Geant4  10.02.p02
G4Molecule.cc
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25 // $Id: G4Molecule.cc 93883 2015-11-03 08:25:04Z gcosmo $
26 //
27 // ---------------------------------------------------------------------
28 // GEANT 4 class header file
29 //
30 // History: first implementation, based on G4DynamicParticle
31 // New dependency : G4VUserTrackInformation
32 //
33 // ---------------- G4Molecule ----------------
34 // first design&implementation by Alfonso Mantero, 7 Apr 2009
35 // New developments Alfonso Mantero & Mathieu Karamitros
36 // Oct/Nov 2009 Class Name changed to G4Molecule
37 // Removed dependency from G4DynamicParticle
38 // New constructors :
39 // copy constructor
40 // direct ionized/excited molecule
41 // New methods :
42 // Get : name,atoms' number,nb electrons,decayChannel
43 // PrintState //To get the electronic level and the
44 // corresponding name of the excitation
45 // Kinematic :
46 // BuildTrack,GetKineticEnergy,GetDiffusionVelocity
47 // Change the way dynCharge and eNb is calculated
48 // ---------------------------------------------------------------------
49 
50 #include "G4Molecule.hh"
52 #include "Randomize.hh"
53 #include "G4PhysicalConstants.hh"
54 #include "G4SystemOfUnits.hh"
55 #include "G4Track.hh"
56 #include "G4MoleculeCounter.hh"
57 
58 using namespace std;
59 
61 // 37°C, used to shoot an energy
62 
64 
66 
67 //______________________________________________________________________________
68 
70 {
71  return (G4Molecule*) (GetIT(track));
72 }
73 
74 //______________________________________________________________________________
75 
77 {
78  return (G4Molecule*) (GetIT(track));
79 }
80 
81 //______________________________________________________________________________
82 
84 {
85  return (G4Molecule*) (GetIT(track));
86 }
87 
88 //______________________________________________________________________________
89 
90 void G4Molecule::Print() const
91 {
92  G4cout << "The user track information is a molecule" << G4endl;
93 }
94 
95 //______________________________________________________________________________
96 
98  G4VUserTrackInformation("G4Molecule"), G4IT(right)
99 {
101 }
102 
103 //______________________________________________________________________________
104 
106 {
107  if (&right == this) return *this;
109  return *this;
110 }
111 
112 //______________________________________________________________________________
113 
115 {
117  {
118  return true;
119  }
120  return false;
121 }
122 
123 //______________________________________________________________________________
124 
126 {
127  return !(*this == right);
128 }
129 
130 //______________________________________________________________________________
137 {
139 }
140 
141 //______________________________________________________________________________
145  G4VUserTrackInformation("G4Molecule"), G4IT()
146 
147 {
149 }
150 
151 //______________________________________________________________________________
152 
154 {
155  if (fpTrack != NULL)
156  {
158  {
161  }
162  fpTrack = 0;
163  }
165 }
166 
167 //______________________________________________________________________________
171 G4Molecule::G4Molecule(G4MoleculeDefinition * moleculeDefinition) :
173  G4VUserTrackInformation("G4Molecule"), G4IT()
175 {
178 }
179 
180 //______________________________________________________________________________
181 
182 G4Molecule::G4Molecule(G4MoleculeDefinition* moleculeDefinition, int charge)
183 {
186  charge);
187 }
188 
189 //______________________________________________________________________________
194 G4Molecule::G4Molecule(G4MoleculeDefinition * moleculeDefinition,
196  G4int OrbitalToFree,
197  G4int OrbitalToFill) :
198  G4VUserTrackInformation("G4Molecule"), G4IT()
200 {
201  if (moleculeDefinition->GetGroundStateElectronOccupancy())
202  {
203  G4ElectronOccupancy dynElectronOccupancy(
204  *moleculeDefinition->GetGroundStateElectronOccupancy());
205 
206  if (OrbitalToFill != 0)
207  {
208  dynElectronOccupancy.RemoveElectron(OrbitalToFree - 1, 1);
209  dynElectronOccupancy.AddElectron(OrbitalToFill - 1, 1);
210  // dynElectronOccupancy.DumpInfo(); // DEBUG
211  }
212 
213  if (OrbitalToFill == 0)
214  {
215  dynElectronOccupancy.RemoveElectron(OrbitalToFree - 1, 1);
216  // dynElectronOccupancy.DumpInfo(); // DEBUG
217  }
218 
221  moleculeDefinition, dynElectronOccupancy);
222  }
223  else
224  {
226  G4Exception(
227  "G4Molecule::G4Molecule(G4MoleculeDefinition * moleculeDefinition, "
228  "G4int OrbitalToFree, G4int OrbitalToFill)",
229  "G4Molecule_wrong_usage_of_constructor",
231  "If you want to use this constructor, the molecule definition has to be "
232  "first defined with electron occupancies");
233  }
234 }
235 
236 //______________________________________________________________________________
243  G4int Level,
244  G4bool Excitation) :
245  G4VUserTrackInformation("G4Molecule"), G4IT()
246 {
247  if (moleculeDefinition->GetGroundStateElectronOccupancy())
248  {
249  G4ElectronOccupancy dynElectronOccupancy(
250  *moleculeDefinition->GetGroundStateElectronOccupancy());
251 
252  if (Excitation == true)
253  {
254  dynElectronOccupancy.RemoveElectron(Level, 1);
255  dynElectronOccupancy.AddElectron(5, 1);
256  // dynElectronOccupancy.DumpInfo(); // DEBUG
257  }
258 
259  if (Excitation == false)
260  {
261  dynElectronOccupancy.RemoveElectron(Level, 1);
262  // dynElectronOccupancy.DumpInfo(); // DEBUG
263  }
264 
267  moleculeDefinition, dynElectronOccupancy);
268  }
269  else
270  {
272  G4Exception(
273  "G4Molecule::G4Molecule(G4MoleculeDefinition * moleculeDefinition, "
274  "G4int OrbitalToFree, G4int OrbitalToFill)",
275  "G4Molecule_wrong_usage_of_constructor",
277  "If you want to use this constructor, the molecule definition has to be "
278  "first defined with electron occupancies");
279 
280  }
281 }
282 
283 //______________________________________________________________________________
284 
286 {
287  fpMolecularConfiguration = molConf;
288 }
289 
290 //______________________________________________________________________________
291 
293 {
297 }
298 
299 //______________________________________________________________________________
300 
304 {
306  ExcitedLevel);
307 }
308 
309 //______________________________________________________________________________
310 
314 {
316  IonizedLevel);
317 }
318 
319 //______________________________________________________________________________
320 
322 {
324  number);
325 }
326 
327 //______________________________________________________________________________
328 
330 {
332  number);
333 }
334 
335 //______________________________________________________________________________
336 
337 void G4Molecule::MoveOneElectron(G4int orbitToFree, G4int orbitToFill)
338 {
340  orbitToFree, orbitToFill);
341 }
342 
343 //______________________________________________________________________________
344 
346 {
348 }
349 
350 //______________________________________________________________________________
351 
353 {
355 }
356 
357 //______________________________________________________________________________
358 
360 {
362 }
363 
364 //______________________________________________________________________________
365 
367 {
369 }
370 
371 //______________________________________________________________________________
372 
374 {
376 }
377 
378 //______________________________________________________________________________
379 
381  const G4ThreeVector& position)
382 {
383  if (fpTrack != 0)
384  {
385  G4Exception("G4Molecule::BuildTrack", "Molecule001", FatalErrorInArgument,
386  "A track was already assigned to this molecule");
387  }
388 
389  // Kinetic Values
390  // Set a random direction to the molecule
391  G4double costheta = (2 * G4UniformRand()-1);
392  G4double theta = acos(costheta);
393  G4double phi = 2 * pi * G4UniformRand();
394 
395  G4double xMomentum = cos(phi) * sin(theta);
396  G4double yMomentum = sin(theta) * sin(phi);
397  G4double zMomentum = costheta;
398 
399  G4ThreeVector MomentumDirection(xMomentum, yMomentum, zMomentum);
400  G4double KineticEnergy = GetKineticEnergy();
401 
402  G4DynamicParticle* dynamicParticle = new G4DynamicParticle(
403  fpMolecularConfiguration->GetDefinition(), MomentumDirection,
404  KineticEnergy);
405 
407  {
409  globalTime);
410  }
411 
412  //Set the Track
413  fpTrack = new G4Track(dynamicParticle, globalTime, position);
415 
416  return fpTrack;
417 }
418 
419 //______________________________________________________________________________
420 
422 {
424  // Ideal Gaz case
425  double v = GetDiffusionVelocity();
426  double E = (fpMolecularConfiguration->GetMass() / (c_squared)) * (v * v) / 2.;
428  return E;
429 }
430 
431 //______________________________________________________________________________
432 
434 {
435  double moleculeMass = fpMolecularConfiguration->GetMass() / (c_squared);
436 
438  // Different possibilities
440  // Ideal Gaz case : Maxwell Boltzmann Distribution
441  // double sigma = k_Boltzmann * fgTemperature / mass;
442  // return G4RandGauss::shoot( 0, sigma );
444  // Ideal Gaz case : mean velocity from equipartition theorem
445  return sqrt(3 * k_Boltzmann *
448  // Using this approximation for liquid is wrong
449  // However the brownian process avoid taking
450  // care of energy consideration and plays only
451  // with positions
452 }
453 
454 //______________________________________________________________________________
455 
456 // added - to be transformed in a "Decay method"
457 const vector<const G4MolecularDissociationChannel*>*
459 {
461 }
462 
463 //______________________________________________________________________________
464 
466 {
468 }
469 
470 //______________________________________________________________________________
471 
473 {
475 }
476 
477 //______________________________________________________________________________
478 
480 {
481  fpMolecularConfiguration->SetDecayTime(dynDecayTime);
482 }
483 
484 //______________________________________________________________________________
485 
487 {
489 }
490 
491 //______________________________________________________________________________
492 
493 void G4Molecule::SetVanDerVaalsRadius(G4double dynVanDerVaalsRadius)
494 {
495  fpMolecularConfiguration->SetVanDerVaalsRadius(dynVanDerVaalsRadius);
496 }
497 
498 //______________________________________________________________________________
499 
501 {
503 }
504 
505 //______________________________________________________________________________
506 
508 {
510 }
511 
512 //______________________________________________________________________________
513 
515 {
517 }
518 
519 //______________________________________________________________________________
520 
522 {
524 }
525 
526 //______________________________________________________________________________
527 
529 {
531 }
532 
533 //______________________________________________________________________________
534 
536 {
538 }
539 
540 //______________________________________________________________________________
541 
542 void G4Molecule::SetDiffusionCoefficient(G4double dynDiffusionCoefficient)
543 {
544  fpMolecularConfiguration->SetDiffusionCoefficient(dynDiffusionCoefficient);
545 }
546 
547 //______________________________________________________________________________
548 
550 {
552 }
553 
554 //______________________________________________________________________________
555 
557  double temperature) const
558 {
560  temperature);
561 }
562 
563 //______________________________________________________________________________
564 
566 {
568 }
569 
570 //______________________________________________________________________________
571 
572 //void G4Molecule::SetGlobalTemperature(G4double temperature)
573 //{
574 // fgTemperature = temperature;
575 //}
576 //
578 //
579 //G4double G4Molecule::GetGlobalTemperature()
580 //{
581 // return fgTemperature;
582 //}
583 
584 //______________________________________________________________________________
585 
587 {
589 }
590 
591 //______________________________________________________________________________
592 
593 void G4Molecule::SetLabel(const G4String& label)
594 {
596 }
597 
598 //______________________________________________________________________________
599 
601 {
602  // TODO check fpMolecularConfiguration already exists
603  // and new one as well
604  // TODO notify for stack change
608 
609  assert(fpMolecularConfiguration!=0);
610 }
The pointer G4MolecularConfiguration will be shared by all the molecules having the same molecule def...
G4double GetDiffusionCoefficient() const
Returns the diffusion coefficient D.
void PrintState() const
Display the electronic state of the molecule.
G4int GetCharge() const
Returns the charge of molecule.
const G4String & GetName() const
Returns the name of the molecule.
void SetDiffusionCoefficient(G4double)
Sets the diffusion coefficient D of the molecule used in diffusion processes to calculate the mean sq...
Definition: G4Molecule.cc:542
const std::vector< const G4MolecularDissociationChannel * > * GetDecayChannel() const
Definition: G4Molecule.cc:458
G4bool operator!=(const G4Molecule &right) const
Definition: G4Molecule.cc:125
CLHEP::Hep3Vector G4ThreeVector
G4Molecule()
Default molecule builder.
Definition: G4Molecule.cc:144
G4bool operator<(const G4Molecule &right) const
The two methods below are the most called of the simulation : compare molecules in the MoleculeStackM...
Definition: G4Molecule.cc:136
static G4Molecule * GetMolecule(const G4Track *)
Definition: G4Molecule.cc:83
G4double GetMass() const
Returns the total mass of the molecule.
Definition: G4Molecule.cc:521
void SetMass(G4double)
Set the total mass of the molecule.
Definition: G4Molecule.cc:514
void SetLabel(const G4String &label)
Definition: G4Molecule.cc:593
static G4MolecularConfiguration * GetMolecularConfiguration(const G4MoleculeDefinition *, const G4String &label)
G4MolecularConfiguration * fpMolecularConfiguration
Definition: G4Molecule.hh:290
G4double GetDiffusionCoefficient() const
Returns the diffusion coefficient D.
Definition: G4Molecule.cc:549
static G4MoleculeCounter * GetMoleculeCounter()
G4double GetNbElectrons() const
Returns the number of electron.
Definition: G4Molecule.cc:366
G4double GetNbElectrons() const
Returns the number of electron.
const std::vector< const G4MolecularDissociationChannel * > * GetDecayChannel() const
virtual void RemoveAMoleculeAtTime(G4MolecularConfiguration *, G4double time, int number=1)
G4MolecularConfiguration * GetMolecularConfiguration() const
Definition: G4Molecule.cc:565
const G4ElectronOccupancy * GetElectronOccupancy() const
Returns the object ElectronOccupancy describing the electronic configuration of the molecule...
#define G4ThreadLocal
Definition: tls.hh:89
virtual ~G4Molecule()
Definition: G4Molecule.cc:153
int G4int
Definition: G4Types.hh:78
void ChangeConfigurationToLabel(const G4String &label)
Definition: G4Molecule.cc:600
const G4String & GetName() const
Returns the name of the molecule.
Definition: G4Molecule.cc:345
G4IT * GetIT(const G4Track *track)
Definition: G4IT.cc:49
void MoveOneElectron(G4int, G4int)
Move one electron from an orbit to another.
Definition: G4Molecule.cc:337
const G4String & GetLabel() const
Returns the label of the molecule configuration.
Definition: G4Molecule.cc:586
#define position
Definition: xmlparse.cc:622
#define G4UniformRand()
Definition: Randomize.hh:97
G4GLOB_DLL std::ostream G4cout
static G4bool InUse()
G4MolecularConfiguration * IonizeMolecule(G4int)
Method used in Geant4-DNA to ionize water molecules.
void SetElectronOccupancy(const G4ElectronOccupancy *)
Will set up the correct molecularConfiguration given an electron configuration.
Definition: G4Molecule.cc:292
G4int GetAtomsNumber() const
Returns the nomber of atoms compouning the molecule.
Definition: G4Molecule.cc:359
G4MolecularConfiguration * AddElectron(G4int orbit, G4int n=1)
Add n electrons to a given orbit.
G4int GetFakeParticleID() const
Definition: G4Molecule.cc:465
bool G4bool
Definition: G4Types.hh:79
G4Track * fpTrack
Definition: G4IT.hh:164
ITImp(G4Molecule) G4ThreadLocal G4Allocator< G4Molecule > *aMoleculeAllocator=0
G4ThreadLocal/G4double G4Molecule::fgTemperature = 310; // 310*kelvin;
G4Molecule * GetMolecule(const G4Track &track)
Definition: G4Molecule.cc:69
void SetVanDerVaalsRadius(G4double)
The Van Der Valls Radius of the molecule.
Definition: G4Molecule.cc:493
G4MolecularConfiguration * MoveOneElectron(G4int, G4int)
Move one electron from an orbit to another.
void SetDiffusionCoefficient(G4double)
Sets the diffusion coefficient D of the molecule used in diffusion processes to calculate the mean sq...
virtual void AddAMoleculeAtTime(G4MolecularConfiguration *, G4double time, int number=1)
G4Molecule & operator=(const G4Molecule &right)
Definition: G4Molecule.cc:105
G4double GetGlobalTime() const
void IonizeMolecule(G4int)
Method used in Geant4-DNA to ionize water molecules.
Definition: G4Molecule.cc:313
static G4MolecularConfiguration * GetOrCreateMolecularConfiguration(const G4MoleculeDefinition *)
const G4MoleculeDefinition * GetDefinition() const
Get molecule definition.
Definition: G4Molecule.cc:535
void G4Exception(const char *originOfException, const char *exceptionCode, G4ExceptionSeverity severity, const char *comments)
Definition: G4Exception.cc:41
G4Track * BuildTrack(G4double globalTime, const G4ThreeVector &Position)
Definition: G4Molecule.cc:380
G4double GetMass() const
Returns the total mass of the molecule.
const G4String & GetFormatedName() const
Returns the formated name of the molecule.
Definition: G4Molecule.cc:352
G4int GetCharge() const
Returns the charge of molecule.
Definition: G4Molecule.cc:507
const G4String & GetFormatedName() const
Returns the formated name of the molecule.
void SetMass(G4double)
Set the total mass of the molecule.
static const double pi
Definition: G4SIunits.hh:74
G4double GetKineticEnergy() const
Definition: G4Molecule.cc:421
void RemoveElectron(G4int, G4int number=1)
Remove n electrons to a given orbit.
Definition: G4Molecule.cc:329
void SetDecayTime(G4double)
Set the decay time of the molecule.
void SetVanDerVaalsRadius(G4double)
The Van Der Valls Radius of the molecule.
G4int GetAtomsNumber() const
Returns the nomber of atoms compouning the molecule.
G4DLLIMPORT G4ThreadLocal G4Allocator< G4Molecule > * aMoleculeAllocator
void PrintState() const
Show the electronic state of the molecule.
Definition: G4Molecule.cc:373
const G4MoleculeDefinition * GetDefinition() const
const G4String & GetLabel() const
#define G4endl
Definition: G4ios.hh:61
G4double GetDiffusionVelocity() const
Definition: G4Molecule.cc:433
Class Description The dynamic molecule holds all the data that change for a molecule It has a pointer...
Definition: G4Molecule.hh:94
G4double GetDecayTime() const
Returns the decay time of the molecule.
double G4double
Definition: G4Types.hh:76
const G4ElectronOccupancy * GetGroundStateElectronOccupancy() const
const G4ElectronOccupancy * GetElectronOccupancy() const
Returns the object ElectronOccupancy describing the electronic configuration of the molecule...
Definition: G4Molecule.cc:528
void SetUserInformation(G4VUserTrackInformation *aValue)
G4MolecularConfiguration * RemoveElectron(G4int, G4int number=1)
Remove n electrons to a given orbit.
G4double GetVanDerVaalsRadius() const
Definition: G4Molecule.cc:500
G4double GetDecayTime() const
Returns the decay time of the molecule.
Definition: G4Molecule.cc:486
G4MolecularConfiguration * ExciteMolecule(G4int)
Method used in Geant4-DNA to excite water molecules.
{ Class description:
virtual void Print() const
Definition: G4IT.hh:94
void AddElectron(G4int orbit, G4int n=1)
Add n electrons to a given orbit.
Definition: G4Molecule.cc:321
G4bool operator==(const G4Molecule &right) const
Definition: G4Molecule.cc:114
void SetDecayTime(G4double)
Set the decay time of the molecule.
Definition: G4Molecule.cc:479
G4int RemoveElectron(G4int orbit, G4int number=1)
void ExciteMolecule(G4int)
Method used in Geant4-DNA to excite water molecules.
Definition: G4Molecule.cc:303
G4int GetMoleculeID() const
Definition: G4Molecule.cc:472