapAxes();

9031

9032

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_MATHEMATICA"))

9033

{

9034

sprintf(buf,"vhcf_%s%s.nb",o->m_pVHDF->m_sName,multibuf);

9035

mprintf(" Saving VHCF Mathematica Notebook as \"%s\"...\n",buf);

9036

o->m_pVHDF->m_pVHDF->WriteMathematicaNb("",buf,"",false);

9037

}

9038

9039

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_GNUPLOT"))

9040

{

9041

sprintf(buf,"vhcf_%s%s",o->m_pVHDF->m_sName,multibuf);

9042

mprintf(" Saving VHCF Gnuplot Input as \"%s.gp\"...\n",buf);

9043

o->m_pVHDF->m_pVHDF->WriteGnuplotInput("",buf,"",false);

9044

}

9045

} // END IF VHDF

9046

9047

if (g_bCDF)

9048

{

9049

if (g_iCDFChannels == 2)

9050

{

9051

mprintf(WHITE,"* Combined Distribution Function (2D)\n");

9052

/* if (o->m_pConditions != NULL)

9053

{

9054

mprintf(" Conditions: %.2f percent of the molecules passed.\n",o->m_pConditions->m_fPassed/(o->m_pConditions->m_fPassed+o->m_pConditions->m_fFailed)*100.0);

9055

mprintf(" After conditions: ");

9056

} else mprintf(" ");*/

9057

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pCDF->m_p2DF->m_fBinEntries,o->m_pCDF->m_p2DF->m_fSkipEntries,ZeroDivide(o->m_pCDF->m_p2DF->m_fSkipEntries,o->m_pCDF->m_p2DF->m_fSkipEntries+o->m_pCDF->m_p2DF->m_fBinEntries)*100.0);

9058

if (o->m_pCDF->m_p2DF->m_fBinEntries == 0)

9059

{

9060

eprintf(" There were no bin entries. Check your CDF definition. Skipping this CDF.\n\n");

9061

goto _skipsdf;

9062

}

9063

for (z2=0;z2<2;z2++)

9064

{

9065

if (g_iObsChannel[z2] == 0)

9066

{

9067

if ((o->m_pRDF[z2]->m_bRadialCorrect) && (o->m_pCDF->m_iNormalize != 3))

9068

{

9069

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

9070

o->m_pCDF->m_p2DF->CorrectRadialDist(z2);

9071

}

9072

}

9073

if (g_iObsChannel[z2] == 1)

9074

{

9075

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine) && (o->m_pCDF->m_iNormalize != 3))

9076

{

9077

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

9078

o->m_pCDF->m_p2DF->CorrectAngle(z2);

9079

}

9080

if (o->m_pADF[z2]->m_bMirror)

9081

{

9082

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

9083

if (o->m_pADF[z2]->m_bCosine)

9084

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

9085

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

9086

}

9087

}

9088

if (g_iObsChannel[z2] == 6)

9089

{

9090

if (o->m_pLiDF[z2]->m_bRadialCorrect)

9091

{

9092

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

9093

o->m_pCDF->m_p2DF->CorrectLiRadialDist(z2);

9094

}

9095

}

9096

}

9097

o->m_pCDF->m_fFactor = 1.0;

9098

switch(o->m_pCDF->m_iNormalize)

9099

{

9100

case 3:

9101

mprintf(" Normalizing CDF to uniform density.\n");

9102

o->m_pCDF->m_p2DF->NormalizeUniform(g_fBoxX*g_fBoxY*g_fBoxZ/g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / ((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize() / o->m_pCDF->m_iCombinationsEnabled);

9103

break;

9104

case 2:

9105

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

9106

o->m_pCDF->m_p2DF->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9107

break;

9108

case 1:

9109

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

9110

o->m_pCDF->m_fFactor = o->m_pCDF->m_p2DF->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9111

break;

9112

case 0:

9113

mprintf(" Not normalizing this CDF.\n");

9114

break;

9115

}

9116

9117

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_TRIPLES"))

9118

{

9119

mprintf(" Saving CDF triples as \"%s%s_triples.csv\"...\n",o->m_pCDF->m_sName,multibuf);

9120

o->m_pCDF->m_p2DF->Write(o->m_pCDF->m_sName,multibuf,"_triples.csv");

9121

}

9122

9123

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_MATRIX"))

9124

{

9125

mprintf(" Saving CDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pCDF->m_sName,multibuf);

9126

o->m_pCDF->m_p2DF->WriteCSV(o->m_pCDF->m_sName,multibuf,"_matrix.csv");

9127

}

9128

9129

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_MATHEMATICA"))

9130

{

9131

mprintf(" Saving CDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9132

o->m_pCDF->m_p2DF->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,".nb",false);

9133

}

9134

9135

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_GNUPLOT"))

9136

{

9137

mprintf(" Saving CDF Gnuplot Input as \"%s%s.gp\"...\n",o->m_pCDF->m_sName,multibuf);

9138

o->m_pCDF->m_p2DF->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"",false);

9139

}

9140

9141

mprintf(" Saving combined plot AGR file as \"%s%s_combined.agr\"...\n",o->m_pCDF->m_sName,multibuf);

9142

o->m_pCDF->m_p2DF->WriteCombinedPlot(o->m_pCDF->m_sName,multibuf,"_combined.agr");

9143

if (o->m_pCDF->m_iHistogramRes != 0)

9144

{

9145

mprintf(" Calculating Histogram...\n");

9146

o->m_pCDF->m_p2DF->CalcHistogram();

9147

sprintf(buf,"his_%s",o->m_pCDF->m_sName);

9148

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

9149

o->m_pCDF->m_p2DF->WriteHistogram(buf,multibuf,".csv");

9150

}

9151

9152

if (o->m_pCDF->m_bGraceBunch)

9153

{

9154

if (o->m_pCDF->m_iGraceBunchC1 > 0)

9155

{

9156

if ((g_iObsChannel[1] == 0) && (o->m_bOthers))

9157

tf = 1.0 / o->m_pCDF->m_fFactor * 3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() /o->m_pRDF[1]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[1]->m_iRefAtomGes;

9158

else tf = 1;

9159

sprintf(buf,"cdf_c1_%s%s.agr",o->m_pCDF->m_sName,multibuf);

9160

mprintf(" Saving CDF Channel 1 Grace Stack as \"%s\"...\n",buf);

9161

o->m_pCDF->m_p2DF->WriteGraceBunch(0,o->m_pCDF->m_iGraceBunchC1,(float)tf,"",buf,"");

9162

}

9163

if (o->m_pCDF->m_iGraceBunchC2 > 0)

9164

{

9165

if ((g_iObsChannel[0] == 0) && (o->m_bOthers))

9166

tf = 1.0 / o->m_pCDF->m_fFactor * 3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() /o->m_pRDF[0]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[0]->m_iRefAtomGes;

9167

else tf = 1;

9168

sprintf(buf,"cdf_c2_%s%s.agr",o->m_pCDF->m_sName,multibuf);

9169

mprintf(" Saving CDF Channel 2 Grace Stack as \"%s\"...\n",buf);

9170

o->m_pCDF->m_p2DF->WriteGraceBunch(1,o->m_pCDF->m_iGraceBunchC2,(float)tf,"",buf,"");

9171

}

9172

}

9173

9174

if (o->m_pCDF->m_bAxisDivide)

9175

{

9176

if (o->m_pCDF->m_bAxisDivideAll)

9177

{

9178

mprintf(" Saving CDF X projection as \"%s%s_pX.csv\"...\n",o->m_pCDF->m_sName,multibuf);

9179

o->m_pCDF->m_p2DF->WriteXProjection(o->m_pCDF->m_sName,multibuf,"_pX.csv");

9180

9181

mprintf(" Saving CDF Y projection as \"%s%s_pY.csv\"...\n",o->m_pCDF->m_sName,multibuf);

9182

o->m_pCDF->m_p2DF->WriteYProjection(o->m_pCDF->m_sName,multibuf,"_pY.csv");

9183

9184

mprintf(" Saving X-normalized CDF Mathematica Notebook as \"%s%s_nX.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9185

9186

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

9187

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9188

9189

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

9190

if (g_iObsChannel[0] == 0)

9191

if (o->m_pRDF[0]->m_bRadialCorrect)

9192

tempc2df->UnCorrectRadialDist(0);

9193

if (g_iObsChannel[0] == 1)

9194

if (o->m_pADF[0]->m_bStat && (!o->m_pADF[0]->m_bCosine))

9195

tempc2df->UnCorrectAngle(0);

9196

tempc2df->NormalizeXCount();

9197

switch(o->m_pCDF->m_iNormalize)

9198

{

9199

case 2:

9200

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9201

break;

9202

case 1:

9203

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9204

break;

9205

case 0:

9206

break;

9207

}

9208

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nX.nb",false);

9209

tempc2df->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_nX",false);

9210

delete tempc2df;

9211

9212

mprintf(" Saving Y-normalized CDF Mathematica Notebook as \"%s%s_nY.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9213

9214

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

9215

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9216

9217

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

9218

if (g_iObsChannel[1] == 0)

9219

if (o->m_pRDF[1]->m_bRadialCorrect)

9220

tempc2df->UnCorrectRadialDist(1);

9221

if (g_iObsChannel[1] == 1)

9222

if (o->m_pADF[1]->m_bStat && (!o->m_pADF[1]->m_bCosine))

9223

tempc2df->UnCorrectAngle(1);

9224

tempc2df->NormalizeYCount();

9225

switch(o->m_pCDF->m_iNormalize)

9226

{

9227

case 2:

9228

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9229

break;

9230

case 1:

9231

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9232

break;

9233

case 0:

9234

break;

9235

}

9236

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nY.nb",false);

9237

tempc2df->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_nY",false);

9238

delete tempc2df;

9239

9240

mprintf(" Saving XY-normalized CDF Mathematica Notebook as \"%s%s_nXY.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9241

9242

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

9243

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9244

9245

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

9246

for (z2=0;z2<2;z2++)

9247

{

9248

if (g_iObsChannel[z2] == 0)

9249

if (o->m_pRDF[z2]->m_bRadialCorrect)

9250

tempc2df->UnCorrectRadialDist(z2);

9251

if (g_iObsChannel[z2] == 1)

9252

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine))

9253

tempc2df->UnCorrectAngle(z2);

9254

}

9255

tempc2df->NormalizeXCount();

9256

tempc2df->NormalizeYCount();

9257

switch(o->m_pCDF->m_iNormalize)

9258

{

9259

case 2:

9260

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9261

break;

9262

case 1:

9263

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9264

break;

9265

case 0:

9266

break;

9267

}

9268

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nXY.nb",false);

9269

tempc2df->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_nXY",false);

9270

delete tempc2df;

9271

}

9272

9273

mprintf(" Calculating tensor product of CDF projections...\n");

9274

9275

try { o->m_pCDF->m_pTensorProduct = new C2DF(); } catch(...) { o->m_pCDF->m_pTensorProduct = NULL; }

9276

if (o->m_pCDF->m_pTensorProduct == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9277

9278

o->m_pCDF->m_pTensorProduct->CopyFrom(o->m_pCDF->m_p2DF);

9279

o->m_pCDF->m_pTensorProduct->MakeTensorProduct(o->m_pCDF->m_p2DF);

9280

switch(o->m_pCDF->m_iNormalize)

9281

{

9282

case 2:

9283

o->m_pCDF->m_pTensorProduct->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9284

break;

9285

case 1:

9286

o->m_pCDF->m_pTensorProduct->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9287

break;

9288

case 0:

9289

break;

9290

}

9291

if (o->m_pCDF->m_bAxisDivideAll)

9292

{

9293

mprintf(" Saving tensor product as \"%s%s_tensor.dat\"...\n",o->m_pCDF->m_sName,multibuf);

9294

o->m_pCDF->m_pTensorProduct->Write(o->m_pCDF->m_sName,multibuf,"_tensor.dat");

9295

mprintf(" Saving tensor product Mathematica Notebook as \"%s%s_tensor.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9296

o->m_pCDF->m_pTensorProduct->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_tensor.nb",false);

9297

mprintf(" Saving tensor product Gnuplot Input as \"%s%s_tensor.gp\"...\n",o->m_pCDF->m_sName,multibuf);

9298

o->m_pCDF->m_pTensorProduct->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_tensor",false);

9299

mprintf(" Calculating difference between CDF and tensor product...\n");

9300

}

9301

o->m_pCDF->m_p2DF->Subtract(o->m_pCDF->m_pTensorProduct);

9302

o->m_pCDF->m_p2DF->CalcMaxEntry();

9303

o->m_pCDF->m_p2DF->m_iColorScale = 4; // PlusMinus Scale

9304

o->m_pCDF->m_p2DF->m_fPlotExp = 1.0;

9305

// o->m_pCDF->m_p2DF->m_fMathematicaColorOffset = max(fabs(o->m_pCDF->m_p2DF->m_fMinEntry),fabs(o->m_pCDF->m_p2DF->m_fMaxEntry)) / 3.0;

9306

// o->m_pCDF->m_p2DF->m_fMathematicaColorScale = o->m_pCDF->m_p2DF->m_fMathematicaColorOffset * 2.0;

9307

mprintf(" Saving +/- correlation plot as \"%s%s_correlation.dat\"...\n",o->m_pCDF->m_sName,multibuf);

9308

o->m_pCDF->m_p2DF->Write(o->m_pCDF->m_sName,multibuf,"_correlation.dat");

9309

mprintf(" Saving +/- correlation plot Mathematica Notebook as \"%s%s_correlation.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9310

o->m_pCDF->m_p2DF->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_correlation.nb",false);

9311

mprintf(" Saving +/- correlation plot Gnuplot Input as \"%s%s_correlation.gp\"...\n",o->m_pCDF->m_sName,multibuf);

9312

o->m_pCDF->m_p2DF->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_correlation",false);

9313

} // END IF AXISDIVIDE

9314

if (o->m_pCDF->m_bDumpDat)

9315

{

9316

fclose(o->m_pCDF->m_fDump);

9317

mprintf(" CDF raw data saved as cdfdump_%dd_%s%s.csv.\n",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

9318

}

9319

if (o->m_bTimeDev)

9320

{

9321

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

9322

{

9323

fclose(o->m_pCDF->m_fTimeDev[0]);

9324

// sprintf(buf,"cdf_timedev_%dd_%s_ref%d%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

9325

mprintf(" Temporal development saved as cdf_timedev_%dd%s%s.csv\n",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

9326

} else

9327

{

9328

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

9329

{

9330

fclose(o->m_pCDF->m_fTimeDev[z2]);

9331

mprintf(" Temporal development saved as cdf_timedev_%dd%s_ref%d%s.csv\n",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

9332

}

9333

}

9334

if (o->m_pCDF->m_bTDAnimation)

9335

{

9336

mprintf(WHITE," * Time dependent animation *\n");

9337

sprintf(buf,"animation_complete_%s%s.agr",o->m_pCDF->m_sName,multibuf);

9338

mprintf(" Saving complete Plot as \"%s\"...\n",buf);

9339

for (z2=0;z2<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z2++)

9340

{

9341

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(z2,2.0f);

9342

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(z2,GraceColor(z2,0.0));

9343

}

9344

o->m_pCDF->m_pTDAPlot->WriteAgr(buf,false);

9345

sprintf(buf,"render_%s%s",o->m_pCDF->m_sName,multibuf);

9346

mprintf(" Saving xmgrace render script for animation as \"%s\"...\n",buf);

9347

a = OpenFileWrite("gracebatch",true);

9348

mfprintf(a,"PRINT TO \"output.png\"\n");

9349

mfprintf(a,"HARDCOPY DEVICE \"PNG\"\n");

9350

mfprintf(a,"PAGE SIZE %d, %d\n",o->m_pCDF->m_iTDAResX,o->m_pCDF->m_iTDAResY);

9351

mfprintf(a,"DEVICE \"PNG\" FONT ANTIALIASING on\n");

9352

mfprintf(a,"DEVICE \"PNG\" OP \"compression:9\"\n");

9353

mfprintf(a,"PRINT\n");

9354

fclose(a);

9355

a = OpenFileWrite(buf,true);

9356

if (o->m_pCDF->m_bTDATrace)

9357

{

9358

for (z2=0;z2<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z2++)

9359

{

9360

o->m_pCDF->m_pTDAPlot->DuplicateSet(z2);

9361

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(z2,2.0f);

9362

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(z2,GraceColor(z2,0.7));

9363

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled+z2,3.0f);

9364

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled+z2,GraceColor(z2,0.0));

9365

}

9366

}

9367

for (z2=0;z2<o->m_pCDF->m_iTDASteps;z2++)

9368

{

9369

if (o->m_pCDF->m_bTDATrace)

9370

{

9371

for (z3=0;z3<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z3++)

9372

{

9373

o->m_pCDF->m_pTDAPlot->SetSetRange(z3+o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled,z2*o->m_pCDF->m_iTDAStride,z2*o->m_pCDF->m_iTDAStride+o->m_pCDF->m_iTDATail);

9374

o->m_pCDF->m_pTDAPlot->SetSetRange(z3,0,z2*o->m_pCDF->m_iTDAStride);

9375

}

9376

} else

9377

{

9378

for (z3=0;z3<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z3++)

9379

o->m_pCDF->m_pTDAPlot->SetSetRange(z3,z2*o->m_pCDF->m_iTDAStride,z2*o->m_pCDF->m_iTDAStride+o->m_pCDF->m_iTDATail);

9380

}

9381

9382

sprintf(buf,"animation_%05d_%s%s.agr",z2+1,o->m_pCDF->m_sName,multibuf);

9383

mprintf(" Saving frame \"%s\"...\n",buf);

9384

o->m_pCDF->m_pTDAPlot->WriteAgr(buf,false);

9385

mfprintf(a,"echo 'Printing frame %d of %d'\n",z2+1,o->m_pCDF->m_iTDASteps);

9386

mfprintf(a,"xmgrace %s -batch gracebatch -nosafe -hardcopy\n",buf);

9387

mfprintf(a,"mv output.png frame%04d.png\n",z2+1);

9388

}

9389

fclose(a);

9390

}

9391

}

9392

} // END IF CHANNELS == 2

9393

9394

if (g_iCDFChannels == 3)

9395

{

9396

mprintf(WHITE,"* Combined Distribution Function (3D)\n");

9397

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pCDF->m_p3DF->m_fBinEntries,o->m_pCDF->m_p3DF->m_fSkipEntries,ZeroDivide(o->m_pCDF->m_p3DF->m_fSkipEntries,o->m_pCDF->m_p3DF->m_fSkipEntries+o->m_pCDF->m_p3DF->m_fBinEntries)*100.0);

9398

if (o->m_pCDF->m_p3DF->m_fBinEntries == 0)

9399

{

9400

eprintf(" There were no bin entries. Check your CDF definition. Skipping this CDF.\n\n");

9401

goto _skipsdf;

9402

}

9403

o->m_pCDF->m_p3DF->CalcMaxEntry();

9404

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9405

for (z2=0;z2<g_iCDFChannels;z2++)

9406

{

9407

if (g_iObsChannel[z2] == 0)

9408

{

9409

if (o->m_pRDF[z2]->m_bRadialCorrect)

9410

{

9411

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

9412

o->m_pCDF->m_p3DF->CorrectRadialDist(z2);

9413

o->m_pCDF->m_p3DF->CalcMaxEntry();

9414

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9415

}

9416

}

9417

if (g_iObsChannel[z2] == 1)

9418

{

9419

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine))

9420

{

9421

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

9422

o->m_pCDF->m_p3DF->CorrectAngle(z2);

9423

o->m_pCDF->m_p3DF->CalcMaxEntry();

9424

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9425

}

9426

if (o->m_pADF[z2]->m_bMirror)

9427

{

9428

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

9429

if (o->m_pADF[z2]->m_bCosine)

9430

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

9431

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

9432

o->m_pCDF->m_p3DF->CalcMaxEntry();

9433

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9434

}

9435

}

9436

}

9437

// o->m_pCDF->m_p3DF->CalcMaxEntry();

9438

// mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9439

o->m_pCDF->m_fFactor = 1.0;

9440

switch(o->m_pCDF->m_iNormalize)

9441

{

9442

case 2:

9443

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

9444

o->m_pCDF->m_p3DF->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9445

o->m_pCDF->m_p3DF->CalcMaxEntry();

9446

mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9447

break;

9448

case 1:

9449

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

9450

o->m_pCDF->m_fFactor = o->m_pCDF->m_p3DF->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9451

mprintf(" Factor was %G.\n",o->m_pCDF->m_fFactor);

9452

o->m_pCDF->m_p3DF->CalcMaxEntry();

9453

mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9454

break;

9455

case 0:

9456

mprintf(" Not normalizing this CDF.\n");

9457

break;

9458

}

9459

9460

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

9461

{

9462

try { temp3DF = new C3DF(); } catch(...) { temp3DF = NULL; }

9463

if (temp3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9464

9465

temp3DF->CopyFrom(o->m_pCDF->m_p3DF);

9466

if (z2 != 0)

9467

{

9468

temp3DF->Smooth(z2);

9469

sprintf(buf,".s%d%s.plt",z2,multibuf);

9470

} else sprintf(buf,"%s.plt",multibuf);

9471

mprintf(" Saving 3D CDF as \"%s%s\"...\n",o->m_pCDF->m_sName,buf);

9472

temp3DF->WritePLT("",o->m_pCDF->m_sName,buf,false);

9473

9474

if (z2 != 0)

9475

sprintf(buf,".s%d%s.cube",z2,multibuf);

9476

else sprintf(buf,"%s.cube",multibuf);

9477

mprintf(" Saving 3D CDF as \"%s%s\"...\n",o->m_pCDF->m_sName,buf);

9478

temp3DF->WriteCube("",o->m_pCDF->m_sName,buf,false);

9479

if (o->m_pCDF->m_iHistogramRes != 0)

9480

{

9481

mprintf(" Calculating Histogram...\n");

9482

temp3DF->CalcHistogram();

9483

if (z2 != 0)

9484

sprintf(buf,"his_%s.s%d",o->m_pCDF->m_sName,z2);

9485

else sprintf(buf,"his_%s",o->m_pCDF->m_sName);

9486

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

9487

temp3DF->WriteHistogram(buf,multibuf,".csv");

9488

}

9489

9490

if (o->m_pCDF->m_b3DSlices)

9491

{

9492

for (z3=0;z3<3;z3++)

9493

{

9494

if (o->m_pCDF->m_i3DSliceIntervals[z3] != 0)

9495

{

9496

if (z2 != 0)

9497

mprintf(WHITE," * Creating channel %d smooth grade %d slices...\n",z3+1,z2);

9498

else mprintf(WHITE," * Creating channel %d slices...\n",z3+1);

9499

9500

try { temp2dfa = new C2DF*[o->m_pCDF->m_i3DSliceIntervals[z3]]; } catch(...) { temp2dfa = NULL; }

9501

if (temp2dfa == NULL) NewException((double)o->m_pCDF->m_i3DSliceIntervals[z3]*sizeof(C2DF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9502

9503

tf = 0;

9504

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

9505

{

9506

try { temp2dfa[z4] = new C2DF(); } catch(...) { temp2dfa[z4] = NULL; }

9507

if (temp2dfa[z4] == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9508

9509

temp3DF->CreateSlice(z3,(int)((double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*o->m_pCDF->m_p3DF->m_iRes[z3]),(int)((z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*o->m_pCDF->m_p3DF->m_iRes[z3]-1),temp2dfa[z4]);

9510

mprintf(" - %2d: %9.4f - %9.4f (%3d - %3d), Intensity range %.3f ... %.3f\n",z4+1,o->m_pCDF->m_p3DF->m_fMinVal[z3]+(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),o->m_pCDF->m_p3DF->m_fMinVal[z3]+(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),int((double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*o->m_pCDF->m_p3DF->m_iRes[z3]),int((z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*o->m_pCDF->m_p3DF->m_iRes[z3]-1),temp2dfa[z4]->m_fMinEntry,temp2dfa[z4]->m_fMaxEntry);

9511

if (temp2dfa[z4]->m_fMaxEntry > tf)

9512

tf = temp2dfa[z4]->m_fMaxEntry;

9513

}

9514

9515

mprintf(" Setting common intensity range to 0 ... %.3f.\n",tf);

9516

9517

mprintf(" Writing out slice files...\n",z3+1);

9518

9519

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

9520

{

9521

temp2dfa[z4]->m_fMinEntry = 0;

9522

temp2dfa[z4]->m_fMaxEntry = tf;

9523

if (z2 != 0)

9524

sprintf(buf,"%s_slice_ch%d_%d_%.3f-%.3f.s%d.nb",o->m_pCDF->m_sName,z3+1,z4+1,o->m_pCDF->m_p3DF->m_fMinVal[z3]+(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),o->m_pCDF->m_p3DF->m_fMinVal[z3]+(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),z2);

9525

else sprintf(buf,"%s_slice_ch%d_%d_%.3f-%.3f.nb",o->m_pCDF->m_sName,z3+1,z4+1,o->m_pCDF->m_p3DF->m_fMinVal[z3]+(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),o->m_pCDF->m_p3DF->m_fMinVal[z3]+(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]));

9526

mprintf(" %s ...\n",buf);

9527

temp2dfa[z4]->WriteMathematicaNb("",buf,"",true);

9528

if (z2 != 0)

9529

sprintf(buf,"%s_slice_ch%d_%d_%.3f-%.3f.s%d",o->m_pCDF->m_sName,z3+1,z4+1,o->m_pCDF->m_p3DF->m_fMinVal[z3]+(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),o->m_pCDF->m_p3DF->m_fMinVal[z3]+(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),z2);

9530

else sprintf(buf,"%s_slice_ch%d_%d_%.3f-%.3f",o->m_pCDF->m_sName,z3+1,z4+1,o->m_pCDF->m_p3DF->m_fMinVal[z3]+(double)z4/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]),o->m_pCDF->m_p3DF->m_fMinVal[z3]+(z4+1.0)/o->m_pCDF->m_i3DSliceIntervals[z3]*(o->m_pCDF->m_p3DF->m_fMaxVal[z3]-o->m_pCDF->m_p3DF->m_fMinVal[z3]));

9531

mprintf(" %s.gp ...\n",buf);

9532

temp2dfa[z4]->WriteGnuplotInput("",buf,"",true);

9533

}

9534

9535

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

9536

delete temp2dfa[z4];

9537

9538

delete[] temp2dfa;

9539

}

9540

}

9541

}

9542

}

9543

9544

mprintf(" Writing out 2D projections...\n");

9545

for (z3=0;z3<3;z3++)

9546

{

9547

mprintf(WHITE," * CDF 2D projection on channel %d\n",z3+1);

9548

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fBinEntries,o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fSkipEntries,ZeroDivide(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fSkipEntries,o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fSkipEntries+o->m_pCDF->m_p3DF->m_p2DF[z3]->m_fBinEntries)*100.0);

9549

switch(z3)

9550

{

9551

case 0:

9552

tia[0] = 0;

9553

tia[1] = 1;

9554

break;

9555

case 1:

9556

tia[0] = 0;

9557

tia[1] = 2;

9558

break;

9559

case 2:

9560

tia[0] = 1;

9561

tia[1] = 2;

9562

break;

9563

}

9564

for (z2=0;z2<2;z2++)

9565

{

9566

if (g_iObsChannel[tia[z2]] == 0)

9567

{

9568

if (o->m_pRDF[tia[z2]]->m_bRadialCorrect)

9569

{

9570

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

9571

o->m_pCDF->m_p3DF->m_p2DF[z3]->CorrectRadialDist(z2);

9572

}

9573

}

9574

if (g_iObsChannel[tia[z2]] == 1)

9575

{

9576

if (o->m_pADF[tia[z2]]->m_bStat && (!o->m_pADF[tia[z2]]->m_bCosine))

9577

{

9578

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

9579

o->m_pCDF->m_p3DF->m_p2DF[z3]->CorrectAngle(z2);

9580

}

9581

/* if (o->m_pADF[z2]->m_bMirror)

9582

{

9583

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

9584

if (o->m_pADF[z2]->m_bCosine)

9585

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

9586

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

9587

}*/

9588

}

9589

}

9590

o->m_pCDF->m_fFactor = 1.0;

9591

switch(o->m_pCDF->m_iNormalize)

9592

{

9593

case 2:

9594

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

9595

o->m_pCDF->m_p3DF->m_p2DF[z3]->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9596

break;

9597

case 1:

9598

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

9599

o->m_pCDF->m_p3DF->m_p2DF[z3]->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9600

break;

9601

case 0:

9602

mprintf(" Not normalizing this CDF.\n");

9603

break;

9604

}

9605

mprintf(" Saving CDF triples as \"%s%s_triples.csv\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9606

o->m_pCDF->m_p3DF->m_p2DF[z3]->Write(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_triples.csv");

9607

mprintf(" Saving CDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9608

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteCSV(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_matrix.csv");

9609

mprintf(" Saving CDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9610

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteMathematicaNb(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,".nb",false);

9611

mprintf(" Saving CDF Gnuplot Input as \"%s%s.gp\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9612

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteGnuplotInput(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"",false);

9613

mprintf(" Saving combined plot AGR file as \"%s%s_combined.agr\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9614

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteCombinedPlot(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_combined.agr");

9615

if (o->m_pCDF->m_iHistogramRes != 0)

9616

{

9617

mprintf(" Calculating Histogram...\n");

9618

o->m_pCDF->m_p3DF->m_p2DF[z3]->CalcHistogram();

9619

sprintf(buf,"his_%s",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName);

9620

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

9621

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteHistogram(buf,multibuf,".csv");

9622

}

9623

}

9624

} // END IF CHANNELS == 3

9625

_skipsdf:;

9626

} // END IF CDF

9627

9628

if (g_bRevSDF)

9629

{

9630

mprintf(WHITE,"* Pseudo SDF\n");

9631

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pRevSDF->m_p2DF->m_fBinEntries,o->m_pRevSDF->m_p2DF->m_fSkipEntries,ZeroDivide(o->m_pRevSDF->m_p2DF->m_fSkipEntries,o->m_pRevSDF->m_p2DF->m_fSkipEntries+o->m_pRevSDF->m_p2DF->m_fBinEntries)*100.0);

9632

if (o->m_pRevSDF->m_p2DF->m_fBinEntries == 0)

9633

{

9634

eprintf(" There were no bin entries. Check your function definition. Skipping this PseudoSDF.\n\n");

9635

goto _skiprevsdf;

9636

}

9637

mprintf(" Normalizing integral value to %.2f.\n",1000000.0f);

9638

o->m_pRevSDF->m_p2DF->NormalizeBinIntegral(1000000.0f);

9639

if (o->m_pRevSDF->m_bDrawAtoms)

9640

{

9641

mprintf(" Inserting reference atoms into the Pseudo SDF plot...\n");

9642

9643

if (((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_fRadius == 0)

9644

o->m_pRevSDF->m_p2DF->AddCircle(0,0,50.0,0.4,0.4,0.4);

9645

else o->m_pRevSDF->m_p2DF->AddCircle(0,0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_iColorB/255.0);

9646

9647

if (((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_fRadius == 0)

9648

o->m_pRevSDF->m_p2DF->AddCircle(0,o->m_pRevSDF->m_fSecondAtomPosX/o->m_pRevSDF->m_fSecondAtomCount,50.0,0.4,0.4,0.4);

9649

else o->m_pRevSDF->m_p2DF->AddCircle(0,o->m_pRevSDF->m_fSecondAtomPosX/o->m_pRevSDF->m_fSecondAtomCount,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_fRadius*0.75,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_iColorB/255.0);

9650

}

9651

mprintf(" Saving PseudoSDF triples as \"%s%s_triples.csv\"...\n",o->m_pRevSDF->m_sName,multibuf);

9652

o->m_pRevSDF->m_p2DF->Write(o->m_pRevSDF->m_sName,multibuf,"_triples.csv");

9653

mprintf(" Saving PseudoSDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pRevSDF->m_sName,multibuf);

9654

o->m_pRevSDF->m_p2DF->WriteCSV(o->m_pRevSDF->m_sName,multibuf,"_matrix.csv");

9655

mprintf(" Saving PseudoSDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pRevSDF->m_sName,multibuf);

9656

o->m_pRevSDF->m_p2DF->WriteMathematicaNb(o->m_pRevSDF->m_sName,multibuf,".nb",false);

9657

mprintf(" Saving PseudoSDF Gnuplot Input as \"%s%s.gp\"...\n",o->m_pRevSDF->m_sName,multibuf);

9658

o->m_pRevSDF->m_p2DF->WriteGnuplotInput(o->m_pRevSDF->m_sName,multibuf,"",false);

9659

if (o->m_pRevSDF->m_iHistogramRes != 0)

8967

mprintf(WHITE,"* Plane Projection Distribution Function\n");

8968

mprintf(" %.0f bin entries, %.0f out of bin range (%.2f percent).\n",o->m_pPlProj->m_p2DF->m_fBinEntries,o->m_pPlProj->m_p2DF->m_fSkipEntries,ZeroDivide(o->m_pPlProj->m_p2DF->m_fSkipEntries,o->m_pPlProj->m_p2DF->m_fBinEntries+o->m_pPlProj->m_p2DF->m_fSkipEntries)*100.0);

8969

if (o->m_pPlProj->m_p2DF->m_fBinEntries == 0)

8970

{

8971

eprintf(" There were no bin entries. Check your function definition. Skipping this Plane Projection DF.\n\n");

8972

goto _skipplproj;

8973

}

8974

8975

o->m_pPlProj->m_p2DF->CalcMaxEntry();

8976

mprintf(" Raw data range from %.0f to %.0f hits.\n",o->m_pPlProj->m_p2DF->m_fMinEntry,o->m_pPlProj->m_p2DF->m_fMaxEntry);

8977

mprintf(" The volume of one bin is %.3f pm^3.\n",(o->m_pPlProj->m_fMaxVal[0]-o->m_pPlProj->m_fMinVal[0])*(o->m_pPlProj->m_fMaxVal[1]-o->m_pPlProj->m_fMinVal[1])*(o->m_pPlProj->m_fSliceBorder[1]-o->m_pPlProj->m_fSliceBorder[0])/o->m_pPlProj->m_iResolution[0]/o->m_pPlProj->m_iResolution[1]);

8978

8979

if ((g_bPeriodicX) && (g_bPeriodicY) && (g_bPeriodicZ))

8980

{

8981

mprintf(" System is periodic, normalizing values to uniform density.\n");

8982

mprintf(" The uniform particle density of this observation is %.6f nm^-3.\n",o->m_pPlProj->m_fParticleDensity);

8983

// mprintf(" (%f)\n",(double)o->m_pPlProj->m_iResolution[0]*o->m_pPlProj->m_iResolution[1]/(o->m_pPlProj->m_fMaxVal[0]-o->m_pPlProj->m_fMinVal[0])/(o->m_pPlProj->m_fMaxVal[1]-o->m_pPlProj->m_fMinVal[1])/(o->m_pPlProj->m_fSliceBorder[1]-o->m_pPlProj->m_fSliceBorder[0])*1.0e9 / (double)g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pPlProj->m_iShowAtomGes * (g_bDoubleBox?g_iDoubleBoxFactor:1));

8984

// mprintf(" o->m_pPlProj->m_iShowAtomGes = %d\n",o->m_pPlProj->m_iShowAtomGes);

8985

// mprintf(" 1/Vol = %f\n",(double)o->m_pPlProj->m_iResolution[0]*o->m_pPlProj->m_iResolution[1]/(o->m_pPlProj->m_fMaxVal[0]-o->m_pPlProj->m_fMinVal[0])/(o->m_pPlProj->m_fMaxVal[1]-o->m_pPlProj->m_fMinVal[1])/(o->m_pPlProj->m_fSliceBorder[1]-o->m_pPlProj->m_fSliceBorder[0])*1.0e9);

8986

o->m_pPlProj->m_p2DF->MultiplyBin((double)o->m_pPlProj->m_iResolution[0]*o->m_pPlProj->m_iResolution[1]/(o->m_pPlProj->m_fMaxVal[0]-o->m_pPlProj->m_fMinVal[0])/(o->m_pPlProj->m_fMaxVal[1]-o->m_pPlProj->m_fMinVal[1])/(o->m_pPlProj->m_fSliceBorder[1]-o->m_pPlProj->m_fSliceBorder[0])*1.0e9 / (double)g_iSteps * g_iStride / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() /* / o->m_pPlProj->m_iShowAtomGes*/ * (g_bDoubleBox?g_iDoubleBoxFactor:1));

8987

// mprintf(" (%f)\n",1.0/o->m_pPlProj->m_fParticleDensity);

8988

o->m_pPlProj->m_p2DF->MultiplyBin(1.0/o->m_pPlProj->m_fParticleDensity);

8989

} else

8990

{

8991

mprintf(" System is non-periodic, normalizing integral value to %.2f.\n",1000000.0f);

8992

o->m_pPlProj->m_p2DF->NormalizeBinIntegral(1000000.0f);

8993

}

8994

8995

o->m_pPlProj->m_p2DF->CalcMaxEntry();

8996

mprintf(" Resulting data range from %.6f to %.6f.\n",o->m_pPlProj->m_p2DF->m_fMinEntry,o->m_pPlProj->m_p2DF->m_fMaxEntry);

8997

8998

if (o->m_pPlProj->m_bDrawAtoms)

8999

{

9000

mprintf(" Inserting reference atoms into the Plane Projection DF plot...\n");

9001

ti = 0;

9002

for (z3=0;z3<o->m_pPlProj->m_oDrawAtoms.m_oaAtoms.GetSize();z3++)

9003

{

9004

ti2 = o->m_pPlProj->m_oDrawAtoms.m_baRealAtomType[z3];

9005

for (z4=0;z4<((CxIntArray*)o->m_pPlProj->m_oDrawAtoms.m_oaAtoms[z3])->GetSize();z4++)

9006

{

9007

if (o->m_pPlProj->m_bAverageAtomPos)

9008

o->m_pPlProj->m_vaAtomPos[ti] /= o->m_pPlProj->m_iAverageCounter;

9009

9010

if (((CAtom*)g_oaAtoms[ti2])->m_pElement->m_fRadius == 0)

9011

o->m_pPlProj->m_p2DF->AddCircle(o->m_pPlProj->m_vaAtomPos[ti][0],o->m_pPlProj->m_vaAtomPos[ti][1],25.0,0.4,0.4,0.4);

9012

else o->m_pPlProj->m_p2DF->AddCircle(o->m_pPlProj->m_vaAtomPos[ti][0],o->m_pPlProj->m_vaAtomPos[ti][1],((CAtom*)g_oaAtoms[ti2])->m_pElement->m_fRadius*0.6,((CAtom*)g_oaAtoms[ti2])->m_pElement->m_iColorR/255.0,((CAtom*)g_oaAtoms[ti2])->m_pElement->m_iColorG/255.0,((CAtom*)g_oaAtoms[ti2])->m_pElement->m_iColorB/255.0);

9013

9014

ti++;

9015

}

9016

}

9017

}

9018

9019

mprintf(" Saving Plane Projection DF triples as \"%s%s_triples.csv\"...\n",o->m_pPlProj->m_sName,multibuf);

9020

o->m_pPlProj->m_p2DF->Write(o->m_pPlProj->m_sName,multibuf,"_triples.csv");

9021

mprintf(" Saving Plane Projection DF matrix as \"%s%s_matrix.csv\"...\n",o->m_pPlProj->m_sName,multibuf);

9022

o->m_pPlProj->m_p2DF->WriteCSV(o->m_pPlProj->m_sName,multibuf,"_matrix.csv");

9023

mprintf(" Saving Plane Projection DF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pPlProj->m_sName,multibuf);

9024

o->m_pPlProj->m_p2DF->WriteMathematicaNb(o->m_pPlProj->m_sName,multibuf,".nb",false);

9025

mprintf(" Saving Plane Projection DF Gnuplot Input as \"%s%s.gp\"...\n",o->m_pPlProj->m_sName,multibuf);

9026

o->m_pPlProj->m_p2DF->WriteGnuplotInput(o->m_pPlProj->m_sName,multibuf,"",false);

9027

if (o->m_pPlProj->m_iHistogramRes != 0)

9660

9028

{

9661

9029

mprintf(" Calculating Histogram...\n");

9662

o->m_pRevSDF->m_p2DF->CalcHistogram();

9663

sprintf(buf,"his_%s",o->m_pRevSDF->m_sName);

9030

o->m_pPlProj->m_p2DF->CalcHistogram();

9031

sprintf(buf,"his_%s",o->m_pPlProj->m_sName);

9664

9032

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

9665

o->m_pRevSDF->m_p2DF->WriteHistogram(buf,multibuf,".csv");

9666

}

9667

if (o->m_pRevSDF->m_bCreateRevSDF)

9668

{

9669

mprintf(" Creating volumetric Revolution SDF...\n");

9670

o->m_pRevSDF->CreateRevSDF();

9671

sprintf(buf,"revsdf_ref_%s.xyz",o->m_pRevSDF->m_sName);

9672

mprintf(" Saving Revolution SDF reference structure as \"%s\"...\n",buf);

9673

a = OpenFileWrite(buf,true);

9674

mfprintf(a,"2\n\n%s 0.0 0.0 0.0\n%s 0.0 %f 0.0\n",((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,o->m_pRevSDF->m_fSecondAtomPosX/o->m_pRevSDF->m_fSecondAtomCount/100.0);

9675

fclose(a);

9676

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

9677

{

9678

try { tempSDF = new C3DF(); } catch(...) { tempSDF = NULL; }

9679

if (tempSDF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9680

9681

tempSDF->CopyFrom(o->m_pRevSDF->m_pRevSDF);

9682

if (z2 != 0)

9683

{

9684

tempSDF->Smooth(z2);

9685

sprintf(buf,".s%d%s.plt",z2,multibuf);

9686

} else sprintf(buf,"%s.plt",multibuf);

9687

mprintf(" Saving Revolution SDF as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

9688

tempSDF->WritePLT("revsdf_",o->m_pRevSDF->m_sName,buf,true);

9689

9690

if (z2 != 0)

9691

sprintf(buf,".s%d%s.cube",z2,multibuf);

9692

else sprintf(buf,"%s.cube",multibuf);

9693

mprintf(" Saving Revolution SDF as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

9694

tempSDF->WriteCube("revsdf_",o->m_pRevSDF->m_sName,buf,true);

9695

9696

if (z2 != 0)

9697

sprintf(buf,".s%d%s.his",z2,multibuf);

9698

else sprintf(buf,"%s.his",multibuf);

9699

mprintf(" Saving Revolution SDF Histogram as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

9700

tempSDF->CalcHistogram();

9701

tempSDF->WriteHistogram("revsdf_",o->m_pRevSDF->m_sName,buf);

9702

if (o->m_pRevSDF->m_iHistogramRes != 0)

9703

{

9704

mprintf(" Calculating Histogram...\n");

9705

tempSDF->CalcHistogram();

9706

sprintf(buf2,"his_revsdf_%s",o->m_pRevSDF->m_sName);

9707

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf2,buf);

9708

tempSDF->WriteHistogram(buf2,buf,".csv");

9709

}

9710

}

9711

}

9712

_skiprevsdf:;

9713

} // END IF REVSDF

9714

}

9715

9716

if (g_bSDF || g_bAvg || g_bVoidSDF)

9717

{

9718

sprintf(buf,"ref_%s_%s%d_%s%d_%s%d%s.xyz",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName,((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_sName,g_iFixAtom[0]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_sName,g_iFixAtom[1]+1,((CAtom*)g_oaAtoms[g_iFixRealAtomType[2]])->m_sName,g_iFixAtom[2]+1,multibuf);

9719

strtolower(buf);

9720

mprintf("\n*** Reference molecule ***\n");

9721

FreeFileName(buf);

9722

mprintf("Saving reference molecule as \"%s\"...",buf);

9723

a = OpenFileWrite(buf,true);

9724

if (a == NULL)

9725

{

9726

eprintf("\nError: Could not open %s for writing.\n",buf);

9727

return 0;

9728

}

9729

if (!g_bSaveVirtAtoms)

9730

mfprintf(a," %d \n\n",(int)(((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes-((CMolecule*)g_oaMolecules[g_iFixMol])->m_laVirtualAtoms.GetSize()));

9731

else mfprintf(a," %d \n\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes);

9732

cc = 0;

9733

for (z=0;z<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z++)

9734

{

9735

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z] == g_iVirtAtomType))

9736

continue;

9737

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z];z2++)

9738

{

9739

if (g_bMiddleAvg)

9740

{

9741

g_pRefMol[cc][0] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

9742

g_pRefMol[cc][1] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

9743

g_pRefMol[cc][2] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

9744

}

9745

if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z] == g_iVirtAtomType)

9746

mfprintf(a," %s %9.6f %9.6f %9.6f\n",((CVirtualAtom*)g_oaVirtualAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_laVirtualAtoms[z2]])->m_sLabel,g_pRefMol[cc][0]/100.0,g_pRefMol[cc][1]/100.0,g_pRefMol[cc][2]/100.0);

9747

else mfprintf(a," %s %9.6f %9.6f %9.6f\n",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z]])->m_sName,g_pRefMol[cc][0]/100.0,g_pRefMol[cc][1]/100.0,g_pRefMol[cc][2]/100.0);

9748

cc++;

9749

}

9750

}

9751

fclose(a);

9752

mprintf("Done.\n");

9753

if (g_iSwapAtoms)

9754

{

9755

mprintf("\n*** This is the swap matrix of reference molecule %s:\n (It shows how often the atoms\n have been swapped with each other)\n\n ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);

9756

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z2++)

9757

{

9758

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z2];z3++)

9759

{

9760

if (((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName[1] == 0)

9761

mprintf(" ");

9762

mprintf("%s%d ",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName,z3+1);

9763

if (z3 < 10)

9764

mprintf(" ");

9765

}

9766

}

9767

mprintf("\n");

9768

cc = 0;

9769

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z2++)

9770

{

9771

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z2];z3++)

9772

{

9773

mprintf("%s%d ",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName,z3+1);

9774

if (((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName[1] == 0)

9775

mprintf(" ");

9776

if (z3 < 9)

9777

mprintf(" ");

9778

cc2 = 0;

9779

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z4++)

9780

{

9781

for (z5=0;z5<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z4];z5++)

9782

{

9783

if ((z2 == z4) && (z3 == z5))

9784

{

9785

mprintf(" *** ");

9786

goto _swm;

9787

}

9788

if (pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc2] != 0)

9789

mprintf("%3.0f%c ",(double)pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc2] * 100.0f / g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize(),'%');

9790

else mprintf(" - ");

9791

_swm:

9792

cc2++;

9793

}

9794

}

9795

mprintf("\n");

9796

cc++;

9797

}

9798

}

9799

}

9800

}

9801

_ende:

9802

9803

if (g_bMultiInterval)

9804

{

9805

mprintf("\n");

9806

mprintf(YELLOW,"***********************************************\n");

9807

mprintf(YELLOW,"*** Interval %2d (%6d - %6d) finished. ***\n",multicounter+1,g_laMultiIntervalStart[multicounter]+1,g_laMultiIntervalEnd[multicounter]+1);

9808

mprintf(YELLOW,"***********************************************\n\n");

9809

multicounter++;

9810

if (multicounter < g_laMultiIntervalStart.GetSize())

9811

goto _multiintervalstart;

9812

}

9813

9814

g_iEndTime = time(NULL);

9815

if (((g_iEndTime-g_iStartTime) > 5) && (g_iStartTime != 0))

9816

{

9817

mprintf(WHITE,"\nAnalysis was running for %dh %dm %ds.\n",(g_iEndTime-g_iStartTime)/3600,((g_iEndTime-g_iStartTime)/60)%60,(g_iEndTime-g_iStartTime)%60);

9818

mprintf(WHITE," (%.3f steps per second)\n\n",g_iSteps/g_iStride/((double)g_iEndTime-g_iStartTime));

9819

} else mprintf("\n");

9820

9821

WriteCredits();

9822

9823

if (g_bSMode)

9824

{

9825

PrintSMode();

9826

} else

9827

{

9828

mprintf(WHITE,"*** The End ***\n\n");

9829

}

9830

UninstallSignalHandler();

9831

if (g_fInput != NULL)

9832

fclose(g_fInput);

9833

if (g_pDatabase != NULL)

9834

{

9835

delete g_pDatabase;

9836

g_pDatabase = NULL;

9837

}

9838

if (g_pTempTimestep != NULL)

9839

{

9840

delete g_pTempTimestep;

9841

g_pTempTimestep = NULL;

9842

}

9843

if (apfa != NULL)

9844

{

9845

delete[] apfa;

9846

apfa = NULL;

9847

}

9848

if (tda != NULL)

9849

{

9850

delete[] tda;

9851

tda = NULL;

9852

}

9853

RemoveAllAnalyses();

9854

RemoveAllElements();

9855

RemoveAllAtoms();

9856

RemoveAllMolecules();

9857

RemoveAllObservations();

9858

BTOUT;

9859

return 0;

9860

}

9861

9862

//////////////// Cross-Correlation Test 1

9863

9864

/* CAutoCorrelation acx, acf;

9865

CCrossCorrelation ccx, ccf;

9866

CxFloatArray i1, i2, opx, opf, opcx, opcf;

9867

9868

i1.SetSize(32);

9869

i2.SetSize(32);

9870

9871

for (z=0;z<32;z++)

9872

{

9873

i1[z] = ((rand()%200)/100.0)-1.0;

9874

i2[z] = i1[z];

9875

}

9876

9877

acx.Init(32,32,false);

9878

acx.AutoCorrelate(&i1,&opx);

9879

9880

acf.Init(32,32,true);

9881

acf.AutoCorrelate(&i1,&opf);

9882

9883

ccx.Init(32,32,false);

9884

ccx.CrossCorrelate(&i1,&i2,&opcx);

9885

9886

ccf.Init(32,32,true);

9887

ccf.CrossCorrelate(&i1,&i2,&opcf);

9888

9889

for (z=0;z<32;z++)

9890

mprintf("%8.4f - %8.4f - %8.4f - %8.4f - %8.4f\n",i1[z],opx[z],opf[z],opcx[z],opcf[z]);

9891

9892

gets(buf);

9893

9894

return 0;*/

9895

9896

//////////////// Cross-Correlation Test 2

9897

9898

/* CCrossCorrelation ccx, ccf;

9899

CxFloatArray i1, i2, opcx, opcf;

9900

9901

i1.SetSize(32);

9902

i2.SetSize(32);

9903

9904

for (z=0;z<32;z++)

9905

{

9906

i1[z] = ((rand()%200)/100.0)-1.0;

9907

i2[z] = ((rand()%200)/100.0)-1.0;

9908

}

9909

9910

ccx.Init(32,32,false);

9911

ccx.CrossCorrelate(&i1,&i2,&opcx);

9912

9913

ccf.Init(32,32,true);

9914

ccf.CrossCorrelate(&i1,&i2,&opcf);

9915

9916

for (z=0;z<32;z++)

9917

mprintf("%8.4f - %8.4f - %8.4f - %8.4f - %8.4f - %8.4f\n",i1[z],i2[z],opcx[z],opcf[z],ccf.m_pFFTback->m_pOutput[2*z]/64.0/(32-z),ccf.m_pFFTback->m_pOutput[2*z+1]/64.0/(32-z));

9918

9919

gets(buf);

9920

9921

return 0;*/

9922

9923

9924

/* a = fopen("E:\\tmptraj.xyz","wt");

9925

9926

for (z=0;z<200000;z++)

9927

{

9928

mfprintf(a,"4\n\n");

9929

mfprintf(a,"Ne %f %f %f\n",sin(pow(z/50.0,1.1))*3.0,cos(pow(z/50.0,1.1))*3.0,0);

9930

mfprintf(a,"Ne %f %f %f\n",-sin(pow(z/50.0,1.1))*3.0,-cos(pow(z/50.0,1.1))*3.0,0);

9931

9932

mfprintf(a,"Ne %f %f %f\n",0.0,0.0,cos(z/33.0)*2.0+4.0);

9933

mfprintf(a,"Ne %f %f %f\n",0.0,0.0,-cos(z/33.0)*2.0-4.0);

9934

}

9935

9936

fclose(a);

9937

return 0;*/

9938

9939

// mprintf("\"%s\"\n\"%d\"\n\"%s\"\n",RemovePath(__FILE__),__LINE__,__PRETTY_FUNCTION__);

9940

9941

/* CClusterAnalysis *can;

9942

can = new CClusterAnalysis();

9943

9944

for (z=0;z<15;z++)

9945

{

9946

can->AddCluster();

9947

can->AddParticle(rand()%20,rand()%20,rand()%20);

9948

9949

}

9950

9951

can->BuildTree();

9952

9953

can->DumpAgr("C:\\Software\\test.csv");

9954

9955

gets(buf);

9956

9957

return 0;*/

9958

9959

/* int maj, min;

9960

CreateTicks(0,540,maj,min);

9961

return 0;*/

9962

9963

/* CExtendedCondition *ec;

9964

9965

ec = new CExtendedCondition();

9966

9967

ec->m_fD[0] = 1;

9968

ec->m_fA[0] = 1;

9969

9970

ec->m_fD[1] = 2;

9971

ec->m_fA[1] = 1;

9972

9973

ec->m_fD[2] = 2;

9974

ec->m_fA[2] = 0;

9975

9976

if (!ec->Evaluate())

9977

{

9978

printf("Fail.\n");

9979

// return 0;

9980

}

9981

9982

printf("%G * d + %G * a %c %G.\n",ec->m_fX,ec->m_fY,ec->m_bLarger?'>':'<',ec->m_fZ);

9983

return 0;*/

9984

9985

/* CLMWrapper w;

9986

double *px, *py, *pp, r, integral;

9987

9988

px = new double[100];

9989

py = new double[100];

9990

pp = new double[6];

9991

9992

pp[0] = 1;

9993

pp[1] = -0.001;

9994

pp[2] = 1;

9995

pp[3] = -0.01;

9996

pp[4] = 1;

9997

pp[5] = -0.0001;

9998

9999

for (z=0;z<100;z++)

10000

{

10001

px[z] = z;

10002

py[z] = 0.2 * exp(-0.004 * z) + 0.3 * exp(-0.05 * z) + 0.5 * exp(-0.15 * z) + 0.1 * exp(-0.1 * z);

10003

}

10004

10005

w.Fit_TriExp(100,px,py,pp,r,integral);

10006

10007

return 0;*/

10008

10009

/* C3DF *df3;

10010

10011

df3 = new C3DF();

10012

df3->m_fMinVal[0] = -100;

10013

df3->m_fMaxVal[0] = 100;

10014

df3->m_fMinVal[1] = -100;

10015

df3->m_fMaxVal[1] = 100;

10016

df3->m_fMinVal[2] = -100;

10017

df3->m_fMaxVal[2] = 100;

10018

df3->m_iRes[0] = 101;

10019

df3->m_iRes[1] = 101;

10020

df3->m_iRes[2] = 101;

10021

df3->Create();

10022

10023

for (z=0;z<101;z++)

10024

for (z2=0;z2<101;z2++)

10025

for (z3=0;z3<101;z3++)

10026

if (sqrt(pow(z-50,2)+pow(z2-50,2)+pow(z3-50,2)) < 30)

10027

df3->AddToBin(CxVector3(z-50,z2-50,z3-50));

10028

10029

df3->WritePLT("","C:\\test.plt","",true);

10030

df3->WriteCube("","C:\\test.cube","",true);

10031

return 0;*/

10032

10033

/* CDF *mdf;

10034

10035

mdf = new CDF();

10036

mdf->m_fMinVal = 0;

10037

mdf->m_fMaxVal = 1;

10038

mdf->m_iResolution = 20;

10039

mdf->Create(true);

10040

10041

srand(time(NULL));

10042

for (z=0;z<1000000;z++)

10043

mdf->AddToBin(z/999999.0);

10044

mdf->Write("","D:\\Software\\out.csv","");

10045

return 0;*/

10046

10047

/* CAutoCorrelation *ac;

10048

10049

ac = new CAutoCorrelation();

10050

10051

#define N 23

10052

10053

ac->Init(N,N,false);

10054

10055

ptfa = new CxFloatArray();

10056

ptfa->SetSize(N);

10057

ptfa2 = new CxFloatArray();

10058

ptfa2->SetSize(N);

10059

10060

for (z=0;z<N;z++)

10061

ptfa->SetAt(z,sin(z/1.3)*exp(-0.01*z));

10062

10063

ac->AutoCorrelate(ptfa,ptfa2);

10064

10065

mprintf("Classic:\n");

10066

for (z=0;z<N;z++)

10067

mprintf("%02d: %.10f\n",z,ptfa2->GetAt(z));

10068

10069

ac->Init(N,N,true);

10070

10071

for (z=0;z<N;z++)

10072

ptfa->SetAt(z,sin(z/1.3)*exp(-0.01*z));

10073

10074

ac->AutoCorrelate(ptfa,ptfa2);

10075

10076

mprintf("\nFFT:\n");

10077

for (z=0;z<N;z++)

10078

mprintf("%02d: %.10f\n",z,ptfa2->GetAt(z));

10079

10080

gets(buf);

10081

10082

return 0;*/

10083

10084

10085

/* fft = new CFFT();

10086

10087

fft->PrepareFFT_R2C(300);

10088

10089

for (z=0;z<300;z++)

10090

{

10091

fft->m_pInput[z*2] = sin(z/3.1) * exp(-10.0/z);

10092

fft->m_pInput[z*2+1] = sin(z/2.7+1.0) * exp(-2.0/z);

10093

}

10094

10095

fft->DoFFT();

10096

10097

for (z=0;z<300;z++)

10098

mprintf("%03d: % 10.6f % 10.6f\n",z+1,fft->m_pOutput[z*2],fft->m_pOutput[z*2+1]);

10099

10100

gets(buf);

10101

return 0;*/

10102

10103

/* CxVector3 v1, v2, v3, v;

10104

10105

v1 = CxVector3(0,0,0);

10106

v2 = CxVector3(1,0,0);

10107

v3 = CxVector3(1,1,0);

10108

10109

v = PointFromRAD(v1,v2,v3,3,3.1415926/2,3.1415926/2);

10110

10111

v.Dump();

10112

10113

gets(buf);

10114

return 0;*/

10115

10116

/* fft = new CFFT();

10117

fft->PrepareFFT_C2C(20);

10118

for (z=0;z<20;z++)

10119

{

10120

if (z < 20)

10121

{

10122

fft->m_pInput[2*z] = sin(2*z*17.89) * exp(-0.1*z*2);

10123

fft->m_pInput[2*z+1] = sin((2*z+1)*17.89) * exp(-0.1*(2*z+1));

10124

} else

10125

{

10126

fft->m_pInput[2*z] = 0;

10127

fft->m_pInput[2*z+1] = 0;

10128

}

10129

printf("%2d: % f + I * % f\n",z+1,fft->m_pInput[2*z],fft->m_pInput[2*z+1]);

10130

}

10131

printf("Transforming...\n");

10132

fft->DoFFT();

10133

for (z=0;z<20;z++)

10134

printf("%2d: % f + I * % f\n",z+1,fft->m_pOutput[2*z],fft->m_pOutput[2*z+1]);

10135

gets(buf);

10136

10137

return 0;*/

10138

10139

10140

/* vec0 = CxVector3(-4.20694017, 9.48010063, -2.43410969);

10141

vec1 = CxVector3(0.159780025, -0.360321045, 0.0924463272);

10142

10143

tf = DotP(vec0,vec1);

10144

10145

tf2 = Angle_Deg(vec0,vec1);

10146

10147

printf("DotP: %f, Length 1: %f, Length 2: %f, DotP/Length1/Length2: %.10f, Angle: %.10f\n",tf,vec0.GetLength(),vec1.GetLength(),tf/vec0.GetLength()/vec1.GetLength(),tf2);

10148

10149

printf("acos(1)=%f, acos(-1)=%f\n",acos(1.0f),acos(-1.0f));

10150

return 0;*/

10151

10152

10153

/* CxVector3 a1, a2, a3;

10154

10155

a1 = CxVector3(0,1.0,0);

10156

a2 = CxVector3(0,-1.0,0.0001);

10157

a3 = CxVector3(1.0,0,0);

10158

10159

mprintf("Dihedral = %.3f\n",Dihedral(a1,a2,a3,false));

10160

getchar();

10161

return 0;*/

10162

10163

/* CGrace *g = new CGrace();

10164

10165

g->m_fMinValX = 1.37;

10166

g->m_fMaxValX = 2.53;

10167

g->m_fMinValY = 225;

10168

g->m_fMaxValY = 8337;

10169

g->MakeTicks();

10170

10171

printf("X: %f - %f Ticks %f\nY: %f - %f Ticks %f\n",g->m_fMinRangeX,g->m_fMaxRangeX,g->m_fTickMajorX,g->m_fMinRangeY,g->m_fMaxRangeY,g->m_fTickMajorY);

10172

10173

10174

/* CDatabaseTable *dt = new CDatabaseTable();

10175

10176

dt->AddInt(0,0,12345);

10177

dt->AddInt(1,1,123456);

10178

dt->AddInt(2,2,123);

10179

dt->AddInt(3,3,1);

10180

dt->AddInt(4,4,123456789);

10181

10182

dt->AddDouble(1,0,13.45);

10183

dt->AddDouble(2,1,3.199);

10184

dt->AddDouble(3,2,1367.4597);

10185

dt->AddDouble(4,3,13.45);

10186

dt->AddDouble(0,4,1.45);

10187

10188

dt->AddString(2,0,"Hallo!");

10189

dt->AddString(3,1,"Hiu");

10190

dt->AddString(4,2,"Hallo Welt!");

10191

dt->AddString(0,3,"Dies ist ein Test");

10192

dt->AddString(1,4,"^^");

10193

10194

dt->AddBool(3,0,true);

10195

dt->AddBool(4,1,false);

10196

dt->AddBool(0,2,true);

10197

dt->AddBool(1,3,false);

10198

dt->AddBool(2,4,true);

10199

10200

dt->DumpTable();

10201

a = fopen("table.dat","wt");

10202

dt->DumpOutputFile(a);

10203

fclose(a);

10204

10205

return 0;*/

10206

10207

/* CFFAtomNode *no;

10208

10209

no = new CFFAtomNode();

10210

10211

no->REC_Parse("O2=O(C,Si(O,S)(C))",0);

10212

10213

no->REC_DumpTree(0,0xFFFFFFFF,false);

10214

10215

10216

gets(buf);

10217

10218

return 0;*/

10219

10220

/* C2DF *t2df;

10221

10222

t2df = new C2DF();

10223

10224

t2df->m_iRes[0] = 100;

10225

t2df->m_iRes[1] = 100;

10226

t2df->m_fMinVal[0] = 0;

10227

t2df->m_fMaxVal[0] = 500.0;

10228

t2df->m_fMinVal[1] = 0;

10229

t2df->m_fMaxVal[1] = 500.0;

10230

t2df->Create();

10231

10232

FILE *aa;

10233

char *pp;

10234

10235

aa = fopen(argv[1],"rt");

10236

10237

z = 0;

10238

while (!feof(aa))

10239

{

10240

z++;

10241

if ((z%5000)==0)

10242

mprintf("\n");

10243

if ((z%100)==0)

10244

mprintf(".");

10245

fgets(buf,256,aa);

10246

if (feof(aa))

10247

break;

10248

buf[strlen(buf)-1] = 0;

10249

pp = strchr(buf,' ');

10250

*pp = 0;

10251

tf = atof(buf);

10252

pp++;

10253

tf2 = atof(pp);

10254

// mprintf("%f | %f\n",tf,tf2);

10255

t2df->AddToBin(tf,tf2);

10256

}

10257

10258

fclose(aa);

10259

10260

mprintf("\n%.0f Entries, %.0f skipped.\n\n",t2df->m_fBinEntries,t2df->m_fSkipEntries);

10261

10262

t2df->CorrectRadialDist(0);

10263

t2df->CorrectRadialDist(1);

10264

t2df->NormalizeBinIntegral(1000000.0);

10265

10266

t2df->WriteMathematicaNb("cdf.nb","","",false);

10267

10268

return 0;*/

10269

10270

10271

/***********************************************************************************************************/

10272

10273

10274

10275

int xv0[] = {

10276

0, 166, 333, 500, 667, 834, 1001, 1168, 1335, 1502,

10277

1669, 1836, 2003, 2170, 2337, 2504, 2671, 2838, 3004, 3171,

10278

3338, 3505, 3672, 3839, 4006, 4173, 4340, 4507, 4674, 4841,

10279

5008, 5175, 5342, 5509, 5676, 5843, 6009, 6176, 6343, 6510,

10280

6677, 6844, 7011, 7178, 7345, 7512, 7679, 7846, 8013, 8180,

10281

8347, 8514, 8681, 8847, 9014, 9181, 9348, 9515, 9682, 9849,

10282

10016, 10183, 10350, 10517, 10684, 10851, 11018, 11185, 11352, 11519,

10283

11686, 11852, 12019, 12186, 12353, 12520, 12687, 12854, 13021, 13188,

10284

13355, 13522, 13689, 13856, 14023, 14190, 14357, 14524, 14691, 14857,

10285

15024, 15191, 15358, 15525, 15692, 15859, 16026, 16193, 16360, 16527,

10286

16694, 16861, 17028, 17195, 17362, 17529, 17695, 17862, 18029, 18196,

10287

18363, 18530, 18697, 18864, 19031, 19198, 19365, 19532, 19699, 19866,

10288

20033, 20200, 20367, 20534, 20700, 20867, 21034, 21201, 21368, 21535,

10289

21702, 21869, 22036, 22203, 22370, 22537, 22704, 22871, 23038, 23205,

10290

23372, 23538, 23705, 23872, 24039, 24206, 24373, 24540, 24707, 24874,

10291

25041, 25208, 25375, 25542, 25709, 25876, 26043, 26210, 26377, 26543,

10292

26710, 26877, 27044, 27211, 27378, 27545, 27712, 27879, 28046, 28213,

10293

28380, 28547, 28714, 28881, 29048, 29215, 29382, 29548, 29715, 29882,

10294

30049, 30216, 30383, 30550, 30717, 30884, 31051, 31218, 31385, 31552,

10295

31719, 31886, 32053, 32220, 32386, 32553, 32720, 32887, 33054, 33221,

10296

33388, 33555, 33722, 33889, 34056, 34223, 34390, 34557, 34724, 34891,

10297

35058, 35225, 35391, 35558, 35725, 35892, 36059, 36226, 36393, 36560,

10298

36727, 36894, 37061, 37228, 37395, 37562, 37729, 37896, 38063, 38230,

10299

38396, 38563, 38730, 38897, 39064, 39231, 39398, 39565, 39732, 39899,

10300

40066, 40233, 40400, 40567, 40734, 40901, 41068, 41234, 41401, 41568,

10301

41735, 41902, 42069, 42236, 42403, 42570, 42737, 42904, 43071, 43238,

10302

43405, 43572, 43739, 43906, 44073, 44239, 44406, 44573, 44740, 44907,

10303

45074, 45241, 45408, 45575, 45742, 45909, 46076, 46243, 46410, 46577,

10304

46744, 46911, 47077, 47244, 47411, 47578, 47745, 47912, 48079, 48246,

10305

48413, 48580, 48747, 48914, 49081, 49248, 49415, 49582, 49749, 49916,

10306

50082, 50249, 50416, 50583, 50750, 50917, 51084, 51251, 51418, 51585,

10307

51752, 51919, 52086, 52253, 52420, 52587, 52754, 52921, 53087, 53254,

10308

53421, 53588, 53755, 53922, 54089, 54256, 54423, 54590, 54757, 54924,

10309

55091, 55258, 55425, 55592, 55759, 55925, 56092, 56259, 56426, 56593,

10310

56760, 56927, 57094, 57261, 57428, 57595, 57762, 57929, 58096, 58263,

10311

58430, 58597, 58764, 58930, 59097, 59264, 59431, 59598, 59765, 59932,

10312

60099, 60266, 60433, 60600, 60767, 60934, 61101, 61268, 61435, 61602,

10313

61768, 61935, 62102, 62269, 62436, 62603, 62770, 62937, 63104, 63271,

10314

63438, 63605, 63772, 63939, 64106, 64273, 64440, 64607, 64773, 64940,

10315

65107, 65274, 65441, 65608, 65775, 65942, 66109, 66276, 66443, 66610,

10316

66777, 66944, 67111, 67278, 67445, 67612, 67778, 67945, 68112, 68279,

10317

68446, 68613, 68780, 68947, 69114, 69281, 69448, 69615, 69782, 69949,

10318

70116, 70283, 70450, 70616, 70783, 70950, 71117, 71284, 71451, 71618,

10319

71785, 71952, 72119, 72286, 72453, 72620, 72787, 72954, 73121, 73288,

10320

73455, 73621, 73788, 73955, 74122, 74289, 74456, 74623, 74790, 74957,

10321

75124, 75291, 75458, 75625, 75792, 75959, 76126, 76293, 76460, 76626,

10322

76793, 76960, 77127, 77294, 77461, 77628, 77795, 77962, 78129, 78296,

10323

78463, 78630, 78797, 78964, 79131, 79298, 79464, 79631, 79798, 79965,

10324

80132, 80299, 80466, 80633, 80800, 80967, 81134, 81301, 81468, 81635,

10325

81802, 81969, 82136, 82303, 82469, 82636, 82803, 82970, 83137, 83304,

10326

83471, 83638, 83805, 83972, 84139, 84306, 84473, 84640, 84807, 84974,

10327

85141, 85307, 85474, 85641, 85808, 85975, 86142, 86309, 86476, 86643,

10328

86810, 86977, 87144, 87311, 87478, 87645, 87812, 87979, 88146, 88312,

10329

88479, 88646, 88813, 88980, 89147, 89314, 89481, 89648, 89815, 89982,

10330

90149, 90316, 90483, 90650, 90817, 90984, 91151, 91317, 91484, 91651,

10331

91818, 91985, 92152, 92319, 92486, 92653, 92820, 92987, 93154, 93321,

10332

93488, 93655, 93822, 93989, 94155, 94322, 94489, 94656, 94823, 94990,

10333

95157, 95324, 95491, 95658, 95825, 95992, 96159, 96326, 96493, 96660,

10334

96827, 96994, 97160, 97327, 97494, 97661, 97828, 97995, 98162, 98329,

10335

98496, 98663, 98830, 98997, 99164, 99331, 99498, 99665, 99832, 99999 };

10336

10337

double yv[] = {

10338

10339

0.535508,

10340

0.393073,

10341

0.296141,

10342

0.226017,

10343

0.174104,

10344

0.13505,

10345

0.105128,

10346

0.0820967,

10347

0.0645619,

10348

0.0510392,

10349

0.0406872,

10350

0.0322757,

10351

0.0257705,

10352

0.0206065,

10353

0.0167599,

10354

0.0135311,

10355

0.0110249,

10356

0.00922048,

10357

0.00751678,

10358

0.0062541,

10359

0.00473929,

10360

0.00376091,

10361

0.00322141,

10362

0.00266083,

10363

0.00230204,

10364

0.00165769,

10365

0.00142532,

10366

0.00146844,

10367

0.00135552,

10368

0.000981507,

10369

0.000500664,

10370

7.63E-05,

10371

-0.00021215,

10372

-0.000345428,

10373

-0.000356055,

10374

-0.000586005,

10375

-0.000365747,

10376

-8.19E-06,

10377

0.000117745,

10378

0.000301018,

10379

0.000153056,

10380

0.000249429,

10381

0.00041901,

10382

0.000272173,

10383

0.000432356,

10384

0.00034246,

10385

0.000253033,

10386

-8.95E-07,

10387

-0.000191937,

10388

-0.000411342,

10389

-0.000388538,

10390

-0.00014581,

10391

-8.29E-05,

10392

5.60E-05,

10393

-5.46E-06,

10394

-0.00012311,

10395

-0.000203272,

10396

-0.000304272,

10397

-0.000385733,

10398

-0.00033551,

10399

-0.000174071,

10400

3.46E-05,

10401

-3.06E-05,

10402

-0.000196145,

10403

-0.00075811,

10404

-0.000873794,

10405

-0.000839649,

10406

-0.000891512,

10407

-0.00109231,

10408

-0.0012406,

10409

-0.00125277,

10410

-0.00116772,

10411

-0.000800529,

10412

-0.000503297,

10413

-0.000388711,

10414

-0.000192247,

10415

-0.000380379,

10416

-0.000626382,

10417

-0.000562528,

10418

-0.000338185,

10419

-0.000261972,

10420

-0.000172413,

10421

-0.00014704,

10422

-0.000147816,

10423

-0.000335954,

10424

-0.000423681,

10425

-0.00077368,

10426

-0.000829694,

10427

-0.000599776,

10428

-0.000274863,

10429

-0.000198762,

10430

2.44E-05,

10431

0.000157793,

10432

3.36E-05,

10433

5.52E-05,

10434

0.000132802,

10435

0.000160182,

10436

0.000267747,

10437

0.000285335,

10438

0.000302909,

10439

0.000112509,

10440

0.00033765,

10441

0.000410808,

10442

0.000399938,

10443

0.000217723,

10444

0.000252189,

10445

0.000413789,

10446

0.000334351,

10447

0.000221592,

10448

-0.000128382,

10449

-0.000407701,

10450

-0.000434761,

10451

-0.000446333,

10452

-0.000268609,

10453

-0.000328874,

10454

-0.000253456,

10455

-0.000364477,

10456

-0.000379713,

10457

-0.000270978,

10458

3.09E-05,

10459

3.43E-05,

10460

0.000132993,

10461

0.000223472,

10462

0.000196531,

10463

0.000394839,

10464

0.000353766,

10465

0.000120042,

10466

0.000186034,

10467

4.34E-05,

10468

-0.000169091,

10469

-0.000463253,

10470

-0.000526637,

10471

-0.000382341,

10472

-0.000317881,

10473

-0.000161383,

10474

-2.10E-05,

10475

-5.39E-05,

10476

-4.20E-05,

10477

-0.000428827,

10478

-0.000372915,

10479

-0.000230522,

10480

3.13E-05,

10481

-5.22E-05,

10482

1.12E-06,

10483

0.00020615,

10484

-3.95E-05,

10485

-0.000188001,

10486

-0.00036392,

10487

-0.000579835,

10488

-0.000763892,

10489

-0.000954471,

10490

-0.000672926,

10491

-0.000424378,

10492

-0.000254547,

10493

-0.000183938,

10494

-2.71E-05,

10495

0.000387271,

10496

0.000741082,

10497

0.00118213,

10498

0.00144803,

10499

0.00149683,

10500

0.00137681,

10501

0.00128621,

10502

0.00110935,

10503

0.000937524,

10504

0.000815979,

10505

0.000710253,

10506

0.000625412,

10507

0.00018105,

10508

-0.000126372,

10509

-0.000286713,

10510

-0.000268511,

10511

-9.48E-05,

10512

2.80E-05,

10513

0.000193522,

10514

0.000218011,

10515

0.000241254,

10516

0.000212373,

10517

-0.000144938,

10518

-0.000317461,

10519

-0.000310367,

10520

5.52E-05,

10521

7.28E-05,

10522

6.31E-06,

10523

-0.000100696,

10524

-0.000231523,

10525

-0.000232838,

10526

-0.000357755,

10527

-0.000312569,

10528

-0.000515436,

10529

-0.000606856,

10530

-0.000662088,

10531

-0.000494031,

10532

-0.000264875,

10533

-0.000439725,

10534

-0.00023842,

10535

-0.000240582,

10536

-0.000521013,

10537

-0.000548953,

10538

-0.000471158,

10539

-0.000383092,

10540

-0.000433934,

10541

-0.000297616,

10542

-0.000263819,

10543

2.98E-05,

10544

0.000241952,

10545

0.000294519,

10546

0.000128055,

10547

-0.000164661,

10548

-0.000125856,

10549

5.48E-05,

10550

0.00017835,

10551

0.000567644,

10552

0.000653388,

10553

0.00072292,

10554

0.00086677,

10555

0.000497185,

10556

0.000419213,

10557

0.000338733,

10558

0.000446219,

10559

0.000775549,

10560

0.00108515,

10561

0.00112122,

10562

0.00103212,

10563

0.000753898,

10564

0.000780644,

10565

0.000633858,

10566

0.000593352,

10567

0.000742397,

10568

0.000461387,

10569

0.000510694,

10570

0.000425991,

10571

0.000106824,

10572

1.30E-05,

10573

-0.000101644,

10574

-0.000247787,

10575

-5.23E-05,

10576

-1.88E-06,

10577

0.000314304,

10578

3.31E-05,

10579

-0.000493994,

10580

-0.000676519,

10581

-0.000815772,

10582

-0.000560616,

10583

-0.000419621,

10584

-0.000246948,

10585

-7.98E-06,

10586

5.47E-05,

10587

3.29E-06,

10588

9.70E-05,

10589

-6.67E-05,

10590

-0.000400225,

10591

-0.000545787,

10592

-0.000536147,

10593

-0.000382494,

10594

-0.000212611,

10595

0.00026384,

10596

0.000870903,

10597

0.00101919,

10598

0.000827203,

10599

0.000977354,

10600

0.000797584,

10601

0.000839661,

10602

0.000891465,

10603

0.000894189,

10604

0.000790827,

10605

0.000859716,

10606

0.00110719,

10607

0.00102985,

10608

0.00116294,

10609

0.00111391,

10610

0.00104187,

10611

0.000972879,

10612

0.000838099,

10613

0.000928914,

10614

0.000839244,

10615

0.000550288,

10616

0.000317816,

10617

0.000128915,

10618

-2.48E-05,

10619

-0.00015162,

10620

-0.000297103,

10621

-0.000498082,

10622

-0.000904425,

10623

-0.000721854,

10624

-0.000218374,

10625

9.71E-05,

10626

0.000350858,

10627

0.000214938,

10628

0.000131151,

10629

0.000248389,

10630

0.00052038,

10631

0.000395342,

10632

0.000123723,

10633

-0.000264557,

10634

-0.000841548,

10635

-0.00122576,

10636

-0.00109667,

10637

-0.0012236,

10638

-0.00124427,

10639

-0.00154254,

10640

-0.00141593,

10641

-0.00130058,

10642

-0.00124156,

10643

-0.000803948,

10644

-0.000595218,

10645

-6.42E-05,

10646

-4.95E-05,

10647

-1.82E-05,

10648

-4.49E-05,

10649

-4.76E-05,

10650

-0.000322162,

10651

-0.000217286,

10652

-0.000200726,

10653

-0.000318639,

10654

-0.000532153,

10655

-0.000347614,

10656

-3.16E-06,

10657

0.000644489,

10658

0.00100808,

10659

0.00107041,

10660

0.0011488,

10661

0.000744875,

10662

0.000428291,

10663

0.000290936,

10664

0.000258901,

10665

0.00057231,

10666

0.000625447,

10667

0.000833305,

10668

0.000679633,

10669

0.000736282,

10670

0.000384085,

10671

0.000100621,

10672

0.000125945,

10673

0.00018803,

10674

0.000247397,

10675

0.000140543,

10676

0.00023271,

10677

0.000206796,

10678

5.84E-05,

10679

1.03E-05,

10680

0.000149909,

10681

0.000621023,

10682

0.000754729,

10683

0.000771421,

10684

0.00105867,

10685

0.000834447,

10686

0.000733547,

10687

0.000612523,

10688

0.000335448,

10689

8.25E-06,

10690

-0.000189546,

10691

-0.000233238,

10692

-0.000519596,

10693

-0.00042089,

10694

-6.40E-06,

10695

7.77E-05,

10696

9.84E-05,

10697

-0.000171139,

10698

-0.000310745,

10699

-0.000261869,

10700

-0.000309991,

10701

-0.000362793,

10702

-0.000151421,

10703

-0.000194398,

10704

-0.00038984,

10705

-0.000337404,

10706

-0.000292472,

10707

-8.61E-05,

10708

5.75E-05,

10709

9.07E-05,

10710

0.000190954,

10711

0.000296186,

10712

0.000278313,

10713

-3.25E-05,

10714

-0.000333689,

10715

-0.000519787,

10716

-0.000496129,

10717

-0.000570476,

10718

-0.000303045,

10719

-0.000160277,

10720

0.000232384,

10721

0.000591203,

10722

0.00071829,

10723

0.000966969,

10724

0.00114479,

10725

0.00115608,

10726

0.00114881,

10727

0.0012485,

10728

0.0013597,

10729

0.00168101,

10730

0.00104358,

10731

0.000856327,

10732

0.000687258,

10733

0.000923271,

10734

0.000879711,

10735

0.000717467,

10736

0.000847053,

10737

0.000710694,

10738

0.000415626,

10739

0.000267475,

10740

0.00017531,

10741

0.000130545,

10742

7.53E-05,

10743

3.66E-05,

10744

0.000127371,

10745

0.000364506,

10746

0.000782998,

10747

0.000713517,

10748

0.000554627,

10749

0.000520172,

10750

0.000294821,

10751

0.000494704,

10752

0.00086818,

10753

0.000818739,

10754

0.000570463,

10755

0.000593457,

10756

0.000274417,

10757

0.000465056,

10758

0.000570629,

10759

0.000410949,

10760

0.000267827,

10761

0.000521008,

10762

0.000639421,

10763

0.000740811,

10764

0.000654325,

10765

0.000120355,

10766

-0.000199765,

10767

-0.000367148,

10768

-0.00050777,

10769

-0.000554528,

10770

-0.000742839,

10771

-0.000954415,

10772

-0.00111473,

10773

-0.00065717,

10774

-0.000384281,

10775

-0.000584488,

10776

-0.000387121,

10777

6.11E-07,

10778

6.18E-05,

10779

2.74E-06,

10780

-0.000239685,

10781

-0.00039921,

10782

-0.000224125,

10783

-4.40E-05,

10784

8.77E-06,

10785

-6.21E-05,

10786

-0.000519798,

10787

-0.000574988,

10788

-0.000376014,

10789

-0.000261826,

10790

0.000255553,

10791

0.000595628,

10792

0.0006648,

10793

0.000842629,

10794

0.000902367,

10795

0.000586933,

10796

0.00018307,

10797

0.000255133,

10798

9.85E-05,

10799

0.000368992,

10800

0.000562369,

10801

0.00085546,

10802

0.000859038,

10803

0.000907761,

10804

0.000390729,

10805

0.00050405,

10806

0.000698643,

10807

0.000572906,

10808

0.000644083,

10809

0.000435071,

10810

0.000530602,

10811

0.00063087,

10812

0.000323015,

10813

0.000115957,

10814

-5.61E-05,

10815

-0.000302566,

10816

-0.000569679,

10817

-0.000301438,

10818

0.000363858,

10819

0.000895815,

10820

0.00128842,

10821

0.00100383,

10822

0.00158317,

10823

0.00128054,

10824

0.000798382,

10825

0.000581018,

10826

0.000703249,

10827

0.000438639,

10828

0.000442378,

10829

0.000251144,

10830

-0.000178674,

10831

-4.74E-05,

10832

-7.63E-05,

10833

-0.000290456,

10834

-0.000425779,

10835

-0.00117202,

10836

-0.00130518,

10837

-0.00135565,

10838

-0.00117334,

10839

-0.000820887,

10840

-0.000492772,

10841

-0.000300751,

10842

0.00020894,

10843

0.000542867,

10844

0.00112235,

10845

0.0013269,

10846

0.0015155,

10847

0.00171764,

10848

0.00160906,

10849

0.00137222,

10850

0.0015151,

10851

0.00146072,

10852

0.000792795,

10853

0.000521727,

10854

0.000575187,

10855

0.000491216,

10856

0.000296697,

10857

0.000245324,

10858

0.000225258,

10859

1.92E-05,

10860

-0.000372311,

10861

-4.10E-05,

10862

-0.000128977,

10863

1.09E-05,

10864

-0.000600517,

10865

-0.0008249,

10866

-0.000992362,

10867

-0.000963039,

10868

-0.00113936,

10869

-0.00146438,

10870

-0.00111718,

10871

-0.00112647,

10872

-0.00135347,

10873

-0.00101142,

10874

-0.000652267,

10875

-0.000734747,

10876

-0.000377075,

10877

-0.00011074,

10878

-0.00051855,

10879

-0.000619458,

10880

-0.000187873,

10881

-0.000102412,

10882

0.000484728,

10883

0.000783395,

10884

0.000441902,

10885

0.000299374,

10886

0.000947764,

10887

0.00141674,

10888

0.00155242,

10889

0.00180191,

10890

0.00230594,

10891

0.00251656,

10892

0.0024539,

10893

0.00254168,

10894

0.0024158,

10895

0.00195566,

10896

0.0019329,

10897

0.00160632,

10898

0.00188157,

10899

0.001764,

10900

0.00108332,

10901

0.000869896,

10902

0.00067471,

10903

0.000615986,

10904

0.000794104,

10905

0.000386439,

10906

-5.17E-05,

10907

-0.000309826,

10908

-0.000247388,

10909

-0.0004103,

10910

-0.000398971,

10911

-0.000322127,

10912

-0.000306698,

10913

-0.000682788,

10914

-0.000919077,

10915

-0.000967931,

10916

-0.00112106,

10917

-0.00105072,

10918

-0.000969028,

10919

-0.000764652,

10920

-0.000580761,

10921

-0.000390856,

10922

-0.000211922,

10923

-0.000408224,

10924

0.000178671,

10925

0.000698164,

10926

0.00156287,

10927

0.00143122,

10928

0.000691728,

10929

-0.000475124,

10930

-0.000888173,

10931

-0.000686491,

10932

-0.0009318,

10933

-0.000852938,

10934

-0.00018467,

10935

-0.000494222,

10936

-0.000801158,

10937

-0.000975636 };

10938

10939

double coeff[] = { 200.00000,191.41233,183.19339,175.32736,167.79909,160.59407,

10940

153.69842,147.09886,140.78267,134.73769,128.95227,123.41527,

10941

118.11602,113.04431,108.19037,103.54485,99.09880,94.84366,

10942

90.77123,86.87366,83.14344,79.57340,76.15664,72.88660,

10943

69.75697,66.76172,63.89508,61.15153,58.52578,56.01278,

10944

53.60768,51.30585,49.10286,46.99446,44.97660,43.04537,

10945

41.19708,39.42814,37.73516,36.11487,34.56416,33.08003,

10946

31.65963,30.30021,28.99917,27.75399,26.56228,25.42174,

10947

24.33017,23.28547,22.28563,21.32872,20.41290,19.53641,

10948

18.69754,17.89470,17.12633,16.39096,15.68715,15.01357,

10949

14.36892,13.75194,13.16145,12.59632,12.05545,11.53781,

10950

11.04240,10.56825,10.11447,9.68017,9.26452,8.86672,

10951

8.48600,8.12162,7.77289,7.43914,7.11971,6.81400,

10952

6.52142,6.24140,5.97341,5.71692,5.47144,5.23651,

10953

5.01166,4.79647,4.59051,4.39341,4.20476,4.02421,

10954

3.85142,3.68605,3.52777,3.37630,3.23132,3.09258,

10955

2.95979,2.83270,2.71107,2.59466,2.48325,2.37662,

10956

2.27457,2.17691,2.08343,1.99397,1.90836,1.82641,

10957

1.74799,1.67293,1.60110,1.53235,1.46656,1.40358,

10958

1.34332,1.28564,1.23043,1.17760,1.12704,1.07864,

10959

1.03233,0.98800,0.94558,0.90498,0.86612,0.82893,

10960

0.79334,0.75927,0.72667,0.69547,0.66561,0.63703,

10961

0.60967,0.58349,0.55844,0.53446,0.51151,0.48955,

10962

0.46853,0.44841,0.42916,0.41073,0.39309,0.37621,

10963

0.36006,0.34460,0.32980,0.31564,0.30209,0.28912,

10964

0.27670,0.26482,0.25345,0.24257,0.23215,0.22218,

10965

0.21264,0.20351,0.19478,0.18641,0.17841,0.17075,

10966

0.16342,0.15640,0.14968,0.14326,0.13711,0.13122,

10967

0.12558,0.12019,0.11503,0.11009,0.10536,0.10084,

10968

0.09651,0.09237,0.08840,0.08460,0.08097,0.07749,

10969

0.07417,0.07098,0.06793,0.06502,0.06223,0.05955,

10970

0.05700,0.05455,0.05221,0.04997,0.04782,0.04577,

10971

0.04380,0.04192,0.04012,0.03840,0.03675,0.03517,

10972

0.03366,0.03222,0.03083,0.02951,0.02824,0.02703,

10973

0.02587,0.02476,0.02369,0.02268,0.02170,0.02077,

10974

0.01988,0.01903,0.01821,0.01743,0.01668,0.01596,

10975

0.01528,0.01462,0.01399,0.01339,0.01282,0.01227,

10976

0.01174,0.01124,0.01075,0.01029,0.00985,0.00943,

10977

0.00902,0.00864,0.00826,0.00791,0.00757,0.00724,

10978

0.00693,0.00664,0.00635,0.00608,0.00582,0.00557,

10979

0.00533,0.00510,0.00488,0.00467,0.00447,0.00428,

10980

0.00409,0.00392,0.00375,0.00359,0.00344,0.00329,

10981

0.00315,0.00301,0.00288,0.00276,0.00264,0.00253,

10982

0.00242,0.00231,0.00222,0.00212,0.00203,0.00194,

10983

0.00186,0.00178,0.00170,0.00163,0.00156,0.00149,

10984

0.00143,0.00137,0.00131,0.00125,0.00120,0.00115,

10985

0.00110,0.00105,0.00101,0.00096,0.00092,0.00088,

10986

0.00084,0.00081,0.00077,0.00074,0.00071,0.00068,

10987

0.00065,0.00062,0.00059,0.00057,0.00054,0.00052,

10988

0.00050,0.00048,0.00046,0.00044,0.00042,0.00040 };

10989

10990

double xv[600];

10991

10992

for (z=0;z<600;z++)

10993

xv[z] = xv0[z]*0.005;

10994

10995

10996

CDF *tmpdf;

10997

CLTSpec *tlsp;

10998

10999

tmpdf = new CDF();

11000

tmpdf->m_fMinVal = 0;

11001

tmpdf->m_fMaxVal = 500.0;

11002

tmpdf->m_iResolution = 600;

11003

tmpdf->m_bLeft = true;

11004

tmpdf->Create();

11005

11006

for (z=0;z<600;z++)

11007

tmpdf->m_pBin[z] = yv[z];

11008

11009

tlsp = new CLTSpec();

11010

tlsp->m_bLSpecDataLin = true;

11011

tlsp->m_fLSpecMinExp = 0.005;

11012

tlsp->m_fLSpecMaxExp = 2500.0;

11013

tlsp->m_iLSpecData = 600;

11014

tlsp->m_iLSpecPoints = 300;

11015

tlsp->m_iMaxLMIter = 200;

11016

tlsp->m_fLSpecZeroWeight = 1.0;

11017

11018

tlsp->ComputeSpectrum("rdyn","bla","","",tmpdf);

11019

11020

11021

return 0;

11022

11023

/****************************************************************************************************************/

11024

9033

o->m_pPlProj->m_p2DF->WriteHistogram(buf,multibuf,".csv");

9034

}

9035

mprintf(WHITE,"\n Note: ");

9036

mprintf("The atoms of the ref. molecule are only drawn in the Mathematica Notebook (.nb)!\n\n");

9037

_skipplproj:;

9038

} // END IF PlProj

9039

9040

if (g_bRDF)

9041

{

9042

for (zr=0;zr<g_iCDFChannels;zr++)

9043

{

9044

if (o->m_pRDF[zr] == NULL)

9045

continue;

9046

mprintf(WHITE,"* Radial Distribution Function\n");

9047

9048

o->m_pRDF[zr]->m_pRDF->CalcMeanSD();

9049

mprintf(" Mean value: %10G pm Standard deviation: %10G pm\n",o->m_pRDF[zr]->m_pRDF->m_fMean,o->m_pRDF[zr]->m_pRDF->m_fSD);

9050

mprintf(" Min. value: %10G pm Max.value: %10G pm\n",o->m_pRDF[zr]->m_pRDF->m_fMinInput,o->m_pRDF[zr]->m_pRDF->m_fMaxInput);

9051

9052

o->m_pRDF[zr]->m_pRDF->MultiplyBin(1.0 / g_iSteps);

9053

9054

if (o->m_pRDF[zr]->m_bCalcSD)

9055

{

9056

mprintf(GREEN,"\n>>> Standard Deviation Engine >>>\n\n");

9057

o->m_pRDF[zr]->m_pRDF->m_pSDEngine->FinishAnalysis();

9058

o->m_pRDF[zr]->m_pRDF->m_pSDEngine->DumpData(o->m_pRDF[zr]->m_pRDF,o->m_pRDF[zr]->m_fSDTimesSigma,o->m_pRDF[zr]->m_bSDVerbose);

9059

mprintf(GREEN,"\n<<< Standard Deviation Engine <<<\n\n");

9060

}

9061

if (o->m_pRDF[zr]->m_bAdaptive)

9062

{

9063

// o->m_pRDF[zr]->m_pRDF->WriteHenry("rdf_",o->m_pRDF[zr]->m_sName,".csv");

9064

o->m_pRDF[zr]->m_pRDF->PrepareAdapt();

9065

o->m_pRDF[zr]->m_pRDF->BinTree_RadialDist();

9066

if (o->m_iShowMol == g_iFixMol)

9067

9068

9069

9070

mprintf(" Saving RDF as \"rdf_%s.csv\"...\n",o->m_pRDF[zr]->m_sName);

9071

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".001.csv",5,10,0.001,true);

9072

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".002.csv",5,10,0.002,true);

9073

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".005.csv",5,10,0.005,true);

9074

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".010.csv",5,10,0.01,true);

9075

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".020.csv",5,10,0.02,true);

9076

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".050.csv",5,10,0.05,true);

9077

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".100.csv",5,10,0.1,true);

9078

9079

/* o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".50.csv",16,0,50,true);

9080

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".100.csv",16,0,100,true);

9081

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".500.csv",16,0,500,true);

9082

o->m_pRDF[zr]->m_pRDF->WriteAdapted("rdf_",o->m_pRDF[zr]->m_sName,".1000.csv",16,0,1000,true);*/

9083

} else

9084

{

9085

if (o->m_pRDF[zr]->m_bRadialCorrect)

9086

{

9087

mprintf(" Correcting radial distribution...\n");

9088

9089

if (o->m_pRDF[zr]->m_bLongMode)

9090

{

9091

o->m_pRDF[zr]->m_pRDF->CorrectRadialDistLong();

9092

} else

9093

{

9094

o->m_pRDF[zr]->m_pRDF->CorrectRadialDist();

9095

}

9096

}

9097

if (o->m_bOthers && o->m_pRDF[zr]->m_bRadialCorrect)

9098

{

9099

if (o->m_pRDF[zr]->m_bProbDens)

9100

{

9101

mprintf(" Scaling RDF to nm^(-3) ...\n");

9102

if (o->m_bObsCertain)

9103

{

9104

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / o->m_waObsRefList.GetSize());

9105

o->m_pRDF[zr]->m_pRDF->MultiplyBin(1e9 / (4.0/3.0*Pi) / o->m_waObsRefList.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

9106

} else

9107

{

9108

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / (double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

9109

o->m_pRDF[zr]->m_pRDF->MultiplyBin(1e9 / (4.0/3.0*Pi) / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

9110

}

9111

if (g_bDoubleBox)

9112

{

9113

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_iDoubleBoxFactor);

9114

o->m_pRDF[zr]->m_pRDF->MultiplyIntegral(g_iDoubleBoxFactor);

9115

}

9116

} else

9117

{

9118

mprintf(" Scaling RDF to uniform density ...\n");

9119

if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)

9120

{

9121

if (o->m_bObsCertain)

9122

{

9123

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / o->m_waObsRefList.GetSize());

9124

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ / (4.0/3.0*Pi) / o->m_waObsRefList.GetSize() / o->m_pRDF[zr]->m_iShowAtomGes / o->m_waObsShowList.GetSize() / o->m_pRDF[zr]->m_iRefAtomGes);

9125

} else

9126

{

9127

if (g_bRegionAnalysis)

9128

{

9129

9130

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_fBoxX*g_fBoxY*g_fBoxZ * g_iSteps / (4.0/3.0*Pi) / (o->m_pRDF[zr]->m_pRDF->m_fBinEntries + o->m_pRDF[zr]->m_pRDF-> m_fSkipEntries) );

9131

} else

9132

{

9133

o->m_pRDF[zr]->m_pRDF->Integrate(true,1.0 / (double)((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

9134

9135

}

9136

}

9137

if (g_bDoubleBox)

9138

{

9139

o->m_pRDF[zr]->m_pRDF->MultiplyBin(g_iDoubleBoxFactor);

9140

o->m_pRDF[zr]->m_pRDF->MultiplyIntegral(g_iDoubleBoxFactor);

9141

}

9142

} else

9143

{

9144

eprintf(" Uniform density not defined if box is not XYZ-periodic!\n");

9145

goto _rdfint1;

9146

}

9147

}

9148

} else

9149

{

9150

_rdfint1:

9151

mprintf(" Scaling RDF to integral value 1000 ...\n");

9152

o->m_pRDF[zr]->m_pRDF->NormBinIntegral(1000.0);

9153

o->m_pRDF[zr]->m_pRDF->Integrate(false,1000.0);

9154

}

9155

sprintf(buf,"rdf_%s%s.csv",o->m_pRDF[zr]->m_sName,multibuf);

9156

mprintf(" Saving RDF as \"%s\"...\n",buf);

9157

o->m_pRDF[zr]->m_pRDF->Write("",buf,"",true);

9158

sprintf(buf,"rdf_%s%s.agr",o->m_pRDF[zr]->m_sName,multibuf);

9159

mprintf(" Saving RDF AGR file as \"%s\"...\n",buf);

9160

o->m_pRDF[zr]->m_pRDF->WriteAgr("",buf,"",o->m_pRDF[zr]->m_sName,true);

9161

if (o->m_pRDF[zr]->m_iHistogramRes != 0)

9162

{

9163

mprintf(" Calculating Histogram...\n");

9164

o->m_pRDF[zr]->m_pRDF->CalcHistogram();

9165

sprintf(buf,"his_rdf_%s%s.csv",o->m_pRDF[zr]->m_sName,multibuf);

9166

mprintf(" Saving Histogram as \"%s\"...\n",buf);

9167

o->m_pRDF[zr]->m_pRDF->WriteHistogram("",buf,"");

9168

}

9169

if (o->m_bObsCertain && o->m_bDecompDist)

9170

{

9171

sprintf(buf,"rdf_decomp_mol_%s%s",o->m_pRDF[zr]->m_sName,multibuf);

9172

mprintf(" Saving RDF molecule decomposition as \"%s.csv\"...\n",buf);

9173

o->m_pRDF[zr]->m_pRDF->WriteMulti("",buf,".csv");

9174

mprintf(" Saving RDF molecule decomposition as \"%s.agr\"...\n",buf);

9175

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr("",buf,".agr",buf,true);

9176

9177

sprintf(buf,"rdf_decomp_nb_%s%s_cumulative",o->m_pRDF[zr]->m_sName,multibuf);

9178

mprintf(" Saving cumulative RDF molecule decomposition as \"%s.csv\"...\n",buf);

9179

o->m_pRDF[zr]->m_pRDF->WriteMulti_Cumulative("",buf,".csv");

9180

mprintf(" Saving cumulative RDF molecule decomposition as \"%s.agr\"...\n",buf);

9181

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr_Cumulative("",buf,".agr",buf,true);

9182

}

9183

if (o->m_bDecompType)

9184

{

9185

sprintf(buf,"rdf_decomp_type_%s%s",o->m_pRDF[zr]->m_sName,multibuf);

9186

mprintf(" Saving RDF type decomposition as \"%s.csv\"...\n",buf);

9187

o->m_pRDF[zr]->m_pRDF->WriteMulti("",buf,".csv");

9188

mprintf(" Saving RDF type decomposition as \"%s.agr\"...\n",buf);

9189

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr("",buf,".agr",buf,true);

9190

9191

sprintf(buf,"rdf_decomp_type_%s%s_cumulative",o->m_pRDF[zr]->m_sName,multibuf);

9192

mprintf(" Saving cumulative RDF type decomposition as \"%s.csv\"...\n",buf);

9193

o->m_pRDF[zr]->m_pRDF->WriteMulti_Cumulative("",buf,".csv");

9194

mprintf(" Saving cumulative RDF type decomposition as \"%s.agr\"...\n",buf);

9195

o->m_pRDF[zr]->m_pRDF->WriteMultiAgr_Cumulative("",buf,".agr",buf,true);

9196

}

9197

9198

if (o->m_bTimeDiff)

9199

o->WriteTimeDiff(o->m_pRDF[zr]->m_pRDF,"RDF","rdf",o->m_pRDF[zr]->m_sName,multibuf,false);

9200

9201

if (o->m_pRDF[zr]->m_bACF)

9202

{

9203

o->m_pRDF[zr]->Autocorrelate();

9204

}

9205

}

9206

if (o->m_bTimeDev)

9207

{

9208

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

9209

{

9210

fclose(o->m_pRDF[zr]->m_fDist[0]);

9211

mprintf(" Saving temporal development as \"rdf_timedev_%s%s.csv\"...\n",o->m_pRDF[zr]->m_sName,multibuf);

9212

} else

9213

{

9214

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

9215

{

9216

fclose(o->m_pRDF[zr]->m_fDist[z2]);

9217

sprintf(buf,"rdf_timedev_%s_ref%d%s.csv",o->m_pRDF[zr]->m_sName,o->m_waSaveRefList[z2]+1,multibuf);

9218

mprintf(" Saving temporal development as \"%s\"...\n",buf);

9219

}

9220

}

9221

delete[] o->m_pRDF[zr]->m_fDist;

9222

o->m_pRDF[zr]->m_fDist = NULL;

9223

if (o->m_bCombinedPlot)

9224

{

9225

sprintf(buf,"combined_%s%s.agr",o->m_pRDF[zr]->m_sName,multibuf);

9226

mprintf(" Saving combined plot as \"%s\"...\n",buf);

9227

o->m_pRDF[zr]->m_pRDF->CreateCombinedPlot(true);

9228

o->m_pRDF[zr]->m_pRDF->m_pCombinedPlot->WriteAgr(buf,false);

9229

}

9230

}

9231

}

9232

} // END IF RDF

9233

9234

if (g_bVHDF)

9235

{

9236

mprintf(WHITE,"* Van Hove Correlation Function\n");

9237

9238

o->m_pVHDF->CorrectCount();

9239

if (o->m_pVHDF->m_bRadialCorrect)

9240

{

9241

mprintf(" Correcting radial distribution...\n");

9242

o->m_pVHDF->m_pVHDF->CorrectRadialDist(1);

9243

if (g_bPeriodicX && g_bPeriodicY && g_bPeriodicZ)

9244

{

9245

mprintf(" Normalizing bin to uniform density...\n");

9246

o->m_pVHDF->m_pVHDF->MultiplyBin(3.0f/4.0f/Pi*g_fBoxX*g_fBoxY*g_fBoxZ);

9247

}

9248

if (g_bDoubleBox)

9249

o->m_pVHDF->m_pVHDF->MultiplyBin(g_iDoubleBoxFactor);

9250

} else

9251

{

9252

mprintf(" Normalizing bin integral to 1000000...\n");

9253

o->m_pVHDF->m_pVHDF->NormalizeBinIntegral(1000000.0);

9254

}

9255

9256

sprintf(buf,"vhcf_%s%s",o->m_pVHDF->m_sName,multibuf);

9257

9258

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_TRIPLES"))

9259

{

9260

mprintf(" Saving VHCF triples as \"%s_triples.csv\"...\n",buf);

9261

o->m_pVHDF->m_pVHDF->Write("",buf,"_triples.csv");

9262

}

9263

9264

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_MATRIX"))

9265

{

9266

mprintf(" Saving VHCF matrix as \"%s_matrix.csv\"...\n",buf);

9267

o->m_pVHDF->m_pVHDF->WriteCSV("",buf,"_matrix.csv");

9268

}

9269

9270

if (o->m_pVHDF->m_iGraceBunchDist > 0)

9271

{

9272

sprintf(buf,"vhcf_dist_%s%s.agr",o->m_pVHDF->m_sName,multibuf);

9273

mprintf(" Saving VHCF distance Grace Stack as \"%s\"...\n",buf);

9274

o->m_pVHDF->m_pVHDF->WriteGraceBunch(0,o->m_pVHDF->m_iGraceBunchDist,1.0f,"",buf,"");

9275

}

9276

9277

if (o->m_pVHDF->m_iGraceBunchTime > 0)

9278

{

9279

sprintf(buf,"vhcf_time_%s%s.agr",o->m_pVHDF->m_sName,multibuf);

9280

mprintf(" Saving VHCF time Grace Stack as \"%s\"...\n",buf);

9281

o->m_pVHDF->m_pVHDF->WriteGraceBunch(1,o->m_pVHDF->m_iGraceBunchTime,1.0f,"",buf,"");

9282

}

9283

9284

if (o->m_pVHDF->m_bSwapAxes)

9285

o->m_pVHDF->m_pVHDF->SwapAxes();

9286

9287

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_MATHEMATICA"))

9288

{

9289

sprintf(buf,"vhcf_%s%s.nb",o->m_pVHDF->m_sName,multibuf);

9290

mprintf(" Saving VHCF Mathematica Notebook as \"%s\"...\n",buf);

9291

o->m_pVHDF->m_pVHDF->WriteMathematicaNb("",buf,"",false);

9292

}

9293

9294

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_GNUPLOT"))

9295

{

9296

sprintf(buf,"vhcf_%s%s",o->m_pVHDF->m_sName,multibuf);

9297

mprintf(" Saving VHCF Gnuplot Input as \"%s.gp\"...\n",buf);

9298

o->m_pVHDF->m_pVHDF->WriteGnuplotInput("",buf,"",false);

9299

}

9300

} // END IF VHDF

9301

9302

if (g_bCDF)

9303

{

9304

if (g_iCDFChannels == 2)

9305

{

9306

mprintf(WHITE,"* Combined Distribution Function (2D)\n");

9307

/* if (o->m_pConditions != NULL)

9308

{

9309

mprintf(" Conditions: %.2f percent of the molecules passed.\n",o->m_pConditions->m_fPassed/(o->m_pConditions->m_fPassed+o->m_pConditions->m_fFailed)*100.0);

9310

mprintf(" After conditions: ");

9311

} else mprintf(" ");*/

9312

9313

if (o->m_pCDF->m_p2DF->m_fBinEntries == 0)

9314

{

9315

eprintf(" There were no bin entries. Check your CDF definition. Skipping this CDF.\n\n");

9316

goto _skipsdf;

9317

}

9318

for (z2=0;z2<2;z2++)

9319

{

9320

if (g_iObsChannel[z2] == 0)

9321

{

9322

if ((o->m_pRDF[z2]->m_bRadialCorrect) && (o->m_pCDF->m_iNormalize != 3))

9323

{

9324

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

9325

o->m_pCDF->m_p2DF->CorrectRadialDist(z2);

9326

}

9327

}

9328

if (g_iObsChannel[z2] == 1)

9329

{

9330

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine) && (o->m_pCDF->m_iNormalize != 3))

9331

{

9332

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

9333

o->m_pCDF->m_p2DF->CorrectAngle(z2);

9334

}

9335

if (o->m_pADF[z2]->m_bMirror)

9336

{

9337

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

9338

if (o->m_pADF[z2]->m_bCosine)

9339

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

9340

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

9341

}

9342

}

9343

if (g_iObsChannel[z2] == 6)

9344

{

9345

if (o->m_pLiDF[z2]->m_bRadialCorrect)

9346

{

9347

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

9348

o->m_pCDF->m_p2DF->CorrectLiRadialDist(z2);

9349

}

9350

}

9351

}

9352

o->m_pCDF->m_fFactor = 1.0;

9353

switch(o->m_pCDF->m_iNormalize)

9354

{

9355

case 3:

9356

mprintf(" Normalizing CDF to uniform density.\n");

9357

9358

break;

9359

case 2:

9360

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

9361

o->m_pCDF->m_p2DF->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9362

break;

9363

case 1:

9364

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

9365

o->m_pCDF->m_fFactor = o->m_pCDF->m_p2DF->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9366

break;

9367

case 0:

9368

mprintf(" Not normalizing this CDF.\n");

9369

break;

9370

}

9371

9372

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_TRIPLES"))

9373

{

9374

mprintf(" Saving CDF triples as \"%s%s_triples.csv\"...\n",o->m_pCDF->m_sName,multibuf);

9375

o->m_pCDF->m_p2DF->Write(o->m_pCDF->m_sName,multibuf,"_triples.csv");

9376

}

9377

9378

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_MATRIX"))

9379

{

9380

mprintf(" Saving CDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pCDF->m_sName,multibuf);

9381

o->m_pCDF->m_p2DF->WriteCSV(o->m_pCDF->m_sName,multibuf,"_matrix.csv");

9382

}

9383

9384

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_MATHEMATICA"))

9385

{

9386

mprintf(" Saving CDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9387

o->m_pCDF->m_p2DF->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,".nb",false);

9388

}

9389

9390

if (g_pDatabase->GetBool("/PLOT2D/FORMATS/WRITE_GNUPLOT"))

9391

{

9392

mprintf(" Saving CDF Gnuplot Input as \"%s%s.gp\"...\n",o->m_pCDF->m_sName,multibuf);

9393

o->m_pCDF->m_p2DF->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"",false);

9394

}

9395

9396

mprintf(" Saving combined plot AGR file as \"%s%s_combined.agr\"...\n",o->m_pCDF->m_sName,multibuf);

9397

o->m_pCDF->m_p2DF->WriteCombinedPlot(o->m_pCDF->m_sName,multibuf,"_combined.agr");

9398

if (o->m_pCDF->m_iHistogramRes != 0)

9399

{

9400

mprintf(" Calculating Histogram...\n");

9401

o->m_pCDF->m_p2DF->CalcHistogram();

9402

sprintf(buf,"his_%s",o->m_pCDF->m_sName);

9403

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

9404

o->m_pCDF->m_p2DF->WriteHistogram(buf,multibuf,".csv");

9405

}

9406

9407

if (o->m_pCDF->m_bGraceBunch)

9408

{

9409

if (o->m_pCDF->m_iGraceBunchC1 > 0)

9410

{

9411

if ((g_iObsChannel[1] == 0) && (o->m_bOthers))

9412

9413

else tf = 1;

9414

sprintf(buf,"cdf_c1_%s%s.agr",o->m_pCDF->m_sName,multibuf);

9415

mprintf(" Saving CDF Channel 1 Grace Stack as \"%s\"...\n",buf);

9416

o->m_pCDF->m_p2DF->WriteGraceBunch(0,o->m_pCDF->m_iGraceBunchC1,(float)tf,"",buf,"");

9417

}

9418

if (o->m_pCDF->m_iGraceBunchC2 > 0)

9419

{

9420

if ((g_iObsChannel[0] == 0) && (o->m_bOthers))

9421

tf = 1.0 / o->m_pCDF->m_fFactor * 3.0f/4.0f/Pi/g_iSteps*g_fBoxX*g_fBoxY*g_fBoxZ/((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize() /o->m_pRDF[0]->m_iShowAtomGes/((CMolecule*)g_oaMolecules[o->m_iShowMol])->m_laSingleMolIndex.GetSize()/o->m_pRDF[0]->m_iRefAtomGes;

9422

else tf = 1;

9423

sprintf(buf,"cdf_c2_%s%s.agr",o->m_pCDF->m_sName,multibuf);

9424

mprintf(" Saving CDF Channel 2 Grace Stack as \"%s\"...\n",buf);

9425

o->m_pCDF->m_p2DF->WriteGraceBunch(1,o->m_pCDF->m_iGraceBunchC2,(float)tf,"",buf,"");

9426

}

9427

}

9428

9429

if (o->m_pCDF->m_bAxisDivide)

9430

{

9431

if (o->m_pCDF->m_bAxisDivideAll)

9432

{

9433

mprintf(" Saving CDF X projection as \"%s%s_pX.csv\"...\n",o->m_pCDF->m_sName,multibuf);

9434

o->m_pCDF->m_p2DF->WriteXProjection(o->m_pCDF->m_sName,multibuf,"_pX.csv");

9435

9436

mprintf(" Saving CDF Y projection as \"%s%s_pY.csv\"...\n",o->m_pCDF->m_sName,multibuf);

9437

o->m_pCDF->m_p2DF->WriteYProjection(o->m_pCDF->m_sName,multibuf,"_pY.csv");

9438

9439

mprintf(" Saving X-normalized CDF Mathematica Notebook as \"%s%s_nX.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9440

9441

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

9442

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9443

9444

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

9445

if (g_iObsChannel[0] == 0)

9446

if (o->m_pRDF[0]->m_bRadialCorrect)

9447

tempc2df->UnCorrectRadialDist(0);

9448

if (g_iObsChannel[0] == 1)

9449

if (o->m_pADF[0]->m_bStat && (!o->m_pADF[0]->m_bCosine))

9450

tempc2df->UnCorrectAngle(0);

9451

tempc2df->NormalizeXCount();

9452

switch(o->m_pCDF->m_iNormalize)

9453

{

9454

case 2:

9455

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9456

break;

9457

case 1:

9458

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9459

break;

9460

case 0:

9461

break;

9462

}

9463

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nX.nb",false);

9464

tempc2df->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_nX",false);

9465

delete tempc2df;

9466

9467

mprintf(" Saving Y-normalized CDF Mathematica Notebook as \"%s%s_nY.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9468

9469

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

9470

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9471

9472

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

9473

if (g_iObsChannel[1] == 0)

9474

if (o->m_pRDF[1]->m_bRadialCorrect)

9475

tempc2df->UnCorrectRadialDist(1);

9476

if (g_iObsChannel[1] == 1)

9477

if (o->m_pADF[1]->m_bStat && (!o->m_pADF[1]->m_bCosine))

9478

tempc2df->UnCorrectAngle(1);

9479

tempc2df->NormalizeYCount();

9480

switch(o->m_pCDF->m_iNormalize)

9481

{

9482

case 2:

9483

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9484

break;

9485

case 1:

9486

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9487

break;

9488

case 0:

9489

break;

9490

}

9491

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nY.nb",false);

9492

tempc2df->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_nY",false);

9493

delete tempc2df;

9494

9495

mprintf(" Saving XY-normalized CDF Mathematica Notebook as \"%s%s_nXY.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9496

9497

try { tempc2df = new C2DF(); } catch(...) { tempc2df = NULL; }

9498

if (tempc2df == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9499

9500

tempc2df->CopyFrom(o->m_pCDF->m_p2DF);

9501

for (z2=0;z2<2;z2++)

9502

{

9503

if (g_iObsChannel[z2] == 0)

9504

if (o->m_pRDF[z2]->m_bRadialCorrect)

9505

tempc2df->UnCorrectRadialDist(z2);

9506

if (g_iObsChannel[z2] == 1)

9507

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine))

9508

tempc2df->UnCorrectAngle(z2);

9509

}

9510

tempc2df->NormalizeXCount();

9511

tempc2df->NormalizeYCount();

9512

switch(o->m_pCDF->m_iNormalize)

9513

{

9514

case 2:

9515

tempc2df->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9516

break;

9517

case 1:

9518

tempc2df->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9519

break;

9520

case 0:

9521

break;

9522

}

9523

tempc2df->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_nXY.nb",false);

9524

tempc2df->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_nXY",false);

9525

delete tempc2df;

9526

}

9527

9528

mprintf(" Calculating tensor product of CDF projections...\n");

9529

9530

try { o->m_pCDF->m_pTensorProduct = new C2DF(); } catch(...) { o->m_pCDF->m_pTensorProduct = NULL; }

9531

if (o->m_pCDF->m_pTensorProduct == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9532

9533

o->m_pCDF->m_pTensorProduct->CopyFrom(o->m_pCDF->m_p2DF);

9534

o->m_pCDF->m_pTensorProduct->MakeTensorProduct(o->m_pCDF->m_p2DF);

9535

switch(o->m_pCDF->m_iNormalize)

9536

{

9537

case 2:

9538

o->m_pCDF->m_pTensorProduct->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9539

break;

9540

case 1:

9541

o->m_pCDF->m_pTensorProduct->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9542

break;

9543

case 0:

9544

break;

9545

}

9546

if (o->m_pCDF->m_bAxisDivideAll)

9547

{

9548

mprintf(" Saving tensor product as \"%s%s_tensor.dat\"...\n",o->m_pCDF->m_sName,multibuf);

9549

o->m_pCDF->m_pTensorProduct->Write(o->m_pCDF->m_sName,multibuf,"_tensor.dat");

9550

mprintf(" Saving tensor product Mathematica Notebook as \"%s%s_tensor.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9551

o->m_pCDF->m_pTensorProduct->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_tensor.nb",false);

9552

mprintf(" Saving tensor product Gnuplot Input as \"%s%s_tensor.gp\"...\n",o->m_pCDF->m_sName,multibuf);

9553

o->m_pCDF->m_pTensorProduct->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_tensor",false);

9554

mprintf(" Calculating difference between CDF and tensor product...\n");

9555

}

9556

o->m_pCDF->m_p2DF->Subtract(o->m_pCDF->m_pTensorProduct);

9557

o->m_pCDF->m_p2DF->CalcMaxEntry();

9558

o->m_pCDF->m_p2DF->m_iColorScale = 4; // PlusMinus Scale

9559

o->m_pCDF->m_p2DF->m_fPlotExp = 1.0;

9560

// o->m_pCDF->m_p2DF->m_fMathematicaColorOffset = max(fabs(o->m_pCDF->m_p2DF->m_fMinEntry),fabs(o->m_pCDF->m_p2DF->m_fMaxEntry)) / 3.0;

9561

// o->m_pCDF->m_p2DF->m_fMathematicaColorScale = o->m_pCDF->m_p2DF->m_fMathematicaColorOffset * 2.0;

9562

mprintf(" Saving +/- correlation plot as \"%s%s_correlation.dat\"...\n",o->m_pCDF->m_sName,multibuf);

9563

o->m_pCDF->m_p2DF->Write(o->m_pCDF->m_sName,multibuf,"_correlation.dat");

9564

mprintf(" Saving +/- correlation plot Mathematica Notebook as \"%s%s_correlation.nb\"...\n",o->m_pCDF->m_sName,multibuf);

9565

o->m_pCDF->m_p2DF->WriteMathematicaNb(o->m_pCDF->m_sName,multibuf,"_correlation.nb",false);

9566

mprintf(" Saving +/- correlation plot Gnuplot Input as \"%s%s_correlation.gp\"...\n",o->m_pCDF->m_sName,multibuf);

9567

o->m_pCDF->m_p2DF->WriteGnuplotInput(o->m_pCDF->m_sName,multibuf,"_correlation",false);

9568

} // END IF AXISDIVIDE

9569

if (o->m_pCDF->m_bDumpDat)

9570

{

9571

fclose(o->m_pCDF->m_fDump);

9572

mprintf(" CDF raw data saved as cdfdump_%dd_%s%s.csv.\n",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

9573

}

9574

if (o->m_bTimeDev)

9575

{

9576

if ((o->m_waSaveRefList.GetSize() == 1) || (!o->m_bSaveSeparateFiles))

9577

{

9578

fclose(o->m_pCDF->m_fTimeDev[0]);

9579

// sprintf(buf,"cdf_timedev_%dd_%s_ref%d%s.csv",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

9580

mprintf(" Temporal development saved as cdf_timedev_%dd%s%s.csv\n",g_iCDFChannels,o->m_pCDF->m_sShortName,multibuf);

9581

} else

9582

{

9583

for (z2=0;z2<o->m_waSaveRefList.GetSize();z2++)

9584

{

9585

fclose(o->m_pCDF->m_fTimeDev[z2]);

9586

mprintf(" Temporal development saved as cdf_timedev_%dd%s_ref%d%s.csv\n",g_iCDFChannels,o->m_pCDF->m_sShortName,z2+1,multibuf);

9587

}

9588

}

9589

if (o->m_pCDF->m_bTDAnimation)

9590

{

9591

mprintf(WHITE," * Time dependent animation *\n");

9592

sprintf(buf,"animation_complete_%s%s.agr",o->m_pCDF->m_sName,multibuf);

9593

mprintf(" Saving complete Plot as \"%s\"...\n",buf);

9594

for (z2=0;z2<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z2++)

9595

{

9596

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(z2,2.0f);

9597

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(z2,GraceColor(z2,0.0));

9598

}

9599

o->m_pCDF->m_pTDAPlot->WriteAgr(buf,false);

9600

sprintf(buf,"render_%s%s",o->m_pCDF->m_sName,multibuf);

9601

mprintf(" Saving xmgrace render script for animation as \"%s\"...\n",buf);

9602

a = OpenFileWrite("gracebatch",true);

9603

mfprintf(a,"PRINT TO \"output.png\"\n");

9604

mfprintf(a,"HARDCOPY DEVICE \"PNG\"\n");

9605

mfprintf(a,"PAGE SIZE %d, %d\n",o->m_pCDF->m_iTDAResX,o->m_pCDF->m_iTDAResY);

9606

mfprintf(a,"DEVICE \"PNG\" FONT ANTIALIASING on\n");

9607

mfprintf(a,"DEVICE \"PNG\" OP \"compression:9\"\n");

9608

mfprintf(a,"PRINT\n");

9609

fclose(a);

9610

a = OpenFileWrite(buf,true);

9611

if (o->m_pCDF->m_bTDATrace)

9612

{

9613

for (z2=0;z2<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z2++)

9614

{

9615

o->m_pCDF->m_pTDAPlot->DuplicateSet(z2);

9616

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(z2,2.0f);

9617

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(z2,GraceColor(z2,0.7));

9618

o->m_pCDF->m_pTDAPlot->SetSetLineWidth(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled+z2,3.0f);

9619

o->m_pCDF->m_pTDAPlot->SetSetLineColorLong(o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled+z2,GraceColor(z2,0.0));

9620

}

9621

}

9622

for (z2=0;z2<o->m_pCDF->m_iTDASteps;z2++)

9623

{

9624

if (o->m_pCDF->m_bTDATrace)

9625

{

9626

for (z3=0;z3<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z3++)

9627

{

9628

9629

o->m_pCDF->m_pTDAPlot->SetSetRange(z3,0,z2*o->m_pCDF->m_iTDAStride);

9630

}

9631

} else

9632

{

9633

for (z3=0;z3<o->m_waSaveRefList.GetSize()*o->m_waSaveShowList.GetSize()*o->m_pCDF->m_iCombinationsEnabled;z3++)

9634

o->m_pCDF->m_pTDAPlot->SetSetRange(z3,z2*o->m_pCDF->m_iTDAStride,z2*o->m_pCDF->m_iTDAStride+o->m_pCDF->m_iTDATail);

9635

}

9636

9637

sprintf(buf,"animation_%05d_%s%s.agr",z2+1,o->m_pCDF->m_sName,multibuf);

9638

mprintf(" Saving frame \"%s\"...\n",buf);

9639

o->m_pCDF->m_pTDAPlot->WriteAgr(buf,false);

9640

mfprintf(a,"echo 'Printing frame %d of %d'\n",z2+1,o->m_pCDF->m_iTDASteps);

9641

mfprintf(a,"xmgrace %s -batch gracebatch -nosafe -hardcopy\n",buf);

9642

mfprintf(a,"mv output.png frame%04d.png\n",z2+1);

9643

}

9644

fclose(a);

9645

}

9646

}

9647

} // END IF CHANNELS == 2

9648

9649

if (g_iCDFChannels == 3)

9650

{

9651

mprintf(WHITE,"* Combined Distribution Function (3D)\n");

9652

9653

if (o->m_pCDF->m_p3DF->m_fBinEntries == 0)

9654

{

9655

eprintf(" There were no bin entries. Check your CDF definition. Skipping this CDF.\n\n");

9656

goto _skipsdf;

9657

}

9658

o->m_pCDF->m_p3DF->CalcMaxEntry();

9659

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9660

for (z2=0;z2<g_iCDFChannels;z2++)

9661

{

9662

if (g_iObsChannel[z2] == 0)

9663

{

9664

if (o->m_pRDF[z2]->m_bRadialCorrect)

9665

{

9666

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

9667

o->m_pCDF->m_p3DF->CorrectRadialDist(z2);

9668

o->m_pCDF->m_p3DF->CalcMaxEntry();

9669

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9670

}

9671

}

9672

if (g_iObsChannel[z2] == 1)

9673

{

9674

if (o->m_pADF[z2]->m_bStat && (!o->m_pADF[z2]->m_bCosine))

9675

{

9676

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

9677

o->m_pCDF->m_p3DF->CorrectAngle(z2);

9678

o->m_pCDF->m_p3DF->CalcMaxEntry();

9679

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9680

}

9681

if (o->m_pADF[z2]->m_bMirror)

9682

{

9683

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

9684

if (o->m_pADF[z2]->m_bCosine)

9685

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

9686

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

9687

o->m_pCDF->m_p3DF->CalcMaxEntry();

9688

mprintf(" Data range from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9689

}

9690

}

9691

}

9692

// o->m_pCDF->m_p3DF->CalcMaxEntry();

9693

// mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9694

o->m_pCDF->m_fFactor = 1.0;

9695

switch(o->m_pCDF->m_iNormalize)

9696

{

9697

case 2:

9698

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

9699

o->m_pCDF->m_p3DF->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9700

o->m_pCDF->m_p3DF->CalcMaxEntry();

9701

mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9702

break;

9703

case 1:

9704

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

9705

o->m_pCDF->m_fFactor = o->m_pCDF->m_p3DF->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9706

mprintf(" Factor was %G.\n",o->m_pCDF->m_fFactor);

9707

o->m_pCDF->m_p3DF->CalcMaxEntry();

9708

mprintf(" Data range now from %G to %G.\n",o->m_pCDF->m_p3DF->m_fMinEntry,o->m_pCDF->m_p3DF->m_fMaxEntry);

9709

break;

9710

case 0:

9711

mprintf(" Not normalizing this CDF.\n");

9712

break;

9713

}

9714

9715

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

9716

{

9717

try { temp3DF = new C3DF(); } catch(...) { temp3DF = NULL; }

9718

if (temp3DF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9719

9720

temp3DF->CopyFrom(o->m_pCDF->m_p3DF);

9721

if (z2 != 0)

9722

{

9723

temp3DF->Smooth(z2);

9724

sprintf(buf,".s%d%s.plt",z2,multibuf);

9725

} else sprintf(buf,"%s.plt",multibuf);

9726

mprintf(" Saving 3D CDF as \"%s%s\"...\n",o->m_pCDF->m_sName,buf);

9727

temp3DF->WritePLT("",o->m_pCDF->m_sName,buf,false);

9728

9729

if (z2 != 0)

9730

sprintf(buf,".s%d%s.cube",z2,multibuf);

9731

else sprintf(buf,"%s.cube",multibuf);

9732

mprintf(" Saving 3D CDF as \"%s%s\"...\n",o->m_pCDF->m_sName,buf);

9733

temp3DF->WriteCube("",o->m_pCDF->m_sName,buf,false);

9734

if (o->m_pCDF->m_iHistogramRes != 0)

9735

{

9736

mprintf(" Calculating Histogram...\n");

9737

temp3DF->CalcHistogram();

9738

if (z2 != 0)

9739

sprintf(buf,"his_%s.s%d",o->m_pCDF->m_sName,z2);

9740

else sprintf(buf,"his_%s",o->m_pCDF->m_sName);

9741

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

9742

temp3DF->WriteHistogram(buf,multibuf,".csv");

9743

}

9744

9745

if (o->m_pCDF->m_b3DSlices)

9746

{

9747

for (z3=0;z3<3;z3++)

9748

{

9749

if (o->m_pCDF->m_i3DSliceIntervals[z3] != 0)

9750

{

9751

if (z2 != 0)

9752

mprintf(WHITE," * Creating channel %d smooth grade %d slices...\n",z3+1,z2);

9753

else mprintf(WHITE," * Creating channel %d slices...\n",z3+1);

9754

9755

try { temp2dfa = new C2DF*[o->m_pCDF->m_i3DSliceIntervals[z3]]; } catch(...) { temp2dfa = NULL; }

9756

if (temp2dfa == NULL) NewException((double)o->m_pCDF->m_i3DSliceIntervals[z3]*sizeof(C2DF*),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9757

9758

tf = 0;

9759

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

9760

{

9761

try { temp2dfa[z4] = new C2DF(); } catch(...) { temp2dfa[z4] = NULL; }

9762

if (temp2dfa[z4] == NULL) NewException((double)sizeof(C2DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9763

9764

9765

9766

if (temp2dfa[z4]->m_fMaxEntry > tf)

9767

tf = temp2dfa[z4]->m_fMaxEntry;

9768

}

9769

9770

mprintf(" Setting common intensity range to 0 ... %.3f.\n",tf);

9771

9772

mprintf(" Writing out slice files...\n",z3+1);

9773

9774

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

9775

{

9776

temp2dfa[z4]->m_fMinEntry = 0;

9777

temp2dfa[z4]->m_fMaxEntry = tf;

9778

if (z2 != 0)

9779

9780

9781

mprintf(" %s ...\n",buf);

9782

temp2dfa[z4]->WriteMathematicaNb("",buf,"",true);

9783

if (z2 != 0)

9784

9785

9786

mprintf(" %s.gp ...\n",buf);

9787

temp2dfa[z4]->WriteGnuplotInput("",buf,"",true);

9788

}

9789

9790

for (z4=0;z4<o->m_pCDF->m_i3DSliceIntervals[z3];z4++)

9791

delete temp2dfa[z4];

9792

9793

delete[] temp2dfa;

9794

}

9795

}

9796

}

9797

}

9798

9799

mprintf(" Writing out 2D projections...\n");

9800

for (z3=0;z3<3;z3++)

9801

{

9802

mprintf(WHITE," * CDF 2D projection on channel %d\n",z3+1);

9803

9804

switch(z3)

9805

{

9806

case 0:

9807

tia[0] = 0;

9808

tia[1] = 1;

9809

break;

9810

case 1:

9811

tia[0] = 0;

9812

tia[1] = 2;

9813

break;

9814

case 2:

9815

tia[0] = 1;

9816

tia[1] = 2;

9817

break;

9818

}

9819

for (z2=0;z2<2;z2++)

9820

{

9821

if (g_iObsChannel[tia[z2]] == 0)

9822

{

9823

if (o->m_pRDF[tia[z2]]->m_bRadialCorrect)

9824

{

9825

mprintf(" Correcting radial distribution for CDF channel %d...\n",z2+1);

9826

o->m_pCDF->m_p3DF->m_p2DF[z3]->CorrectRadialDist(z2);

9827

}

9828

}

9829

if (g_iObsChannel[tia[z2]] == 1)

9830

{

9831

if (o->m_pADF[tia[z2]]->m_bStat && (!o->m_pADF[tia[z2]]->m_bCosine))

9832

{

9833

mprintf(" Correcting angular distribution for CDF channel %d...\n",z2+1);

9834

o->m_pCDF->m_p3DF->m_p2DF[z3]->CorrectAngle(z2);

9835

}

9836

/* if (o->m_pADF[z2]->m_bMirror)

9837

{

9838

mprintf(" Making channel %d mirror-symmetric...\n",z2+1);

9839

if (o->m_pADF[z2]->m_bCosine)

9840

o->m_pCDF->m_p2DF->Mirror(0.0f,z2);

9841

else o->m_pCDF->m_p2DF->Mirror(90.0f,z2);

9842

}*/

9843

}

9844

}

9845

o->m_pCDF->m_fFactor = 1.0;

9846

switch(o->m_pCDF->m_iNormalize)

9847

{

9848

case 2:

9849

mprintf(" Normalizing maximum value to %.2f.\n",o->m_pCDF->m_fNormValue);

9850

o->m_pCDF->m_p3DF->m_p2DF[z3]->NormalizeBin(0.0,o->m_pCDF->m_fNormValue);

9851

break;

9852

case 1:

9853

mprintf(" Normalizing integral value to %.2f.\n",o->m_pCDF->m_fNormValue);

9854

o->m_pCDF->m_p3DF->m_p2DF[z3]->NormalizeBinIntegral(o->m_pCDF->m_fNormValue);

9855

break;

9856

case 0:

9857

mprintf(" Not normalizing this CDF.\n");

9858

break;

9859

}

9860

mprintf(" Saving CDF triples as \"%s%s_triples.csv\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9861

o->m_pCDF->m_p3DF->m_p2DF[z3]->Write(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_triples.csv");

9862

mprintf(" Saving CDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9863

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteCSV(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_matrix.csv");

9864

mprintf(" Saving CDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9865

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteMathematicaNb(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,".nb",false);

9866

mprintf(" Saving CDF Gnuplot Input as \"%s%s.gp\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9867

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteGnuplotInput(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"",false);

9868

mprintf(" Saving combined plot AGR file as \"%s%s_combined.agr\"...\n",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf);

9869

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteCombinedPlot(o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName,multibuf,"_combined.agr");

9870

if (o->m_pCDF->m_iHistogramRes != 0)

9871

{

9872

mprintf(" Calculating Histogram...\n");

9873

o->m_pCDF->m_p3DF->m_p2DF[z3]->CalcHistogram();

9874

sprintf(buf,"his_%s",o->m_pCDF->m_p3DF->m_p2DF[z3]->m_sName);

9875

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

9876

o->m_pCDF->m_p3DF->m_p2DF[z3]->WriteHistogram(buf,multibuf,".csv");

9877

}

9878

}

9879

} // END IF CHANNELS == 3

9880

_skipsdf:;

9881

} // END IF CDF

9882

9883

if (g_bRevSDF)

9884

{

9885

mprintf(WHITE,"* Pseudo SDF\n");

9886

9887

if (o->m_pRevSDF->m_p2DF->m_fBinEntries == 0)

9888

{

9889

eprintf(" There were no bin entries. Check your function definition. Skipping this PseudoSDF.\n\n");

9890

goto _skiprevsdf;

9891

}

9892

mprintf(" Normalizing integral value to %.2f.\n",1000000.0f);

9893

o->m_pRevSDF->m_p2DF->NormalizeBinIntegral(1000000.0f);

9894

if (o->m_pRevSDF->m_bDrawAtoms)

9895

{

9896

mprintf(" Inserting reference atoms into the Pseudo SDF plot...\n");

9897

9898

if (((CAtom*)g_oaAtoms[g_iFixRealAtomType[0]])->m_pElement->m_fRadius == 0)

9899

o->m_pRevSDF->m_p2DF->AddCircle(0,0,50.0,0.4,0.4,0.4);

9900

9901

9902

if (((CAtom*)g_oaAtoms[g_iFixRealAtomType[1]])->m_pElement->m_fRadius == 0)

9903

o->m_pRevSDF->m_p2DF->AddCircle(0,o->m_pRevSDF->m_fSecondAtomPosX/o->m_pRevSDF->m_fSecondAtomCount,50.0,0.4,0.4,0.4);

9904

9905

}

9906

mprintf(" Saving PseudoSDF triples as \"%s%s_triples.csv\"...\n",o->m_pRevSDF->m_sName,multibuf);

9907

o->m_pRevSDF->m_p2DF->Write(o->m_pRevSDF->m_sName,multibuf,"_triples.csv");

9908

mprintf(" Saving PseudoSDF matrix as \"%s%s_matrix.csv\"...\n",o->m_pRevSDF->m_sName,multibuf);

9909

o->m_pRevSDF->m_p2DF->WriteCSV(o->m_pRevSDF->m_sName,multibuf,"_matrix.csv");

9910

mprintf(" Saving PseudoSDF Mathematica Notebook as \"%s%s.nb\"...\n",o->m_pRevSDF->m_sName,multibuf);

9911

o->m_pRevSDF->m_p2DF->WriteMathematicaNb(o->m_pRevSDF->m_sName,multibuf,".nb",false);

9912

mprintf(" Saving PseudoSDF Gnuplot Input as \"%s%s.gp\"...\n",o->m_pRevSDF->m_sName,multibuf);

9913

o->m_pRevSDF->m_p2DF->WriteGnuplotInput(o->m_pRevSDF->m_sName,multibuf,"",false);

9914

if (o->m_pRevSDF->m_iHistogramRes != 0)

9915

{

9916

mprintf(" Calculating Histogram...\n");

9917

o->m_pRevSDF->m_p2DF->CalcHistogram();

9918

sprintf(buf,"his_%s",o->m_pRevSDF->m_sName);

9919

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf,multibuf);

9920

o->m_pRevSDF->m_p2DF->WriteHistogram(buf,multibuf,".csv");

9921

}

9922

if (o->m_pRevSDF->m_bCreateRevSDF)

9923

{

9924

mprintf(" Creating volumetric Revolution SDF...\n");

9925

o->m_pRevSDF->CreateRevSDF();

9926

sprintf(buf,"revsdf_ref_%s.xyz",o->m_pRevSDF->m_sName);

9927

mprintf(" Saving Revolution SDF reference structure as \"%s\"...\n",buf);

9928

a = OpenFileWrite(buf,true);

9929

9930

fclose(a);

9931

for (z2=0;z2<=g_iSDFSmoothGrade;z2++)

9932

{

9933

try { tempSDF = new C3DF(); } catch(...) { tempSDF = NULL; }

9934

if (tempSDF == NULL) NewException((double)sizeof(C3DF),__FILE__,__LINE__,__PRETTY_FUNCTION__);

9935

9936

tempSDF->CopyFrom(o->m_pRevSDF->m_pRevSDF);

9937

if (z2 != 0)

9938

{

9939

tempSDF->Smooth(z2);

9940

sprintf(buf,".s%d%s.plt",z2,multibuf);

9941

} else sprintf(buf,"%s.plt",multibuf);

9942

mprintf(" Saving Revolution SDF as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

9943

tempSDF->WritePLT("revsdf_",o->m_pRevSDF->m_sName,buf,true);

9944

9945

if (z2 != 0)

9946

sprintf(buf,".s%d%s.cube",z2,multibuf);

9947

else sprintf(buf,"%s.cube",multibuf);

9948

mprintf(" Saving Revolution SDF as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

9949

tempSDF->WriteCube("revsdf_",o->m_pRevSDF->m_sName,buf,true);

9950

9951

if (z2 != 0)

9952

sprintf(buf,".s%d%s.his",z2,multibuf);

9953

else sprintf(buf,"%s.his",multibuf);

9954

mprintf(" Saving Revolution SDF Histogram as \"revsdf_%s%s\"...\n",o->m_pRevSDF->m_sName,buf);

9955

tempSDF->CalcHistogram();

9956

tempSDF->WriteHistogram("revsdf_",o->m_pRevSDF->m_sName,buf);

9957

if (o->m_pRevSDF->m_iHistogramRes != 0)

9958

{

9959

mprintf(" Calculating Histogram...\n");

9960

tempSDF->CalcHistogram();

9961

sprintf(buf2,"his_revsdf_%s",o->m_pRevSDF->m_sName);

9962

mprintf(" Saving Histogram as \"%s%s.csv\"...\n",buf2,buf);

9963

tempSDF->WriteHistogram(buf2,buf,".csv");

9964

}

9965

}

9966

}

9967

_skiprevsdf:;

9968

} // END IF REVSDF

9969

}

9970

9971

if (g_bSDF || g_bAvg || g_bVoidSDF)

9972

{

9973

9974

strtolower(buf);

9975

mprintf("\n*** Reference molecule ***\n");

9976

FreeFileName(buf);

9977

mprintf("Saving reference molecule as \"%s\"...",buf);

9978

a = OpenFileWrite(buf,true);

9979

if (a == NULL)

9980

{

9981

eprintf("\nError: Could not open %s for writing.\n",buf);

9982

return 0;

9983

}

9984

if (!g_bSaveVirtAtoms)

9985

mfprintf(a," %d \n\n",(int)(((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes-((CMolecule*)g_oaMolecules[g_iFixMol])->m_laVirtualAtoms.GetSize()));

9986

else mfprintf(a," %d \n\n",((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes);

9987

cc = 0;

9988

for (z=0;z<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z++)

9989

{

9990

if ((!g_bSaveVirtAtoms) && (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z] == g_iVirtAtomType))

9991

continue;

9992

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z];z2++)

9993

{

9994

if (g_bMiddleAvg)

9995

{

9996

g_pRefMol[cc][0] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

9997

g_pRefMol[cc][1] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

9998

g_pRefMol[cc][2] /= ((float)g_iSteps * ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize());

9999

}

10000

if (((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z] == g_iVirtAtomType)

10001

10002

else mfprintf(a," %s %9.6f %9.6f %9.6f\n",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z]])->m_sName,g_pRefMol[cc][0]/100.0,g_pRefMol[cc][1]/100.0,g_pRefMol[cc][2]/100.0);

10003

cc++;

10004

}

10005

}

10006

fclose(a);

10007

mprintf("Done.\n");

10008

if (g_iSwapAtoms)

10009

{

10010

mprintf("\n*** This is the swap matrix of reference molecule %s:\n (It shows how often the atoms\n have been swapped with each other)\n\n ",((CMolecule*)g_oaMolecules[g_iFixMol])->m_sName);

10011

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z2++)

10012

{

10013

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z2];z3++)

10014

{

10015

if (((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName[1] == 0)

10016

mprintf(" ");

10017

mprintf("%s%d ",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName,z3+1);

10018

if (z3 < 10)

10019

mprintf(" ");

10020

}

10021

}

10022

mprintf("\n");

10023

cc = 0;

10024

for (z2=0;z2<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z2++)

10025

{

10026

for (z3=0;z3<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z2];z3++)

10027

{

10028

mprintf("%s%d ",((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName,z3+1);

10029

if (((CAtom*)g_oaAtoms[((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex[z2]])->m_sName[1] == 0)

10030

mprintf(" ");

10031

if (z3 < 9)

10032

mprintf(" ");

10033

cc2 = 0;

10034

for (z4=0;z4<((CMolecule*)g_oaMolecules[g_iFixMol])->m_baAtomIndex.GetSize();z4++)

10035

{

10036

for (z5=0;z5<((CMolecule*)g_oaMolecules[g_iFixMol])->m_waAtomCount[z4];z5++)

10037

{

10038

if ((z2 == z4) && (z3 == z5))

10039

{

10040

mprintf(" *** ");

10041

goto _swm;

10042

}

10043

if (pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc2] != 0)

10044

mprintf("%3.0f%c ",(double)pSwapMatrix[cc*((CMolecule*)g_oaMolecules[g_iFixMol])->m_iAtomGes+cc2] * 100.0f / g_iSteps / ((CMolecule*)g_oaMolecules[g_iFixMol])->m_laSingleMolIndex.GetSize(),'%');

10045

else mprintf(" - ");

10046

_swm:

10047

cc2++;

10048

}

10049

}

10050

mprintf("\n");

10051

cc++;

10052

}

10053

}

10054

}

10055

}

10056

_ende:

10057

10058

if (g_bMultiInterval)

10059

{

10060

mprintf("\n");

10061

mprintf(YELLOW,"***********************************************\n");

10062

mprintf(YELLOW,"*** Interval %2d (%6d - %6d) finished. ***\n",multicounter+1,g_laMultiIntervalStart[multicounter]+1,g_laMultiIntervalEnd[multicounter]+1);

10063

mprintf(YELLOW,"***********************************************\n\n");

10064

multicounter++;

10065

if (multicounter < g_laMultiIntervalStart.GetSize())

10066

goto _multiintervalstart;

10067

}

10068

10069

g_iEndTime = time(NULL);

10070

if (((g_iEndTime-g_iStartTime) > 5) && (g_iStartTime != 0))

10071

{

10072

mprintf(WHITE,"\nAnalysis was running for %dh %dm %ds.\n",(g_iEndTime-g_iStartTime)/3600,((g_iEndTime-g_iStartTime)/60)%60,(g_iEndTime-g_iStartTime)%60);

10073

mprintf(WHITE," (%.3f steps per second)\n\n",g_iSteps/g_iStride/((double)g_iEndTime-g_iStartTime));

10074

} else mprintf("\n");

10075

10076

WriteCredits();

10077

10078

if (g_bSMode)

10079

{

10080

PrintSMode();

10081

} else

10082

{

10083

mprintf(WHITE,"*** The End ***\n\n");

10084

}

10085

UninstallSignalHandler();

10086

if (g_fInput != NULL)

10087

fclose(g_fInput);

10088

if (g_pDatabase != NULL)

10089

{

10090

delete g_pDatabase;

10091

g_pDatabase = NULL;

10092

}

10093

if (g_pTempTimestep != NULL)

10094

{

10095

delete g_pTempTimestep;

10096

g_pTempTimestep = NULL;

10097

}

10098

if (apfa != NULL)

10099

{

10100

delete[] apfa;

10101

apfa = NULL;

10102

}

10103

if (tda != NULL)

10104

{

10105

delete[] tda;

10106

tda = NULL;

10107

}

10108

RemoveAllAnalyses();

10109

RemoveAllElements();

10110

RemoveAllAtoms();

10111

RemoveAllMolecules();

10112

RemoveAllObservations();

10113

BTOUT;

10114

return 0;

10115

}

10116

10117

//////////////// Cross-Correlation Test 1

10118

10119

/* CAutoCorrelation acx, acf;

10120

CCrossCorrelation ccx, ccf;

10121

CxFloatArray i1, i2, opx, opf, opcx, opcf;

10122

10123

i1.SetSize(32);

10124

i2.SetSize(32);

10125

10126

for (z=0;z<32;z++)

10127

{

10128

i1[z] = ((rand()%200)/100.0)-1.0;

10129

i2[z] = i1[z];

10130

}

10131

10132

acx.Init(32,32,false);

10133

acx.AutoCorrelate(&i1,&opx);

10134

10135

acf.Init(32,32,true);

10136

acf.AutoCorrelate(&i1,&opf);

10137

10138

ccx.Init(32,32,false);

10139

ccx.CrossCorrelate(&i1,&i2,&opcx);

10140

10141

ccf.Init(32,32,true);

10142

ccf.CrossCorrelate(&i1,&i2,&opcf);

10143

10144

for (z=0;z<32;z++)

10145

mprintf("%8.4f - %8.4f - %8.4f - %8.4f - %8.4f\n",i1[z],opx[z],opf[z],opcx[z],opcf[z]);

10146

10147

gets(buf);

10148

10149

return 0;*/

10150

10151

//////////////// Cross-Correlation Test 2

10152

10153

/* CCrossCorrelation ccx, ccf;

10154

CxFloatArray i1, i2, opcx, opcf;

10155

10156

i1.SetSize(32);

10157

i2.SetSize(32);

10158

10159

for (z=0;z<32;z++)

10160

{

10161

i1[z] = ((rand()%200)/100.0)-1.0;

10162

i2[z] = ((rand()%200)/100.0)-1.0;

10163

}

10164

10165

ccx.Init(32,32,false);

10166

ccx.CrossCorrelate(&i1,&i2,&opcx);

10167

10168

ccf.Init(32,32,true);

10169

ccf.CrossCorrelate(&i1,&i2,&opcf);

10170

10171

for (z=0;z<32;z++)

10172

mprintf("%8.4f - %8.4f - %8.4f - %8.4f - %8.4f - %8.4f\n",i1[z],i2[z],opcx[z],opcf[z],ccf.m_pFFTback->m_pOutput[2*z]/64.0/(32-z),ccf.m_pFFTback->m_pOutput[2*z+1]/64.0/(32-z));

10173

10174

gets(buf);

10175

10176

return 0;*/

10177

10178

10179

/* a = fopen("E:\\tmptraj.xyz","wt");

10180

10181

for (z=0;z<200000;z++)

10182

{

10183

mfprintf(a,"4\n\n");

10184

mfprintf(a,"Ne %f %f %f\n",sin(pow(z/50.0,1.1))*3.0,cos(pow(z/50.0,1.1))*3.0,0);

10185

mfprintf(a,"Ne %f %f %f\n",-sin(pow(z/50.0,1.1))*3.0,-cos(pow(z/50.0,1.1))*3.0,0);

10186

10187

mfprintf(a,"Ne %f %f %f\n",0.0,0.0,cos(z/33.0)*2.0+4.0);

10188

mfprintf(a,"Ne %f %f %f\n",0.0,0.0,-cos(z/33.0)*2.0-4.0);

10189

}

10190

10191

fclose(a);

10192

return 0;*/

10193

10194

// mprintf("\"%s\"\n\"%d\"\n\"%s\"\n",RemovePath(__FILE__),__LINE__,__PRETTY_FUNCTION__);

10195

10196

/* CClusterAnalysis *can;

10197

can = new CClusterAnalysis();

10198

10199

for (z=0;z<15;z++)

10200

{

10201

can->AddCluster();

10202

can->AddParticle(rand()%20,rand()%20,rand()%20);

10203

10204

}

10205

10206

can->BuildTree();

10207

10208

can->DumpAgr("C:\\Software\\test.csv");

10209

10210

gets(buf);

10211

10212

return 0;*/

10213

10214

/* int maj, min;

10215

CreateTicks(0,540,maj,min);

10216

return 0;*/

10217

10218

/* CExtendedCondition *ec;

10219

10220

ec = new CExtendedCondition();

10221

10222

ec->m_fD[0] = 1;

10223

ec->m_fA[0] = 1;

10224

10225

ec->m_fD[1] = 2;

10226

ec->m_fA[1] = 1;

10227

10228

ec->m_fD[2] = 2;

10229

ec->m_fA[2] = 0;

10230

10231

if (!ec->Evaluate())

10232

{

10233

printf("Fail.\n");

10234

// return 0;

10235

}

10236

10237

printf("%G * d + %G * a %c %G.\n",ec->m_fX,ec->m_fY,ec->m_bLarger?'>':'<',ec->m_fZ);

10238

return 0;*/

10239

10240

/* CLMWrapper w;

10241

double *px, *py, *pp, r, integral;

10242

10243

px = new double[100];

10244

py = new double[100];

10245

pp = new double[6];

10246

10247

pp[0] = 1;

10248

pp[1] = -0.001;

10249

pp[2] = 1;

10250

pp[3] = -0.01;

10251

pp[4] = 1;

10252

pp[5] = -0.0001;

10253

10254

for (z=0;z<100;z++)

10255

{

10256

px[z] = z;

10257

py[z] = 0.2 * exp(-0.004 * z) + 0.3 * exp(-0.05 * z) + 0.5 * exp(-0.15 * z) + 0.1 * exp(-0.1 * z);

10258

}

10259

10260

w.Fit_TriExp(100,px,py,pp,r,integral);

10261

10262

return 0;*/

10263

10264

/* C3DF *df3;

10265

10266

df3 = new C3DF();

10267

df3->m_fMinVal[0] = -100;

10268

df3->m_fMaxVal[0] = 100;

10269

df3->m_fMinVal[1] = -100;

10270

df3->m_fMaxVal[1] = 100;

10271

df3->m_fMinVal[2] = -100;

10272

df3->m_fMaxVal[2] = 100;

10273

df3->m_iRes[0] = 101;

10274

df3->m_iRes[1] = 101;

10275

df3->m_iRes[2] = 101;

10276

df3->Create();

10277

10278

for (z=0;z<101;z++)

10279

for (z2=0;z2<101;z2++)

10280

for (z3=0;z3<101;z3++)

10281

if (sqrt(pow(z-50,2)+pow(z2-50,2)+pow(z3-50,2)) < 30)

10282

df3->AddToBin(CxVector3(z-50,z2-50,z3-50));

10283

10284

df3->WritePLT("","C:\\test.plt","",true);

10285

df3->WriteCube("","C:\\test.cube","",true);

10286

return 0;*/

10287

10288

/* CDF *mdf;

10289

10290

mdf = new CDF();

10291

mdf->m_fMinVal = 0;

10292

mdf->m_fMaxVal = 1;

10293

mdf->m_iResolution = 20;

10294

mdf->Create(true);

10295

10296

srand(time(NULL));

10297

for (z=0;z<1000000;z++)

10298

mdf->AddToBin(z/999999.0);

10299

mdf->Write("","D:\\Software\\out.csv","");

10300

return 0;*/

10301

10302

/* CAutoCorrelation *ac;

10303

10304

ac = new CAutoCorrelation();

10305

10306

#define N 23

10307

10308

ac->Init(N,N,false);

10309

10310

ptfa = new CxFloatArray();

10311

ptfa->SetSize(N);

10312

ptfa2 = new CxFloatArray();

10313

ptfa2->SetSize(N);

10314

10315

for (z=0;z<N;z++)

10316

ptfa->SetAt(z,sin(z/1.3)*exp(-0.01*z));

10317

10318

ac->AutoCorrelate(ptfa,ptfa2);

10319

10320

mprintf("Classic:\n");

10321

for (z=0;z<N;z++)

10322

mprintf("%02d: %.10f\n",z,ptfa2->GetAt(z));

10323

10324

ac->Init(N,N,true);

10325

10326

for (z=0;z<N;z++)

10327

ptfa->SetAt(z,sin(z/1.3)*exp(-0.01*z));

10328

10329

ac->AutoCorrelate(ptfa,ptfa2);

10330

10331

mprintf("\nFFT:\n");

10332

for (z=0;z<N;z++)

10333

mprintf("%02d: %.10f\n",z,ptfa2->GetAt(z));

10334

10335

gets(buf);

10336

10337

return 0;*/

10338

10339

10340

/* fft = new CFFT();

10341

10342

fft->PrepareFFT_R2C(300);

10343

10344

for (z=0;z<300;z++)

10345

{

10346

fft->m_pInput[z*2] = sin(z/3.1) * exp(-10.0/z);

10347

fft->m_pInput[z*2+1] = sin(z/2.7+1.0) * exp(-2.0/z);

10348

}

10349

10350

fft->DoFFT();

10351

10352

for (z=0;z<300;z++)

10353

mprintf("%03d: % 10.6f % 10.6f\n",z+1,fft->m_pOutput[z*2],fft->m_pOutput[z*2+1]);

10354

10355

gets(buf);

10356

return 0;*/

10357

10358

/* CxVector3 v1, v2, v3, v;

10359

10360

v1 = CxVector3(0,0,0);

10361

v2 = CxVector3(1,0,0);

10362

v3 = CxVector3(1,1,0);

10363

10364

v = PointFromRAD(v1,v2,v3,3,3.1415926/2,3.1415926/2);

10365

10366

v.Dump();

10367

10368

gets(buf);

10369

return 0;*/

10370

10371

/* fft = new CFFT();

10372

fft->PrepareFFT_C2C(20);

10373

for (z=0;z<20;z++)

10374

{

10375

if (z < 20)

10376

{

10377

fft->m_pInput[2*z] = sin(2*z*17.89) * exp(-0.1*z*2);

10378

fft->m_pInput[2*z+1] = sin((2*z+1)*17.89) * exp(-0.1*(2*z+1));

10379

} else

10380

{

10381

fft->m_pInput[2*z] = 0;

10382

fft->m_pInput[2*z+1] = 0;

10383

}

10384

printf("%2d: % f + I * % f\n",z+1,fft->m_pInput[2*z],fft->m_pInput[2*z+1]);

10385

}

10386

printf("Transforming...\n");

10387

fft->DoFFT();

10388

for (z=0;z<20;z++)

10389

printf("%2d: % f + I * % f\n",z+1,fft->m_pOutput[2*z],fft->m_pOutput[2*z+1]);

10390

gets(buf);

10391

10392

return 0;*/

10393

10394

10395

/* vec0 = CxVector3(-4.20694017, 9.48010063, -2.43410969);

10396

vec1 = CxVector3(0.159780025, -0.360321045, 0.0924463272);

10397

10398

tf = DotP(vec0,vec1);

10399

10400

tf2 = Angle_Deg(vec0,vec1);

10401

10402

printf("DotP: %f, Length 1: %f, Length 2: %f, DotP/Length1/Length2: %.10f, Angle: %.10f\n",tf,vec0.GetLength(),vec1.GetLength(),tf/vec0.GetLength()/vec1.GetLength(),tf2);

10403

10404

printf("acos(1)=%f, acos(-1)=%f\n",acos(1.0f),acos(-1.0f));

10405

return 0;*/

10406

10407

10408

/* CxVector3 a1, a2, a3;

10409

10410

a1 = CxVector3(0,1.0,0);

10411

a2 = CxVector3(0,-1.0,0.0001);

10412

a3 = CxVector3(1.0,0,0);

10413

10414

mprintf("Dihedral = %.3f\n",Dihedral(a1,a2,a3,false));

10415

getchar();

10416

return 0;*/

10417

10418

/* CGrace *g = new CGrace();

10419

10420

g->m_fMinValX = 1.37;

10421

g->m_fMaxValX = 2.53;

10422

g->m_fMinValY = 225;

10423

g->m_fMaxValY = 8337;

10424

g->MakeTicks();

10425

10426

printf("X: %f - %f Ticks %f\nY: %f - %f Ticks %f\n",g->m_fMinRangeX,g->m_fMaxRangeX,g->m_fTickMajorX,g->m_fMinRangeY,g->m_fMaxRangeY,g->m_fTickMajorY);

10427

10428

10429

/* CDatabaseTable *dt = new CDatabaseTable();

10430

10431

dt->AddInt(0,0,12345);

10432

dt->AddInt(1,1,123456);

10433

dt->AddInt(2,2,123);

10434

dt->AddInt(3,3,1);

10435

dt->AddInt(4,4,123456789);

10436

10437

dt->AddDouble(1,0,13.45);

10438

dt->AddDouble(2,1,3.199);

10439

dt->AddDouble(3,2,1367.4597);

10440

dt->AddDouble(4,3,13.45);

10441

dt->AddDouble(0,4,1.45);

10442

10443

dt->AddString(2,0,"Hallo!");

10444

dt->AddString(3,1,"Hiu");

10445

dt->AddString(4,2,"Hallo Welt!");

10446

dt->AddString(0,3,"Dies ist ein Test");

10447

dt->AddString(1,4,"^^");

10448

10449

dt->AddBool(3,0,true);

10450

dt->AddBool(4,1,false);

10451

dt->AddBool(0,2,true);

10452

dt->AddBool(1,3,false);

10453

dt->AddBool(2,4,true);

10454

10455

dt->DumpTable();

10456

a = fopen("table.dat","wt");

10457

dt->DumpOutputFile(a);

10458

fclose(a);

10459

10460

return 0;*/

10461

10462

/* CFFAtomNode *no;

10463

10464

no = new CFFAtomNode();

10465

10466

no->REC_Parse("O2=O(C,Si(O,S)(C))",0);

10467

10468

no->REC_DumpTree(0,0xFFFFFFFF,false);

10469

10470

10471

gets(buf);

10472

10473

return 0;*/

10474

10475

/* C2DF *t2df;

10476

10477

t2df = new C2DF();

10478

10479

t2df->m_iRes[0] = 100;

10480

t2df->m_iRes[1] = 100;

10481

t2df->m_fMinVal[0] = 0;

10482

t2df->m_fMaxVal[0] = 500.0;

10483

t2df->m_fMinVal[1] = 0;

10484

t2df->m_fMaxVal[1] = 500.0;

10485

t2df->Create();

10486

10487

FILE *aa;

10488

char *pp;

10489

10490

aa = fopen(argv[1],"rt");

10491

10492

z = 0;

10493

while (!feof(aa))

10494

{

10495

z++;

10496

if ((z%5000)==0)

10497

mprintf("\n");

10498

if ((z%100)==0)

10499

mprintf(".");

10500

fgets(buf,256,aa);

10501

if (feof(aa))

10502

break;

10503

buf[strlen(buf)-1] = 0;

10504

pp = strchr(buf,' ');

10505

*pp = 0;

10506

tf = atof(buf);

10507

pp++;

10508

tf2 = atof(pp);

10509

// mprintf("%f | %f\n",tf,tf2);

10510

t2df->AddToBin(tf,tf2);

10511

}

10512

10513

fclose(aa);

10514

10515

mprintf("\n%.0f Entries, %.0f skipped.\n\n",t2df->m_fBinEntries,t2df->m_fSkipEntries);

10516

10517

t2df->CorrectRadialDist(0);

10518

t2df->CorrectRadialDist(1);

10519

t2df->NormalizeBinIntegral(1000000.0);

10520

10521

t2df->WriteMathematicaNb("cdf.nb","","",false);

10522

10523

return 0;*/

10524

10525

10526

/***********************************************************************************************************/

10527

10528

10529

10530

int xv0[] = {

10531

0, 166, 333, 500, 667, 834, 1001, 1168, 1335, 1502,

10532

1669, 1836, 2003, 2170, 2337, 2504, 2671, 2838, 3004, 3171,

10533

3338, 3505, 3672, 3839, 4006, 4173, 4340, 4507, 4674, 4841,

10534

5008, 5175, 5342, 5509, 5676, 5843, 6009, 6176, 6343, 6510,

10535

6677, 6844, 7011, 7178, 7345, 7512, 7679, 7846, 8013, 8180,

10536

8347, 8514, 8681, 8847, 9014, 9181, 9348, 9515, 9682, 9849,

10537

10016, 10183, 10350, 10517, 10684, 10851, 11018, 11185, 11352, 11519,

10538

11686, 11852, 12019, 12186, 12353, 12520, 12687, 12854, 13021, 13188,

10539

13355, 13522, 13689, 13856, 14023, 14190, 14357, 14524, 14691, 14857,

10540

15024, 15191, 15358, 15525, 15692, 15859, 16026, 16193, 16360, 16527,

10541

16694, 16861, 17028, 17195, 17362, 17529, 17695, 17862, 18029, 18196,

10542

18363, 18530, 18697, 18864, 19031, 19198, 19365, 19532, 19699, 19866,

10543

20033, 20200, 20367, 20534, 20700, 20867, 21034, 21201, 21368, 21535,

10544

21702, 21869, 22036, 22203, 22370, 22537, 22704, 22871, 23038, 23205,

10545

23372, 23538, 23705, 23872, 24039, 24206, 24373, 24540, 24707, 24874,

10546

25041, 25208, 25375, 25542, 25709, 25876, 26043, 26210, 26377, 26543,

10547

26710, 26877, 27044, 27211, 27378, 27545, 27712, 27879, 28046, 28213,

10548

28380, 28547, 28714, 28881, 29048, 29215, 29382, 29548, 29715, 29882,

10549

30049, 30216, 30383, 30550, 30717, 30884, 31051, 31218, 31385, 31552,

10550

31719, 31886, 32053, 32220, 32386, 32553, 32720, 32887, 33054, 33221,

10551

33388, 33555, 33722, 33889, 34056, 34223, 34390, 34557, 34724, 34891,

10552

35058, 35225, 35391, 35558, 35725, 35892, 36059, 36226, 36393, 36560,

10553

36727, 36894, 37061, 37228, 37395, 37562, 37729, 37896, 38063, 38230,

10554

38396, 38563, 38730, 38897, 39064, 39231, 39398, 39565, 39732, 39899,

10555

40066, 40233, 40400, 40567, 40734, 40901, 41068, 41234, 41401, 41568,

10556

41735, 41902, 42069, 42236, 42403, 42570, 42737, 42904, 43071, 43238,

10557

43405, 43572, 43739, 43906, 44073, 44239, 44406, 44573, 44740, 44907,

10558

45074, 45241, 45408, 45575, 45742, 45909, 46076, 46243, 46410, 46577,

10559

46744, 46911, 47077, 47244, 47411, 47578, 47745, 47912, 48079, 48246,

10560

48413, 48580, 48747, 48914, 49081, 49248, 49415, 49582, 49749, 49916,

10561

50082, 50249, 50416, 50583, 50750, 50917, 51084, 51251, 51418, 51585,

10562

51752, 51919, 52086, 52253, 52420, 52587, 52754, 52921, 53087, 53254,

10563

53421, 53588, 53755, 53922, 54089, 54256, 54423, 54590, 54757, 54924,

10564

55091, 55258, 55425, 55592, 55759, 55925, 56092, 56259, 56426, 56593,

10565

56760, 56927, 57094, 57261, 57428, 57595, 57762, 57929, 58096, 58263,

10566

58430, 58597, 58764, 58930, 59097, 59264, 59431, 59598, 59765, 59932,

10567

60099, 60266, 60433, 60600, 60767, 60934, 61101, 61268, 61435, 61602,

10568

61768, 61935, 62102, 62269, 62436, 62603, 62770, 62937, 63104, 63271,

10569

63438, 63605, 63772, 63939, 64106, 64273, 64440, 64607, 64773, 64940,

10570

65107, 65274, 65441, 65608, 65775, 65942, 66109, 66276, 66443, 66610,

10571

66777, 66944, 67111, 67278, 67445, 67612, 67778, 67945, 68112, 68279,

10572

68446, 68613, 68780, 68947, 69114, 69281, 69448, 69615, 69782, 69949,

10573

70116, 70283, 70450, 70616, 70783, 70950, 71117, 71284, 71451, 71618,

10574

71785, 71952, 72119, 72286, 72453, 72620, 72787, 72954, 73121, 73288,

10575

73455, 73621, 73788, 73955, 74122, 74289, 74456, 74623, 74790, 74957,

10576

75124, 75291, 75458, 75625, 75792, 75959, 76126, 76293, 76460, 76626,

10577

76793, 76960, 77127, 77294, 77461, 77628, 77795, 77962, 78129, 78296,

10578

78463, 78630, 78797, 78964, 79131, 79298, 79464, 79631, 79798, 79965,

10579

80132, 80299, 80466, 80633, 80800, 80967, 81134, 81301, 81468, 81635,

10580

81802, 81969, 82136, 82303, 82469, 82636, 82803, 82970, 83137, 83304,

10581

83471, 83638, 83805, 83972, 84139, 84306, 84473, 84640, 84807, 84974,

10582

85141, 85307, 85474, 85641, 85808, 85975, 86142, 86309, 86476, 86643,

10583

86810, 86977, 87144, 87311, 87478, 87645, 87812, 87979, 88146, 88312,

10584

88479, 88646, 88813, 88980, 89147, 89314, 89481, 89648, 89815, 89982,

10585

90149, 90316, 90483, 90650, 90817, 90984, 91151, 91317, 91484, 91651,

10586

91818, 91985, 92152, 92319, 92486, 92653, 92820, 92987, 93154, 93321,

10587

93488, 93655, 93822, 93989, 94155, 94322, 94489, 94656, 94823, 94990,

10588

95157, 95324, 95491, 95658, 95825, 95992, 96159, 96326, 96493, 96660,

10589

96827, 96994, 97160, 97327, 97494, 97661, 97828, 97995, 98162, 98329,

10590

98496, 98663, 98830, 98997, 99164, 99331, 99498, 99665, 99832, 99999 };

10591

10592

double yv[] = {

10593

10594

0.535508,

10595

0.393073,

10596

0.296141,

10597

0.226017,

10598

0.174104,

10599

0.13505,

10600

0.105128,

10601

0.0820967,

10602

0.0645619,

10603

0.0510392,

10604

0.0406872,

10605

0.0322757,

10606

0.0257705,

10607

0.0206065,

10608

0.0167599,

10609

0.0135311,

10610

0.0110249,

10611

0.00922048,

10612

0.00751678,

10613

0.0062541,

10614

0.00473929,

10615

0.00376091,

10616

0.00322141,

10617

0.00266083,

10618

0.00230204,

10619

0.00165769,

10620

0.00142532,

10621

0.00146844,

10622

0.00135552,

10623

0.000981507,

10624

0.000500664,

10625

7.63E-05,

10626

-0.00021215,

10627

-0.000345428,

10628

-0.000356055,

10629

-0.000586005,

10630

-0.000365747,

10631

-8.19E-06,

10632

0.000117745,

10633

0.000301018,

10634

0.000153056,

10635

0.000249429,

10636

0.00041901,

10637

0.000272173,

10638

0.000432356,

10639

0.00034246,

10640

0.000253033,

10641

-8.95E-07,

10642

-0.000191937,

10643

-0.000411342,

10644

-0.000388538,

10645

-0.00014581,

10646

-8.29E-05,

10647

5.60E-05,

10648

-5.46E-06,

10649

-0.00012311,

10650

-0.000203272,

10651

-0.000304272,

10652

-0.000385733,

10653

-0.00033551,

10654

-0.000174071,

10655

3.46E-05,

10656

-3.06E-05,

10657

-0.000196145,

10658

-0.00075811,

10659

-0.000873794,

10660

-0.000839649,

10661

-0.000891512,

10662

-0.00109231,

10663

-0.0012406,

10664

-0.00125277,

10665

-0.00116772,

10666

-0.000800529,

10667

-0.000503297,

10668

-0.000388711,

10669

-0.000192247,

10670

-0.000380379,

10671

-0.000626382,

10672

-0.000562528,

10673

-0.000338185,

10674

-0.000261972,

10675

-0.000172413,

10676

-0.00014704,

10677

-0.000147816,

10678

-0.000335954,

10679

-0.000423681,

10680

-0.00077368,

10681

-0.000829694,

10682

-0.000599776,

10683

-0.000274863,

10684

-0.000198762,

10685

2.44E-05,

10686

0.000157793,

10687

3.36E-05,

10688

5.52E-05,

10689

0.000132802,

10690

0.000160182,

10691

0.000267747,

10692

0.000285335,

10693

0.000302909,

10694

0.000112509,

10695

0.00033765,

10696

0.000410808,

10697

0.000399938,

10698

0.000217723,

10699

0.000252189,

10700

0.000413789,

10701

0.000334351,

10702

0.000221592,

10703

-0.000128382,

10704

-0.000407701,

10705

-0.000434761,

10706

-0.000446333,

10707

-0.000268609,

10708

-0.000328874,

10709

-0.000253456,

10710

-0.000364477,

10711

-0.000379713,

10712

-0.000270978,

10713

3.09E-05,

10714

3.43E-05,

10715

0.000132993,

10716

0.000223472,

10717

0.000196531,

10718

0.000394839,

10719

0.000353766,

10720

0.000120042,

10721

0.000186034,

10722

4.34E-05,

10723

-0.000169091,

10724

-0.000463253,

10725

-0.000526637,

10726

-0.000382341,

10727

-0.000317881,

10728

-0.000161383,

10729

-2.10E-05,

10730

-5.39E-05,

10731

-4.20E-05,

10732

-0.000428827,

10733

-0.000372915,

10734

-0.000230522,

10735

3.13E-05,

10736

-5.22E-05,

10737

1.12E-06,

10738

0.00020615,

10739

-3.95E-05,

10740

-0.000188001,

10741

-0.00036392,

10742

-0.000579835,

10743

-0.000763892,

10744

-0.000954471,

10745

-0.000672926,

10746

-0.000424378,

10747

-0.000254547,

10748

-0.000183938,

10749

-2.71E-05,

10750

0.000387271,

10751

0.000741082,

10752

0.00118213,

10753

0.00144803,

10754

0.00149683,

10755

0.00137681,

10756

0.00128621,

10757

0.00110935,

10758

0.000937524,

10759

0.000815979,

10760

0.000710253,

10761

0.000625412,

10762

0.00018105,

10763

-0.000126372,

10764

-0.000286713,

10765

-0.000268511,

10766

-9.48E-05,

10767

2.80E-05,

10768

0.000193522,

10769

0.000218011,

10770

0.000241254,

10771

0.000212373,

10772

-0.000144938,

10773

-0.000317461,

10774

-0.000310367,

10775

5.52E-05,

10776

7.28E-05,

10777

6.31E-06,

10778

-0.000100696,

10779

-0.000231523,

10780

-0.000232838,

10781

-0.000357755,

10782

-0.000312569,

10783

-0.000515436,

10784

-0.000606856,

10785

-0.000662088,

10786

-0.000494031,

10787

-0.000264875,

10788

-0.000439725,

10789

-0.00023842,

10790

-0.000240582,

10791

-0.000521013,

10792

-0.000548953,

10793

-0.000471158,

10794

-0.000383092,

10795

-0.000433934,

10796

-0.000297616,

10797

-0.000263819,

10798

2.98E-05,

10799

0.000241952,

10800

0.000294519,

10801

0.000128055,

10802

-0.000164661,

10803

-0.000125856,

10804

5.48E-05,

10805

0.00017835,

10806

0.000567644,

10807

0.000653388,

10808

0.00072292,

10809

0.00086677,

10810

0.000497185,

10811

0.000419213,

10812

0.000338733,

10813

0.000446219,

10814

0.000775549,

10815

0.00108515,

10816

0.00112122,

10817

0.00103212,

10818

0.000753898,

10819

0.000780644,

10820

0.000633858,

10821

0.000593352,

10822

0.000742397,

10823

0.000461387,

10824

0.000510694,

10825

0.000425991,

10826

0.000106824,

10827

1.30E-05,

10828

-0.000101644,

10829

-0.000247787,

10830

-5.23E-05,

10831

-1.88E-06,

10832

0.000314304,

10833

3.31E-05,

10834

-0.000493994,

10835

-0.000676519,

10836

-0.000815772,

10837

-0.000560616,

10838

-0.000419621,

10839

-0.000246948,

10840

-7.98E-06,

10841

5.47E-05,

10842

3.29E-06,

10843

9.70E-05,

10844

-6.67E-05,

10845

-0.000400225,

10846

-0.000545787,

10847

-0.000536147,

10848

-0.000382494,

10849

-0.000212611,

10850

0.00026384,

10851

0.000870903,

10852

0.00101919,

10853

0.000827203,

10854

0.000977354,

10855

0.000797584,

10856

0.000839661,

10857

0.000891465,

10858

0.000894189,

10859

0.000790827,

10860

0.000859716,

10861

0.00110719,

10862

0.00102985,

10863

0.00116294,

10864

0.00111391,

10865

0.00104187,

10866

0.000972879,

10867

0.000838099,

10868

0.000928914,

10869

0.000839244,

10870

0.000550288,

10871

0.000317816,

10872

0.000128915,

10873

-2.48E-05,

10874

-0.00015162,

10875

-0.000297103,

10876

-0.000498082,

10877

-0.000904425,

10878

-0.000721854,

10879

-0.000218374,

10880

9.71E-05,

10881

0.000350858,

10882

0.000214938,

10883

0.000131151,

10884

0.000248389,

10885

0.00052038,

10886

0.000395342,

10887

0.000123723,

10888

-0.000264557,

10889

-0.000841548,

10890

-0.00122576,

10891

-0.00109667,

10892

-0.0012236,

10893

-0.00124427,

10894

-0.00154254,

10895

-0.00141593,

10896

-0.00130058,

10897

-0.00124156,

10898

-0.000803948,

10899

-0.000595218,

10900

-6.42E-05,

10901

-4.95E-05,

10902

-1.82E-05,

10903

-4.49E-05,

10904

-4.76E-05,

10905

-0.000322162,

10906

-0.000217286,

10907

-0.000200726,

10908

-0.000318639,

10909

-0.000532153,

10910

-0.000347614,

10911

-3.16E-06,

10912

0.000644489,

10913

0.00100808,

10914

0.00107041,

10915

0.0011488,

10916

0.000744875,

10917

0.000428291,

10918

0.000290936,

10919

0.000258901,

10920

0.00057231,

10921

0.000625447,

10922

0.000833305,

10923

0.000679633,

10924

0.000736282,

10925

0.000384085,

10926

0.000100621,

10927

0.000125945,

10928

0.00018803,

10929

0.000247397,

10930

0.000140543,

10931

0.00023271,

10932

0.000206796,

10933

5.84E-05,

10934

1.03E-05,

10935

0.000149909,

10936

0.000621023,

10937

0.000754729,

10938

0.000771421,

10939

0.00105867,

10940

0.000834447,

10941

0.000733547,

10942

0.000612523,

10943

0.000335448,

10944

8.25E-06,

10945

-0.000189546,

10946

-0.000233238,

10947

-0.000519596,

10948

-0.00042089,

10949

-6.40E-06,

10950

7.77E-05,

10951

9.84E-05,

10952

-0.000171139,

10953

-0.000310745,

10954

-0.000261869,

10955

-0.000309991,

10956

-0.000362793,

10957

-0.000151421,

10958

-0.000194398,

10959

-0.00038984,

10960

-0.000337404,

10961

-0.000292472,

10962

-8.61E-05,

10963

5.75E-05,

10964

9.07E-05,

10965

0.000190954,

10966

0.000296186,

10967

0.000278313,

10968

-3.25E-05,

10969

-0.000333689,

10970

-0.000519787,

10971

-0.000496129,

10972

-0.000570476,

10973

-0.000303045,

10974

-0.000160277,

10975

0.000232384,

10976

0.000591203,

10977

0.00071829,

10978

0.000966969,

10979

0.00114479,

10980

0.00115608,

10981

0.00114881,

10982

0.0012485,

10983

0.0013597,

10984

0.00168101,

10985

0.00104358,

10986

0.000856327,

10987

0.000687258,

10988

0.000923271,

10989

0.000879711,

10990

0.000717467,

10991

0.000847053,

10992

0.000710694,

10993

0.000415626,

10994

0.000267475,

10995

0.00017531,

10996

0.000130545,

10997

7.53E-05,

10998

3.66E-05,

10999

0.000127371,

11000

0.000364506,

11001

0.000782998,

11002

0.000713517,

11003

0.000554627,

11004

0.000520172,

11005

0.000294821,

11006

0.000494704,

11007

0.00086818,

11008

0.000818739,

11009

0.000570463,

11010

0.000593457,

11011

0.000274417,

11012

0.000465056,

11013

0.000570629,

11014

0.000410949,

11015

0.000267827,

11016

0.000521008,

11017

0.000639421,

11018

0.000740811,

11019

0.000654325,

11020

0.000120355,

11021

-0.000199765,

11022

-0.000367148,

11023

-0.00050777,

11024

-0.000554528,

11025

-0.000742839,

11026

-0.000954415,

11027

-0.00111473,

11028

-0.00065717,

11029

-0.000384281,

11030

-0.000584488,

11031

-0.000387121,

11032

6.11E-07,

11033

6.18E-05,

11034

2.74E-06,

11035

-0.000239685,

11036

-0.00039921,

11037

-0.000224125,

11038

-4.40E-05,

11039

8.77E-06,

11040

-6.21E-05,

11041

-0.000519798,

11042

-0.000574988,

11043

-0.000376014,

11044

-0.000261826,

11045

0.000255553,

11046

0.000595628,

11047

0.0006648,

11048

0.000842629,

11049

0.000902367,

11050

0.000586933,

11051

0.00018307,

11052

0.000255133,

11053

9.85E-05,

11054

0.000368992,

11055

0.000562369,

11056

0.00085546,

11057

0.000859038,

11058

0.000907761,

11059

0.000390729,

11060

0.00050405,

11061

0.000698643,

11062

0.000572906,

11063

0.000644083,

11064

0.000435071,

11065

0.000530602,

11066

0.00063087,

11067

0.000323015,

11068

0.000115957,

11069

-5.61E-05,

11070

-0.000302566,

11071

-0.000569679,

11072

-0.000301438,

11073

0.000363858,

11074

0.000895815,

11075

0.00128842,

11076

0.00100383,

11077

0.00158317,

11078

0.00128054,

11079

0.000798382,

11080

0.000581018,

11081

0.000703249,

11082

0.000438639,

11083

0.000442378,

11084

0.000251144,

11085

-0.000178674,

11086

-4.74E-05,

11087

-7.63E-05,

11088

-0.000290456,

11089

-0.000425779,

11090

-0.00117202,

11091

-0.00130518,

11092

-0.00135565,

11093

-0.00117334,

11094

-0.000820887,

11095

-0.000492772,

11096

-0.000300751,

11097

0.00020894,

11098

0.000542867,

11099

0.00112235,

11100

0.0013269,

11101

0.0015155,

11102

0.00171764,

11103

0.00160906,

11104

0.00137222,

11105

0.0015151,

11106

0.00146072,

11107

0.000792795,

11108

0.000521727,

11109

0.000575187,

11110

0.000491216,

11111

0.000296697,

11112

0.000245324,

11113

0.000225258,

11114

1.92E-05,

11115

-0.000372311,

11116

-4.10E-05,

11117

-0.000128977,

11118

1.09E-05,

11119

-0.000600517,

11120

-0.0008249,

11121

-0.000992362,

11122

-0.000963039,

11123

-0.00113936,

11124

-0.00146438,

11125

-0.00111718,

11126

-0.00112647,

11127

-0.00135347,

11128

-0.00101142,

11129

-0.000652267,

11130

-0.000734747,

11131

-0.000377075,

11132

-0.00011074,

11133

-0.00051855,

11134

-0.000619458,

11135

-0.000187873,

11136

-0.000102412,

11137

0.000484728,

11138

0.000783395,

11139

0.000441902,

11140

0.000299374,

11141

0.000947764,

11142

0.00141674,

11143

0.00155242,

11144

0.00180191,

11145

0.00230594,

11146

0.00251656,

11147

0.0024539,

11148

0.00254168,

11149

0.0024158,

11150

0.00195566,

11151

0.0019329,

11152

0.00160632,

11153

0.00188157,

11154

0.001764,

11155

0.00108332,

11156

0.000869896,

11157

0.00067471,

11158

0.000615986,

11159

0.000794104,

11160

0.000386439,

11161

-5.17E-05,

11162

-0.000309826,

11163

-0.000247388,

11164

-0.0004103,

11165

-0.000398971,

11166

-0.000322127,

11167

-0.000306698,

11168

-0.000682788,

11169

-0.000919077,

11170

-0.000967931,

11171

-0.00112106,

11172

-0.00105072,

11173

-0.000969028,

11174

-0.000764652,

11175

-0.000580761,

11176

-0.000390856,

11177

-0.000211922,

11178

-0.000408224,

11179

0.000178671,

11180

0.000698164,

11181

0.00156287,

11182

0.00143122,

11183

0.000691728,

11184

-0.000475124,

11185

-0.000888173,

11186

-0.000686491,

11187

-0.0009318,

11188

-0.000852938,

11189

-0.00018467,

11190

-0.000494222,

11191

-0.000801158,

11192

-0.000975636 };

11193

11194

double coeff[] = { 200.00000,191.41233,183.19339,175.32736,167.79909,160.59407,

11195

153.69842,147.09886,140.78267,134.73769,128.95227,123.41527,

11196

118.11602,113.04431,108.19037,103.54485,99.09880,94.84366,

11197

90.77123,86.87366,83.14344,79.57340,76.15664,72.88660,

11198

69.75697,66.76172,63.89508,61.15153,58.52578,56.01278,

11199

53.60768,51.30585,49.10286,46.99446,44.97660,43.04537,

11200

41.19708,39.42814,37.73516,36.11487,34.56416,33.08003,

11201

31.65963,30.30021,28.99917,27.75399,26.56228,25.42174,

11202

24.33017,23.28547,22.28563,21.32872,20.41290,19.53641,

11203

18.69754,17.89470,17.12633,16.39096,15.68715,15.01357,

11204

14.36892,13.75194,13.16145,12.59632,12.05545,11.53781,

11205

11.04240,10.56825,10.11447,9.68017,9.26452,8.86672,

11206

8.48600,8.12162,7.77289,7.43914,7.11971,6.81400,

11207

6.52142,6.24140,5.97341,5.71692,5.47144,5.23651,

11208

5.01166,4.79647,4.59051,4.39341,4.20476,4.02421,

11209

3.85142,3.68605,3.52777,3.37630,3.23132,3.09258,

11210

2.95979,2.83270,2.71107,2.59466,2.48325,2.37662,

11211

2.27457,2.17691,2.08343,1.99397,1.90836,1.82641,

11212

1.74799,1.67293,1.60110,1.53235,1.46656,1.40358,

11213

1.34332,1.28564,1.23043,1.17760,1.12704,1.07864,

11214

1.03233,0.98800,0.94558,0.90498,0.86612,0.82893,

11215

0.79334,0.75927,0.72667,0.69547,0.66561,0.63703,

11216

0.60967,0.58349,0.55844,0.53446,0.51151,0.48955,

11217

0.46853,0.44841,0.42916,0.41073,0.39309,0.37621,

11218

0.36006,0.34460,0.32980,0.31564,0.30209,0.28912,

11219

0.27670,0.26482,0.25345,0.24257,0.23215,0.22218,

11220

0.21264,0.20351,0.19478,0.18641,0.17841,0.17075,

11221

0.16342,0.15640,0.14968,0.14326,0.13711,0.13122,

11222

0.12558,0.12019,0.11503,0.11009,0.10536,0.10084,

11223

0.09651,0.09237,0.08840,0.08460,0.08097,0.07749,

11224

0.07417,0.07098,0.06793,0.06502,0.06223,0.05955,

11225

0.05700,0.05455,0.05221,0.04997,0.04782,0.04577,

11226

0.04380,0.04192,0.04012,0.03840,0.03675,0.03517,

11227

0.03366,0.03222,0.03083,0.02951,0.02824,0.02703,

11228

0.02587,0.02476,0.02369,0.02268,0.02170,0.02077,

11229

0.01988,0.01903,0.01821,0.01743,0.01668,0.01596,

11230

0.01528,0.01462,0.01399,0.01339,0.01282,0.01227,

11231

0.01174,0.01124,0.01075,0.01029,0.00985,0.00943,

11232

0.00902,0.00864,0.00826,0.00791,0.00757,0.00724,

11233

0.00693,0.00664,0.00635,0.00608,0.00582,0.00557,

11234

0.00533,0.00510,0.00488,0.00467,0.00447,0.00428,

11235

0.00409,0.00392,0.00375,0.00359,0.00344,0.00329,

11236

0.00315,0.00301,0.00288,0.00276,0.00264,0.00253,

11237

0.00242,0.00231,0.00222,0.00212,0.00203,0.00194,

11238

0.00186,0.00178,0.00170,0.00163,0.00156,0.00149,

11239

0.00143,0.00137,0.00131,0.00125,0.00120,0.00115,

11240

0.00110,0.00105,0.00101,0.00096,0.00092,0.00088,

11241

0.00084,0.00081,0.00077,0.00074,0.00071,0.00068,

11242

0.00065,0.00062,0.00059,0.00057,0.00054,0.00052,

11243

0.00050,0.00048,0.00046,0.00044,0.00042,0.00040 };

11244

11245

double xv[600];

11246

11247

for (z=0;z<600;z++)

11248

xv[z] = xv0[z]*0.005;

11249

11250

11251

CDF *tmpdf;

11252

CLTSpec *tlsp;

11253

11254

tmpdf = new CDF();

11255

tmpdf->m_fMinVal = 0;

11256

tmpdf->m_fMaxVal = 500.0;

11257

tmpdf->m_iResolution = 600;

11258

tmpdf->m_bLeft = true;

11259

tmpdf->Create();

11260

11261

for (z=0;z<600;z++)

11262

tmpdf->m_pBin[z] = yv[z];

11263

11264

tlsp = new CLTSpec();

11265

tlsp->m_bLSpecDataLin = true;

11266

tlsp->m_fLSpecMinExp = 0.005;

11267

tlsp->m_fLSpecMaxExp = 2500.0;

11268

tlsp->m_iLSpecData = 600;

11269

tlsp->m_iLSpecPoints = 300;

11270

tlsp->m_iMaxLMIter = 200;

11271

tlsp->m_fLSpecZeroWeight = 1.0;

11272

11273

tlsp->ComputeSpectrum("rdyn","bla","","",tmpdf);

11274

11275

11276

return 0;

11277

11278

/****************************************************************************************************************/

11279

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