| Geant4 Cross Reference |
1 // 1
2 // *******************************************
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4 // *
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17 // *
18 // * This code implementation is the result
19 // * technical work of the GEANT4 collaboratio
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23 // * acceptance of all terms of the Geant4 Sof
24 // *******************************************
25 //
26 #include "EmDNAChemistry.hh"
27
28 #include "G4DNAChemistryManager.hh"
29 #include "G4DNAWaterDissociationDisplacer.hh"
30 #include "G4ProcessManager.hh"
31 #include "G4SystemOfUnits.hh"
32
33 // *** Processes and models for Geant4-DNA
34
35 #include "BoundedBrownianAction.hh"
36
37 #include "G4DNABrownianTransportation.hh"
38 #include "G4DNAElectronHoleRecombination.hh"
39 #include "G4DNAElectronSolvation.hh"
40 #include "G4DNAMolecularDissociation.hh"
41 #include "G4DNAMolecularReactionTable.hh"
42 #include "G4DNAMolecularStepByStepModel.hh"
43 #include "G4DNASancheExcitationModel.hh"
44 #include "G4DNASmoluchowskiReactionModel.hh"
45 #include "G4DNAVibExcitation.hh"
46 // particles
47
48 #include "G4Electron.hh"
49 #include "G4Electron_aq.hh"
50 #include "G4H2O.hh"
51 #include "G4H2O2.hh"
52 #include "G4H3O.hh"
53 #include "G4HO2.hh"
54 #include "G4Hydrogen.hh"
55 #include "G4MoleculeTable.hh"
56 #include "G4O2.hh"
57 #include "G4O3.hh"
58 #include "G4OH.hh"
59 #include "G4Oxygen.hh"
60 #include "G4PhysicsListHelper.hh"
61 /****/
62 #include "G4DNAMoleculeEncounterStepper.hh"
63 #include "G4DNAScavengerProcess.hh"
64 #include "G4MolecularConfiguration.hh"
65 #include "G4ProcessTable.hh"
66 #include "G4VChemistryWorld.hh"
67 /****/
68 #include "G4ChemicalMoleculeFinder.hh"
69 // factory
70 #include "ChemOxygenWaterBuilder.hh"
71 #include "ChemPureWaterBuilder.hh"
72
73 #include "G4ChemDissociationChannels_option1.h
74 #include "G4PhysicsConstructorFactory.hh"
75
76 G4_DECLARE_PHYSCONSTR_FACTORY(EmDNAChemistry);
77
78 EmDNAChemistry::EmDNAChemistry() : G4VUserChem
79 {
80 G4DNAChemistryManager::Instance()->SetChemis
81 }
82
83 //....oooOO0OOooo........oooOO0OOooo........oo
84
85 EmDNAChemistry::~EmDNAChemistry() = default;
86
87 //....oooOO0OOooo........oooOO0OOooo........oo
88
89 void EmDNAChemistry::ConstructMolecule()
90 {
91 G4ChemDissociationChannels_option1::Construc
92 auto table = G4MoleculeTable::Instance();
93
94 auto H3OpB = table->GetConfiguration("H3Op(B
95 H3OpB->SetDiffusionCoefficient(9.46e-9 * (m2
96
97 auto OHm = table->GetConfiguration("OHm(B)")
98 OHm->SetDiffusionCoefficient(5.3e-9 * (m2 /
99 table->CreateConfiguration("H2O", G4H2O::Def
100
101 auto G4NO2 = new G4MoleculeDefinition("NO_2"
102 /*D*/
103 /*char
104 /*elec
105 /*radi
106
107 auto G4NO3 = new G4MoleculeDefinition("NO_3"
108 /*D*/
109 /*char
110 /*elec
111 /*radi
112
113 table->CreateConfiguration("NO2", G4NO2);
114 table->CreateConfiguration("NO2m", G4NO2,
115 -1, // charge
116 0 * (m2 / s));
117 table->CreateConfiguration("NO2mm", G4NO2,
118 -2, // charge
119 0 * (m2 / s));
120
121 table->CreateConfiguration("NO3m", G4NO3,
122 -1, // charge
123 0 * (m2 / s));
124
125 table->CreateConfiguration("NO3mm", G4NO3,
126 -2, // charge
127 0 * (m2 / s));
128
129 // FrickeDosimeter
130 auto G4Fe = new G4MoleculeDefinition("Fe",
131 /*mass*
132 /*D*/ 0
133 /*charg
134 /*elect
135 /*radiu
136
137 table->CreateConfiguration("Fe0", G4Fe);
138
139 table->CreateConfiguration("Feppp", G4Fe,
140 3, // charge
141 4.86e-10 * (m2 /
142
143 table->CreateConfiguration("Fepp", G4Fe,
144 2, // charge
145 5.78e-10 * (m2 /
146 // HSO4-
147 auto G4HSO4 = new G4MoleculeDefinition("HSO4
148 /*mas
149 /*D*/
150 /*cha
151 /*ele
152 /*rad
153 table->CreateConfiguration("HSO4m", G4HSO4,
154 -1, // charge
155 0 * (m2 / s));
156
157 // SO4-
158 auto G4SO4 = new G4MoleculeDefinition("SO4",
159 /*mass
160 /*D*/
161 /*char
162 /*elec
163 /*radi
164 table->CreateConfiguration("SO4m", G4SO4,
165 -1, // charge
166 0 * (m2 / s));
167 }
168
169 //....oooOO0OOooo........oooOO0OOooo........oo
170
171 void EmDNAChemistry::ConstructDissociationChan
172 {
173 G4ChemDissociationChannels_option1::Construc
174 }
175
176 //....oooOO0OOooo........oooOO0OOooo........oo
177
178 void EmDNAChemistry::ConstructReactionTable(G4
179 {
180 ChemOxygenWaterBuilder::OxygenScavengerReact
181 ChemOxygenWaterBuilder::SecondOrderReactionE
182 ChemPureWaterBuilder::WaterScavengerReaction
183 }
184
185 //....oooOO0OOooo........oooOO0OOooo........oo
186
187 void EmDNAChemistry::ConstructProcess()
188 {
189 auto table = G4MoleculeTable::Instance();
190 auto O2 = table->GetConfiguration("O2");
191 auto O2m = table->GetConfiguration("O2m");
192 auto HO2 = table->GetConfiguration("HO2°");
193
194 auto e_aq = table->GetConfiguration("e_aq");
195 auto OH = table->GetConfiguration("°OH");
196 auto OHm = table->GetConfiguration("OHm");
197
198 auto NO2 = table->GetConfiguration("NO2");
199 auto NO2m = table->GetConfiguration("NO2m");
200 auto NO2mm = table->GetConfiguration("NO2mm"
201 auto NO3m = table->GetConfiguration("NO3m");
202 auto NO3mm = table->GetConfiguration("NO3mm"
203
204 auto H2O2 = table->GetConfiguration("H2O2");
205 auto H = table->GetConfiguration("H");
206
207 auto* H3OpB = table->GetConfiguration("H3Op(
208 auto* OHmB = table->GetConfiguration("OHm(B)
209 auto* HO2m = table->GetConfiguration("HO2m")
210 auto* Om = table->GetConfiguration("Om");
211 auto* O3m = table->GetConfiguration("O3m");
212 auto* H3Op = table->GetConfiguration("H3Op")
213
214 fpChemistryWorld->ConstructChemistryComponen
215 auto confinedBox = fpChemistryWorld->GetChem
216
217 auto* ph = G4PhysicsListHelper::GetPhysicsLi
218
219 //==========================================
220 // Extend vibrational to low energy
221 // Anyway, solvation of electrons is taken i
222 // So below this threshold, for now, no accu
223 //
224 G4VProcess* process =
225 G4ProcessTable::GetProcessTable()->FindPro
226
227 if (process) {
228 auto vibExcitation = (G4DNAVibExcitation*)
229 G4VEmModel* model = vibExcitation->EmModel
230 auto sancheExcitationMod = dynamic_cast<G4
231 if (sancheExcitationMod) {
232 sancheExcitationMod->ExtendLowEnergyLimi
233 }
234 }
235
236 //==========================================
237 // *** Electron Solvatation ***
238 //
239 process = G4ProcessTable::GetProcessTable()-
240
241 if (process == nullptr) {
242 ph->RegisterProcess(new G4DNAElectronSolva
243 G4Electron::Definition
244 }
245
246 //==========================================
247 // Define processes for molecules
248 //
249 auto* theMoleculeTable = G4MoleculeTable::In
250 auto iterator = theMoleculeTable->GetDefinti
251 iterator.reset();
252
253 while (iterator()) {
254 auto* moleculeDef = iterator.value();
255
256 if (moleculeDef != G4H2O::Definition()) {
257 auto brown = new G4DNABrownianTransporta
258 // hoang exp
259 auto brownTransport = new BoundedBrownia
260 brownTransport->SetBoundary(*confinedBox
261 brown->SetUserBrownianAction(brownTransp
262 // hoang exp
263
264 ph->RegisterProcess(brown, moleculeDef);
265 }
266 else {
267 moleculeDef->GetProcessManager()->AddRes
268 auto brownTransport = new BoundedBrownia
269 brownTransport->SetBoundary(*confinedBox
270 auto dissociationProcess = new G4DNAMole
271 dissociationProcess->SetUserBrownianActi
272 dissociationProcess->SetDisplacer(molecu
273 moleculeDef->GetProcessManager()->AddRes
274 }
275
276 if (moleculeDef == G4Hydrogen::Definition(
277 // O2
278 auto scanvergerProcess = new G4DNAScaven
279 //--------------------------------------
280 // H + O2(B) -> HO2
281 auto reactionData = new G4DNAMolecularRe
282 reactionData->AddProduct(HO2);
283 scanvergerProcess->SetReaction(H, reacti
284 //--------------------------------------
285 // H + OH-(B) -> H2O + eaq- 2.49e3 / s
286 reactionData = new G4DNAMolecularReactio
287
288 reactionData->AddProduct(e_aq);
289 scanvergerProcess->SetReaction(H, reacti
290
291 // H2O2
292 //--------------------------------------
293 // H + H202 -> OH + H20
294 // reactionData = new G4DNAMo
295 // 9.0e7 * (1e-3 * m3
296 // reactionData->AddProduct(O
297 // scanvergerProcess->SetReac
298 ph->RegisterProcess(scanvergerProcess, m
299 }
300 if (moleculeDef == G4Electron_aq::Definiti
301 auto scanvergerProcess = new G4DNAScaven
302 G4DNAMolecularReactionData* reactionData
303 //--------------------------------------
304 // e_aq + O2(B) -> O2-
305 reactionData = new G4DNAMolecularReactio
306 reactionData->AddProduct(O2m);
307 scanvergerProcess->SetReaction(e_aq, rea
308 //--------------------------------------
309 // eaq- + H3O+(B) -> H + H2O 2.09e3 / s
310 reactionData =
311 new G4DNAMolecularReactionData(2.25e10
312 H3OpB);
313 reactionData->AddProduct(H);
314 scanvergerProcess->SetReaction(e_aq, rea
315 //--------------------------------------
316 // e_aq + NO2- -> NO2--
317 reactionData = new G4DNAMolecularReactio
318 reactionData->AddProduct(NO2mm);
319 scanvergerProcess->SetReaction(e_aq, rea
320 //--------------------------------------
321 // e_aq + NO3- -> NO3--
322 reactionData = new G4DNAMolecularReactio
323 reactionData->AddProduct(NO3mm);
324 scanvergerProcess->SetReaction(e_aq, rea
325 //--------------------------------------
326
327 // H2O2 + e aq → OHm + OH
328 // reactionData = new G4DNAMo
329 // 1.1e10 * (1e-3 * m
330 // reactionData->AddProduct(O
331 // reactionData->AddProduct(O
332 // scanvergerProcess->SetReac
333
334 ph->RegisterProcess(scanvergerProcess, m
335 }
336 if (moleculeDef == G4O2::Definition()) {
337 auto scanvergerProcess = new G4DNAScaven
338 G4DNAMolecularReactionData* reactionData
339 //--------------------------------------
340 // O2- + H3O+(B) -> HO2 + H2O 4.73e3 / s
341 reactionData =
342 new G4DNAMolecularReactionData(4.78e10
343 H3OpB);
344 reactionData->AddProduct(HO2);
345 scanvergerProcess->SetReaction(O2m, reac
346 ph->RegisterProcess(scanvergerProcess, m
347 }
348 if (moleculeDef == G4ParticleTable::GetPar
349 auto scanvergerProcess = new G4DNAScaven
350 G4DNAMolecularReactionData* reactionData
351 //--------------------------------------
352 // OH- + H3O+(B) -> 2H2O 1.11e4 / s
353 reactionData =
354 new G4DNAMolecularReactionData(1.13e11
355 H3OpB);
356 scanvergerProcess->SetReaction(OHm, reac
357 ph->RegisterProcess(scanvergerProcess, m
358 }
359 if (moleculeDef == G4OH::Definition()) {
360 auto scanvergerProcess = new G4DNAScaven
361 G4DNAMolecularReactionData* reactionData
362
363 //--------------------------------------
364 // OH + OH-(B) -> O- + H2O 6.24e2 / s
365 reactionData =
366 new G4DNAMolecularReactionData(1.27e10
367 OHmB);
368 reactionData->AddProduct(Om);
369 scanvergerProcess->SetReaction(OH, react
370
371 //--------------------------------------
372 // OH + NO2- -> NO2 + OH-
373 reactionData = new G4DNAMolecularReactio
374 reactionData->AddProduct(NO2);
375 reactionData->AddProduct(OHm);
376 scanvergerProcess->SetReaction(OH, react
377 ph->RegisterProcess(scanvergerProcess, m
378 }
379 if (moleculeDef == G4ParticleTable::GetPar
380 auto scanvergerProcess = new G4DNAScaven
381 G4DNAMolecularReactionData* reactionData
382 //--------------------------------------
383 // HO2- + H3O+(B) -> H2O2 + H2O 4.98e3 /
384 reactionData =
385 new G4DNAMolecularReactionData(4.78e10
386 H3OpB);
387 reactionData->AddProduct(H2O2);
388 scanvergerProcess->SetReaction(HO2m, rea
389 ph->RegisterProcess(scanvergerProcess, m
390 }
391
392 if (moleculeDef == G4HO2::Definition()) {
393 auto scanvergerProcess = new G4DNAScaven
394 G4DNAMolecularReactionData* reactionData
395 //--------------------------------------
396 // HO2 + OH-(B) -> O2- + H2O 6.24e2 / s
397 reactionData = new G4DNAMolecularReactio
398
399 reactionData->AddProduct(O2m);
400 scanvergerProcess->SetReaction(HO2, reac
401 //--------------------------------------
402 ph->RegisterProcess(scanvergerProcess, m
403 }
404 if (moleculeDef == G4Oxygen::Definition())
405 auto scanvergerProcess = new G4DNAScaven
406 G4DNAMolecularReactionData* reactionData
407 //--------------------------------------
408 // O- + H3O+(B) -> OH + H2O 4.73e3 / s
409 reactionData =
410 new G4DNAMolecularReactionData(4.78e10
411 H3OpB);
412 reactionData->AddProduct(OH);
413 scanvergerProcess->SetReaction(Om, react
414 ph->RegisterProcess(scanvergerProcess, m
415 }
416 if (moleculeDef == G4O3::Definition()) {
417 auto scanvergerProcess = new G4DNAScaven
418 G4DNAMolecularReactionData* reactionData
419 //--------------------------------------
420 // O3- + H3O+(B) -> OH + O2 + H2O 8.91e3
421 reactionData =
422 new G4DNAMolecularReactionData(9.0e10
423 H3OpB);
424 reactionData->AddProduct(OH);
425 reactionData->AddProduct(O2);
426 //--------------------------------------
427 scanvergerProcess->SetReaction(O3m, reac
428 ph->RegisterProcess(scanvergerProcess, m
429 }
430 if (moleculeDef == G4H3O::Definition()) {
431 auto scanvergerProcess = new G4DNAScaven
432 G4DNAMolecularReactionData* reactionData
433 //--------------------------------------
434 // H3O+ + OH-(B) -> 2H2O 1.11e4 / s
435 reactionData =
436 new G4DNAMolecularReactionData(1.13e11
437 OHmB);
438 scanvergerProcess->SetReaction(H3Op, rea
439 ph->RegisterProcess(scanvergerProcess, m
440 }
441 if (moleculeDef == G4H2O2::Definition()) {
442 auto scanvergerProcess = new G4DNAScaven
443 G4DNAMolecularReactionData* reactionData
444 //--------------------------------------
445 // H2O2 + OH-(B) -> HO2- + H2O 4.66e2 /
446 reactionData =
447 new G4DNAMolecularReactionData(1.27e10
448 OHmB);
449 reactionData->AddProduct(HO2m);
450 scanvergerProcess->SetReaction(H2O2, rea
451 ph->RegisterProcess(scanvergerProcess, m
452 }
453 }
454 G4DNAChemistryManager::Instance()->Initializ
455 }
456
457 //....oooOO0OOooo........oooOO0OOooo........oo
458
459 void EmDNAChemistry::ConstructTimeStepModel(G4
460 {
461 auto reactionRadiusComputer = new G4DNASmolu
462 reactionTable->PrintTable(reactionRadiusComp
463 auto stepByStep = new G4DNAMolecularStepBySt
464 stepByStep->SetReactionModel(reactionRadiusC
465 RegisterTimeStepModel(stepByStep, 0);
466 }
467
468 //....oooOO0OOooo........oooOO0OOooo........oo
469