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25 // 20/2/2019
26 // Author: HoangTRAN
27
28 #include "G4DNAIndependentReactionTimeStepper.
29
30 #include "G4ChemicalMoleculeFinder.hh"
31 #include "G4DNAChemistryManager.hh"
32 #include "G4DNAMakeReaction.hh"
33 #include "G4DNAMolecularReactionTable.hh"
34 #include "G4DiffusionControlledReactionModel.h
35 #include "G4IRTUtils.hh"
36 #include "G4ITReactionChange.hh"
37 #include "G4Molecule.hh"
38 #include "G4Scheduler.hh"
39 #include "G4UnitsTable.hh"
40 #include "G4VDNAReactionModel.hh"
41 #include "Randomize.hh"
42
43 #include <memory>
44 using namespace std;
45 using namespace CLHEP;
46
47 G4DNAIndependentReactionTimeStepper::Utils::Ut
48 : fTrackA(trackA), fTrackB(trackB)
49 {
50 fpMoleculeA = GetMolecule(trackA);
51 fpMoleculeB = GetMolecule(trackA);
52 }
53
54 G4DNAIndependentReactionTimeStepper::G4DNAInde
55 {
56 fReactionSet->SortByTime();
57 }
58
59 void G4DNAIndependentReactionTimeStepper::Prep
60 {
61 G4VITTimeStepComputer::Prepare();
62 fSampledPositions.clear();
63 BuildChemicalMoleculeFinder()
64 }
65
66 void G4DNAIndependentReactionTimeStepper::Init
67 {
68 if (fReactants != nullptr) {
69 fReactants.reset();
70 }
71 fSampledMinTimeStep = DBL_MAX;
72 fHasAlreadyReachedNullTime = false;
73 }
74
75 G4double G4DNAIndependentReactionTimeStepper::
76
77 {
78 auto pMoleculeA = GetMolecule(trackA);
79 InitializeForNewTrack();
80 fUserMinTimeStep = userMinTimeStep;
81 fCheckedTracks.insert(trackA.GetTrackID());
82
83 #ifdef G4VERBOSE
84 if (fVerbose != 0) {
85 G4cout << "_______________________________
86 "_______"
87 << G4endl;
88 G4cout << "G4DNAIndependentReactionTimeSte
89 G4cout << "Check done for molecule : " <<
90 << ") " << G4endl;
91 }
92 #endif
93
94 auto pMolConfA = pMoleculeA->GetMolecularCon
95
96 const auto pReactantList = fMolecularReactio
97
98 if (pReactantList == nullptr) {
99 if(fVerbose > 1) {
100 G4ExceptionDescription msg;
101 msg << "G4DNAIndependentReactionTimeStep
102 "for the reaction because the mol
103 << pMoleculeA->GetName() << " does n
104 << G4endl;
105 G4Exception("G4DNAIndependentReactionTim
106 "G4DNAIndependentReactionTim
107 }
108 return DBL_MAX;
109 }
110
111 auto nbReactives = (G4int)pReactantList->siz
112
113 if (nbReactives == 0) {
114 if(fVerbose != 0){
115 G4ExceptionDescription msg;
116 msg << "G4DNAIndependentReactionTimeStep
117 "return infinity "
118 "for the reaction because the mol
119 << pMoleculeA->GetName() << " does n
120 << "This message can also result fro
121 "the reaction table."
122 << G4endl;
123 G4Exception("G4DNAIndependentReactionTim
124 "G4DNAIndependentReactionTim
125 }
126 return DBL_MAX;
127 }
128 fReactants = std::make_shared<vector<G4Track
129 fReactionModel->Initialise(pMolConfA, trackA
130 for (G4int i = 0; i < nbReactives; ++i) {
131 auto pMoleculeB = (*pReactantList)[i];
132 G4int key = pMoleculeB->GetMoleculeID();
133
134 // fRCutOff = G4IRTUtils::GetRCutOff(1 * p
135 fRCutOff = G4IRTUtils::GetRCutOff();
136 //________________________________________
137 // Retrieve reaction range
138 const G4double Reff = fReactionModel->GetR
139 std::vector<std::pair<G4TrackList::iterato
140 resultIndices.clear();
141 G4ChemicalMoleculeFinder::Instance()->Find
142
143 if (resultIndices.empty()) {
144 continue;
145 }
146 for (auto& it : resultIndices) {
147 G4Track* pTrackB = *(std::get<0>(it));
148
149 if (pTrackB == &trackA) {
150 continue;
151 }
152 if (pTrackB == nullptr) {
153 G4ExceptionDescription exceptionDescri
154 exceptionDescription << "No trackB no
155 G4Exception(
156 "G4DNAIndependentReactionTimeStepper
157 "::CalculateStep()",
158 "G4DNAIndependentReactionTimeStepper
159 }
160 else {
161 if (fCheckedTracks.find(pTrackB->GetTr
162 continue;
163 }
164
165 Utils utils(trackA, *pTrackB);
166
167 auto pMolB = GetMolecule(pTrackB);
168 auto pMolConfB = pMolB->GetMolecularCo
169 G4double distance = (trackA.GetPositio
170 if (distance * distance < Reff * Reff)
171 auto reactionData = fMolecularReacti
172 if (G4Scheduler::Instance()->GetGlob
173 if (reactionData->GetProbability()
174 if (!fHasAlreadyReachedNullTime)
175 fReactants->clear();
176 fHasAlreadyReachedNullTime = t
177 }
178 fSampledMinTimeStep = 0.;
179 CheckAndRecordResults(utils);
180 }
181 }
182 }
183 else {
184 G4double tempMinET = GetTimeToEncoun
185 if (tempMinET < 0 || tempMinET > G4S
186 continue;
187 }
188 if (tempMinET >= fSampledMinTimeStep
189 continue;
190 }
191 fSampledMinTimeStep = tempMinET;
192 fReactants->clear();
193 CheckAndRecordResults(utils);
194 }
195 }
196 }
197 }
198
199 #ifdef G4VERBOSE
200 if (fVerbose != 0) {
201 G4cout << "G4DNAIndependentReactionTimeSte
202 "return :"
203 << G4BestUnit(fSampledMinTimeStep,
204
205 if (fVerbose > 1) {
206 G4cout << "Selected reactants for trackA
207 << trackA.GetTrackID() << ") are:
208
209 vector<G4Track*>::iterator it;
210 for (it = fReactants->begin(); it != fRe
211 G4Track* trackB = *it;
212 G4cout << GetMolecule(trackB)->GetName
213 }
214 G4cout << G4endl;
215 }
216 }
217 #endif
218 return fSampledMinTimeStep;
219 }
220
221 void G4DNAIndependentReactionTimeStepper::Chec
222 {
223 if (utils.fTrackB.GetTrackStatus() != fAlive
224 return;
225 }
226
227 if (&utils.fTrackB == &utils.fTrackA) {
228 G4ExceptionDescription msg;
229 msg << "A track is reacting with itself"
230 " (which is imposs
231 << G4endl;
232 msg << "Molecule A is of type : " << utils
233 << " with trackID : "
234 << " and B : " << uti
235 << " with trackID : "
236 G4Exception("G4DNAIndependentReactionTimeS
237 "G4DNAIndependentReactionTimeS
238 msg);
239 }
240
241 if (fabs(utils.fTrackB.GetGlobalTime() - uti
242 > utils.fTrackA.GetGlobalTime() * (1. -
243 {
244 // DEBUG
245 G4ExceptionDescription msg;
246 msg << "The interacting tracks are not syn
247 msg << "trackB->GetGlobalTime() != fpTrack
248
249 msg << "fpTrackA : trackID : " << utils.fT
250 << "\t Name :" << uti
251 << "\t fpTrackA->GetG
252 << G4BestUnit(utils.f
253
254 msg << "trackB : trackID : " << utils.fTra
255 << "\t Name :" << uti
256 << "\t trackB->GetGlo
257 << G4BestUnit(utils.f
258
259 G4Exception("G4DNAIndependentReactionTimeS
260 "G4DNAIndependentReactionTimeS
261 msg);
262 }
263 fReactants->push_back(const_cast<G4Track*>(&
264 }
265
266 std::unique_ptr<G4ITReactionChange> G4DNAIndep
267 G4ITReactionSet* pReactionSet, const G4doubl
268 const G4double& /*previousStepTime*/, const
269 {
270 if (pReactionSet == nullptr) {
271 return nullptr;
272 }
273
274 G4ITReactionPerTime& reactionPerTime = pReac
275 if (reactionPerTime.empty()) {
276 return nullptr;
277 }
278 for (auto reaction_i = reactionPerTime.begin
279 reaction_i = reactionPerTime.begin())
280 {
281 if ((*reaction_i)->GetTime() > currentStep
282 fReactionSet->CleanAllReaction();
283 return nullptr;
284 }
285
286 G4Track* pTrackA = (*reaction_i)->GetReact
287 if (pTrackA->GetTrackStatus() == fStopAndK
288 continue;
289 }
290 G4Track* pTrackB = (*reaction_i)->GetReact
291 if (pTrackB->GetTrackStatus() == fStopAndK
292 continue;
293 }
294
295 if (pTrackB == pTrackA) {
296 G4ExceptionDescription msg;
297 msg << "The IT reaction process sent bac
298 "between trackA
299 msg << "The problem is trackA == trackB"
300 G4Exception("G4DNAIndependentReactionTim
301 "G4DNAIndependentReactionTim
302 msg);
303 }
304 pReactionSet->SelectThisReaction(*reaction
305 if (fpReactionProcess != nullptr
306 && fpReactionProcess->TestReactibility
307 {
308 if ((fSampledPositions.find(pTrackA->Get
309 && (fSampledPositions.find(pTrackB-
310 {
311 G4ExceptionDescription msg;
312 msg << "The positions of trackA and tr
313 G4Exception("G4DNAIndependentReactionT
314 "G4DNAIndependentReactionT
315 msg);
316 }
317
318 pTrackA->SetPosition(fSampledPositions[p
319 pTrackB->SetPosition(fSampledPositions[p
320 auto pReactionChange = fpReactionProcess
321 if (pReactionChange == nullptr) {
322 return nullptr;
323 }
324 return pReactionChange;
325 }
326 }
327 return nullptr;
328 }
329
330 void G4DNAIndependentReactionTimeStepper::SetR
331 {
332 fReactionModel = pReactionModel;
333 }
334
335 G4VDNAReactionModel* G4DNAIndependentReactionT
336 {
337 return fReactionModel;
338 }
339
340 void G4DNAIndependentReactionTimeStepper::SetV
341 {
342 fVerbose = flag;
343 }
344
345 G4double G4DNAIndependentReactionTimeStepper::
346
347 {
348 G4double timeToReaction = dynamic_cast<G4Dif
349 ->GetTimeToEncou
350 return timeToReaction;
351 }
352
353 void G4DNAIndependentReactionTimeStepper::SetR
354 {
355 fpReactionProcess = pReactionProcess;
356 }
357 G4double G4DNAIndependentReactionTimeStepper::
358
359 {
360 G4double fTSTimeStep = DBL_MAX;
361 fCheckedTracks.clear();
362
363 for (auto pTrack : *fpTrackContainer->GetMai
364 if (pTrack == nullptr) {
365 G4ExceptionDescription msg;
366 msg << "No track found.";
367 G4Exception("G4DNAIndependentReactionTim
368 "G4DNAIndependentReactionTim
369 msg);
370 continue;
371 }
372
373 G4TrackStatus trackStatus = pTrack->GetTra
374 if (trackStatus == fStopAndKill || trackSt
375 continue;
376 }
377
378 G4double sampledMinTimeStep = CalculateSte
379 G4TrackVectorHandle reactants = GetReactan
380
381 if (sampledMinTimeStep < fTSTimeStep) {
382 fTSTimeStep = sampledMinTimeStep;
383 if (reactants) {
384 fReactionSet->AddReactions(fTSTimeStep
385
386 fSampledPositions[pTrack->GetTrackID()
387 for (const auto& it : *fReactants) {
388 auto pTrackB = it;
389 fSampledPositions[pTrackB->GetTrackI
390 }
391 ResetReactants();
392 }
393 }
394 else if (fTSTimeStep == sampledMinTimeStep
395 fReactionSet->AddReactions(fTSTimeStep,
396
397 fSampledPositions[pTrack->GetTrackID()]
398 for (const auto& it : *fReactants) {
399 auto pTrackB = it;
400 fSampledPositions[pTrackB->GetTrackID(
401 }
402 ResetReactants();
403 }
404 else if (reactants) {
405 ResetReactants();
406 }
407 }
408 return fTSTimeStep;
409 }
410