| Geant4 Cross Reference |
1 // 1
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25 //
26 //
27 // Author: Mathieu Karamitros (kara (AT) cenbg
28 //
29 // History:
30 // -----------
31 // 10 Oct 2011 M.Karamitros created
32 //
33 // -------------------------------------------
34
35 #include "G4MolecularConfiguration.hh"
36 #include "G4MoleculeDefinition.hh"
37 #include "G4UIcommand.hh"
38 #include "G4AllocatorList.hh"
39 #include "G4AutoLock.hh"
40 #include "G4MoleculeTable.hh"
41 #include "G4Serialize.hh"
42 #include <fstream>
43
44 using CLHEP::m2;
45 using CLHEP::s;
46 using CLHEP::kelvin;
47
48 using namespace std;
49
50 #if defined ( WIN32 )
51 #define __func__ __FUNCTION__
52 #endif
53
54 /*G4ThreadLocal*/G4double G4MolecularConfigura
55 // 25°C, used to shoot an energy
56
57 //____________________________________________
58 // G4MolecularConfigurationManager
59 using MolecularConfigurationManager = G4Molecu
60
61 MolecularConfigurationManager* G4MolecularConf
62
63 G4Mutex MolecularConfigurationManager::fManage
64
65 int G4MolecularConfiguration::GetNumberOfSpeci
66 {
67 return GetManager()->GetNumberOfCreatedSpeci
68 }
69
70 double G4MolecularConfiguration::ReturnDefault
71 double,
72 const G4M
73 molConf)
74 {
75 return molConf->fDynDiffusionCoefficient;
76 }
77
78 G4MolecularConfiguration::G4MolecularConfigura
79
80
81 {
82 fMoleculeDefinition = moleculeDef;
83
84 fLabel = new G4String(label);
85
86 fMoleculeID = GetManager()->Insert(moleculeD
87 label,
88 this);
89 fElectronOccupancy = nullptr;
90
91 fDynCharge = charge;
92
93 fDynMass = fMoleculeDefinition->GetMass();
94
95 fDynDiffusionCoefficient = fMoleculeDefiniti
96 fDynVanDerVaalsRadius = fMoleculeDefinition-
97 fDynDecayTime = fMoleculeDefinition->GetDeca
98
99 fName = fMoleculeDefinition->GetName();
100 fName += "^";
101 fName += G4UIcommand::ConvertToString(fDynCh
102
103 fFormatedName = fMoleculeDefinition->GetForm
104 fFormatedName += "^";
105 fFormatedName += "{";
106 fFormatedName += G4UIcommand::ConvertToStrin
107 fFormatedName += "}";
108
109 fDiffParam = &G4MolecularConfiguration::Retu
110 fIsFinalized = false;
111 }
112
113 void G4MolecularConfiguration::MakeExceptionIf
114 {
115 if(fIsFinalized)
116 {
117 G4ExceptionDescription errMsg;
118 errMsg << "This molecular configuration "
119 << " is already finalized. Therefor
120 " properties cannot be changed.";
121 G4Exception("G4MolecularConfiguration::Mak
122 "CONF_FINALIZED",FatalExceptio
123 }
124 }
125
126 //____________________________________________
127
128 G4MolecularConfiguration::G4MolecularConfigura
129 G4MolecularConfiguration::GetManager()
130 {
131 if (fgManager == nullptr)
132 {
133 G4AutoLock lock(&MolecularConfigurationMan
134 if (fgManager == nullptr) // double check
135 {
136 fgManager = new G4MolecularConfiguration
137 G4MolecularConfigurationManager();
138 }
139 lock.unlock();
140 }
141
142 return fgManager;
143 }
144
145 //____________________________________________
146
147 G4MolecularConfiguration::
148 G4MolecularConfigurationManager::~G4MolecularC
149 {
150 // G4cout << "Does G4AllocatorList exists= ";
151 // G4cout << (G4AllocatorList::GetAllocatorLi
152 // << G4endl;
153
154 G4MolecularConfigurationManager::MolElectron
155 G4MolecularConfigurationManager::ElectronOcc
156 iterator it2;
157
158 for (it1 = fElecOccTable.begin(); it1 != fEl
159 {
160 for (it2 = it1->second.begin(); it2 != it1
161 {
162
163
164 delete it2->second;
165
166 }
167 }
168 fElecOccTable.clear();
169 fgManager = nullptr;
170 }
171
172 //____________________________________________
173 // G4MolecularConfigurationManager
174 G4int G4MolecularConfiguration::
175 G4MolecularConfigurationManager::
176 Insert(const G4MoleculeDefinition* molDef,
177 const G4ElectronO
178 G4MolecularConfig
179 {
180 //G4AutoLock lock(&fMoleculeCreationMutex);
181
182 ElectronOccupancyTable& table2 = fElecOccTab
183 auto it = table2.find(eOcc);
184
185 if(it == table2.end())
186 {
187 table2[eOcc] = molConf;
188 }
189 else
190 {
191 G4ExceptionDescription errMsg;
192 errMsg << "The same molecular configuratio
193 G4Exception("G4MolecularConfigurationManag
194 "SetMolecularConfiguration(con
195 "const G4ElectronOccupancy& eO
196 "G4MolecularConfiguration* mol
197 "",
198 FatalException,
199 errMsg
200 );
201 }
202
203 fLastMoleculeID++;
204
205 fMolConfPerID.push_back(molConf);
206
207 //lock.unlock();
208 return fLastMoleculeID;
209 }
210
211 //____________________________________________
212
213 const G4ElectronOccupancy*
214 G4MolecularConfiguration::G4MolecularConfigura
215 FindCommonElectronOccupancy(const G4MoleculeDe
216 const G4ElectronOc
217 {
218 //G4AutoLock lock(&fMoleculeCreationMutex);
219
220 auto it1 = fElecOccTable.find(molDef);
221
222 if(it1 == fElecOccTable.end())
223 {
224 // TODO = handle exception ?
225 return nullptr;
226 }
227
228 ElectronOccupancyTable& table2 = it1->second
229 auto it2 = table2.find(eOcc);
230
231 //lock.unlock();
232
233 if (it2 == table2.end())
234 {
235 // TODO = handle exception ?
236 return nullptr;
237 }
238
239 return &(it2->first);
240 }
241
242 //____________________________________________
243
244 G4MolecularConfiguration*
245 G4MolecularConfiguration::G4MolecularConfigura
246 GetMolecularConfiguration(const G4MoleculeDefi
247 const G4ElectronOccu
248 {
249 auto it1 = fElecOccTable.find(molDef);
250
251 if(it1 == fElecOccTable.end()) return nullpt
252
253 ElectronOccupancyTable& table2 = it1->second
254 auto it = table2.find(eOcc);
255
256 if(it == table2.end())
257 {
258 return nullptr;
259 }
260
261 return it->second;
262 }
263
264 //____________________________________________
265
266 G4int G4MolecularConfiguration::G4MolecularCon
267 Insert(const G4MoleculeDefinition* molDef,
268 int charge,
269 G4MolecularConfiguration* molConf)
270 {
271
272 //G4AutoLock lock(&fMoleculeCreationMutex);
273 ChargeTable& table2 = fChargeTable[molDef];
274 auto it = table2.find(charge);
275
276 if(it == table2.end())
277 {
278 table2[charge] = molConf;
279 }
280 else
281 {
282 //lock.unlock();
283 G4ExceptionDescription errMsg;
284 errMsg << "The same molecular configuratio
285 G4Exception("G4MolecularConfigurationManag
286 "SetMolecularConfiguration(con
287 "int charge,"
288 "G4MolecularConfiguration* mol
289 "", FatalException, errMsg);
290 }
291
292 fLastMoleculeID++;
293 fMolConfPerID.push_back(molConf);
294 //lock.unlock();
295 return fLastMoleculeID;
296 }
297
298 //____________________________________________
299
300 G4MolecularConfiguration*
301 G4MolecularConfiguration::G4MolecularConfigura
302 GetMolecularConfiguration(const G4MoleculeDefi
303 int charge)
304 {
305 //G4AutoLock lock(&fMoleculeCreationMutex);
306
307 auto it1 = fChargeTable.find(molDef);
308
309 if(it1 == fChargeTable.end()) return nullptr
310
311 ChargeTable& table2 = it1->second;
312 auto it = table2.find(charge);
313
314 if(it == table2.end())
315 {
316 return nullptr;
317 }
318
319 return it->second;
320
321 }
322
323 //____________________________________________
324 // Static method in G4MolecularConfiguration
325 G4MolecularConfiguration*
326 G4MolecularConfiguration::
327 GetOrCreateMolecularConfiguration(const G4Mole
328 {
329 if (molDef->GetGroundStateElectronOccupancy(
330 {
331 const G4ElectronOccupancy& elecOcc =
332 *molDef->GetGroundStateElectronOccupan
333 G4MolecularConfiguration* molConf =
334 GetManager()->GetMolecularConfiguratio
335
336 if (molConf != nullptr)
337 {
338 return molConf;
339 }
340
341 auto newConf =
342 new G4MolecularConfiguration(molDef,
343 elecOcc);
344 newConf->SetUserID(molDef->GetName());
345 return newConf;
346 }
347
348 G4MolecularConfiguration* molConf =
349 GetManager()->GetMolecularConfiguration(
350 if(molConf != nullptr)
351 {
352 return molConf;
353 }
354
355 auto newConf =
356 new G4MolecularConfiguration(molDef, mol
357 newConf->SetUserID(molDef->GetName());
358 return newConf;
359 }
360
361 //____________________________________________
362
363 G4MolecularConfiguration*
364 G4MolecularConfiguration::
365 GetOrCreateMolecularConfiguration(const G4Mole
366 const G4Elec
367 {
368 return GetManager()->GetOrCreateMolecularCon
369
370 // G4MolecularConfiguration* molConf =
371 // GetManager()->GetMolecularConfiguratio
372 //
373 // if (molConf)
374 // {
375 // return molConf;
376 // }
377 // else
378 // {
379 // G4MolecularConfiguration* newConf =
380 // new G4MolecularConfiguration(molDef,
381 // return newConf;
382 // }
383 }
384
385 //____________________________________________
386
387 G4MolecularConfiguration*
388 G4MolecularConfiguration::
389 GetOrCreateMolecularConfiguration(const G4Mole
390 int charge)
391 {
392 G4MolecularConfiguration* molConf =
393 GetManager()->GetMolecularConfiguration(
394
395 if(molConf != nullptr)
396 {
397 return molConf;
398 }
399
400 auto newConf =
401 new G4MolecularConfiguration(molDef, cha
402 return newConf;
403 }
404
405 //____________________________________________
406
407 void G4MolecularConfiguration::DeleteManager()
408 {
409 G4AutoLock lock(&MolecularConfigurationManag
410 delete fgManager;
411 fgManager = nullptr;
412 lock.unlock();
413 }
414
415 //____________________________________________
416 // G4MolecularConfiguration
417 G4MolecularConfiguration::
418 G4MolecularConfiguration(const G4MoleculeDefin
419 const G4ElectronOccup
420 const G4String& label
421 {
422 fMoleculeDefinition = moleculeDef;
423
424 fMoleculeID = GetManager()->Insert(moleculeD
425 elecOcc,
426 this);
427 fElectronOccupancy = GetManager()->FindCommo
428
429
430 /*
431 fgManager->fTable[fMoleculeDefinition][elec
432 std::map<G4ElectronOccupancy, G4MolecularCo
433 it = fgManager->fTable[moleculeDef].find(el
434 fElectronOccupancy = &(it->first);
435 */
436
437 fDynCharge = fMoleculeDefinition->GetNbElect
438 - fElectronOccupancy->GetTotalOccupancy(
439 + moleculeDef->GetCharge();
440 fDynMass = fMoleculeDefinition->GetMass();
441
442 fDynDiffusionCoefficient = fMoleculeDefiniti
443 fDynVanDerVaalsRadius = fMoleculeDefinition-
444 fDynDecayTime = fMoleculeDefinition->GetDeca
445
446 fName = fMoleculeDefinition->GetName();
447 fName += "^";
448 fName += G4UIcommand::ConvertToString(fDynCh
449
450 fFormatedName = fMoleculeDefinition->GetForm
451 fFormatedName += "^";
452 fFormatedName += "{";
453 fFormatedName += G4UIcommand::ConvertToStrin
454 fFormatedName += "}";
455
456 fLabel = nullptr; // let it here
457
458 if(!label.empty())
459 {
460 SetLabel(label);
461 }
462
463 fDiffParam = &G4MolecularConfiguration::Retu
464
465 fIsFinalized = false;
466 }
467
468 //____________________________________________
469
470 G4MolecularConfiguration::
471 G4MolecularConfiguration(const G4MoleculeDefin
472 int charge)
473 {
474 fMoleculeDefinition = moleculeDef;
475
476 fMoleculeID = GetManager()->Insert(moleculeD
477 charge,
478 this);
479 fElectronOccupancy = nullptr;
480
481 fDynCharge = charge;
482 fDynMass = fMoleculeDefinition->GetMass();
483
484 fDynDiffusionCoefficient = fMoleculeDefiniti
485 fDynVanDerVaalsRadius = fMoleculeDefinition-
486 fDynDecayTime = fMoleculeDefinition->GetDeca
487
488 fName = fMoleculeDefinition->GetName();
489 fName += "^";
490 fName += G4UIcommand::ConvertToString(fDynCh
491
492 fFormatedName = fMoleculeDefinition->GetForm
493 fFormatedName += "^";
494 fFormatedName += "{";
495 fFormatedName += G4UIcommand::ConvertToStrin
496 fFormatedName += "}";
497
498 fLabel = nullptr;
499
500 fDiffParam = &G4MolecularConfiguration::Retu
501
502 fIsFinalized = false;
503 }
504
505 //____________________________________________
506
507 G4MolecularConfiguration::~G4MolecularConfigur
508 {
509 if (fgManager != nullptr) fgManager->RemoveM
510
511 // if (G4AllocatorList::GetAllocatorListIfExi
512 // {
513 // if (fElectronOccupancy)
514 // {
515 // delete fElectronOccupancy;
516 // fElectronOccupancy = 0;
517 // }
518 // }
519 }
520
521 //____________________________________________
522
523 G4MolecularConfiguration*
524 G4MolecularConfiguration::
525 ChangeConfiguration(const G4ElectronOccupancy&
526 {
527 G4MolecularConfiguration* output =
528 GetManager()->GetMolecularConfiguration(
529
530
531 if (output == nullptr)
532 {
533 output = new G4MolecularConfiguration(fMol
534 newE
535 }
536 return output;
537 }
538
539 //____________________________________________
540
541 G4MolecularConfiguration*
542 G4MolecularConfiguration::ChangeConfiguration(
543 {
544 G4MolecularConfiguration* output =
545 GetManager()->GetMolecularConfiguration(
546
547 if (output == nullptr)
548 {
549 output = new G4MolecularConfiguration(fMol
550 }
551 return output;
552 }
553
554 //____________________________________________
555
556 G4MolecularConfiguration&
557 G4MolecularConfiguration::operator=(G4Molecula
558 {
559 // if (&right == this) return *this;
560 return *this;
561 }
562
563 //____________________________________________
564
565 /** Method used in Geant4-DNA to excite water
566 */
567 G4MolecularConfiguration*
568 G4MolecularConfiguration::ExciteMolecule(G4int
569 {
570 // MakeExceptionIfFinalized();
571 CheckElectronOccupancy(__func__);
572 G4ElectronOccupancy newElectronOccupancy(*fE
573
574 newElectronOccupancy.RemoveElectron(ExcitedL
575 newElectronOccupancy.AddElectron(5, 1);
576
577 return ChangeConfiguration(newElectronOccupa
578 }
579
580 //____________________________________________
581
582 /** Method used in Geant4-DNA to ionize water
583 */
584 G4MolecularConfiguration*
585 G4MolecularConfiguration::IonizeMolecule(G4int
586 {
587 // MakeExceptionIfFinalized();
588 CheckElectronOccupancy(__func__);
589 G4ElectronOccupancy newElectronOccupancy(*fE
590
591 if (newElectronOccupancy.GetOccupancy(Ionize
592 {
593 newElectronOccupancy.RemoveElectron(Ionize
594 }
595 else
596 {
597 G4String errMsg = "There is no electron on
598 + G4UIcommand::ConvertToString(Ionized
599 + " you want to free. The molecule's n
600 + GetName();
601 G4Exception("G4MolecularConfiguration::Ion
602 "",
603 FatalErrorInArgument,
604 errMsg);
605 PrintState();
606 }
607
608 // DEBUG
609 // PrintState();
610
611 return ChangeConfiguration(newElectronOccupa
612 }
613
614 //____________________________________________
615
616 G4MolecularConfiguration* G4MolecularConfigura
617
618 {
619 // MakeExceptionIfFinalized();
620 CheckElectronOccupancy(__func__);
621 G4ElectronOccupancy newElectronOccupancy(*fE
622 newElectronOccupancy.AddElectron(orbit, numb
623 return ChangeConfiguration(newElectronOccupa
624 }
625
626 //____________________________________________
627
628 G4MolecularConfiguration*
629 G4MolecularConfiguration::RemoveElectron(G4int
630 G4int
631 {
632 // MakeExceptionIfFinalized();
633 CheckElectronOccupancy(__func__);
634 G4ElectronOccupancy newElectronOccupancy(*fE
635
636 if (newElectronOccupancy.GetOccupancy(orbit)
637 {
638 newElectronOccupancy.RemoveElectron(orbit,
639 }
640 else
641 {
642 G4String errMsg = "There is already no ele
643 + G4UIcommand::ConvertToString(orbit)
644 + " you want to free. The molecule's n
645 G4Exception("G4MolecularConfiguration::Rem
646 "",
647 JustWarning,
648 errMsg);
649 PrintState();
650 }
651
652 return ChangeConfiguration(newElectronOccupa
653 }
654
655 //____________________________________________
656
657 G4MolecularConfiguration*
658 G4MolecularConfiguration::MoveOneElectron(G4in
659 G4in
660 {
661 // MakeExceptionIfFinalized();
662 CheckElectronOccupancy(__func__);
663 G4ElectronOccupancy newElectronOccupancy(*fE
664
665 if (newElectronOccupancy.GetOccupancy(orbitT
666 {
667 newElectronOccupancy.RemoveElectron(orbitT
668 newElectronOccupancy.AddElectron(orbitToFi
669 }
670 else
671 {
672 G4String errMsg = "There is no electron on
673 + G4UIcommand::ConvertToString(orbitTo
674 + " you want to free. The molecule's n
675 G4Exception("G4MolecularConfiguration::Mov
676 "",
677 FatalErrorInArgument,
678 errMsg);
679 PrintState();
680 }
681
682 return ChangeConfiguration(newElectronOccupa
683 }
684
685 //____________________________________________
686
687 const G4String& G4MolecularConfiguration::GetN
688 {
689 return fName;
690 }
691
692 //____________________________________________
693
694 const G4String& G4MolecularConfiguration::GetF
695 {
696 return fFormatedName;
697 }
698
699 //____________________________________________
700
701 G4int G4MolecularConfiguration::GetAtomsNumber
702 {
703 return fMoleculeDefinition->GetAtomsNumber()
704 }
705
706 //____________________________________________
707
708 G4double G4MolecularConfiguration::GetNbElectr
709 {
710 CheckElectronOccupancy(__func__);
711 return fElectronOccupancy->GetTotalOccupancy
712 }
713
714 //____________________________________________
715
716 void G4MolecularConfiguration::PrintState() co
717 {
718 G4cout << "-------------- Start Printing Sta
719 << " ---------------" << G4endl;
720
721 if (fElectronOccupancy != nullptr)
722 {
723 G4cout << "--------------Print electronic
724 << "---------------" << G4endl;
725 fElectronOccupancy->DumpInfo();
726 if(fElectronOccupancy==fMoleculeDefinition
727 {
728 G4cout<<"At ground state"<<G4endl;
729 }
730 }
731 else
732 {
733 G4cout << "--- No electron occupancy set u
734 }
735
736 G4cout << "Charge :"
737 << fDynCharge
738 << G4endl;
739
740 if(fLabel != nullptr)
741 {
742 G4cout << "Label :"
743 << GetLabel()
744 << G4endl;
745 }
746 G4cout << "-------------- End Of State " <<
747 << " -----------------------" << G4e
748 }
749
750 //____________________________________________
751
752 // added - to be transformed in a "Decay metho
753 const vector<const G4MolecularDissociationChan
754 G4MolecularConfiguration::GetDissociationCha
755 {
756 // if (fElectronOccupancy == 0) return 0;
757 return fMoleculeDefinition->GetDecayChannels
758 }
759
760 //____________________________________________
761
762 G4int G4MolecularConfiguration::GetFakeParticl
763 {
764 if(fMoleculeDefinition != nullptr) return fM
765 G4Exception("G4MolecularConfiguration::GetMo
766 "",
767 FatalErrorInArgument,
768 "You should first enter a m
769
770 return INT_MAX;
771 }
772
773 //____________________________________________
774
775 const char* removePath(const char* path)
776 {
777 const char* pDelimeter = strrchr(path, '\\')
778 if (pDelimeter != nullptr) path = pDelimeter
779
780 pDelimeter = strrchr(path, '/');
781 if (pDelimeter != nullptr) path = pDelimeter
782
783 return path;
784 }
785
786 //____________________________________________
787
788 void G4MolecularConfiguration::CheckElectronOc
789 {
790 if (fElectronOccupancy == nullptr)
791 {
792 G4String functionName(function);
793 G4ExceptionDescription description;
794 description
795 << "No G4ElectronOccupancy was defined
796 << fMoleculeDefinition->GetName()
797 << ". The definition was probably defi
798 "rather than electron state.";
799
800 G4Exception(functionName, "", FatalErrorIn
801 }
802 }
803
804 //____________________________________________
805
806 void G4MolecularConfiguration::G4MolecularConf
807 RecordNewlyLabeledConfiguration(G4MolecularCon
808 {
809 //G4AutoLock lock(&fMoleculeCreationMutex);
810
811 LabelTable& tmpMap = fLabelTable[molConf->fM
812
813 auto it = tmpMap.find(*molConf->fLabel);
814
815 if(it == tmpMap.end())
816 {
817 tmpMap[*(molConf->fLabel)] = molConf;
818 }
819 else
820 {
821 G4ExceptionDescription errMsg;
822 errMsg << "The same molecular configuratio
823 G4Exception("G4MolecularConfigurationManag
824 "SetMolecularConfiguration(con
825 "const G4String& label,"
826 "G4MolecularConfiguration* mol
827 "", FatalException, errMsg);
828 }
829
830 //lock.unlock();
831 }
832
833 void G4MolecularConfiguration::G4MolecularConf
834
835 {
836 auto it = fUserIDTable.find(userID);
837
838 if(it == fUserIDTable.end())
839 {
840 fUserIDTable[userID] = molecule;
841 }
842 else if(molecule != it->second)
843 {
844 // TODO improve exception
845 // exception
846 G4ExceptionDescription description;
847 description << "The user identifier " << u
848 << " was already given in anot
849 << G4endl;
850 G4Exception("G4MolecularConfiguration::G4Mol
851 "CONF_ALREADY_RECORDED",
852 FatalException,
853 description);
854 }
855 }
856
857 //____________________________________________
858
859 void G4MolecularConfiguration::G4MolecularConf
860 RemoveMolecularConfigurationFromTable(G4Molecu
861 {
862 auto it1 =
863 fElecOccTable.find(configuration->GetDef
864 auto end = fElecOccTable.end();
865
866 if (it1 == end) return;
867
868 auto it2 =
869 it1->second.find(*configuration->GetElec
870
871 if (it2 == it1->second.end()) return;
872
873 it2->second = 0;
874 // it1->second.erase(it2);
875
876 configuration->fElectronOccupancy = nullptr;
877 }
878
879 //____________________________________________
880
881 G4MolecularConfiguration*
882 G4MolecularConfiguration::G4MolecularConfigura
883 GetMolecularConfiguration(const G4MoleculeDefi
884 const G4String& labe
885 {
886 //G4AutoLock lock(&fMoleculeCreationMutex);
887
888 auto it1 = fLabelTable.find(molDef);
889
890 if(it1 == fLabelTable.end()) return nullptr;
891
892 LabelTable& table2 = it1->second;
893
894 auto it2 = table2.find(label);
895
896 //lock.unlock();
897
898 if(it2 == table2.end()) return nullptr;
899 return it2->second;
900 }
901
902 //____________________________________________
903
904 G4MolecularConfiguration*
905 G4MolecularConfiguration::G4MolecularConfigura
906 GetMolecularConfiguration(int moleculeID)
907 {
908 if(moleculeID > (int) fMolConfPerID.size() |
909 moleculeID < 0) return nullptr;
910
911 return fMolConfPerID[moleculeID];
912 }
913
914 //____________________________________________
915
916 G4int
917 G4MolecularConfiguration::G4MolecularConfigura
918 Insert(const G4MoleculeDefinition* molDef,
919 const G4String& l
920 G4MolecularConfig
921 {
922 G4AutoLock lock(&fMoleculeCreationMutex);
923 LabelTable& tmpMap = fLabelTable[molDef];
924 auto it = tmpMap.find(label);
925
926 if(it == tmpMap.end())
927 {
928 fLastMoleculeID++;
929 tmpMap[label] = molConf;
930 lock.unlock();
931 }
932 else
933 {
934 lock.unlock();
935 G4ExceptionDescription errMsg;
936 errMsg << "The same molecular configuratio
937 G4Exception("G4MolecularConfigurationManag
938 "SetMolecularConfiguration(con
939 "const G4String& label,"
940 "G4MolecularConfiguration* mol
941 "", FatalException, errMsg);
942 }
943
944 fMolConfPerID.push_back(molConf);
945
946 return fLastMoleculeID;
947 }
948
949 //____________________________________________
950
951 G4MolecularConfiguration*
952 G4MolecularConfiguration::GetMolecularConfigur
953
954 {
955 return GetManager()->GetMolecularConfigurati
956 }
957
958 //____________________________________________
959
960 G4MolecularConfiguration*
961 G4MolecularConfiguration::GetMolecularConfigur
962 {
963 return GetManager()->GetMolecularConfigurati
964 }
965
966 //____________________________________________
967
968 G4MolecularConfiguration*
969 G4MolecularConfiguration::CreateMolecularConfi
970
971
972
973
974 {
975 wasAlreadyCreated = false;
976 G4MolecularConfiguration* molConf =
977 GetManager()->GetMolecularConfiguration(
978
979 if (molConf != nullptr)
980 {
981 if(molConf->fLabel == nullptr)
982 {
983 molConf->SetLabel(label);
984 G4ExceptionDescription wMsg ;
985 wMsg << "The molecular configuration for
986 << molDef->GetName()
987 << " with charge " << charge << "
988 "but with NO label";
989 G4Exception("G4MolecularConfiguration::C
990 "DOUBLE_CREATION",
991 JustWarning,
992 wMsg);
993 }
994 else if(molConf->fLabel->empty() )
995 {
996 molConf->SetLabel(label);
997 }
998 else if(*(molConf->fLabel) != label)
999 {
1000 G4ExceptionDescription errMsg ;
1001 errMsg << "The molecular configuration
1002 << molDef->GetName()
1003 << " with charge " << charge <<
1004 "but with a different label
1005 << molConf->GetLabel();
1006 G4Exception("G4MolecularConfiguration::
1007 "DOUBLE_CREATION",
1008 FatalErrorInArgument,
1009 errMsg);
1010 // KILL APP
1011 }
1012
1013 if(molConf->fUserIdentifier.empty())
1014 {
1015 molConf->fUserIdentifier = userIdentifi
1016
1017 G4ExceptionDescription wMsg ;
1018 wMsg << "The molecular configuration fo
1019 << molDef->GetName()
1020 << " with label " << label << "
1021 G4Exception("G4MolecularConfiguration::
1022 "DOUBLE_CREATION",
1023 JustWarning,
1024 wMsg);
1025 }
1026 else if(molConf->fUserIdentifier != userI
1027 {
1028 G4ExceptionDescription errMsg ;
1029 errMsg << "The molecular configuration
1030 << molDef->GetName()
1031 << " with label " << label << "
1032 "BUT with a different user I
1033 << molConf->fUserIdentifier;
1034 G4Exception("G4MolecularConfiguration::
1035 "DOUBLE_CREATION",
1036 FatalErrorInArgument,
1037 errMsg);
1038 // KILL APP
1039 }
1040
1041 wasAlreadyCreated = true;
1042 return molConf;
1043 }
1044
1045 auto newConf =
1046 new G4MolecularConfiguration(molDef, la
1047 newConf->fUserIdentifier = userIdentifier;
1048
1049 GetManager()->AddUserID(userIdentifier, new
1050
1051 // G4MoleculeTable::Instance()->RecordMole
1052 //
1053 return newConf;
1054 }
1055
1056 //___________________________________________
1057
1058 G4MolecularConfiguration*
1059 G4MolecularConfiguration::
1060 CreateMolecularConfiguration(const G4String&
1061 const G4Molecule
1062 bool& wasAlready
1063 {
1064 wasAlreadyCreated = false;
1065 G4MolecularConfiguration* preRegisteredMolC
1066 GetManager()->GetMolecularConfiguration
1067
1068 if(preRegisteredMolConf != nullptr)
1069 {
1070 if(preRegisteredMolConf->GetDefinition()
1071 {
1072 wasAlreadyCreated = true;
1073 return preRegisteredMolConf;
1074 }
1075 }
1076
1077 if(molDef->GetGroundStateElectronOccupancy(
1078 {
1079 const G4ElectronOccupancy& elecOcc = *mol
1080 ->GetGroundStateElectronOccupancy();
1081 G4MolecularConfiguration* molConf =
1082 GetManager()->GetMolecularConfigurati
1083
1084 if(molConf != nullptr)
1085 {
1086 if(molConf->fUserIdentifier.empty())
1087 {
1088 molConf->fUserIdentifier = userIdenti
1089 }
1090 else if(molConf->fUserIdentifier != use
1091 {
1092 G4ExceptionDescription errMsg;
1093 errMsg << "A molecular configuration
1094 << molDef->GetName() << " has
1095 "and recorded with a different
1096 << molConf->fUserIdentifier;
1097 G4Exception("G4MolecularConfiguration
1098 "DOUBLE_CREATION",
1099 FatalErrorInArgument,
1100 errMsg);
1101 }
1102 // TODO exception
1103 G4ExceptionDescription errMsg;
1104 errMsg << "A molecular configuration fo
1105 << molDef->GetName() << " has al
1106 G4Exception("G4MolecularConfiguration::
1107 "DOUBLE_CREATION",
1108 JustWarning,
1109 errMsg);
1110 wasAlreadyCreated = true;
1111 return molConf;
1112 }
1113
1114 // G4cout << "Create molConf for " << mol
1115 auto newConf = new G4MolecularConfigurat
1116
1117 newConf->fUserIdentifier = userIdentifier
1118
1119 GetManager()->AddUserID(userIdentifier, n
1120
1121 // G4MoleculeTable::Instance()->RecordMo
1122 //
1123 return newConf;
1124 }
1125
1126 return CreateMolecularConfiguration(userIde
1127 molDef,
1128 molDef-
1129 molDef-
1130 wasAlre
1131 }
1132
1133 //___________________________________________
1134
1135 G4MolecularConfiguration*
1136 G4MolecularConfiguration::
1137 CreateMolecularConfiguration(const G4String&
1138 const G4Molecule
1139 const G4String&
1140 bool& wasAlready
1141 {
1142 assert(label != "");
1143 wasAlreadyCreated = false;
1144
1145 G4MolecularConfiguration* molConf =
1146 GetManager()->GetMolecularConfiguration
1147 if(molConf != nullptr)
1148 {
1149 if((molConf->fLabel != nullptr)
1150 && *molConf->fLabel == label)
1151 {
1152 wasAlreadyCreated = true;
1153 return molConf;
1154 }
1155 if(molConf->fLabel == nullptr)
1156 {
1157 wasAlreadyCreated = true;
1158 molConf->SetLabel(label);
1159 return molConf;
1160 }
1161 if(molConf->fLabel->empty())
1162 {
1163 wasAlreadyCreated = true;
1164 molConf->SetLabel(label);
1165 return molConf;
1166 }
1167
1168 molConf->PrintState();
1169 G4ExceptionDescription errMsg ;
1170 errMsg << "A molecular configuration for
1171 << molDef->GetName()
1172 << " has already been created "
1173 "with user ID "
1174 << molConf->fUserIdentifier << " a
1175 << molConf->GetLabel();
1176 G4Exception("G4MolecularConfiguration::Cr
1177 "DOUBLE_CREATION",
1178 FatalErrorInArgument,
1179 errMsg);
1180 // KILL APP
1181 }
1182 else
1183 {
1184 auto newConf =
1185 new G4MolecularConfiguration(molDef,
1186 label,
1187 molDef->Ge
1188 newConf->fUserIdentifier = userIdentifier
1189
1190 GetManager()->AddUserID(userIdentifier, n
1191
1192 // G4MoleculeTable::Instance()->
1193 // RecordMolecularConfiguration(userId
1194 return newConf;
1195 }
1196 return molConf;
1197 }
1198
1199 //___________________________________________
1200
1201 G4MolecularConfiguration*
1202 G4MolecularConfiguration::
1203 CreateMolecularConfiguration(const G4String&
1204 const G4Molecule
1205 const G4String&
1206 const G4Electron
1207 bool& wasAlready
1208 {
1209 assert(label != "");
1210 wasAlreadyCreated = false;
1211
1212 G4MolecularConfiguration* molConf =
1213 GetManager()->GetMolecularConfiguration
1214
1215 if(molConf != nullptr)
1216 {
1217 if(molConf->GetElectronOccupancy() != nul
1218 {
1219 if(*molConf->GetElectronOccupancy() ==
1220 {
1221 if((molConf->fLabel != nullptr) && *m
1222 {
1223 wasAlreadyCreated = true;
1224 return molConf;
1225 }
1226 if(molConf->fLabel == nullptr)
1227 {
1228 wasAlreadyCreated = true;
1229 molConf->SetLabel(label);
1230 return molConf;
1231 }
1232 if(molConf->fLabel->empty())
1233 {
1234 wasAlreadyCreated = true;
1235 molConf->SetLabel(label);
1236 return molConf;
1237 }
1238 }
1239 }
1240
1241
1242 molConf->PrintState();
1243 G4ExceptionDescription errMsg ;
1244 errMsg << "A molecular configuration for
1245 << molDef->GetName()
1246 << " has already been created "
1247 "with user ID "
1248 << molConf->fUserIdentifier
1249 << " and possible different electr
1250 G4Exception("G4MolecularConfiguration::Cr
1251 "DOUBLE_CREATION",
1252 FatalErrorInArgument,
1253 errMsg);
1254 }
1255 else
1256 {
1257 auto newConf =
1258 new G4MolecularConfiguration(molDef,
1259 eOcc,
1260 label);
1261 newConf->fUserIdentifier = userIdentifier
1262
1263 GetManager()->AddUserID(userIdentifier, n
1264
1265 // G4MoleculeTable::Instance()->
1266 // RecordMolecularConfiguration(userId
1267 return newConf;
1268 }
1269 return molConf;
1270 }
1271
1272
1273 //___________________________________________
1274
1275 G4MolecularConfiguration*
1276 G4MolecularConfiguration::G4MolecularConfigur
1277 GetOrCreateMolecularConfiguration(const G4Mol
1278 const G4Ele
1279 {
1280 auto it1 = fElecOccTable.find(molDef);
1281
1282 if(it1 == fElecOccTable.end())
1283 {
1284 return new G4MolecularConfiguration(molDe
1285 }
1286
1287 ElectronOccupancyTable& table2 = it1->secon
1288 auto it = table2.find(eOcc);
1289
1290 if(it == table2.end())
1291 {
1292 auto molConf =
1293 new G4MolecularConfiguration(molDef,
1294 // molConf->Finalize();
1295 return molConf;
1296 }
1297
1298 return it->second;
1299 }
1300
1301 //___________________________________________
1302
1303 G4MolecularConfiguration*
1304 G4MolecularConfiguration::G4MolecularConfigur
1305 GetOrCreateMolecularConfiguration(const G4Mol
1306 int charge)
1307 {
1308 auto it1 = fChargeTable.find(molDef);
1309
1310 if(it1 == fChargeTable.end())
1311 {
1312 G4AutoLock lock(&fMoleculeCreationMutex);
1313
1314 auto newConf = new G4MolecularConfigurat
1315 return newConf ;
1316 }
1317
1318 ChargeTable& table2 = it1->second;
1319 auto it = table2.find(charge);
1320
1321 if(it == table2.end())
1322 {
1323 G4AutoLock lock(&fMoleculeCreationMutex);
1324
1325 auto newConf =
1326 new G4MolecularConfiguration(molDef,
1327 // newConf->Finalize();
1328 return newConf ;
1329 }
1330
1331 return it->second;
1332 }
1333
1334 //___________________________________________
1335
1336 void G4MolecularConfiguration::Serialize(std:
1337 {
1338 G4String moleculeName = fMoleculeDefinition
1339 WRITE(out, moleculeName);
1340
1341 // if(fLabel)
1342 // out << fLabel;
1343 // else
1344 // out << "";
1345 WRITE(out,fDynDiffusionCoefficient);
1346 WRITE(out,fDynVanDerVaalsRadius);
1347 WRITE(out,fDynDecayTime);
1348 WRITE(out,fDynMass);
1349 WRITE(out,fDynCharge);
1350 WRITE(out,fMoleculeID);
1351 WRITE(out,fFormatedName);
1352 WRITE(out,fName);
1353 WRITE(out,fIsFinalized);
1354 }
1355
1356 //___________________________________________
1357
1358 void G4MolecularConfiguration::Unserialize(st
1359 {
1360 G4String moleculeName;
1361 READ(in, moleculeName);
1362 fMoleculeDefinition =
1363 G4MoleculeTable::Instance()->GetMolecul
1364
1365 // G4String label;
1366 //
1367 // in.read((char*)(&label), sizeof(label));
1368 //
1369 // if(label)
1370 // fLabel = new G4String(label);
1371 // else
1372 // fLabel = 0;
1373 READ(in,fDynDiffusionCoefficient);
1374 READ(in,fDynVanDerVaalsRadius);
1375 READ(in,fDynDecayTime);
1376 READ(in,fDynMass);
1377 READ(in,fDynCharge);
1378 READ(in,fMoleculeID);
1379 READ(in,fFormatedName);
1380 READ(in,fName);
1381 READ(in,fIsFinalized);
1382 }
1383
1384 //___________________________________________
1385
1386 G4MolecularConfiguration* G4MolecularConfigur
1387 {
1388 return new G4MolecularConfiguration(in);
1389 }
1390
1391 //___________________________________________
1392
1393 G4MolecularConfiguration::G4MolecularConfigur
1394 {
1395 fLabel = nullptr; // TODO: for now not seri
1396 Unserialize(in);
1397 fMoleculeDefinition = nullptr;
1398 fElectronOccupancy = nullptr;
1399 if(fElectronOccupancy != nullptr)
1400 {
1401 GetManager()->Insert(fMoleculeDefinition,
1402 fElectronOccupancy =
1403 GetManager()->FindCommonElectronOccup
1404
1405
1406 if(fLabel != nullptr)
1407 {
1408 GetManager()->RecordNewlyLabeledConfigu
1409 }
1410 }
1411 else if(fLabel != nullptr)
1412 {
1413 fMoleculeID = GetManager()->Insert(fMolec
1414 }
1415 else if(fDynCharge != 0)
1416 {
1417 fMoleculeID = GetManager()->Insert(fMolec
1418 }
1419 }
1420
1421 //___________________________________________
1422
1423 void G4MolecularConfiguration::SetUserID(cons
1424 {
1425 fUserIdentifier = userID;
1426 GetManager()->AddUserID(userID, this);
1427 // G4MoleculeTable::Instance()->RecordMolecu
1428 }
1429
1430 //___________________________________________
1431
1432 double G4MolecularConfiguration::DiffCoeffWat
1433 {
1434 return pow(10, 4.311
1435 - 2.722e3/temperature_K
1436 + 8.565e5/(temperature_K *temper
1437 - 1.181e8/(temperature_K*tempera
1438 }
1439
1440 //___________________________________________
1441
1442 void
1443 G4MolecularConfiguration::
1444 ScaleAllDiffusionCoefficientsOnWater(double t
1445 {
1446 double D_water_0 = DiffCoeffWater(fgTempera
1447 double D_water_f = DiffCoeffWater(temperatu
1448
1449 G4cout << "Scaling factor = " << D_water_f/
1450
1451 G4ConfigurationIterator it =
1452 G4MoleculeTable::Instance()->GetConfigu
1453
1454 while(it())
1455 {
1456 G4MolecularConfiguration* conf = it.value
1457 double D_0 = conf->GetDiffusionCoefficien
1458 double D_f = D_water_f * D_0 /D_water_0;
1459 conf->SetDiffusionCoefficient(D_f);
1460 };
1461 }
1462
1463 //___________________________________________
1464
1465 void G4MolecularConfiguration::CreateDefaultD
1466 {
1467 if(!static_cast<bool>(fDiffParam))
1468 {
1469 fDiffParam = &G4MolecularConfiguration::R
1470 }
1471 }
1472
1473 //___________________________________________
1474
1475 void G4MolecularConfiguration::SetGlobalTempe
1476 {
1477 ScaleAllDiffusionCoefficientsOnWater(temper
1478 fgTemperature = temperature;
1479 }
1480
1481 //___________________________________________
1482
1483 G4double G4MolecularConfiguration::GetGlobalT
1484 {
1485 return fgTemperature;
1486 }
1487
1488 //___________________________________________
1489
1490 G4MolecularConfiguration*
1491 G4MolecularConfiguration::
1492 G4MolecularConfigurationManager::GetMolecular
1493 {
1494 for(auto it : fMolConfPerID)
1495 {
1496 if(it->GetUserID() == userID) return it;
1497 }
1498 return nullptr;
1499 }
1500
1501 //___________________________________________
1502
1503 G4MolecularConfiguration*
1504 G4MolecularConfiguration::GetMolecularConfigu
1505 {
1506 return GetManager()->GetMolecularConfigurat
1507 }
1508
1509 //___________________________________________
1510
1511 void G4MolecularConfiguration::FinalizeAll()
1512 {
1513 const std::vector<G4MolecularConfiguration*
1514 GetManager()->GetAllSpecies();
1515
1516 for(auto specie : species)
1517 {
1518 specie->Finalize();
1519 }
1520
1521 }
1522
1523 void G4MolecularConfiguration::PrintAll() //h
1524 {
1525 const std::vector<G4MolecularConfiguration*
1526 GetManager()->GetAllSpecies();
1527 G4cout<<G4endl;
1528 G4cout<<"Molecular Config"<<std::setw(25)<<
1529 G4cout<<"__________________________________
1530 "________________________________
1531 for(auto specie : species)
1532 {
1533 G4cout<<specie->GetName()
1534 <<std::setw(G4int(30 - specie->Get
1535 <<right<<specie->GetDiffusionCoeff
1536 <<specie->GetVanDerVaalsRadius()/C
1537 G4cout<<"________________________________
1538 "______________________________
1539 }
1540
1541 }
1542