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25 //
26 //
27 // Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
28 //
29 // WARNING : This class is released as a prototype.
30 // It might strongly evolve or even disappear in the next releases.
31 //
32 // History:
33 // -----------
34 // 10 Oct 2011 M.Karamitros created
35 //
36 // -------------------------------------------------------------------
37
38 #include "G4DNAChemistryManager.hh"
39
40 #include "G4AutoLock.hh"
41 #include "G4DNAMolecularReactionTable.hh"
42 #include "G4DNAWaterExcitationStructure.hh"
43 #include "G4DNAWaterIonisationStructure.hh"
44 #include "G4Electron_aq.hh"
45 #include "G4GeometryManager.hh"
46 #include "G4H2O.hh"
47 #include "G4MolecularConfiguration.hh"
48 #include "G4Molecule.hh"
49 #include "G4MoleculeFinder.hh"
50 #include "G4MoleculeTable.hh"
51 #include "G4PhysChemIO.hh"
52 #include "G4Scheduler.hh"
53 #include "G4StateManager.hh"
54 #include "G4SystemOfUnits.hh"
55 #include "G4UIcmdWithABool.hh"
56 #include "G4UIcmdWithADoubleAndUnit.hh"
57 #include "G4UIcmdWithAnInteger.hh"
58 #include "G4UIcmdWithoutParameter.hh"
59 #include "G4VITTrackHolder.hh"
60 #include "G4VMoleculeCounter.hh"
61 #include "G4VUserChemistryList.hh"
62 #include "G4VUserPulseInfo.hh"
63
64 #include <memory>
65
66 G4DNAChemistryManager* G4DNAChemistryManager::fgInstance = nullptr;
67
68 G4ThreadLocal G4DNAChemistryManager::ThreadLocalData*
69 G4DNAChemistryManager::fpThreadData = nullptr;
70
71 G4Mutex chemManExistence;
72
73 //------------------------------------------------------------------------------
74
75 G4DNAChemistryManager::ThreadLocalData::ThreadLocalData()
76 {
77 fpPhysChemIO = nullptr;
78 fThreadInitialized = false;
79 }
80
81 //------------------------------------------------------------------------------
82
83 G4DNAChemistryManager::ThreadLocalData::~ThreadLocalData()
84 {
85 fpThreadData = nullptr;
86 }
87
88 //------------------------------------------------------------------------------
89
90 void G4DNAChemistryManager::SetPhysChemIO(std::unique_ptr<G4VPhysChemIO> pPhysChemIO)
91 {
92 fpThreadData->fpPhysChemIO = std::move(pPhysChemIO);
93 }
94
95 //------------------------------------------------------------------------------
96
97 //------------------------------------------------------------------------------
98 /*
99 * The chemistry manager is shared between threads
100 * It is initialized both on the master thread and on the worker threads
101 */
102 //------------------------------------------------------------------------------
103 G4DNAChemistryManager::G4DNAChemistryManager()
104 :
105 fpChemDNADirectory(new G4UIdirectory("/chem/"))
106 , fpActivateChem(new G4UIcmdWithABool("/chem/activate", this))
107 , fpRunChem(new G4UIcmdWithAnInteger("/chem/run", this))
108 , fpSkipReactionsFromChemList(new G4UIcmdWithoutParameter("/chem/skipReactionsFromChemList", this))
109 , fpScaleForNewTemperature(new G4UIcmdWithADoubleAndUnit("/chem/temperature", this))
110 , fpInitChem(new G4UIcmdWithoutParameter("/chem/init", this))
111 ,
112 fpExcitationLevel(nullptr)
113 , fpIonisationLevel(nullptr)
114 , fpUserChemistryList(nullptr)
115 {
116 fpRunChem->SetParameterName("Number of runs to execute for the chemistry module"
117 "(this works when used in standalone", true, true);
118 fpRunChem->SetDefaultValue(1);
119 fpScaleForNewTemperature->SetUnitCategory("Temperature");
120 }
121
122 //------------------------------------------------------------------------------
123
124 G4DNAChemistryManager* G4DNAChemistryManager::Instance()
125 {
126 if (fgInstance == nullptr)
127 {
128 G4AutoLock lock(&chemManExistence);
129 if (fgInstance == nullptr) // MT : double check at initialisation
130 {
131 fgInstance = new G4DNAChemistryManager();
132 }
133 lock.unlock();
134 }
135
136 // make sure thread local data is initialized for all threads
137 if (fpThreadData == nullptr)
138 {
139 fpThreadData = new ThreadLocalData();
140 }
141
142 assert(fpThreadData != nullptr);
143
144 return fgInstance;
145 }
146
147 //------------------------------------------------------------------------------
148
149 G4DNAChemistryManager* G4DNAChemistryManager::GetInstanceIfExists()
150 {
151 return fgInstance;
152 }
153
154 //------------------------------------------------------------------------------
155
156 G4DNAChemistryManager::~G4DNAChemistryManager()
157 {
158 Clear();
159 fgInstance = nullptr;
160 }
161
162 //------------------------------------------------------------------------------
163
164 void G4DNAChemistryManager::Clear()
165 {
166 fpIonisationLevel.reset();
167 fpExcitationLevel.reset();
168
169 if (fpUserChemistryList)
170 {
171 Deregister(*fpUserChemistryList);
172 }
173
174 fpChemDNADirectory.reset();
175 fpActivateChem.reset();
176 fpRunChem.reset();
177
178 fpSkipReactionsFromChemList.reset();
179 fpInitChem.reset();
180
181 if (fpThreadData != nullptr)
182 {
183 delete fpThreadData;
184 fpThreadData = nullptr;
185 }
186
187 G4DNAMolecularReactionTable::DeleteInstance();
188 G4MolecularConfiguration::DeleteManager();
189 G4VMoleculeCounter::DeleteInstance();
190 }
191
192 //------------------------------------------------------------------------------
193
194 void G4DNAChemistryManager::DeleteInstance()
195 {
196 G4AutoLock lock(&chemManExistence);
197
198 if (fgInstance != nullptr)
199 {
200 G4DNAChemistryManager* pDeleteMe = fgInstance;
201 fgInstance = nullptr;
202 lock.unlock();
203 delete pDeleteMe;
204 }
205 else
206 {
207 G4cerr << "G4DNAChemistryManager already deleted" << G4endl;
208 }
209 lock.unlock();
210 }
211
212 //------------------------------------------------------------------------------
213
214 G4bool G4DNAChemistryManager::Notify(G4ApplicationState requestedState)
215 {
216 if (requestedState == G4State_Quit)
217 {
218 if (fVerbose != 0)
219 {
220 G4cout << "G4DNAChemistryManager::Notify ---> received G4State_Quit"
221 << G4endl;
222 }
223 Clear();
224 }
225 else if (requestedState == G4State_GeomClosed)
226 {
227 fGeometryClosed = true;
228 }
229 else if (requestedState == G4State_Idle)
230 {
231 InitializeThreadSharedData();
232 }
233
234 return true;
235 }
236
237 //------------------------------------------------------------------------------
238
239 void G4DNAChemistryManager::SetNewValue(G4UIcommand* pCommand, G4String value)
240 {
241 if (pCommand == fpActivateChem.get())
242 {
243 SetChemistryActivation(G4UIcmdWithABool::GetNewBoolValue(value));
244 }
245 else if (pCommand == fpRunChem.get())
246 {
247 int nbExec = value.empty() ? 1 : G4UIcommand::ConvertToInt(value);
248 for (int i = 0 ; i < nbExec ; ++i)
249 {
250 Run();
251 }
252 }
253 else if (pCommand == fpSkipReactionsFromChemList.get())
254 {
255 fSkipReactions = true;
256 }
257 else if (pCommand == fpScaleForNewTemperature.get())
258 {
259 SetGlobalTemperature(fpScaleForNewTemperature->ConvertToDimensionedDouble(value));
260 }
261 else if (pCommand == fpInitChem.get())
262 {
263 Initialize();
264 InitializeThread();
265 }
266 }
267
268 //------------------------------------------------------------------------------
269
270 G4String G4DNAChemistryManager::GetCurrentValue(G4UIcommand* pCommand)
271 {
272 if (pCommand == fpActivateChem.get())
273 {
274 return G4UIcmdWithABool::ConvertToString(fActiveChemistry);
275 }
276 if (pCommand == fpScaleForNewTemperature.get())
277 {
278 return fpScaleForNewTemperature->ConvertToStringWithBestUnit(G4MolecularConfiguration::GetGlobalTemperature());
279 }
280 if (pCommand == fpSkipReactionsFromChemList.get())
281 {
282 return G4UIcmdWithABool::ConvertToString(fSkipReactions);
283 }
284
285 return "";
286 }
287
288 //------------------------------------------------------------------------------
289
290 void G4DNAChemistryManager::InitializeThreadSharedData()
291 {
292 if (!G4Threading::IsMasterThread())
293 {
294 return;
295 }
296
297 G4MoleculeTable::Instance()->PrepareMolecularConfiguration();
298 G4MoleculeTable::Instance()->Finalize();
299 }
300
301 //------------------------------------------------------------------------------
302 void G4DNAChemistryManager::Run()
303 {
304 if (!fActiveChemistry)
305 {
306 return;
307 }
308
309 InitializeThread();
310
311 if (!fMasterInitialized)
312 {
313 G4ExceptionDescription description;
314 description << "Global components were not initialized.";
315 G4Exception("G4DNAChemistryManager::Run", "MASTER_INIT", FatalException,
316 description);
317 }
318
319 if (!fpThreadData->fThreadInitialized)
320 {
321 G4ExceptionDescription description;
322 description << "Thread local components were not initialized.";
323 G4Exception("G4DNAChemistryManager::Run", "THREAD_INIT", FatalException,
324 description);
325 }
326
327 G4MoleculeTable::Instance()->Finalize();
328 G4Scheduler::Instance()->Process();
329 if (fResetCounterWhenRunEnds)
330 {
331 G4VMoleculeCounter::Instance()->ResetCounter();
332 }
333 CloseFile();
334 }
335
336 //------------------------------------------------------------------------------
337
338 void G4DNAChemistryManager::UseAsStandalone(G4bool flag)
339 {
340 fUseInStandalone = flag;
341 }
342
343 //------------------------------------------------------------------------------
344
345 void G4DNAChemistryManager::SetGun(G4ITGun* pChemGun)
346 {
347 G4Scheduler::Instance()->SetGun(pChemGun);
348 }
349
350 //------------------------------------------------------------------------------
351
352 void G4DNAChemistryManager::Initialize()
353 {
354 //===========================================================================
355 // MT MODE
356 //===========================================================================
357 if (G4Threading::IsMultithreadedApplication())
358 {
359 //==========================================================================
360 // ON WORKER THREAD
361 //==========================================================================
362 if (G4Threading::IsWorkerThread())
363 {
364 InitializeThread(); // Will create and initialize G4Scheduler
365 return;
366 }
367 //==========================================================================
368 // ON MASTER THREAD
369 //==========================================================================
370
371 InitializeMaster();
372 InitializeThreadSharedData();
373 return;
374 }
375 //===========================================================================
376 // IS NOT IN MT MODE
377 //===========================================================================
378
379 InitializeMaster();
380 InitializeThreadSharedData();
381 // In this case: InitializeThread is called when Run() is called
382 return;
383 }
384
385 //------------------------------------------------------------------------------
386
387 void G4DNAChemistryManager::InitializeMaster()
388 {
389 if (fMasterInitialized)
390 {
391 return;
392 }
393
394 if (fVerbose != 0)
395 {
396 G4cout << "G4DNAChemistryManager::InitializeMaster() is called" << G4endl;
397 }
398
399
400 if (fpUserChemistryList == nullptr)
401 {
402 G4ExceptionDescription description;
403 description << "No user chemistry list has been provided.";
404 G4Exception("G4DNAChemistryManager::InitializeMaster", "NO_CHEM_LIST",
405 FatalException, description);
406 }else
407 {
408 fpUserChemistryList->ConstructDissociationChannels();
409 if (!fSkipReactions)
410 {
411 fpUserChemistryList->ConstructReactionTable(G4DNAMolecularReactionTable::GetReactionTable());
412 }
413 else
414 {
415 G4DNAMolecularReactionTable::GetReactionTable(); // init pointer
416 }
417 }
418
419 G4Scheduler::Instance();
420 // creates a concrete object of the scheduler
421 fMasterInitialized = true;
422 }
423
424 //------------------------------------------------------------------------------
425
426 void G4DNAChemistryManager::HandleStandaloneInitialization()
427 {
428 if (!fUseInStandalone || fPhysicsTableBuilt)
429 {
430 return;
431 }
432
433 if (fVerbose != 0)
434 {
435 G4cout << "G4DNAChemistryManager: Build the physics tables for "
436 "molecule definition only."
437 << G4endl;
438 }
439
440 fpUserChemistryList->BuildPhysicsTable();
441
442 if (!fGeometryClosed)
443 {
444 if (fVerbose != 0)
445 {
446 G4cout << "G4DNAChemistryManager: Close geometry" << G4endl;
447 }
448
449 G4GeometryManager* pGeomManager = G4GeometryManager::GetInstance();
450 pGeomManager->OpenGeometry();
451 pGeomManager->CloseGeometry(true, true);
452 fGeometryClosed = true;
453 }
454
455 fPhysicsTableBuilt = true;
456 }
457
458 //------------------------------------------------------------------------------
459
460 void G4DNAChemistryManager::InitializeThread()
461 {
462 if (fpThreadData->fThreadInitialized && !fForceThreadReinitialization)
463 {
464 return;
465 }
466
467 if (fpUserChemistryList == nullptr)
468 {
469 G4ExceptionDescription description;
470 description << "No user chemistry list has been provided.";
471 G4Exception("G4DNAChemistryManager::InitializeThread", "NO_CHEM_LIST",
472 FatalException, description);
473 }else
474 {
475 HandleStandaloneInitialization();// To make coverty happy
476 fpUserChemistryList->ConstructTimeStepModel(G4DNAMolecularReactionTable::GetReactionTable());
477 }
478
479 if (fVerbose != 0)
480 {
481 G4cout << "G4DNAChemistryManager::InitializeThread() is called"
482 << G4endl;
483 }
484
485 G4Scheduler::Instance()->Initialize();
486
487 fpThreadData->fThreadInitialized = true;
488
489 G4VMoleculeCounter::InitializeInstance();
490
491 InitializeFile();
492 }
493
494 //------------------------------------------------------------------------------
495
496 void G4DNAChemistryManager::InitializeFile()
497 {
498 if (fVerbose != 0)
499 {
500 G4cout << "G4DNAChemistryManager::InitializeFile() is called"
501 << G4endl;
502 }
503
504 if (fpThreadData->fpPhysChemIO)
505 {
506 fpThreadData->fpPhysChemIO->InitializeFile();
507 }
508 }
509
510 //------------------------------------------------------------------------------
511
512 G4bool G4DNAChemistryManager::IsActivated()
513 {
514 return fgInstance != nullptr ? fgInstance->IsChemistryActivated() : false;
515 }
516
517 //------------------------------------------------------------------------------
518
519 G4bool G4DNAChemistryManager::IsChemistryActivated()
520 {
521 return fActiveChemistry;
522 }
523
524 //------------------------------------------------------------------------------
525
526 void G4DNAChemistryManager::SetChemistryActivation(G4bool flag)
527 {
528 fActiveChemistry = flag;
529 }
530
531 //------------------------------------------------------------------------------
532
533 void G4DNAChemistryManager::WriteInto(const G4String& output,
534 std::ios_base::openmode mode)
535 {
536 if (fVerbose != 0)
537 {
538 G4cout << "G4DNAChemistryManager: Write chemical stage into "
539 << output.data() << G4endl;
540 }
541
542 if (!fpThreadData->fpPhysChemIO)
543 {
544 fpThreadData->fpPhysChemIO = std::make_unique<G4PhysChemIO::FormattedText>();
545 }
546
547 fpThreadData->fpPhysChemIO->WriteInto(output, mode);
548
549 }
550
551 //------------------------------------------------------------------------------
552
553 void G4DNAChemistryManager::AddEmptyLineInOutputFile()
554 {
555 if (fpThreadData->fpPhysChemIO)
556 {
557 fpThreadData->fpPhysChemIO->AddEmptyLineInOutputFile();
558 }
559 }
560
561 //------------------------------------------------------------------------------
562
563 void G4DNAChemistryManager::CloseFile()
564 {
565 if (fpThreadData->fpPhysChemIO)
566 {
567 fpThreadData->fpPhysChemIO->CloseFile();
568 }
569 }
570
571 //------------------------------------------------------------------------------
572
573 G4DNAWaterExcitationStructure* G4DNAChemistryManager::GetExcitationLevel()
574 {
575 if (!fpExcitationLevel)
576 {
577 fpExcitationLevel = std::make_unique<G4DNAWaterExcitationStructure>();
578 }
579 return fpExcitationLevel.get();
580 }
581
582 //------------------------------------------------------------------------------
583
584 G4DNAWaterIonisationStructure* G4DNAChemistryManager::GetIonisationLevel()
585 {
586 if (!fpIonisationLevel)
587 {
588 fpIonisationLevel = std::make_unique<G4DNAWaterIonisationStructure>();
589 }
590 return fpIonisationLevel.get();
591 }
592
593 //------------------------------------------------------------------------------
594
595 void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modification,
596 G4int electronicLevel,
597 const G4Track* pIncomingTrack)
598 {
599 if (fpThreadData->fpPhysChemIO)
600 {
601 G4double energy = -1.;
602
603 switch (modification)
604 {
605 case eDissociativeAttachment:
606 energy = 0.;
607 break;
608 case eExcitedMolecule:
609 energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
610 break;
611 case eIonizedMolecule:
612 energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
613 break;
614 }
615
616 fpThreadData->fpPhysChemIO->CreateWaterMolecule(modification,
617 4 - electronicLevel,
618 energy,
619 pIncomingTrack);
620 }
621
622 if (fActiveChemistry)
623 {
624 auto pH2OMolecule = new G4Molecule(G4H2O::Definition());
625
626 switch (modification)
627 {
628 case eDissociativeAttachment:
629 pH2OMolecule->AddElectron(5, 1);
630 break;
631 case eExcitedMolecule:
632 pH2OMolecule->ExciteMolecule(4 - electronicLevel);
633 break;
634 case eIonizedMolecule:
635 pH2OMolecule->IonizeMolecule(4 - electronicLevel);
636 break;
637 }
638
639 G4double delayedTime = 0.;
640 if(pIncomingTrack->GetUserInformation() != nullptr)
641 {
642 auto pPulseInfo = dynamic_cast<G4VUserPulseInfo*>
643 (pIncomingTrack->GetUserInformation());
644 if(pPulseInfo != nullptr)
645 {
646 delayedTime = pPulseInfo->GetDelayedTime();
647 }
648 }
649
650 G4Track* pH2OTrack = pH2OMolecule->BuildTrack(picosecond + delayedTime,
651 pIncomingTrack->GetPosition());
652
653 pH2OTrack->SetParentID(pIncomingTrack->GetTrackID());
654 pH2OTrack->SetTrackStatus(fStopButAlive);
655 pH2OTrack->SetKineticEnergy(0.);
656 PushTrack(pH2OTrack);
657 }
658 }
659
660 //------------------------------------------------------------------------------
661 // pFinalPosition is optional
662 void G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* pIncomingTrack,
663 G4ThreeVector* pFinalPosition)
664 {
665 if (fpThreadData->fpPhysChemIO)
666 {
667 fpThreadData->fpPhysChemIO->CreateSolvatedElectron(pIncomingTrack,
668 pFinalPosition);
669 }
670
671 if (fActiveChemistry)
672 {
673 G4double delayedTime = 0.;
674 if(pIncomingTrack->GetUserInformation() != nullptr)
675 {
676 auto pPulseInfo = dynamic_cast<G4VUserPulseInfo*>
677 (pIncomingTrack->GetUserInformation());
678 if(pPulseInfo != nullptr)
679 {
680 delayedTime = pPulseInfo->GetDelayedTime();
681 }
682 }
683
684 PushMolecule(std::make_unique<G4Molecule>(G4Electron_aq::Definition()),
685 picosecond + delayedTime,
686 pFinalPosition != nullptr ? *pFinalPosition : pIncomingTrack->GetPosition(),
687 pIncomingTrack->GetTrackID());
688 }
689 }
690
691 //------------------------------------------------------------------------------
692
693 void G4DNAChemistryManager::PushMolecule(std::unique_ptr<G4Molecule> pMolecule,
694 double time,
695 const G4ThreeVector& position,
696 int parentID)
697 {
698 assert(fActiveChemistry
699 && "To inject chemical species, the chemistry must be activated. "
700 "Check chemistry activation before injecting species.");
701 G4Track* pTrack = pMolecule->BuildTrack(time, position);
702 pTrack->SetTrackStatus(fAlive);
703 pTrack->SetParentID(parentID);
704 pMolecule.release();
705 PushTrack(pTrack);
706 }
707
708 //------------------------------------------------------------------------------
709
710 void G4DNAChemistryManager::SetGlobalTemperature(G4double temp_K)
711 {
712 G4MolecularConfiguration::SetGlobalTemperature(temp_K);
713 G4DNAMolecularReactionTable::Instance()->ScaleReactionRateForNewTemperature(temp_K);
714 }
715
716 //------------------------------------------------------------------------------
717 // [[deprecated]] : chemistry list should never be nullptr
718 void G4DNAChemistryManager::SetChemistryList(G4VUserChemistryList* pChemistryList)
719 {
720 fpUserChemistryList.reset(pChemistryList);
721 fOwnChemistryList = false;
722 SetChemistryActivation(true);
723 }
724
725 void G4DNAChemistryManager::SetChemistryList(G4VUserChemistryList& chemistryList)
726 {
727 fpUserChemistryList.reset(&chemistryList);
728 fOwnChemistryList = false;
729 SetChemistryActivation(true);
730 }
731
732 void G4DNAChemistryManager::SetChemistryList(std::unique_ptr<G4VUserChemistryList> pChemistryList)
733 {
734 fpUserChemistryList = std::move(pChemistryList);
735 fOwnChemistryList = true;
736 SetChemistryActivation(true);
737 }
738
739 //------------------------------------------------------------------------------
740
741 void G4DNAChemistryManager::Deregister(G4VUserChemistryList& chemistryList)
742 {
743 if (fpUserChemistryList.get() == &chemistryList)
744 {
745 if (!fpUserChemistryList->IsPhysicsConstructor() || fOwnChemistryList)
746 {
747 fpUserChemistryList.reset();
748 }
749
750 fpUserChemistryList.release();
751 }
752 }
753
754 //------------------------------------------------------------------------------
755
756 void G4DNAChemistryManager::PushTrack(G4Track* pTrack)
757 {
758 G4ITTrackHolder::Instance()->Push(pTrack);
759 }
760
761 //------------------------------------------------------------------------------
762
763 void G4DNAChemistryManager::SetVerbose(G4int verbose)
764 {
765 fVerbose = verbose;
766 }
767
768 //------------------------------------------------------------------------------
769
770 G4bool G4DNAChemistryManager::IsCounterResetWhenRunEnds() const
771 {
772 return fResetCounterWhenRunEnds;
773 }
774
775 //------------------------------------------------------------------------------
776
777 void G4DNAChemistryManager::ResetCounterWhenRunEnds(G4bool resetCounterWhenRunEnds)
778 {
779 fResetCounterWhenRunEnds = resetCounterWhenRunEnds;
780 }
781
782 //------------------------------------------------------------------------------
783
784 void G4DNAChemistryManager::ForceRebuildingPhysicsTable()
785 {
786 fPhysicsTableBuilt = false;
787 }
788
789 //------------------------------------------------------------------------------
790
791 void G4DNAChemistryManager::ForceMasterReinitialization()
792 {
793 fMasterInitialized = false;
794 InitializeMaster();
795 }
796
797 //------------------------------------------------------------------------------
798
799 void G4DNAChemistryManager::ForceThreadReinitialization()
800 {
801 fForceThreadReinitialization = true;
802 }
803
804 //------------------------------------------------------------------------------
805
806 void G4DNAChemistryManager::TagThreadForReinitialization()
807 {
808 fpThreadData->fThreadInitialized = false;
809 }
810