| Geant4 Cross Reference |
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
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 #pragma once
47
48 #include "G4ITReactionTable.hh"
49 #include "G4MolecularConfiguration.hh"
50 #include "G4ReferenceCast.hh"
51 #include "G4VDNAMolecularGeometry.hh"
52 #include <vector>
53 #include <map>
54 #include <functional>
55 #include <memory>
56
57 class G4VDNAReactionModel;
58 class G4DNAMolecularReactionTable;
59 class G4ReactionTableMessenger;
60
61 /**
62 * G4DNAMolecularReactionData contains the information
63 * relative to a given reaction (eg : °OH + °OH -> H2O2)
64 */
65 class G4DNAMolecularReactionData
66 {
67 public:
68 //----------------------------------------------------------------------------
69
70 G4DNAMolecularReactionData(G4double reactionRate,
71 const G4MolecularConfiguration* reactive1,
72 const G4MolecularConfiguration* reactive2);
73
74 G4DNAMolecularReactionData(G4double reactionRate,
75 const G4String& reactive1,
76 const G4String& reactive2);
77 ~G4DNAMolecularReactionData();
78
79 using Reactant = const G4MolecularConfiguration;
80 using ReactantPair = std::pair<Reactant*, Reactant*>;
81 using ReactionProducts = std::vector<Reactant*>;
82
83 int GetReactionID() const;
84 void SetReactionID(int ID);
85
86 ReactantPair GetReactants();
87
88 Reactant* GetReactant1() const;
89 Reactant* GetReactant2() const;
90
91 void SetObservedReactionRateConstant(G4double rate);
92 G4double GetObservedReactionRateConstant() const;
93 G4double GetActivationRateConstant() const;
94 G4double GetDiffusionRateConstant() const;
95
96 void SetReactionRadius(G4double radius);
97 G4double GetReactionRadius() const;
98
99 void SetEffectiveReactionRadius(G4double radius);
100 G4double GetEffectiveReactionRadius() const;
101 G4double GetOnsagerRadius() const;
102
103 void SetProbability(G4double prob);
104 G4double GetProbability() const;
105
106 void SetReactionType(G4int type);
107 G4int GetReactionType() const;
108
109 void SetReactant1(Reactant* reactive);
110 void SetReactant2(Reactant* reactive);
111
112 void SetReactants(Reactant* reactive1,
113 Reactant* reactive2);
114
115 void AddProduct(Reactant* molecule);
116
117 void SetReactant1(const G4String& reactive);
118 void SetReactant2(const G4String& reactive);
119 void SetReactants(const G4String& reactive1, const G4String& reactive2);
120 void AddProduct(const G4String& molecule);
121
122 G4int GetNbProducts() const;
123 Reactant* GetProduct(G4int i) const;
124
125 const ReactionProducts* GetProducts() const;
126 void RemoveProducts();
127
128 //----------------------------------------------------------------------------
129 // Temperature scaling
130 using RateParam = std::function<double (double)>;
131
132 static double PolynomialParam(double temp_K, std::vector<double> P);
133 static double ArrehniusParam(double temp_K, std::vector<double> P);
134 static double ScaledParameterization(double temp_K,
135 double temp_init,
136 double rateCste_init);
137
138 void SetPolynomialParameterization(const std::vector<double>& P);
139
140 void SetArrehniusParameterization(double A0, double E_R);
141 void SetScaledParameterization(double temperature_K,
142 double rateCste);
143
144 void ScaleForNewTemperature(double temp_K);
145
146 void ComputeEffectiveRadius();
147
148 protected:
149 G4DNAMolecularReactionData();
150 Reactant* fpReactant1;
151 Reactant* fpReactant2;
152
153 G4double fObservedReactionRate;
154 G4double fActivationRate;
155 G4double fDiffusionRate;
156
157 G4double fOnsagerRadius;
158
159 G4double fReactionRadius;
160 G4double fEffectiveReactionRadius;
161
162 G4double fProbability;
163 G4int fType;
164
165 ReactionProducts fProducts;
166 RateParam fRateParam;
167 int fReactionID;
168 };
169
170 /**
171 * G4DNAMolecularReactionTable sorts out the G4DNAMolecularReactionData
172 * for bimolecular reaction
173 */
174 class G4DNAMolecularReactionTable : public G4ITReactionTable
175 {
176 protected:
177 G4DNAMolecularReactionTable();
178 static G4DNAMolecularReactionTable* fpInstance;
179
180 public:
181 static G4DNAMolecularReactionTable* GetReactionTable();
182 static G4DNAMolecularReactionTable* Instance();
183 static void DeleteInstance();
184 ~G4DNAMolecularReactionTable() override;
185
186 using Reactant = const G4MolecularConfiguration;
187 using Data = const G4DNAMolecularReactionData;
188 using ReactantList = std::vector<Reactant*>;
189 using DataList = std::vector<Data*>;
190 using SpecificDataList = std::map<Reactant*, Data*>;
191
192 using ReactionDataMap = std::map<Reactant*, SpecificDataList>;
193 using ReactivesMV = std::map<Reactant*, ReactantList>;
194 using ReactionDataMV = std::map<Reactant*, DataList>;
195
196 /**
197 * Define a reaction :
198 * First argument : reaction rate
199 * Second argument : reactant 1
200 * Third argument : reactant 2
201 * Fourth argument : a std::vector holding the molecular products
202 * if this last argument is NULL then it will be interpreted as
203 * a reaction giving no products
204 */
205 void SetReaction(G4double observedReactionRate,
206 Reactant* reactive1,
207 Reactant* reactive2);
208
209 void SetReaction(G4DNAMolecularReactionData*);
210
211 void SetGeometry(G4VDNAMolecularGeometry* geometry){fGeometry = geometry;};
212 G4VDNAMolecularGeometry* GetGeometry() const;
213
214 Data* GetReactionData(Reactant*, Reactant*) const;
215
216 Data* GetReactionData(const G4String&, const G4String&) const;
217
218 Data* GetReaction(int reactionID) const;
219
220 size_t GetNReactions() const;
221
222 //_________________________________________________________________
223 /**
224 * Given a molecule's type, it returns with which a reaction is allowed
225 */
226 const ReactantList* CanReactWith(Reactant*) const;
227
228 const SpecificDataList* GetReativesNData(const G4MolecularConfiguration*) const;
229
230 const DataList* GetReactionData(const G4MolecularConfiguration*) const;
231
232 const ReactionDataMap& GetAllReactionData();
233
234 DataList GetVectorOfReactionData();
235
236 void ScaleReactionRateForNewTemperature(double temp_K);
237
238 //_________________________________________________________________
239 void PrintTable(G4VDNAReactionModel* = nullptr);
240
241 void Reset();
242
243 protected:
244 G4bool fVerbose{false};
245
246 G4VDNAMolecularGeometry* fGeometry{nullptr};
247 ReactionDataMap fReactionData;
248 ReactivesMV fReactantsMV;
249 ReactionDataMV fReactionDataMV;
250 std::vector<std::unique_ptr<Data>> fVectorOfReactionData;
251 std::unique_ptr<G4ReactionTableMessenger> fpMessenger;
252 };
253