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25 //
26 // ---------------------------------------------------------------------
27 // GEANT 4 class header file
28 //
29 // History: first implementation, based on G4DynamicParticle
30 // New dependency : G4VUserTrackInformation
31 //
32 // ---------------- G4Molecule ----------------
33 // first design&implementation by Alfonso Mantero, 7 Apr 2009
34 // New developments Alfonso Mantero & Mathieu Karamitros
35 // Oct/Nov 2009 Class Name changed to G4Molecule
36 // Removed dependency from G4DynamicParticle
37 // New constructors :
38 // copy constructor
39 // direct ionized/excited molecule
40 // New methods :
41 // Get : name,atoms' number,nb electrons,decayChannel
42 // PrintState //To get the electronic level and the
43 // corresponding name of the excitation
44 // Kinematic :
45 // BuildTrack,GetKineticEnergy,GetDiffusionVelocity
46 // Change the way dynCharge and eNb is calculated
47 // ---------------------------------------------------------------------
48
49 #include "G4Molecule.hh"
50 #include "G4MolecularConfiguration.hh"
51 #include "Randomize.hh"
52 #include "G4PhysicalConstants.hh"
53 #include "G4SystemOfUnits.hh"
54 #include "G4Track.hh"
55 #include "G4VMoleculeCounter.hh"
56
57 using namespace std;
58
59 G4Allocator<G4Molecule>*& aMoleculeAllocator()
60 {
61 G4ThreadLocalStatic G4Allocator<G4Molecule>* _instance = nullptr;
62 return _instance;
63 }
64
65 //______________________________________________________________________________
66
67 template<>
68 G4KDNode<G4Molecule>::~G4KDNode() {
69 fPoint->SetNode(nullptr);
70 }
71
72 //______________________________________________________________________________
73
74 G4Molecule* GetMolecule(const G4Track& track)
75 {
76 return (G4Molecule*)(GetIT(track));
77 }
78
79 //______________________________________________________________________________
80
81 G4Molecule* GetMolecule(const G4Track* track)
82 {
83 return (G4Molecule*)(GetIT(track));
84 }
85
86 //______________________________________________________________________________
87
88 G4Molecule* G4Molecule::GetMolecule(const G4Track* track)
89 {
90 return (G4Molecule*)(GetIT(track));
91 }
92
93 //______________________________________________________________________________
94
95 void G4Molecule::Print() const
96 {
97 G4cout << "The user track information is a molecule" << G4endl;
98 }
99
100 //______________________________________________________________________________
101
102 G4Molecule::G4Molecule(const G4Molecule& right)
103 : G4VUserTrackInformation("G4Molecule")
104 , G4IT(right)
105 {
106 fpMolecularConfiguration = right.fpMolecularConfiguration;
107 }
108
109 //______________________________________________________________________________
110
111 G4Molecule& G4Molecule::operator=(const G4Molecule& right)
112 {
113 if (&right == this) return *this;
114 fpMolecularConfiguration = right.fpMolecularConfiguration;
115 return *this;
116 }
117
118 //______________________________________________________________________________
119
120 G4bool G4Molecule::operator==(const G4Molecule& right) const
121 {
122 return fpMolecularConfiguration == right.fpMolecularConfiguration;
123 }
124
125 //______________________________________________________________________________
126
127 G4bool G4Molecule::operator!=(const G4Molecule& right) const
128 {
129 return !(*this == right);
130 }
131
132 //______________________________________________________________________________
133 /** The two methods below are the most called of the simulation :
134 * compare molecules in the MoleculeStackManager or in
135 * the InteractionTable
136 */
137
138 G4bool G4Molecule::operator<(const G4Molecule& right) const
139 {
140 return fpMolecularConfiguration < right.fpMolecularConfiguration;
141 }
142
143 //______________________________________________________________________________
144
145 G4Molecule::G4Molecule()
146 : G4VUserTrackInformation("G4Molecule")
147 {
148 fpMolecularConfiguration = nullptr;
149 }
150
151 //______________________________________________________________________________
152
153 G4Molecule::~G4Molecule()
154 {
155 if (fpTrack != nullptr)
156 {
157 if (G4VMoleculeCounter::Instance()->InUse())
158 {
159 G4VMoleculeCounter::Instance()->
160 RemoveAMoleculeAtTime(fpMolecularConfiguration,
161 fpTrack->GetGlobalTime(),
162 &(fpTrack->GetPosition()));
163 }
164 fpTrack = nullptr;
165 }
166 fpMolecularConfiguration = nullptr;
167 }
168
169 //______________________________________________________________________________
170 /** Build a molecule at ground state according to a given
171 * G4MoleculeDefinition that can be obtained from G4GenericMoleculeManager
172 */
173 G4Molecule::G4Molecule(G4MoleculeDefinition* pMoleculeDefinition)
174 : G4VUserTrackInformation("G4Molecule")
175 {
176 fpMolecularConfiguration = G4MolecularConfiguration::GetOrCreateMolecularConfiguration(pMoleculeDefinition);
177 }
178
179 //______________________________________________________________________________
180
181 G4Molecule::G4Molecule(G4MoleculeDefinition* pMoleculeDefinition, int charge)
182 {
183 fpMolecularConfiguration = G4MolecularConfiguration::GetOrCreateMolecularConfiguration(pMoleculeDefinition,
184 charge);
185 }
186
187 //______________________________________________________________________________
188 /** Build a molecule at a specific excitation/ionisation state according
189 * to a ground state that can be obtained from G4GenericMoleculeManager.
190 * Put 0 in the second option if this is a ionisation.
191 */
192 G4Molecule::G4Molecule(G4MoleculeDefinition* pMoleculeDefinition,
193 G4int OrbitalToFree,
194 G4int OrbitalToFill)
195 : G4VUserTrackInformation("G4Molecule")
196 {
197 if (pMoleculeDefinition->GetGroundStateElectronOccupancy() != nullptr)
198 {
199 G4ElectronOccupancy dynElectronOccupancy(*pMoleculeDefinition->GetGroundStateElectronOccupancy());
200
201 if (OrbitalToFill != 0)
202 {
203 dynElectronOccupancy.RemoveElectron(OrbitalToFree - 1, 1);
204 dynElectronOccupancy.AddElectron(OrbitalToFill - 1, 1);
205 // dynElectronOccupancy.DumpInfo(); // DEBUG
206 }
207
208 if (OrbitalToFill == 0)
209 {
210 dynElectronOccupancy.RemoveElectron(OrbitalToFree - 1, 1);
211 // dynElectronOccupancy.DumpInfo(); // DEBUG
212 }
213
214 fpMolecularConfiguration =
215 G4MolecularConfiguration::GetOrCreateMolecularConfiguration(
216 pMoleculeDefinition, dynElectronOccupancy);
217 }
218 else
219 {
220 fpMolecularConfiguration = nullptr;
221 G4Exception(
222 "G4Molecule::G4Molecule(G4MoleculeDefinition* pMoleculeDefinition, "
223 "G4int OrbitalToFree, G4int OrbitalToFill)",
224 "G4Molecule_wrong_usage_of_constructor",
225 FatalErrorInArgument,
226 "If you want to use this constructor, the molecule definition has to be "
227 "first defined with electron occupancies");
228 }
229 }
230
231 //______________________________________________________________________________
232 /** Specific builder for water molecules to be used in Geant4-DNA,
233 * the last option Excitation is true if the molecule is excited, is
234 * false is the molecule is ionized.
235 */
236 G4Molecule::G4Molecule(G4MoleculeDefinition* pMoleculeDefinition,
237 G4int level,
238 G4bool excitation)
239 : G4VUserTrackInformation("G4Molecule")
240 {
241 if (pMoleculeDefinition->GetGroundStateElectronOccupancy() != nullptr)
242 {
243 G4ElectronOccupancy dynElectronOccupancy(*pMoleculeDefinition->GetGroundStateElectronOccupancy());
244
245 if (excitation)
246 {
247 dynElectronOccupancy.RemoveElectron(level, 1);
248 dynElectronOccupancy.AddElectron(5, 1);
249 // dynElectronOccupancy.DumpInfo(); // DEBUG
250 }
251 else
252 {
253 dynElectronOccupancy.RemoveElectron(level, 1);
254 // dynElectronOccupancy.DumpInfo(); // DEBUG
255 }
256
257 fpMolecularConfiguration = G4MolecularConfiguration::GetOrCreateMolecularConfiguration(pMoleculeDefinition,
258 dynElectronOccupancy);
259 }
260 else
261 {
262 fpMolecularConfiguration = nullptr;
263 G4Exception(
264 "G4Molecule::G4Molecule(G4MoleculeDefinition* pMoleculeDefinition, "
265 "G4int OrbitalToFree, G4int OrbitalToFill)",
266 "G4Molecule_wrong_usage_of_constructor",
267 FatalErrorInArgument,
268 "If you want to use this constructor, the molecule definition has to be "
269 "first defined with electron occupancies");
270 }
271 }
272
273 //______________________________________________________________________________
274
275 G4Molecule::G4Molecule(const G4MolecularConfiguration* pMolecularConfiguration)
276 {
277 fpMolecularConfiguration = pMolecularConfiguration;
278 }
279
280 //______________________________________________________________________________
281
282 void G4Molecule::SetElectronOccupancy(const G4ElectronOccupancy* pElectronOcc)
283 {
284 fpMolecularConfiguration =
285 G4MolecularConfiguration::GetOrCreateMolecularConfiguration(fpMolecularConfiguration->GetDefinition(),
286 *pElectronOcc);
287 }
288
289 //______________________________________________________________________________
290
291 void G4Molecule::ExciteMolecule(G4int excitationLevel)
292 {
293 fpMolecularConfiguration = fpMolecularConfiguration->ExciteMolecule(excitationLevel);
294 }
295
296 //______________________________________________________________________________
297
298 void G4Molecule::IonizeMolecule(G4int ionizationLevel)
299 {
300 fpMolecularConfiguration = fpMolecularConfiguration->IonizeMolecule(ionizationLevel);
301 }
302
303 //______________________________________________________________________________
304
305 void G4Molecule::AddElectron(G4int orbit, G4int number)
306 {
307 fpMolecularConfiguration = fpMolecularConfiguration->AddElectron(orbit, number);
308 }
309
310 //______________________________________________________________________________
311
312 void G4Molecule::RemoveElectron(G4int orbit, G4int number)
313 {
314 fpMolecularConfiguration =
315 fpMolecularConfiguration->RemoveElectron(orbit, number);
316 }
317
318 //______________________________________________________________________________
319
320 void G4Molecule::MoveOneElectron(G4int orbitToFree, G4int orbitToFill)
321 {
322 fpMolecularConfiguration =
323 fpMolecularConfiguration->MoveOneElectron(orbitToFree, orbitToFill);
324 }
325
326 //______________________________________________________________________________
327
328 const G4String& G4Molecule::GetName() const
329 {
330 return fpMolecularConfiguration->GetName();
331 }
332
333 //______________________________________________________________________________
334
335 const G4String& G4Molecule::GetFormatedName() const
336 {
337 return fpMolecularConfiguration->GetFormatedName();
338 }
339
340 //______________________________________________________________________________
341
342 G4int G4Molecule::GetAtomsNumber() const
343 {
344 return fpMolecularConfiguration->GetAtomsNumber();
345 }
346
347 //______________________________________________________________________________
348
349 G4double G4Molecule::GetNbElectrons() const
350 {
351 return fpMolecularConfiguration->GetNbElectrons();
352 }
353
354 //______________________________________________________________________________
355
356 void G4Molecule::PrintState() const
357 {
358 fpMolecularConfiguration->PrintState();
359 }
360
361 //______________________________________________________________________________
362
363 G4Track* G4Molecule::BuildTrack(G4double globalTime,
364 const G4ThreeVector& position)
365 {
366 if (fpTrack != nullptr)
367 {
368 G4Exception("G4Molecule::BuildTrack", "Molecule001", FatalErrorInArgument,
369 "A track was already assigned to this molecule");
370 }
371
372 // Kinetic Values
373 // Set a random direction to the molecule
374 G4double costheta = (2 * G4UniformRand() - 1);
375 G4double theta = acos(costheta);
376 G4double phi = 2 * pi * G4UniformRand();
377
378 G4double xMomentum = cos(phi) * sin(theta);
379 G4double yMomentum = sin(theta) * sin(phi);
380 G4double zMomentum = costheta;
381
382 G4ThreeVector MomentumDirection(xMomentum, yMomentum, zMomentum);
383 G4double KineticEnergy = GetKineticEnergy();
384
385 auto dynamicParticle = new G4DynamicParticle(
386 fpMolecularConfiguration->GetDefinition(), MomentumDirection,
387 KineticEnergy);
388
389 if (G4VMoleculeCounter::Instance()->InUse())
390 {
391 G4VMoleculeCounter::Instance()->
392 AddAMoleculeAtTime(fpMolecularConfiguration,
393 globalTime,
394 &(fpTrack->GetPosition()));
395 }
396
397 //Set the Track
398 fpTrack = new G4Track(dynamicParticle, globalTime, position);
399 fpTrack->SetUserInformation(this);
400
401 return fpTrack;
402 }
403
404 //______________________________________________________________________________
405
406 G4double G4Molecule::GetKineticEnergy() const
407 {
408 ////
409 // Ideal Gaz case
410 double v = GetDiffusionVelocity();
411 double E = (fpMolecularConfiguration->GetMass() / (c_squared)) * (v * v) / 2.;
412 ////
413 return E;
414 }
415
416 //______________________________________________________________________________
417
418 G4double G4Molecule::GetDiffusionVelocity() const
419 {
420 double moleculeMass = fpMolecularConfiguration->GetMass() / (c_squared);
421
422 ////
423 // Different possibilities
424 ////
425 // Ideal Gaz case : Maxwell Boltzmann Distribution
426 // double sigma = k_Boltzmann * fgTemperature / mass;
427 // return G4RandGauss::shoot( 0, sigma );
428 ////
429 // Ideal Gaz case : mean velocity from equipartition theorem
430 return sqrt(3 * k_Boltzmann *
431 G4MolecularConfiguration::GetGlobalTemperature() / moleculeMass);
432 ////
433 // Using this approximation for liquid is wrong
434 // However the brownian process avoid taking
435 // care of energy consideration and plays only
436 // with positions
437 }
438
439 //______________________________________________________________________________
440
441 // added - to be transformed in a "Decay method"
442 const vector<const G4MolecularDissociationChannel*>*
443 G4Molecule::GetDissociationChannels() const
444 {
445 return fpMolecularConfiguration->GetDissociationChannels();
446 }
447
448 //______________________________________________________________________________
449
450 G4int G4Molecule::GetFakeParticleID() const
451 {
452 return fpMolecularConfiguration->GetFakeParticleID();
453 }
454
455 //______________________________________________________________________________
456
457 G4int G4Molecule::GetMoleculeID() const
458 {
459 return fpMolecularConfiguration->GetMoleculeID();
460 }
461
462 //______________________________________________________________________________
463
464 G4double G4Molecule::GetDecayTime() const
465 {
466 return fpMolecularConfiguration->GetDecayTime();
467 }
468
469 //______________________________________________________________________________
470
471 G4double G4Molecule::GetVanDerVaalsRadius() const
472 {
473 return fpMolecularConfiguration->GetVanDerVaalsRadius();
474 }
475
476 //______________________________________________________________________________
477
478 G4int G4Molecule::GetCharge() const
479 {
480 return fpMolecularConfiguration->GetCharge();
481 }
482
483 //______________________________________________________________________________
484
485 G4double G4Molecule::GetMass() const
486 {
487 return fpMolecularConfiguration->GetMass();
488 }
489
490 //______________________________________________________________________________
491
492 const G4ElectronOccupancy* G4Molecule::GetElectronOccupancy() const
493 {
494 return fpMolecularConfiguration->GetElectronOccupancy();
495 }
496
497 //______________________________________________________________________________
498
499 const G4MoleculeDefinition* G4Molecule::GetDefinition() const
500 {
501 return fpMolecularConfiguration->GetDefinition();
502 }
503
504 //______________________________________________________________________________
505
506 G4double G4Molecule::GetDiffusionCoefficient() const
507 {
508 return fpMolecularConfiguration->GetDiffusionCoefficient();
509 }
510
511 //______________________________________________________________________________
512
513 G4double G4Molecule::GetDiffusionCoefficient(const G4Material* pMaterial,
514 double temperature) const
515 {
516 return fpMolecularConfiguration->GetDiffusionCoefficient(pMaterial,
517 temperature);
518 }
519
520 //______________________________________________________________________________
521
522 const G4MolecularConfiguration* G4Molecule::GetMolecularConfiguration() const
523 {
524 return fpMolecularConfiguration;
525 }
526
527 //______________________________________________________________________________
528
529 const G4String& G4Molecule::GetLabel() const
530 {
531 return fpMolecularConfiguration->GetLabel();
532 }
533
534 //______________________________________________________________________________
535
536 void G4Molecule::ChangeConfigurationToLabel(const G4String& label)
537 {
538 // TODO check fpMolecularConfiguration already exists
539 // and new one as well
540 // TODO notify for stack change
541 fpMolecularConfiguration = G4MolecularConfiguration::GetMolecularConfiguration(
542 fpMolecularConfiguration->GetDefinition(), label);
543
544 assert(fpMolecularConfiguration != nullptr);
545 }
546