Geant4  10.02
G4MolecularConfiguration.hh
Go to the documentation of this file.
1 //
2 // ********************************************************************
3 // * License and Disclaimer *
4 // * *
5 // * The Geant4 software is copyright of the Copyright Holders of *
6 // * the Geant4 Collaboration. It is provided under the terms and *
7 // * conditions of the Geant4 Software License, included in the file *
8 // * LICENSE and available at http://cern.ch/geant4/license . These *
9 // * include a list of copyright holders. *
10 // * *
11 // * Neither the authors of this software system, nor their employing *
12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warranty, express or implied, *
14 // * regarding this software system or assume any liability for its *
15 // * use. Please see the license in the file LICENSE and URL above *
16 // * for the full disclaimer and the limitation of liability. *
17 // * *
18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboration. *
20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publications, and indicate your *
23 // * acceptance of all terms of the Geant4 Software license. *
24 // ********************************************************************
25 //
26 //
27 // Author: Mathieu Karamitros, kara@cenbg.in2p3.fr
28 
29 // The code is developed in the framework of the ESA AO7146
30 //
31 // We would be very happy hearing from you, send us your feedback! :)
32 //
33 // In order for Geant4-DNA to be maintained and still open-source,
34 // article citations are crucial.
35 // If you use Geant4-DNA chemistry and you publish papers about your software,
36 // in addition to the general paper on Geant4-DNA:
37 //
38 // Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
39 //
40 // we would be very happy if you could please also cite the following
41 // reference papers on chemistry:
42 //
43 // J. Comput. Phys. 274 (2014) 841-882
44 // Prog. Nucl. Sci. Tec. 2 (2011) 503-508
45 
46 #ifndef G4MolecularConfiguration_
47 #define G4MolecularConfiguration_ 1
48 
49 #include <vector>
50 #include <map>
51 #include "G4Threading.hh"
52 #include "G4ElectronOccupancy.hh"
53 #include <cassert>
54 #include <functional>
55 
58 class G4Material;
60 
61 struct comparator
62 {
63  bool operator()(const G4ElectronOccupancy& occ1,
64  const G4ElectronOccupancy& occ2) const
65  {
66  G4int totalOcc1 = occ1.GetTotalOccupancy();
67  G4int totalOcc2 = occ2.GetTotalOccupancy();
68  if (totalOcc1 != totalOcc2)
69  {
70  return totalOcc1 < totalOcc2;
71  }
72  else
73  {
74  G4int occupancy1 = -1;
75  G4int occupancy2 = -1;
76  const G4int sizeOrbit = occ1.GetSizeOfOrbit();
77  for (G4int i = 0; i < sizeOrbit; i++)
78  {
79  occupancy1 = occ1.GetOccupancy(i);
80  occupancy2 = occ2.GetOccupancy(i);
81 
82  if (occupancy1 != occupancy2)
83  {
84  return occupancy1 < occupancy2;
85  }
86  }
87  }
88  return false;
89  }
90 };
91 
99 {
100 public:
101 
102  typedef std::function<double(const G4Material*,
103  double,
105 
106  //____________________________________________________________________________
107  // Static methods
108 
110  // CREATE FINALIZED SPECIES
111  // Get ground state electronic configuration
114 
115  // Get for a given moleculeDefinition and a given electronic configuration,
116  // the molecular configuration
119  const G4ElectronOccupancy& eOcc);
120 
121  // Get for a given moleculeDefinition and a given electronic configuration,
122  // the molecular configuration
125 
127  // CREATE UNFINALIZED SPECIES
128  // Create ground state electronic configuration - to be finalized
130  CreateMolecularConfiguration(const G4String& userIdentifier,
131  const G4MoleculeDefinition*,
132  bool& wasAlreadyCreated);
133 
135  CreateMolecularConfiguration(const G4String& userIdentifier,
136  const G4MoleculeDefinition*,
137  const G4String& label,
138  const G4ElectronOccupancy& eOcc,
139  bool& wasAlreadyCreated);
140 
142  CreateMolecularConfiguration(const G4String& userIdentifier,
143  const G4MoleculeDefinition*,
144  int charge,
145  const G4String& label,
146  bool& wasAlreadyCreated);
147 
149  CreateMolecularConfiguration(const G4String& userIdentifier,
150  const G4MoleculeDefinition*,
151  const G4String& label,
152  bool& wasAlreadyCreated);
153 
155  // GET MOL CONF
156  //
159  const G4String& label);
160 
162  GetMolecularConfiguration(int moleculeID);
163 
165  GetMolecularConfiguration(const G4String& userID);
166 
167  static int GetNumberOfSpecies();
168 
169  static std::map<G4String, G4MolecularConfiguration*>& GetUserIDTable()
170  {
171  return GetManager()->GetUserIDTable();
172  }
173 
174  // Release memory of the mol conf manager
175  static void DeleteManager();
176 
177  static double DiffCoeffWater(double temperature_K);
178 
180 
181  //____________________________________________________________________________
182 
183  const G4MoleculeDefinition* GetDefinition() const;
184 
187  const G4String& GetName() const;
188 
191  const G4String& GetFormatedName() const;
192 
195  G4int GetAtomsNumber() const;
196 
200 
204 
210 
214 
217  G4MolecularConfiguration* MoveOneElectron(G4int /*orbit*/, G4int /*orbit*/);
218 
221  G4double GetNbElectrons() const;
222 
225  void PrintState() const;
226 
227  const std::vector<const G4MolecularDissociationChannel*>*
228  GetDecayChannel() const;
229 
230  G4int GetFakeParticleID() const;
231 
232  inline G4int GetMoleculeID() const;
233 
245  inline void SetDiffusionCoefficient(G4double);
246 
249  inline G4double GetDiffusionCoefficient() const;
250 
252  double temperature) const;
253 
256  inline void SetDecayTime(G4double);
257 
260  inline G4double GetDecayTime() const;
261 
264  inline void SetVanDerVaalsRadius(G4double);
265  inline G4double GetVanDerVaalsRadius() const;
266 
270  inline const G4ElectronOccupancy* GetElectronOccupancy() const;
271 
274  inline G4int GetCharge() const;
275 
278  inline void SetMass(G4double);
279 
282  inline G4double GetMass() const;
283 
284  /*
285  * Adds a label to the molecular configuration
286  * (Can be used for vibrational states for instance)
287  */
288  inline void SetLabel(const G4String&);
289 
290  /*
291  * Returns the label assigned by the user
292  */
293  inline const G4String& GetLabel() const;
294 
295  inline void Finalize();
296  static void FinalizeAll();
297 
298  inline const G4String& GetUserID() const;
299 
300  static void SetGlobalTemperature(G4double);
302 
303  //___________________________________________________________________________
304  // EXPERIMENTAL
305 
306  static G4MolecularConfiguration* Load(std::istream&);
307 
308  void Serialize(std::ostream&);
309  void Unserialize(std::istream&);
310  //___________________________________________________________________________
311 
312 
313 protected:
315  const G4ElectronOccupancy&,
316  const G4String& label = "");
317 
319  int charge);
320 
322  const G4String& label,
323  int charge);
324 
325  G4MolecularConfiguration(std::istream&);
326 
332 
333  void CheckElectronOccupancy(const char* line) const;
335  void SetUserID(const G4String& userID);
336 
338  static void ScaleAllDiffusionCoefficientsOnWater(double temperature_K);
339 
340 public:
342  {
343  public:
346  {
347  fLastMoleculeID = -1;
348  }
350 
352  {
353  return fLastMoleculeID+1;
354  }
355 
356  // TODO: TO BE IMPLEMENTED
357 // void InsertMolecularConfiguration(G4MolecularConfiguration*);
358 
359  //------------------------------------------------------------------------
360  // CALLED FROM CONSTRUCTORS
361  G4int Insert(const G4MoleculeDefinition* molDef,
362  const G4ElectronOccupancy& eOcc,
363  G4MolecularConfiguration* molConf);
364 
365  G4int Insert(const G4MoleculeDefinition* molDef,
366  int charge,
367  G4MolecularConfiguration* molConf);
368 
369  G4int Insert(const G4MoleculeDefinition* molDef,
370  const G4String& label,
371  G4MolecularConfiguration* molConf);
372 
373  //------------------------------------------------------------------------
374  // CALLED WHEN USER ADD SPECIES
375  void AddUserID(const G4String& name,
376  G4MolecularConfiguration* molecule);
377 
379 
380  const G4ElectronOccupancy*
382  const G4ElectronOccupancy& eOcc);
383 
386  const G4ElectronOccupancy& eOcc);
387 
390  int charge);
391 
394  const G4String& label);
395 
397 
399 
402  const G4ElectronOccupancy& eOcc);
403 
406  int charge);
407 
409 
411 
412  const std::vector<G4MolecularConfiguration*>& GetAllSpecies()
413  {
414  return fMolConfPerID;
415  }
416 
417  std::map<G4String, G4MolecularConfiguration*>& GetUserIDTable()
418  {
419  return fUserIDTable;
420  }
421 
422  private:
423 
424  //__________________________________________________________________________
425  typedef std::map<G4ElectronOccupancy,
428  typedef std::map<const G4MoleculeDefinition*,
429  ElectronOccupancyTable > MolElectronConfTable;
430  MolElectronConfTable fElecOccTable;
431 
432  //__________________________________________________________________________
433  typedef std::map<int,
434  G4MolecularConfiguration*> ChargeTable;
435  typedef std::map<const G4MoleculeDefinition*,
436  ChargeTable> MolChargeConfTable;
437  MolChargeConfTable fChargeTable;
438 
439  //__________________________________________________________________________
440  typedef std::map<const G4String,
441  G4MolecularConfiguration*> LabelTable;
442  typedef std::map<const G4MoleculeDefinition*,
443  std::map<const G4String, G4MolecularConfiguration*> > MolLabelConfTable;
444  MolLabelConfTable fLabelTable;
445 
446  //__________________________________________________________________________
447  typedef std::map<G4String, G4MolecularConfiguration*> UserIDTable;
448  UserIDTable fUserIDTable;
449 
450  //__________________________________________________________________________
451  std::vector<G4MolecularConfiguration*> fMolConfPerID;
452  // Indexed by molecule ID
453 
454  //__________________________________________________________________________
457  };
458 
459 protected:
462 
465 
466  mutable G4String* fLabel;
467 
474  /*mutable*/ G4String fFormatedName;
475  /*mutable*/ G4String fName;
478 
480  static /*G4ThreadLocal*/double fgTemperature;
481 
482  static double ReturnDefaultDiffCoeff(const G4Material*,
483  double,
485  molConf);
486 };
487 
489 {
490  return fMoleculeDefinition;
491 }
492 
494 {
495  return fElectronOccupancy;
496 }
497 
499 {
501  fDynDiffusionCoefficient = dynDiffusionCoefficient;
502 }
503 
505 {
507 }
508 
510 {
512  fDynDecayTime = dynDecayTime;
513 }
514 
516 {
517  return fDynDecayTime;
518 }
519 
521 {
523  fDynVanDerVaalsRadius = dynVanDerVaalsRadius;
524 }
525 
527 {
528  return fDynVanDerVaalsRadius;
529 }
530 
532 {
533  return fDynCharge;
534 }
535 
537 {
539  fDynMass = aMass;
540 }
541 
543 {
544  return fDynMass;
545 }
546 
548 {
549  return fMoleculeID;
550 }
551 
553 {
554  assert(fLabel == 0 || *fLabel == "");
555  if(fLabel == 0)
556  {
557  fLabel = new G4String(label);
558  }
559  else
560  {
561  *fLabel = label;
562  }
563  fgManager->RecordNewlyLabeledConfiguration(this);
564 }
565 
567 {
568  if(fLabel == 0)
569  fLabel = new G4String();
570 
571  return (*fLabel);
572 }
573 
575 {
577  fIsFinalized = true;
578 }
579 
581 {
582  return fUserIdentifier;
583 }
584 
586 (const G4DiffCoeffParam& para)
587 {
588  fDiffParam = para;
589 }
590 
591 inline G4double
593  double temperature) const
594 {
595  return fDiffParam(material, temperature, this);
596 }
597 
598 #endif
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.
static G4MolecularConfiguration * Load(std::istream &)
const G4String & GetName() const
Returns the name of the molecule.
G4int GetTotalOccupancy() const
G4MolecularConfiguration * ChangeConfiguration(const G4ElectronOccupancy &newElectronOccupancy)
G4String name
Definition: TRTMaterials.hh:40
static G4MolecularConfiguration * GetMolecularConfiguration(const G4MoleculeDefinition *, const G4String &label)
void AddUserID(const G4String &name, G4MolecularConfiguration *molecule)
std::function< double(const G4Material *, double, const G4MolecularConfiguration *)> G4DiffCoeffParam
G4double GetNbElectrons() const
Returns the number of electron.
G4int GetSizeOfOrbit() const
const std::vector< const G4MolecularDissociationChannel * > * GetDecayChannel() const
G4MolecularConfiguration * GetOrCreateMolecularConfiguration(const G4MoleculeDefinition *molDef, const G4ElectronOccupancy &eOcc)
const G4String & GetUserID() const
const G4ElectronOccupancy * FindCommonElectronOccupancy(const G4MoleculeDefinition *molDef, const G4ElectronOccupancy &eOcc)
const G4ElectronOccupancy * GetElectronOccupancy() const
Returns the object ElectronOccupancy describing the electronic configuration of the molecule...
G4int Insert(const G4MoleculeDefinition *molDef, const G4ElectronOccupancy &eOcc, G4MolecularConfiguration *molConf)
int G4int
Definition: G4Types.hh:78
void SetUserID(const G4String &userID)
G4double(* function)(G4double)
static std::map< G4String, G4MolecularConfiguration * > & GetUserIDTable()
static G4MolecularConfigurationManager * fgManager
std::map< G4String, G4MolecularConfiguration * > & GetUserIDTable()
bool operator()(const G4ElectronOccupancy &occ1, const G4ElectronOccupancy &occ2) const
static void ScaleAllDiffusionCoefficientsOnWater(double temperature_K)
void RecordNewlyLabeledConfiguration(G4MolecularConfiguration *molConf)
G4int GetOccupancy(G4int orbit) const
G4MolecularConfiguration * IonizeMolecule(G4int)
Method used in Geant4-DNA to ionize water molecules.
G4MolecularConfiguration * AddElectron(G4int orbit, G4int n=1)
Add n electrons to a given orbit.
bool G4bool
Definition: G4Types.hh:79
void CheckElectronOccupancy(const char *line) const
static double DiffCoeffWater(double temperature_K)
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...
G4MolecularConfiguration & operator=(G4MolecularConfiguration &right)
static void SetGlobalTemperature(G4double)
const G4int n
static G4MolecularConfigurationManager * GetManager()
static G4MolecularConfiguration * GetOrCreateMolecularConfiguration(const G4MoleculeDefinition *)
static double ReturnDefaultDiffCoeff(const G4Material *, double, const G4MolecularConfiguration *molConf)
G4MolecularConfiguration(const G4MoleculeDefinition *, const G4ElectronOccupancy &, const G4String &label="")
G4double GetMass() const
Returns the total mass of the molecule.
G4int G4Mutex
Definition: G4Threading.hh:173
const G4String & GetFormatedName() const
Returns the formated name of the molecule.
std::map< G4ElectronOccupancy, G4MolecularConfiguration *, comparator > ElectronOccupancyTable
void SetMass(G4double)
Set the total mass of the molecule.
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.
const std::vector< G4MolecularConfiguration * > & GetAllSpecies()
const G4MoleculeDefinition * GetDefinition() const
std::map< const G4MoleculeDefinition *, ElectronOccupancyTable > MolElectronConfTable
const G4String & GetLabel() const
G4MolecularConfiguration * GetMolecularConfiguration(const G4MoleculeDefinition *molDef, const G4ElectronOccupancy &eOcc)
std::map< G4String, G4MolecularConfiguration * > UserIDTable
std::map< const G4MoleculeDefinition *, ChargeTable > MolChargeConfTable
G4double GetDecayTime() const
Returns the decay time of the molecule.
double G4double
Definition: G4Types.hh:76
G4MolecularConfiguration * RemoveElectron(G4int, G4int number=1)
Remove n electrons to a given orbit.
std::map< const G4String, G4MolecularConfiguration * > LabelTable
const G4ElectronOccupancy * fElectronOccupancy
G4MolecularConfiguration * ExciteMolecule(G4int)
Method used in Geant4-DNA to excite water molecules.
const G4MoleculeDefinition * fMoleculeDefinition
void AddDiffCoeffParameterization(const G4DiffCoeffParam &)
static G4MolecularConfiguration * CreateMolecularConfiguration(const G4String &userIdentifier, const G4MoleculeDefinition *, bool &wasAlreadyCreated)
std::map< const G4MoleculeDefinition *, std::map< const G4String, G4MolecularConfiguration * > > MolLabelConfTable