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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
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 "globals.hh"
49 #include "G4MoleculeIterator.hh" 49 #include "G4MoleculeIterator.hh"
50 #include "G4ElectronOccupancy.hh" 50 #include "G4ElectronOccupancy.hh"
51 51
52 #include <memory> <<
53 <<
54 class G4MoleculeDefinition; 52 class G4MoleculeDefinition;
55 class G4MolecularConfiguration; 53 class G4MolecularConfiguration;
56 class G4MoleculeTableMessenger; <<
57 54
58 using G4MoleculeDefinitionIterator = G4Molecul << 55 typedef G4MoleculeIterator<G4MoleculeDefinition> G4MoleculeDefinitionIterator;
59 using G4ConfigurationIterator = G4MoleculeIter << 56 typedef G4MoleculeIterator<G4MolecularConfiguration> G4ConfigurationIterator;
60 57
61 class G4MoleculeTable 58 class G4MoleculeTable
62 { 59 {
63 public: 60 public:
64 static G4MoleculeTable* Instance(); 61 static G4MoleculeTable* Instance();
65 static G4MoleculeTable* GetMoleculeTable(); 62 static G4MoleculeTable* GetMoleculeTable();
66 virtual ~G4MoleculeTable(); 63 virtual ~G4MoleculeTable();
67 64
68 //__________________________________________ 65 //____________________________________________________________________________
69 // The methods below enable to create G4Mole 66 // The methods below enable to create G4MoleculeDefinition &
70 // G4MolecularConfiguration with a user iden 67 // G4MolecularConfiguration with a user identifier so that they can be retrieved
71 // from this molecule table 68 // from this molecule table
72 // 69 //
73 70
74 //__________________________________________ 71 //____________________________________________________________________________
75 72
76 G4MoleculeDefinition* CreateMoleculeDefiniti 73 G4MoleculeDefinition* CreateMoleculeDefinition(const G4String& userIdentifier,
77 74 double diffusion_coefficient);
78 75
79 //__________________________________________ 76 //____________________________________________________________________________
80 77
81 G4MolecularConfiguration* 78 G4MolecularConfiguration*
82 CreateConfiguration(const G4String& userIden 79 CreateConfiguration(const G4String& userIdentifier,
83 const G4MoleculeDefiniti 80 const G4MoleculeDefinition* molDef,
84 const G4String& configur 81 const G4String& configurationLabel,
85 const G4ElectronOccupanc 82 const G4ElectronOccupancy& eOcc);
86 83
87 G4MolecularConfiguration* 84 G4MolecularConfiguration*
88 CreateConfiguration(const G4String& userIden 85 CreateConfiguration(const G4String& userIdentifier,
89 G4MoleculeDefinition*, 86 G4MoleculeDefinition*,
90 int charge, 87 int charge,
91 double diffusion_coeffic 88 double diffusion_coefficient = -1);
92 89
93 G4MolecularConfiguration* 90 G4MolecularConfiguration*
94 CreateConfiguration(const G4String& userIden 91 CreateConfiguration(const G4String& userIdentifier,
95 G4MoleculeDefinition*); 92 G4MoleculeDefinition*);
96 93
97 G4MolecularConfiguration* 94 G4MolecularConfiguration*
98 CreateConfiguration(const G4String& userIden 95 CreateConfiguration(const G4String& userIdentifier,
99 G4MoleculeDefinition*, 96 G4MoleculeDefinition*,
100 const G4String& configur 97 const G4String& configurationLabel,
101 int charge = 0); 98 int charge = 0);
102 99
103 //__________________________________________ 100 //____________________________________________________________________________
104 101
105 G4MoleculeDefinition* GetMoleculeDefinition( 102 G4MoleculeDefinition* GetMoleculeDefinition(const G4String&,
106 103 bool mustExist = true);
107 104
108 G4MolecularConfiguration* GetConfiguration(c 105 G4MolecularConfiguration* GetConfiguration(const G4String&,
109 b 106 bool mustExist = true);
110 G4MolecularConfiguration* GetConfiguration(G 107 G4MolecularConfiguration* GetConfiguration(G4int id);
111 108
112 //__________________________________________ 109 //____________________________________________________________________________
113 110
114 void Insert(G4MoleculeDefinition*); 111 void Insert(G4MoleculeDefinition*);
115 void Finalize(G4MoleculeDefinition*){} 112 void Finalize(G4MoleculeDefinition*){}
116 void Finalize(); 113 void Finalize();
117 //__________________________________________ 114 //____________________________________________________________________________
118 115
119 G4MoleculeDefinitionIterator GetDefintionIte 116 G4MoleculeDefinitionIterator GetDefintionIterator()
120 { 117 {
121 return G4MoleculeDefinitionIterator(this-> 118 return G4MoleculeDefinitionIterator(this->fMoleculeDefTable);
122 } 119 }
123 120
124 G4ConfigurationIterator GetConfigurationIter 121 G4ConfigurationIterator GetConfigurationIterator();
125 122
126 void PrepareMolecularConfiguration(); 123 void PrepareMolecularConfiguration();
127 124
128 int GetNumberOfDefinedSpecies(); 125 int GetNumberOfDefinedSpecies();
129 126
130 protected: 127 protected:
131 G4MoleculeTable(); 128 G4MoleculeTable();
132 129
133 static G4MoleculeTable* fpgMoleculeTable; 130 static G4MoleculeTable* fpgMoleculeTable;
134 using MoleculeDefTable = std::map<G4String, << 131 typedef std::map<G4String, G4MoleculeDefinition*> MoleculeDefTable;
135 132
136 MoleculeDefTable fMoleculeDefTable; 133 MoleculeDefTable fMoleculeDefTable;
137 std::unique_ptr<G4MoleculeTableMessenger> fM <<
138 <<
139 }; 134 };
140 135
141 #endif /* G4MOLECULETABLE_HH_ */ 136 #endif /* G4MOLECULETABLE_HH_ */
142 137