| 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
28 // Author: Mathieu Karamitros
29 //
30 // The code is developed in the framework of the ESA AO7146
31 //
32 // We would be very happy hearing from you, send us your feedback! :)
33 //
34 // In order for Geant4-DNA to be maintained and still open-source,
35 // article citations are crucial.
36 // If you use Geant4-DNA chemistry and you publish papers about your software,
37 // in addition to the general paper on Geant4-DNA:
38 //
39 // Int. J. Model. Simul. Sci. Comput. 1 (2010) 157–178
40 //
41 // we would be very happy if you could please also cite the following
42 // reference papers on chemistry:
43 //
44 // J. Comput. Phys. 274 (2014) 841-882
45 // Prog. Nucl. Sci. Tec. 2 (2011) 503-508
46
47 #pragma once
48
49 #include "globals.hh"
50 #include "G4ThreeVector.hh"
51 #include <fstream>
52 #include <memory>
53 #include "G4UImessenger.hh"
54 #include "G4VStateDependent.hh"
55
56 class G4Track;
57 class G4DNAWaterExcitationStructure;
58 class G4DNAWaterIonisationStructure;
59 class G4Molecule;
60 class G4VUserChemistryList;
61 class G4UIcmdWithABool;
62 class G4UIcmdWithADoubleAndUnit;
63 class G4UIcmdWithoutParameter;
64 class G4UIcmdWithAnInteger;
65 class G4ITGun;
66 class G4VPhysChemIO;
67
68 enum ElectronicModification
69 {
70 eIonizedMolecule,
71 eExcitedMolecule,
72 eDissociativeAttachment
73 };
74
75 /**
76 * WARNING: THIS CLASS IS A PROTOTYPE
77 * G4DNAChemistryManager is called from the physics models.
78 * It creates the water molecules and the solvated electrons and
79 * and send them to G4ITStepManager to be treated in the chemistry stage.
80 * For this, the fActiveChemistry flag needs to be on.
81 * It is also possible to give already molecule's pointers already built.
82 * G4DNAChemistryManager will then be in charge of creating the track and loading
83 * it to the IT system.
84 * The user can also ask to create a file containing a information about the
85 * creation of water molecules and solvated electrons.
86 */
87 class G4DNAChemistryManager: public G4UImessenger,
88 public G4VStateDependent
89 {
90 protected:
91 ~G4DNAChemistryManager() override;
92
93 public:
94 //============================================================================
95 // STATIC METHODS
96 //============================================================================
97 static G4DNAChemistryManager* Instance();
98 static G4DNAChemistryManager* GetInstanceIfExists();
99
100 static void DeleteInstance();
101 static G4bool IsActivated();
102
103 //============================================================================
104 // VIRTUAL METHODS
105 //============================================================================
106 // G4VStateDependent
107 G4bool Notify(G4ApplicationState requestedState) override;
108 // G4UImessenger
109 void SetNewValue(G4UIcommand*, G4String) override;
110 G4String GetCurrentValue(G4UIcommand* pCommand) override;
111
112 //============================================================================
113 // INITIALIZATION AND FINALIZATION METHODS
114 //============================================================================
115 G4bool IsChemistryActivated();
116 void SetChemistryActivation(G4bool);
117
118 /** Chemistry list is managed outside the chemistry manager (eg. constructor). */
119 void SetChemistryList(G4VUserChemistryList&);
120
121 /** Not a constructor or when used in standalone? Prefer this method. */
122 void SetChemistryList(std::unique_ptr<G4VUserChemistryList>);
123
124 // [[deprecated]] : chemistry list should never be nullptr
125 void SetChemistryList(G4VUserChemistryList*);
126
127 void Deregister(G4VUserChemistryList&);
128
129 void Initialize();
130 void Run();
131 void Clear();
132
133 /**
134 * @brief Inject custom species to the simulation
135 * @details This method should be called per thread, possibly from
136 * ActionInitialisation::Build.
137 * One can decide to set the same gun for all threads.
138 * It is the user responsibility to handle the pointer deletion.
139 */
140 void SetGun(G4ITGun* pChemSpeciesGun);
141
142 void SetPhysChemIO(std::unique_ptr<G4VPhysChemIO> pPhysChemIO);
143
144 void SetVerbose(G4int verbose);
145
146 /**
147 * If the chemistry module is used in standalone (ie. without running the physics
148 * stage beforehand), the physics table still needs to be built.
149 * It is therefore necessary to flag the chemistry module as being run
150 * in standalone.
151 */
152 void UseAsStandalone(G4bool flag);
153 G4bool IsCounterResetWhenRunEnds() const;
154
155 void ResetCounterWhenRunEnds(G4bool resetCounterWhenRunEnds);
156
157 void ForceMasterReinitialization();
158 void TagThreadForReinitialization();
159 void ForceThreadReinitialization();
160 void ForceRebuildingPhysicsTable();
161
162 //============================================================================
163 // FILE OPERATIONS
164 //============================================================================
165 /**
166 * Tells the chemMan to write into a file
167 * the position and electronic state of the water molecule
168 * and the position thermalized or not of the solvated electron
169 */
170 void WriteInto(const G4String&, std::ios_base::openmode mode =
171 std::ios_base::out);
172 void AddEmptyLineInOutputFile();
173
174 /**
175 * Close the file specified with WriteInto
176 */
177 void CloseFile();
178
179 //============================================================================
180 // PUSH MOLECULES
181 //============================================================================
182 /**
183 * Method used by DNA physics model to create a water molecule.
184 * The ElectronicModification is a flag telling whether the molecule
185 * is ionized or excited, the electronic level is calculated by the
186 * model and the IncomingTrack is the track responsible for the creation
187 * of this molecule (electron, proton...).
188 */
189 void CreateWaterMolecule(ElectronicModification,
190 G4int /*electronicLevel*/,
191 const G4Track* /*pIncomingTrack*/);
192
193 /**
194 * This method should be used by the physics model of the ElectronSolvatation
195 * process.
196 */
197 void CreateSolvatedElectron(const G4Track* /*pIncomingTrack*/,
198 G4ThreeVector* pFinalPosition = nullptr);
199
200 void PushMolecule(std::unique_ptr<G4Molecule> pMolecule,
201 G4double time,
202 const G4ThreeVector& position,
203 G4int parentID);
204
205 protected:
206 void HandleStandaloneInitialization();
207 void PushTrack(G4Track*);
208 void SetGlobalTemperature(G4double temperatureKelvin);
209
210 G4DNAWaterExcitationStructure* GetExcitationLevel();
211 G4DNAWaterIonisationStructure* GetIonisationLevel();
212 void InitializeFile();
213 void InitializeMaster();
214 void InitializeThread();
215 void InitializeThreadSharedData();
216
217 G4DNAChemistryManager();
218
219 private:
220 std::unique_ptr<G4UIdirectory> fpChemDNADirectory;
221 std::unique_ptr<G4UIcmdWithABool> fpActivateChem;
222 std::unique_ptr<G4UIcmdWithAnInteger> fpRunChem;
223 std::unique_ptr<G4UIcmdWithoutParameter> fpSkipReactionsFromChemList;
224 std::unique_ptr<G4UIcmdWithADoubleAndUnit> fpScaleForNewTemperature;
225 std::unique_ptr<G4UIcmdWithoutParameter> fpInitChem;
226
227 static G4DNAChemistryManager* fgInstance;
228 G4bool fActiveChemistry{false};
229
230 struct ThreadLocalData{
231 ThreadLocalData();
232 ~ThreadLocalData();
233 std::unique_ptr<G4VPhysChemIO> fpPhysChemIO;
234 G4bool fThreadInitialized = false;
235 };
236
237 static G4ThreadLocal ThreadLocalData* fpThreadData;
238
239 G4bool fMasterInitialized{false};
240 G4bool fForceThreadReinitialization{false};
241
242 std::unique_ptr<G4DNAWaterExcitationStructure> fpExcitationLevel;
243 std::unique_ptr<G4DNAWaterIonisationStructure> fpIonisationLevel;
244
245 std::unique_ptr<G4VUserChemistryList> fpUserChemistryList;
246 G4bool fOwnChemistryList{false};
247 G4bool fUseInStandalone{false};
248 G4bool fPhysicsTableBuilt{false};
249 G4bool fSkipReactions{false};
250
251 G4bool fGeometryClosed{false};
252
253 G4int fVerbose{0};
254 G4bool fResetCounterWhenRunEnds{true};
255 };
256