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24 // ********************************************************************
25 // 20/2/2019
26 // Author: HoangTRAN
27
28 #include "G4DNAIndependentReactionTimeStepper.hh"
29
30 #include "G4ChemicalMoleculeFinder.hh"
31 #include "G4DNAChemistryManager.hh"
32 #include "G4DNAMakeReaction.hh"
33 #include "G4DNAMolecularReactionTable.hh"
34 #include "G4DiffusionControlledReactionModel.hh"
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::Utils(const G4Track& trackA, const G4Track& trackB)
48 : fTrackA(trackA), fTrackB(trackB)
49 {
50 fpMoleculeA = GetMolecule(trackA);
51 fpMoleculeB = GetMolecule(trackA);
52 }
53
54 G4DNAIndependentReactionTimeStepper::G4DNAIndependentReactionTimeStepper()
55 {
56 fReactionSet->SortByTime();
57 }
58
59 void G4DNAIndependentReactionTimeStepper::Prepare()
60 {
61 G4VITTimeStepComputer::Prepare();
62 fSampledPositions.clear();
63 BuildChemicalMoleculeFinder()
64 }
65
66 void G4DNAIndependentReactionTimeStepper::InitializeForNewTrack()
67 {
68 if (fReactants != nullptr) {
69 fReactants.reset();
70 }
71 fSampledMinTimeStep = DBL_MAX;
72 fHasAlreadyReachedNullTime = false;
73 }
74
75 G4double G4DNAIndependentReactionTimeStepper::CalculateStep(const G4Track& trackA,
76 const G4double& userMinTimeStep)
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 << "G4DNAIndependentReactionTimeStepper::CalculateStep" << G4endl;
89 G4cout << "Check done for molecule : " << pMoleculeA->GetName() << " (" << trackA.GetTrackID()
90 << ") " << G4endl;
91 }
92 #endif
93
94 auto pMolConfA = pMoleculeA->GetMolecularConfiguration();
95
96 const auto pReactantList = fMolecularReactionTable->CanReactWith(pMolConfA);
97
98 if (pReactantList == nullptr) {
99 if(fVerbose > 1) {
100 G4ExceptionDescription msg;
101 msg << "G4DNAIndependentReactionTimeStepper::CalculateStep will return infinity "
102 "for the reaction because the molecule "
103 << pMoleculeA->GetName() << " does not have any reactants given in the reaction table."
104 << G4endl;
105 G4Exception("G4DNAIndependentReactionTimeStepper::CalculateStep",
106 "G4DNAIndependentReactionTimeStepper03", JustWarning, msg);
107 }
108 return DBL_MAX;
109 }
110
111 auto nbReactives = (G4int)pReactantList->size();
112
113 if (nbReactives == 0) {
114 if(fVerbose != 0){
115 G4ExceptionDescription msg;
116 msg << "G4DNAIndependentReactionTimeStepper::CalculateStep will "
117 "return infinity "
118 "for the reaction because the molecule "
119 << pMoleculeA->GetName() << " does not have any reactants given in the reaction table."
120 << "This message can also result from a wrong implementation of "
121 "the reaction table."
122 << G4endl;
123 G4Exception("G4DNAIndependentReactionTimeStepper::CalculateStep",
124 "G4DNAIndependentReactionTimeStepper04", JustWarning, msg);
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 * ps);
135 fRCutOff = G4IRTUtils::GetRCutOff();
136 //______________________________________________________________
137 // Retrieve reaction range
138 const G4double Reff = fReactionModel->GetReactionRadius(i);
139 std::vector<std::pair<G4TrackList::iterator, G4double>> resultIndices;
140 resultIndices.clear();
141 G4ChemicalMoleculeFinder::Instance()->FindNearestInRange(trackA, key, fRCutOff, resultIndices);
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 exceptionDescription;
154 exceptionDescription << "No trackB no valid";
155 G4Exception(
156 "G4DNAIndependentReactionTimeStepper"
157 "::CalculateStep()",
158 "G4DNAIndependentReactionTimeStepper007", FatalException, exceptionDescription);
159 }
160 else {
161 if (fCheckedTracks.find(pTrackB->GetTrackID()) != fCheckedTracks.end()) {
162 continue;
163 }
164
165 Utils utils(trackA, *pTrackB);
166
167 auto pMolB = GetMolecule(pTrackB);
168 auto pMolConfB = pMolB->GetMolecularConfiguration();
169 G4double distance = (trackA.GetPosition() - pTrackB->GetPosition()).mag();
170 if (distance * distance < Reff * Reff) {
171 auto reactionData = fMolecularReactionTable->GetReactionData(pMolConfA, pMolConfB);
172 if (G4Scheduler::Instance()->GetGlobalTime() == G4Scheduler::Instance()->GetStartTime()) {
173 if (reactionData->GetProbability() > G4UniformRand()) {
174 if (!fHasAlreadyReachedNullTime) {
175 fReactants->clear();
176 fHasAlreadyReachedNullTime = true;
177 }
178 fSampledMinTimeStep = 0.;
179 CheckAndRecordResults(utils);
180 }
181 }
182 }
183 else {
184 G4double tempMinET = GetTimeToEncounter(trackA, *pTrackB);
185 if (tempMinET < 0 || tempMinET > G4Scheduler::Instance()->GetEndTime()) {
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 << "G4DNAIndependentReactionTimeStepper::CalculateStep will finally "
202 "return :"
203 << G4BestUnit(fSampledMinTimeStep, "Time") << G4endl;
204
205 if (fVerbose > 1) {
206 G4cout << "Selected reactants for trackA: " << pMoleculeA->GetName() << " ("
207 << trackA.GetTrackID() << ") are: ";
208
209 vector<G4Track*>::iterator it;
210 for (it = fReactants->begin(); it != fReactants->end(); it++) {
211 G4Track* trackB = *it;
212 G4cout << GetMolecule(trackB)->GetName() << " (" << trackB->GetTrackID() << ") \t ";
213 }
214 G4cout << G4endl;
215 }
216 }
217 #endif
218 return fSampledMinTimeStep;
219 }
220
221 void G4DNAIndependentReactionTimeStepper::CheckAndRecordResults(const Utils& utils)
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 impossible) ie fpTrackA == trackB"
231 << G4endl;
232 msg << "Molecule A is of type : " << utils.fpMoleculeA->GetName()
233 << " with trackID : " << utils.fTrackA.GetTrackID()
234 << " and B : " << utils.fpMoleculeB->GetName()
235 << " with trackID : " << utils.fTrackB.GetTrackID() << G4endl;
236 G4Exception("G4DNAIndependentReactionTimeStepper::RetrieveResults",
237 "G4DNAIndependentReactionTimeStepper003", FatalErrorInArgument,
238 msg);
239 }
240
241 if (fabs(utils.fTrackB.GetGlobalTime() - utils.fTrackA.GetGlobalTime())
242 > utils.fTrackA.GetGlobalTime() * (1. - 1. / 100))
243 {
244 // DEBUG
245 G4ExceptionDescription msg;
246 msg << "The interacting tracks are not synchronized in time" << G4endl;
247 msg << "trackB->GetGlobalTime() != fpTrackA.GetGlobalTime()" << G4endl;
248
249 msg << "fpTrackA : trackID : " << utils.fTrackA.GetTrackID()
250 << "\t Name :" << utils.fpMoleculeA->GetName()
251 << "\t fpTrackA->GetGlobalTime() = "
252 << G4BestUnit(utils.fTrackA.GetGlobalTime(), "Time") << G4endl;
253
254 msg << "trackB : trackID : " << utils.fTrackB.GetTrackID()
255 << "\t Name :" << utils.fpMoleculeB->GetName()
256 << "\t trackB->GetGlobalTime() = "
257 << G4BestUnit(utils.fTrackB.GetGlobalTime(), "Time") << G4endl;
258
259 G4Exception("G4DNAIndependentReactionTimeStepper::RetrieveResults",
260 "G4DNAIndependentReactionTimeStepper004", FatalErrorInArgument,
261 msg);
262 }
263 fReactants->push_back(const_cast<G4Track*>(&utils.fTrackB));
264 }
265
266 std::unique_ptr<G4ITReactionChange> G4DNAIndependentReactionTimeStepper::FindReaction(
267 G4ITReactionSet* pReactionSet, const G4double& currentStepTime,
268 const G4double& /*previousStepTime*/, const G4bool& /*reachedUserStepTimeLimit*/)
269 {
270 if (pReactionSet == nullptr) {
271 return nullptr;
272 }
273
274 G4ITReactionPerTime& reactionPerTime = pReactionSet->GetReactionsPerTime();
275 if (reactionPerTime.empty()) {
276 return nullptr;
277 }
278 for (auto reaction_i = reactionPerTime.begin(); reaction_i != reactionPerTime.end();
279 reaction_i = reactionPerTime.begin())
280 {
281 if ((*reaction_i)->GetTime() > currentStepTime) {
282 fReactionSet->CleanAllReaction();
283 return nullptr;
284 }
285
286 G4Track* pTrackA = (*reaction_i)->GetReactants().first;
287 if (pTrackA->GetTrackStatus() == fStopAndKill) {
288 continue;
289 }
290 G4Track* pTrackB = (*reaction_i)->GetReactant(pTrackA);
291 if (pTrackB->GetTrackStatus() == fStopAndKill) {
292 continue;
293 }
294
295 if (pTrackB == pTrackA) {
296 G4ExceptionDescription msg;
297 msg << "The IT reaction process sent back a reaction "
298 "between trackA and trackB. ";
299 msg << "The problem is trackA == trackB";
300 G4Exception("G4DNAIndependentReactionTimeStepper::FindReaction",
301 "G4DNAIndependentReactionTimeStepper02", FatalErrorInArgument,
302 msg);
303 }
304 pReactionSet->SelectThisReaction(*reaction_i);
305 if (fpReactionProcess != nullptr
306 && fpReactionProcess->TestReactibility(*pTrackA, *pTrackB, currentStepTime, false))
307 {
308 if ((fSampledPositions.find(pTrackA->GetTrackID()) == fSampledPositions.end()
309 && (fSampledPositions.find(pTrackB->GetTrackID()) == fSampledPositions.end())))
310 {
311 G4ExceptionDescription msg;
312 msg << "The positions of trackA and trackB have no counted ";
313 G4Exception("G4DNAIndependentReactionTimeStepper::FindReaction",
314 "G4DNAIndependentReactionTimeStepper0001", FatalErrorInArgument,
315 msg);
316 }
317
318 pTrackA->SetPosition(fSampledPositions[pTrackA->GetTrackID()]);
319 pTrackB->SetPosition(fSampledPositions[pTrackB->GetTrackID()]);
320 auto pReactionChange = fpReactionProcess->MakeReaction(*pTrackA, *pTrackB);
321 if (pReactionChange == nullptr) {
322 return nullptr;
323 }
324 return pReactionChange;
325 }
326 }
327 return nullptr;
328 }
329
330 void G4DNAIndependentReactionTimeStepper::SetReactionModel(G4VDNAReactionModel* pReactionModel)
331 {
332 fReactionModel = pReactionModel;
333 }
334
335 G4VDNAReactionModel* G4DNAIndependentReactionTimeStepper::GetReactionModel()
336 {
337 return fReactionModel;
338 }
339
340 void G4DNAIndependentReactionTimeStepper::SetVerbose(G4int flag)
341 {
342 fVerbose = flag;
343 }
344
345 G4double G4DNAIndependentReactionTimeStepper::GetTimeToEncounter(const G4Track& trackA,
346 const G4Track& trackB)
347 {
348 G4double timeToReaction = dynamic_cast<G4DiffusionControlledReactionModel*>(fReactionModel)
349 ->GetTimeToEncounter(trackA, trackB);
350 return timeToReaction;
351 }
352
353 void G4DNAIndependentReactionTimeStepper::SetReactionProcess(G4VITReactionProcess* pReactionProcess)
354 {
355 fpReactionProcess = pReactionProcess;
356 }
357 G4double G4DNAIndependentReactionTimeStepper::CalculateMinTimeStep(G4double /*currentGlobalTime*/,
358 G4double definedMinTimeStep)
359 {
360 G4double fTSTimeStep = DBL_MAX;
361 fCheckedTracks.clear();
362
363 for (auto pTrack : *fpTrackContainer->GetMainList()) {
364 if (pTrack == nullptr) {
365 G4ExceptionDescription msg;
366 msg << "No track found.";
367 G4Exception("G4DNAIndependentReactionTimeStepper::CalculateMinTimeStep",
368 "G4DNAIndependentReactionTimeStepper006", FatalErrorInArgument,
369 msg);
370 continue;
371 }
372
373 G4TrackStatus trackStatus = pTrack->GetTrackStatus();
374 if (trackStatus == fStopAndKill || trackStatus == fStopButAlive) {
375 continue;
376 }
377
378 G4double sampledMinTimeStep = CalculateStep(*pTrack, definedMinTimeStep);
379 G4TrackVectorHandle reactants = GetReactants();
380
381 if (sampledMinTimeStep < fTSTimeStep) {
382 fTSTimeStep = sampledMinTimeStep;
383 if (reactants) {
384 fReactionSet->AddReactions(fTSTimeStep, const_cast<G4Track*>(pTrack), std::move(reactants));
385
386 fSampledPositions[pTrack->GetTrackID()] = pTrack->GetPosition();
387 for (const auto& it : *fReactants) {
388 auto pTrackB = it;
389 fSampledPositions[pTrackB->GetTrackID()] = pTrackB->GetPosition();
390 }
391 ResetReactants();
392 }
393 }
394 else if (fTSTimeStep == sampledMinTimeStep && G4bool(reactants)) {
395 fReactionSet->AddReactions(fTSTimeStep, const_cast<G4Track*>(pTrack), std::move(reactants));
396
397 fSampledPositions[pTrack->GetTrackID()] = pTrack->GetPosition();
398 for (const auto& it : *fReactants) {
399 auto pTrackB = it;
400 fSampledPositions[pTrackB->GetTrackID()] = pTrackB->GetPosition();
401 }
402 ResetReactants();
403 }
404 else if (reactants) {
405 ResetReactants();
406 }
407 }
408 return fTSTimeStep;
409 }
410