| Geant4 Cross Reference |
1 // 1 //
2 // ******************************************* 2 // ********************************************************************
3 // * License and Disclaimer 3 // * License and Disclaimer *
4 // * 4 // * *
5 // * The Geant4 software is copyright of th 5 // * The Geant4 software is copyright of the Copyright Holders of *
6 // * the Geant4 Collaboration. It is provided 6 // * the Geant4 Collaboration. It is provided under the terms and *
7 // * conditions of the Geant4 Software License 7 // * conditions of the Geant4 Software License, included in the file *
8 // * LICENSE and available at http://cern.ch/ 8 // * LICENSE and available at http://cern.ch/geant4/license . These *
9 // * include a list of copyright holders. 9 // * include a list of copyright holders. *
10 // * 10 // * *
11 // * Neither the authors of this software syst 11 // * Neither the authors of this software system, nor their employing *
12 // * institutes,nor the agencies providing fin 12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warran 13 // * work make any representation or warranty, express or implied, *
14 // * regarding this software system or assum 14 // * regarding this software system or assume any liability for its *
15 // * use. Please see the license in the file 15 // * use. Please see the license in the file LICENSE and URL above *
16 // * for the full disclaimer and the limitatio 16 // * for the full disclaimer and the limitation of liability. *
17 // * 17 // * *
18 // * This code implementation is the result 18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboratio 19 // * technical work of the GEANT4 collaboration. *
20 // * By using, copying, modifying or distri 20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you ag 21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publicati 22 // * use in resulting scientific publications, and indicate your *
23 // * acceptance of all terms of the Geant4 Sof 23 // * acceptance of all terms of the Geant4 Software license. *
24 // ******************************************* 24 // ********************************************************************
25 // 25 //
26 // Author: Mathieu Karamitros << 26 // Author: Mathieu Karamitros, kara@cenbg.in2p3.fr
27 27
28 // The code is developed in the framework of t 28 // The code is developed in the framework of the ESA AO7146
29 // 29 //
30 // We would be very happy hearing from you, se 30 // We would be very happy hearing from you, send us your feedback! :)
31 // 31 //
32 // In order for Geant4-DNA to be maintained an 32 // In order for Geant4-DNA to be maintained and still open-source,
33 // article citations are crucial. 33 // article citations are crucial.
34 // If you use Geant4-DNA chemistry and you pub 34 // If you use Geant4-DNA chemistry and you publish papers about your software,
35 // in addition to the general paper on Geant4- 35 // in addition to the general paper on Geant4-DNA:
36 // 36 //
37 // Int. J. Model. Simul. Sci. Comput. 1 (2010) 37 // Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
38 // 38 //
39 // we would be very happy if you could please 39 // we would be very happy if you could please also cite the following
40 // reference papers on chemistry: 40 // reference papers on chemistry:
41 // 41 //
42 // J. Comput. Phys. 274 (2014) 841-882 42 // J. Comput. Phys. 274 (2014) 841-882
43 // Prog. Nucl. Sci. Tec. 2 (2011) 503-508 43 // Prog. Nucl. Sci. Tec. 2 (2011) 503-508
44 44
45 #ifndef G4MOLECULETABLE_HH_ 45 #ifndef G4MOLECULETABLE_HH_
46 #define G4MOLECULETABLE_HH_ 46 #define G4MOLECULETABLE_HH_
47 47
48 #include "globals.hh" << 48 #include "G4MoleculeDefinition.hh"
>> 49 #include "G4Molecule.hh"
49 #include "G4MoleculeIterator.hh" 50 #include "G4MoleculeIterator.hh"
50 #include "G4ElectronOccupancy.hh" <<
51 51
52 #include <memory> << 52 typedef G4MoleculeIterator<G4MoleculeDefinition> G4MoleculeDefinitionIterator;
53 << 53 typedef G4MoleculeIterator<G4Molecule> G4MoleculeModelIterator;
54 class G4MoleculeDefinition; <<
55 class G4MolecularConfiguration; <<
56 class G4MoleculeTableMessenger; <<
57 <<
58 using G4MoleculeDefinitionIterator = G4Molecul <<
59 using G4ConfigurationIterator = G4MoleculeIter <<
60 54
61 class G4MoleculeTable 55 class G4MoleculeTable
62 { 56 {
63 public: 57 public:
64 static G4MoleculeTable* Instance(); 58 static G4MoleculeTable* Instance();
65 static G4MoleculeTable* GetMoleculeTable(); 59 static G4MoleculeTable* GetMoleculeTable();
66 virtual ~G4MoleculeTable(); 60 virtual ~G4MoleculeTable();
67 61
68 //__________________________________________ << 62 G4MoleculeDefinition* CreateMoleculeDefinition(const G4String&,
69 // The methods below enable to create G4Mole <<
70 // G4MolecularConfiguration with a user iden <<
71 // from this molecule table <<
72 // <<
73 <<
74 //__________________________________________ <<
75 <<
76 G4MoleculeDefinition* CreateMoleculeDefiniti <<
77 63 double diffusion_coefficient);
78 << 64 G4Molecule* CreateMoleculeModel(const G4String&,
79 //__________________________________________ << 65 G4MoleculeDefinition*,
80 << 66 int charge,
81 G4MolecularConfiguration* << 67 double diffusion_coefficient = -1);
82 CreateConfiguration(const G4String& userIden << 68 G4Molecule* CreateMoleculeModel(const G4String&, G4MoleculeDefinition*);
83 const G4MoleculeDefiniti << 69
84 const G4String& configur << 70 void RecordMoleculeModel(const G4String& name, G4Molecule*);
85 const G4ElectronOccupanc << 71
86 << 72 G4MoleculeDefinition* GetMoleculeDefinition(const G4String&, bool mustExist = true);
87 G4MolecularConfiguration* << 73 G4Molecule* GetMoleculeModel(const G4String&, bool mustExist = true);
88 CreateConfiguration(const G4String& userIden << 74 G4Molecule* GetMoleculeModel(G4int id);
89 G4MoleculeDefinition*, <<
90 int charge, <<
91 double diffusion_coeffic <<
92 <<
93 G4MolecularConfiguration* <<
94 CreateConfiguration(const G4String& userIden <<
95 G4MoleculeDefinition*); <<
96 <<
97 G4MolecularConfiguration* <<
98 CreateConfiguration(const G4String& userIden <<
99 G4MoleculeDefinition*, <<
100 const G4String& configur <<
101 int charge = 0); <<
102 <<
103 //__________________________________________ <<
104 <<
105 G4MoleculeDefinition* GetMoleculeDefinition( <<
106 <<
107 <<
108 G4MolecularConfiguration* GetConfiguration(c <<
109 b <<
110 G4MolecularConfiguration* GetConfiguration(G <<
111 <<
112 //__________________________________________ <<
113 75
114 void Insert(G4MoleculeDefinition*); 76 void Insert(G4MoleculeDefinition*);
115 void Finalize(G4MoleculeDefinition*){} <<
116 void Finalize(); <<
117 //__________________________________________ <<
118 <<
119 G4MoleculeDefinitionIterator GetDefintionIte 77 G4MoleculeDefinitionIterator GetDefintionIterator()
120 { 78 {
121 return G4MoleculeDefinitionIterator(this-> 79 return G4MoleculeDefinitionIterator(this->fMoleculeDefTable);
122 } 80 }
123 81
124 G4ConfigurationIterator GetConfigurationIter << 82 G4MoleculeModelIterator GetModelIterator()
125 << 83 {
126 void PrepareMolecularConfiguration(); << 84 return G4MoleculeModelIterator(this->fMoleculeTable);
127 << 85 }
128 int GetNumberOfDefinedSpecies(); <<
129 86
130 protected: 87 protected:
131 G4MoleculeTable(); 88 G4MoleculeTable();
132 89
133 static G4MoleculeTable* fpgMoleculeTable; 90 static G4MoleculeTable* fpgMoleculeTable;
134 using MoleculeDefTable = std::map<G4String, << 91 typedef std::map<G4String, G4MoleculeDefinition*> MoleculeDefTable;
>> 92 typedef std::map<G4String, G4Molecule*> MoleculeTable;
>> 93 typedef std::map<G4int, G4Molecule*> MoleculeTablePerID;
>> 94 // TODO: replace with sets
135 95
136 MoleculeDefTable fMoleculeDefTable; 96 MoleculeDefTable fMoleculeDefTable;
137 std::unique_ptr<G4MoleculeTableMessenger> fM << 97 MoleculeTable fMoleculeTable;
138 << 98 MoleculeTablePerID fMoleculeTablePerID;
139 }; 99 };
140 100
141 #endif /* G4MOLECULETABLE_HH_ */ 101 #endif /* G4MOLECULETABLE_HH_ */
142 102