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25 //
26 #include "G4EmDNAChemistry_option1.hh"
27 #include "G4SystemOfUnits.hh"
28 #include "G4DNAWaterDissociationDisplacer.hh"
29 #include "G4DNAChemistryManager.hh"
30 #include "G4ProcessManager.hh"
31
32 #include "G4DNAGenericIonsManager.hh"
33
34 // *** Processes and models for Geant4-DNA
35
36 #include "G4DNAElectronSolvation.hh"
37
38 #include "G4DNAVibExcitation.hh"
39 #include "G4DNASancheExcitationModel.hh"
40
41 #include "G4DNAMolecularDissociation.hh"
42 #include "G4DNABrownianTransportation.hh"
43 #include "G4DNAMolecularReactionTable.hh"
44 #include "G4DNAMolecularStepByStepModel.hh"
45 #include "G4VDNAReactionModel.hh"
46 #include "G4DNASmoluchowskiReactionModel.hh"
47 #include "G4DNAElectronHoleRecombination.hh"
48 #include "G4ChemDissociationChannels.hh"
49 // particles
50 #include "G4Electron.hh"
51 #include "G4MoleculeTable.hh"
52 #include "G4H2O.hh"
53 #include "G4PhysicsListHelper.hh"
54 /****/
55 #include "G4DNAMoleculeEncounterStepper.hh"
56 #include "G4ProcessTable.hh"
57 #include "G4MolecularConfiguration.hh"
58 /****/
59
60 // factory
61 #include "G4PhysicsConstructorFactory.hh"
62
63 G4_DECLARE_PHYSCONSTR_FACTORY(G4EmDNAChemistry_option1);
64
65 G4EmDNAChemistry_option1::G4EmDNAChemistry_option1() :
66 G4VUserChemistryList(true)
67 {
68 G4DNAChemistryManager::Instance()->SetChemistryList(this);
69 }
70
71 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
72
73 void G4EmDNAChemistry_option1::ConstructMolecule()
74 {
75 G4ChemDissociationChannels::ConstructMolecule();
76
77 //____________________________________________________________________________
78
79 G4MoleculeTable::Instance()->GetConfiguration("H3Op")->SetDiffusionCoefficient(
80 9.46e-9 * (m2/s));
81 G4MoleculeTable::Instance()->GetConfiguration("OHm")->SetDiffusionCoefficient(
82 5.3e-9 * (m2 / s));
83 G4MoleculeTable::Instance()->GetConfiguration("°OH")->SetDiffusionCoefficient(
84 2.2e-9 * (m2/s));
85 G4MoleculeTable::Instance()->GetConfiguration("H2")->SetDiffusionCoefficient(
86 4.8e-9 * (m2/s));
87 G4MoleculeTable::Instance()->GetConfiguration("H2O2")->SetDiffusionCoefficient(
88 2.3e-9 * (m2/s));
89 }
90
91 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
92
93 void G4EmDNAChemistry_option1::ConstructDissociationChannels()
94 {
95 G4ChemDissociationChannels::ConstructDissociationChannels();
96 }
97
98 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
99
100 void G4EmDNAChemistry_option1::ConstructReactionTable(G4DNAMolecularReactionTable*
101 theReactionTable)
102 {
103 //-----------------------------------
104 //Get the molecular configuration
105 G4MolecularConfiguration* OH =
106 G4MoleculeTable::Instance()->GetConfiguration("°OH");
107 G4MolecularConfiguration* OHm =
108 G4MoleculeTable::Instance()->GetConfiguration("OHm");
109 G4MolecularConfiguration* e_aq =
110 G4MoleculeTable::Instance()->GetConfiguration("e_aq");
111 G4MolecularConfiguration* H2 =
112 G4MoleculeTable::Instance()->GetConfiguration("H2");
113 G4MolecularConfiguration* H3Op =
114 G4MoleculeTable::Instance()->GetConfiguration("H3Op");
115 G4MolecularConfiguration* H =
116 G4MoleculeTable::Instance()->GetConfiguration("H");
117 G4MolecularConfiguration* H2O2 =
118 G4MoleculeTable::Instance()->GetConfiguration("H2O2");
119
120 //------------------------------------------------------------------
121 // e_aq + e_aq + 2H2O -> H2 + 2OH-
122 G4DNAMolecularReactionData* reactionData =
123 new G4DNAMolecularReactionData(0.636e10 * (1e-3 * m3 / (mole * s)), e_aq, e_aq);
124 reactionData->AddProduct(OHm);
125 reactionData->AddProduct(OHm);
126 reactionData->AddProduct(H2);
127 theReactionTable->SetReaction(reactionData);
128 //------------------------------------------------------------------
129 // e_aq + *OH -> OH-
130 reactionData = new G4DNAMolecularReactionData(
131 2.95e10 * (1e-3 * m3 / (mole * s)), e_aq, OH);
132 reactionData->AddProduct(OHm);
133 theReactionTable->SetReaction(reactionData);
134 //------------------------------------------------------------------
135 // e_aq + H* + H2O -> H2 + OH-
136 reactionData = new G4DNAMolecularReactionData(
137 2.50e10 * (1e-3 * m3 / (mole * s)), e_aq, H);
138 reactionData->AddProduct(OHm);
139 reactionData->AddProduct(H2);
140 theReactionTable->SetReaction(reactionData);
141 //------------------------------------------------------------------
142 // e_aq + H3O+ -> H* + H2O
143 reactionData = new G4DNAMolecularReactionData(
144 2.11e10 * (1e-3 * m3 / (mole * s)), e_aq, H3Op);
145 reactionData->AddProduct(H);
146 theReactionTable->SetReaction(reactionData);
147 //------------------------------------------------------------------
148 // e_aq + H2O2 -> OH- + *OH
149 reactionData = new G4DNAMolecularReactionData(
150 1.10e10 * (1e-3 * m3 / (mole * s)), e_aq, H2O2);
151 reactionData->AddProduct(OHm);
152 reactionData->AddProduct(OH);
153 theReactionTable->SetReaction(reactionData);
154 //------------------------------------------------------------------
155 // *OH + *OH -> H2O2
156 reactionData = new G4DNAMolecularReactionData(
157 0.55e10 * (1e-3 * m3 / (mole * s)), OH, OH);
158 reactionData->AddProduct(H2O2);
159 theReactionTable->SetReaction(reactionData);
160 //------------------------------------------------------------------
161 // *OH + *H -> H2O
162 theReactionTable->SetReaction(1.55e10 * (1e-3 * m3 / (mole * s)), OH, H);
163 //------------------------------------------------------------------
164 // *H + *H -> H2
165 reactionData = new G4DNAMolecularReactionData(
166 0.503e10 * (1e-3 * m3 / (mole * s)), H, H);
167 reactionData->AddProduct(H2);
168 theReactionTable->SetReaction(reactionData);
169 //------------------------------------------------------------------
170 // H3O+ + OH- -> 2H2O
171 theReactionTable->SetReaction(1.13e11 * (1e-3 * m3 / (mole * s)), H3Op, OHm);
172 //------------------------------------------------------------------
173 }
174
175 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
176
177 void G4EmDNAChemistry_option1::ConstructProcess()
178 {
179 G4PhysicsListHelper* ph = G4PhysicsListHelper::GetPhysicsListHelper();
180
181 //===============================================================
182 // Extend vibrational to low energy
183 // Anyway, solvation of electrons is taken into account from 7.4 eV
184 // So below this threshold, for now, no accurate modeling is done
185 //
186 G4VProcess* process =
187 G4ProcessTable::GetProcessTable()->
188 FindProcess("e-_G4DNAVibExcitation", "e-");
189
190 if (process)
191 {
192 G4DNAVibExcitation* vibExcitation = (G4DNAVibExcitation*) process;
193 G4VEmModel* model = vibExcitation->EmModel();
194 G4DNASancheExcitationModel* sancheExcitationMod =
195 dynamic_cast<G4DNASancheExcitationModel*>(model);
196 if(sancheExcitationMod)
197 {
198 sancheExcitationMod->ExtendLowEnergyLimit(0.025 * eV);
199 }
200 }
201
202 //===============================================================
203 // *** Electron Solvatation ***
204 //
205 process =
206 G4ProcessTable::GetProcessTable()->
207 FindProcess("e-_G4DNAElectronSolvation", "e-");
208
209 if (process == 0)
210 {
211 ph->RegisterProcess(
212 new G4DNAElectronSolvation("e-_G4DNAElectronSolvation"),
213 G4Electron::Definition());
214 }
215
216 //===============================================================
217 // Define processes for molecules
218 //
219 G4MoleculeTable* theMoleculeTable = G4MoleculeTable::Instance();
220 G4MoleculeDefinitionIterator iterator =
221 theMoleculeTable->GetDefintionIterator();
222 iterator.reset();
223 while (iterator())
224 {
225 G4MoleculeDefinition* moleculeDef = iterator.value();
226
227 if (moleculeDef != G4H2O::Definition())
228 {
229 // G4cout << "Brownian motion added for : "
230 // << moleculeDef->GetName() << G4endl;
231 G4DNABrownianTransportation* brown = new G4DNABrownianTransportation();
232 // brown->SetVerboseLevel(4);
233 ph->RegisterProcess(brown, moleculeDef);
234 }
235 else
236 {
237 moleculeDef->GetProcessManager()
238 ->AddRestProcess(new G4DNAElectronHoleRecombination(), 2);
239 G4DNAMolecularDissociation* dissociationProcess =
240 new G4DNAMolecularDissociation("H2O_DNAMolecularDecay");
241 dissociationProcess->SetDisplacer(
242 moleculeDef, new G4DNAWaterDissociationDisplacer);
243 dissociationProcess->SetVerboseLevel(1);
244 // ph->RegisterProcess(dissociationProcess, moleculeDef);
245
246 moleculeDef->GetProcessManager()
247 ->AddRestProcess(dissociationProcess, 1);
248 }
249 /*
250 * Warning : end of particles and processes are needed by
251 * EM Physics builders
252 */
253 }
254
255 G4DNAChemistryManager::Instance()->Initialize();
256 }
257
258 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
259
260 void G4EmDNAChemistry_option1::ConstructTimeStepModel(G4DNAMolecularReactionTable*
261 reactionTable)
262 {
263
264 //=========================================
265 // Diffusion controlled reaction model
266 //=========================================
267 /**
268 * The reaction model defines how to compute the reaction range between
269 * molecules
270 */
271
272 G4VDNAReactionModel* reactionRadiusComputer =
273 new G4DNASmoluchowskiReactionModel();
274 reactionTable->PrintTable(reactionRadiusComputer);
275
276 /**
277 * The StepByStep model tells the step manager how to behave before and
278 * after each step, how to compute the time steps.
279 */
280
281 G4DNAMolecularStepByStepModel* stepByStep =
282 new G4DNAMolecularStepByStepModel();
283 stepByStep->SetReactionModel(reactionRadiusComputer);
284 // ((G4DNAMoleculeEncounterStepper*) stepByStep->GetTimeStepper())->
285 // SetVerbose(5);
286
287 RegisterTimeStepModel(stepByStep, 0);
288 }
289