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25 // 25 //
26 // 26 //
27 // Author: Mathieu Karamitros (kara@cenbg.in2p 27 // Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
28 // 28 //
29 // WARNING : This class is released as a proto 29 // WARNING : This class is released as a prototype.
30 // It might strongly evolve or even disappear 30 // It might strongly evolve or even disappear in the next releases.
31 // 31 //
32 // History: 32 // History:
33 // ----------- 33 // -----------
34 // 10 Oct 2011 M.Karamitros created 34 // 10 Oct 2011 M.Karamitros created
35 // 35 //
36 // ------------------------------------------- 36 // -------------------------------------------------------------------
37 37
38 #include "G4DNAChemistryManager.hh" 38 #include "G4DNAChemistryManager.hh"
39 39
40 #include "G4AutoLock.hh" << 40 #include "G4Scheduler.hh"
>> 41 #include "G4SystemOfUnits.hh"
>> 42 #include "G4Molecule.hh"
>> 43 #include "G4VITTrackHolder.hh"
>> 44 #include "G4H2O.hh"
41 #include "G4DNAMolecularReactionTable.hh" 45 #include "G4DNAMolecularReactionTable.hh"
42 #include "G4DNAWaterExcitationStructure.hh" 46 #include "G4DNAWaterExcitationStructure.hh"
43 #include "G4DNAWaterIonisationStructure.hh" 47 #include "G4DNAWaterIonisationStructure.hh"
44 #include "G4Electron_aq.hh" 48 #include "G4Electron_aq.hh"
45 #include "G4GeometryManager.hh" <<
46 #include "G4H2O.hh" <<
47 #include "G4MolecularConfiguration.hh" 49 #include "G4MolecularConfiguration.hh"
48 #include "G4Molecule.hh" << 50 #include "G4VMoleculeCounter.hh"
49 #include "G4MoleculeFinder.hh" << 51 #include "G4VUserChemistryList.hh"
50 #include "G4MoleculeTable.hh" << 52 #include "G4AutoLock.hh"
51 #include "G4PhysChemIO.hh" <<
52 #include "G4Scheduler.hh" <<
53 #include "G4StateManager.hh" <<
54 #include "G4SystemOfUnits.hh" <<
55 #include "G4UIcmdWithABool.hh" 53 #include "G4UIcmdWithABool.hh"
56 #include "G4UIcmdWithADoubleAndUnit.hh" 54 #include "G4UIcmdWithADoubleAndUnit.hh"
57 #include "G4UIcmdWithAnInteger.hh" <<
58 #include "G4UIcmdWithoutParameter.hh" 55 #include "G4UIcmdWithoutParameter.hh"
59 #include "G4VITTrackHolder.hh" << 56 #include "G4UIcmdWithAnInteger.hh"
60 #include "G4VMoleculeCounter.hh" << 57 #include "G4GeometryManager.hh"
61 #include "G4VUserChemistryList.hh" << 58 #include "G4StateManager.hh"
62 #include "G4VUserPulseInfo.hh" << 59 #include "G4MoleculeFinder.hh"
>> 60 #include "G4MoleculeTable.hh"
>> 61 #include "G4PhysChemIO.hh"
63 62
64 #include <memory> <<
65 63
66 G4DNAChemistryManager* G4DNAChemistryManager:: 64 G4DNAChemistryManager* G4DNAChemistryManager::fgInstance = nullptr;
67 65
68 G4ThreadLocal G4DNAChemistryManager::ThreadLoc 66 G4ThreadLocal G4DNAChemistryManager::ThreadLocalData*
69 G4DNAChemistryManager::fpThreadData = null 67 G4DNAChemistryManager::fpThreadData = nullptr;
70 68
71 G4Mutex chemManExistence; 69 G4Mutex chemManExistence;
72 70
73 //-------------------------------------------- 71 //------------------------------------------------------------------------------
74 72
75 G4DNAChemistryManager::ThreadLocalData::Thread 73 G4DNAChemistryManager::ThreadLocalData::ThreadLocalData()
76 { 74 {
77 fpPhysChemIO = nullptr; 75 fpPhysChemIO = nullptr;
78 fThreadInitialized = false; 76 fThreadInitialized = false;
79 } 77 }
80 78
81 //-------------------------------------------- 79 //------------------------------------------------------------------------------
82 80
83 G4DNAChemistryManager::ThreadLocalData::~Threa 81 G4DNAChemistryManager::ThreadLocalData::~ThreadLocalData()
84 { 82 {
85 fpThreadData = nullptr; 83 fpThreadData = nullptr;
86 } 84 }
87 85
88 //-------------------------------------------- 86 //------------------------------------------------------------------------------
89 87
90 void G4DNAChemistryManager::SetPhysChemIO(std: 88 void G4DNAChemistryManager::SetPhysChemIO(std::unique_ptr<G4VPhysChemIO> pPhysChemIO)
91 { 89 {
92 fpThreadData->fpPhysChemIO = std::move(pPh 90 fpThreadData->fpPhysChemIO = std::move(pPhysChemIO);
93 } 91 }
94 92
95 //-------------------------------------------- 93 //------------------------------------------------------------------------------
96 94
97 //-------------------------------------------- 95 //------------------------------------------------------------------------------
98 /* 96 /*
99 * The chemistry manager is shared between thr 97 * The chemistry manager is shared between threads
100 * It is initialized both on the master thread 98 * It is initialized both on the master thread and on the worker threads
101 */ 99 */
102 //-------------------------------------------- 100 //------------------------------------------------------------------------------
103 G4DNAChemistryManager::G4DNAChemistryManager() 101 G4DNAChemistryManager::G4DNAChemistryManager()
104 : << 102 : G4UImessenger()
105 fpChemDNADirectory(new G4UIdirectory( << 103 , G4VStateDependent()
>> 104 , fpChemDNADirectory(new G4UIdirectory("/chem/"))
106 , fpActivateChem(new G4UIcmdWithABool( 105 , fpActivateChem(new G4UIcmdWithABool("/chem/activate", this))
107 , fpRunChem(new G4UIcmdWithAnInteger(" 106 , fpRunChem(new G4UIcmdWithAnInteger("/chem/run", this))
108 , fpSkipReactionsFromChemList(new G4UI 107 , fpSkipReactionsFromChemList(new G4UIcmdWithoutParameter("/chem/skipReactionsFromChemList", this))
109 , fpScaleForNewTemperature(new G4UIcmd 108 , fpScaleForNewTemperature(new G4UIcmdWithADoubleAndUnit("/chem/temperature", this))
110 , fpInitChem(new G4UIcmdWithoutParamet 109 , fpInitChem(new G4UIcmdWithoutParameter("/chem/init", this))
111 , << 110 , fActiveChemistry(false)
112 fpExcitationLevel(nullptr) << 111 , fMasterInitialized(false)
>> 112 , fForceThreadReinitialization(false)
>> 113 , fpExcitationLevel(nullptr)
113 , fpIonisationLevel(nullptr) 114 , fpIonisationLevel(nullptr)
114 , fpUserChemistryList(nullptr) 115 , fpUserChemistryList(nullptr)
>> 116 , fOwnChemistryList(false)
>> 117 , fUseInStandalone(false)
>> 118 , fPhysicsTableBuilt(false)
>> 119 , fSkipReactions(false)
>> 120 , fGeometryClosed(false)
>> 121 , fVerbose(0)
>> 122 , fResetCounterWhenRunEnds(true)
115 { 123 {
116 fpRunChem->SetParameterName("Number of run 124 fpRunChem->SetParameterName("Number of runs to execute for the chemistry module"
117 "(this works w 125 "(this works when used in standalone", true, true);
118 fpRunChem->SetDefaultValue(1); 126 fpRunChem->SetDefaultValue(1);
119 fpScaleForNewTemperature->SetUnitCategory( 127 fpScaleForNewTemperature->SetUnitCategory("Temperature");
120 } 128 }
121 129
122 //-------------------------------------------- 130 //------------------------------------------------------------------------------
123 131
124 G4DNAChemistryManager* G4DNAChemistryManager:: 132 G4DNAChemistryManager* G4DNAChemistryManager::Instance()
125 { 133 {
126 if (fgInstance == nullptr) 134 if (fgInstance == nullptr)
127 { 135 {
128 G4AutoLock lock(&chemManExistence); 136 G4AutoLock lock(&chemManExistence);
129 if (fgInstance == nullptr) // MT : dou 137 if (fgInstance == nullptr) // MT : double check at initialisation
130 { 138 {
131 fgInstance = new G4DNAChemistryMan 139 fgInstance = new G4DNAChemistryManager();
132 } 140 }
133 lock.unlock(); 141 lock.unlock();
134 } 142 }
135 143
136 // make sure thread local data is initiali 144 // make sure thread local data is initialized for all threads
137 if (fpThreadData == nullptr) 145 if (fpThreadData == nullptr)
138 { 146 {
139 fpThreadData = new ThreadLocalData(); 147 fpThreadData = new ThreadLocalData();
140 } 148 }
141 149
142 assert(fpThreadData != nullptr); 150 assert(fpThreadData != nullptr);
143 151
144 return fgInstance; 152 return fgInstance;
145 } 153 }
146 154
147 //-------------------------------------------- 155 //------------------------------------------------------------------------------
148 156
149 G4DNAChemistryManager* G4DNAChemistryManager:: 157 G4DNAChemistryManager* G4DNAChemistryManager::GetInstanceIfExists()
150 { 158 {
151 return fgInstance; 159 return fgInstance;
152 } 160 }
153 161
154 //-------------------------------------------- 162 //------------------------------------------------------------------------------
155 163
156 G4DNAChemistryManager::~G4DNAChemistryManager( 164 G4DNAChemistryManager::~G4DNAChemistryManager()
157 { 165 {
158 Clear(); 166 Clear();
159 fgInstance = nullptr; 167 fgInstance = nullptr;
160 } 168 }
161 169
162 //-------------------------------------------- 170 //------------------------------------------------------------------------------
163 171
164 void G4DNAChemistryManager::Clear() 172 void G4DNAChemistryManager::Clear()
165 { 173 {
166 fpIonisationLevel.reset(); 174 fpIonisationLevel.reset();
167 fpExcitationLevel.reset(); 175 fpExcitationLevel.reset();
168 176
169 if (fpUserChemistryList) 177 if (fpUserChemistryList)
170 { 178 {
171 Deregister(*fpUserChemistryList); 179 Deregister(*fpUserChemistryList);
172 } 180 }
173 181
174 fpChemDNADirectory.reset(); 182 fpChemDNADirectory.reset();
175 fpActivateChem.reset(); 183 fpActivateChem.reset();
176 fpRunChem.reset(); 184 fpRunChem.reset();
177 185
178 fpSkipReactionsFromChemList.reset(); 186 fpSkipReactionsFromChemList.reset();
179 fpInitChem.reset(); 187 fpInitChem.reset();
180 188
181 if (fpThreadData != nullptr) 189 if (fpThreadData != nullptr)
182 { 190 {
183 delete fpThreadData; 191 delete fpThreadData;
184 fpThreadData = nullptr; 192 fpThreadData = nullptr;
185 } 193 }
186 194
187 G4DNAMolecularReactionTable::DeleteInstanc 195 G4DNAMolecularReactionTable::DeleteInstance();
188 G4MolecularConfiguration::DeleteManager(); 196 G4MolecularConfiguration::DeleteManager();
189 G4VMoleculeCounter::DeleteInstance(); 197 G4VMoleculeCounter::DeleteInstance();
190 } 198 }
191 199
192 //-------------------------------------------- 200 //------------------------------------------------------------------------------
193 201
194 void G4DNAChemistryManager::DeleteInstance() 202 void G4DNAChemistryManager::DeleteInstance()
195 { 203 {
196 G4AutoLock lock(&chemManExistence); 204 G4AutoLock lock(&chemManExistence);
197 205
198 if (fgInstance != nullptr) 206 if (fgInstance != nullptr)
199 { 207 {
200 G4DNAChemistryManager* pDeleteMe = fgI 208 G4DNAChemistryManager* pDeleteMe = fgInstance;
201 fgInstance = nullptr; 209 fgInstance = nullptr;
202 lock.unlock(); 210 lock.unlock();
203 delete pDeleteMe; 211 delete pDeleteMe;
204 } 212 }
205 else 213 else
206 { 214 {
207 G4cerr << "G4DNAChemistryManager alrea 215 G4cerr << "G4DNAChemistryManager already deleted" << G4endl;
208 } 216 }
209 lock.unlock(); 217 lock.unlock();
210 } 218 }
211 219
212 //-------------------------------------------- 220 //------------------------------------------------------------------------------
213 221
214 G4bool G4DNAChemistryManager::Notify(G4Applica 222 G4bool G4DNAChemistryManager::Notify(G4ApplicationState requestedState)
215 { 223 {
216 if (requestedState == G4State_Quit) 224 if (requestedState == G4State_Quit)
217 { 225 {
218 if (fVerbose != 0) << 226 if (fVerbose)
219 { 227 {
220 G4cout << "G4DNAChemistryManager:: 228 G4cout << "G4DNAChemistryManager::Notify ---> received G4State_Quit"
221 << G4endl; 229 << G4endl;
222 } 230 }
223 Clear(); 231 Clear();
224 } 232 }
225 else if (requestedState == G4State_GeomClo 233 else if (requestedState == G4State_GeomClosed)
226 { 234 {
227 fGeometryClosed = true; 235 fGeometryClosed = true;
228 } 236 }
229 else if (requestedState == G4State_Idle) 237 else if (requestedState == G4State_Idle)
230 { 238 {
231 InitializeThreadSharedData(); 239 InitializeThreadSharedData();
232 } 240 }
233 241
234 return true; 242 return true;
235 } 243 }
236 244
237 //-------------------------------------------- 245 //------------------------------------------------------------------------------
238 246
239 void G4DNAChemistryManager::SetNewValue(G4UIco 247 void G4DNAChemistryManager::SetNewValue(G4UIcommand* pCommand, G4String value)
240 { 248 {
241 if (pCommand == fpActivateChem.get()) 249 if (pCommand == fpActivateChem.get())
242 { 250 {
243 SetChemistryActivation(G4UIcmdWithABoo 251 SetChemistryActivation(G4UIcmdWithABool::GetNewBoolValue(value));
244 } 252 }
245 else if (pCommand == fpRunChem.get()) 253 else if (pCommand == fpRunChem.get())
246 { 254 {
247 int nbExec = value.empty() ? 1 : G4UIc 255 int nbExec = value.empty() ? 1 : G4UIcommand::ConvertToInt(value);
248 for (int i = 0 ; i < nbExec ; ++i) 256 for (int i = 0 ; i < nbExec ; ++i)
249 { 257 {
250 Run(); 258 Run();
251 } 259 }
252 } 260 }
253 else if (pCommand == fpSkipReactionsFromCh 261 else if (pCommand == fpSkipReactionsFromChemList.get())
254 { 262 {
255 fSkipReactions = true; 263 fSkipReactions = true;
256 } 264 }
257 else if (pCommand == fpScaleForNewTemperat 265 else if (pCommand == fpScaleForNewTemperature.get())
258 { 266 {
259 SetGlobalTemperature(fpScaleForNewTemp 267 SetGlobalTemperature(fpScaleForNewTemperature->ConvertToDimensionedDouble(value));
260 } 268 }
261 else if (pCommand == fpInitChem.get()) 269 else if (pCommand == fpInitChem.get())
262 { 270 {
263 Initialize(); 271 Initialize();
264 InitializeThread(); 272 InitializeThread();
265 } 273 }
266 } 274 }
267 275
268 //-------------------------------------------- 276 //------------------------------------------------------------------------------
269 277
270 G4String G4DNAChemistryManager::GetCurrentValu 278 G4String G4DNAChemistryManager::GetCurrentValue(G4UIcommand* pCommand)
271 { 279 {
272 if (pCommand == fpActivateChem.get()) 280 if (pCommand == fpActivateChem.get())
273 { 281 {
274 return G4UIcmdWithABool::ConvertToStri 282 return G4UIcmdWithABool::ConvertToString(fActiveChemistry);
275 } 283 }
276 if (pCommand == fpScaleForNewTemperature.g << 284 else if (pCommand == fpScaleForNewTemperature.get())
277 { 285 {
278 return fpScaleForNewTemperature->Conve 286 return fpScaleForNewTemperature->ConvertToStringWithBestUnit(G4MolecularConfiguration::GetGlobalTemperature());
279 } 287 }
280 if (pCommand == fpSkipReactionsFromChemLis << 288 else if (pCommand == fpSkipReactionsFromChemList.get())
281 { 289 {
282 return G4UIcmdWithABool::ConvertToStri 290 return G4UIcmdWithABool::ConvertToString(fSkipReactions);
283 } 291 }
284 292
285 return ""; 293 return "";
286 } 294 }
287 295
288 //-------------------------------------------- 296 //------------------------------------------------------------------------------
289 297
290 void G4DNAChemistryManager::InitializeThreadSh 298 void G4DNAChemistryManager::InitializeThreadSharedData()
291 { 299 {
292 if (!G4Threading::IsMasterThread()) 300 if (!G4Threading::IsMasterThread())
293 { 301 {
294 return; 302 return;
295 } 303 }
296 304
297 G4MoleculeTable::Instance()->PrepareMolecu 305 G4MoleculeTable::Instance()->PrepareMolecularConfiguration();
298 G4MoleculeTable::Instance()->Finalize(); 306 G4MoleculeTable::Instance()->Finalize();
299 } 307 }
300 308
301 //-------------------------------------------- 309 //------------------------------------------------------------------------------
302 void G4DNAChemistryManager::Run() 310 void G4DNAChemistryManager::Run()
303 { 311 {
304 if (!fActiveChemistry) 312 if (!fActiveChemistry)
305 { 313 {
306 return; 314 return;
307 } 315 }
308 316
309 InitializeThread(); 317 InitializeThread();
310 318
311 if (!fMasterInitialized) 319 if (!fMasterInitialized)
312 { 320 {
313 G4ExceptionDescription description; 321 G4ExceptionDescription description;
314 description << "Global components were 322 description << "Global components were not initialized.";
315 G4Exception("G4DNAChemistryManager::Ru 323 G4Exception("G4DNAChemistryManager::Run", "MASTER_INIT", FatalException,
316 description); 324 description);
317 } 325 }
318 326
319 if (!fpThreadData->fThreadInitialized) 327 if (!fpThreadData->fThreadInitialized)
320 { 328 {
321 G4ExceptionDescription description; 329 G4ExceptionDescription description;
322 description << "Thread local component 330 description << "Thread local components were not initialized.";
323 G4Exception("G4DNAChemistryManager::Ru 331 G4Exception("G4DNAChemistryManager::Run", "THREAD_INIT", FatalException,
324 description); 332 description);
325 } 333 }
326 334
327 G4MoleculeTable::Instance()->Finalize(); 335 G4MoleculeTable::Instance()->Finalize();
328 G4Scheduler::Instance()->Process(); 336 G4Scheduler::Instance()->Process();
329 if (fResetCounterWhenRunEnds) 337 if (fResetCounterWhenRunEnds)
330 { 338 {
331 G4VMoleculeCounter::Instance()->ResetC 339 G4VMoleculeCounter::Instance()->ResetCounter();
332 } 340 }
333 CloseFile(); 341 CloseFile();
334 } 342 }
335 343
336 //-------------------------------------------- 344 //------------------------------------------------------------------------------
337 345
338 void G4DNAChemistryManager::UseAsStandalone(G4 346 void G4DNAChemistryManager::UseAsStandalone(G4bool flag)
339 { 347 {
340 fUseInStandalone = flag; 348 fUseInStandalone = flag;
341 } 349 }
342 350
343 //-------------------------------------------- 351 //------------------------------------------------------------------------------
344 352
345 void G4DNAChemistryManager::SetGun(G4ITGun* pC 353 void G4DNAChemistryManager::SetGun(G4ITGun* pChemGun)
346 { 354 {
347 G4Scheduler::Instance()->SetGun(pChemGun); 355 G4Scheduler::Instance()->SetGun(pChemGun);
348 } 356 }
349 357
350 //-------------------------------------------- 358 //------------------------------------------------------------------------------
351 359
352 void G4DNAChemistryManager::Initialize() 360 void G4DNAChemistryManager::Initialize()
353 { 361 {
354 //======================================== 362 //===========================================================================
355 // MT MODE 363 // MT MODE
356 //======================================== 364 //===========================================================================
357 if (G4Threading::IsMultithreadedApplicatio 365 if (G4Threading::IsMultithreadedApplication())
358 { 366 {
359 //==================================== 367 //==========================================================================
360 // ON WORKER THREAD 368 // ON WORKER THREAD
361 //==================================== 369 //==========================================================================
362 if (G4Threading::IsWorkerThread()) 370 if (G4Threading::IsWorkerThread())
363 { 371 {
364 InitializeThread(); // Will create 372 InitializeThread(); // Will create and initialize G4Scheduler
365 return; 373 return;
366 } 374 }
367 //==================================== 375 //==========================================================================
368 // ON MASTER THREAD 376 // ON MASTER THREAD
369 //==================================== 377 //==========================================================================
370 << 378 else
371 InitializeMaster(); << 379 {
372 InitializeThreadSharedData(); << 380 InitializeMaster();
373 return; << 381 InitializeThreadSharedData();
>> 382 return;
>> 383 }
374 } 384 }
375 //======================================== 385 //===========================================================================
376 // IS NOT IN MT MODE 386 // IS NOT IN MT MODE
377 //======================================== 387 //===========================================================================
378 << 388 else
379 InitializeMaster(); << 389 {
380 InitializeThreadSharedData(); << 390 InitializeMaster();
381 // In this case: InitializeThread is calle << 391 InitializeThreadSharedData();
382 return; << 392 // In this case: InitializeThread is called when Run() is called
>> 393 return;
>> 394 }
383 } 395 }
384 396
385 //-------------------------------------------- 397 //------------------------------------------------------------------------------
386 398
387 void G4DNAChemistryManager::InitializeMaster() 399 void G4DNAChemistryManager::InitializeMaster()
388 { 400 {
389 if (fMasterInitialized) 401 if (fMasterInitialized)
390 { 402 {
391 return; 403 return;
392 } 404 }
393 405
394 if (fVerbose != 0) << 406 if (fVerbose)
395 { 407 {
396 G4cout << "G4DNAChemistryManager::Init 408 G4cout << "G4DNAChemistryManager::InitializeMaster() is called" << G4endl;
397 } 409 }
398 410
399 411
400 if (fpUserChemistryList == nullptr) 412 if (fpUserChemistryList == nullptr)
401 { 413 {
402 G4ExceptionDescription description; 414 G4ExceptionDescription description;
403 description << "No user chemistry list 415 description << "No user chemistry list has been provided.";
404 G4Exception("G4DNAChemistryManager::In 416 G4Exception("G4DNAChemistryManager::InitializeMaster", "NO_CHEM_LIST",
405 FatalException, descriptio 417 FatalException, description);
406 }else 418 }else
407 { 419 {
408 fpUserChemistryList->ConstructDissociati 420 fpUserChemistryList->ConstructDissociationChannels();
409 if (!fSkipReactions) 421 if (!fSkipReactions)
410 { 422 {
411 fpUserChemistryList->ConstructReacti 423 fpUserChemistryList->ConstructReactionTable(G4DNAMolecularReactionTable::GetReactionTable());
412 } 424 }
413 else 425 else
414 { 426 {
415 G4DNAMolecularReactionTable::GetReac 427 G4DNAMolecularReactionTable::GetReactionTable(); // init pointer
416 } 428 }
417 } 429 }
418 430
419 G4Scheduler::Instance(); 431 G4Scheduler::Instance();
420 // creates a concrete object of the schedu 432 // creates a concrete object of the scheduler
421 fMasterInitialized = true; 433 fMasterInitialized = true;
422 } 434 }
423 435
424 //-------------------------------------------- 436 //------------------------------------------------------------------------------
425 437
426 void G4DNAChemistryManager::HandleStandaloneIn 438 void G4DNAChemistryManager::HandleStandaloneInitialization()
427 { 439 {
428 if (!fUseInStandalone || fPhysicsTableBuil 440 if (!fUseInStandalone || fPhysicsTableBuilt)
429 { 441 {
430 return; 442 return;
431 } 443 }
432 444
433 if (fVerbose != 0) << 445 if (fVerbose)
434 { 446 {
435 G4cout << "G4DNAChemistryManager: Buil 447 G4cout << "G4DNAChemistryManager: Build the physics tables for "
436 "molecule definition only." 448 "molecule definition only."
437 << G4endl; 449 << G4endl;
438 } 450 }
439 451
440 fpUserChemistryList->BuildPhysicsTable(); 452 fpUserChemistryList->BuildPhysicsTable();
441 453
442 if (!fGeometryClosed) 454 if (!fGeometryClosed)
443 { 455 {
444 if (fVerbose != 0) << 456 if (fVerbose)
445 { 457 {
446 G4cout << "G4DNAChemistryManager: 458 G4cout << "G4DNAChemistryManager: Close geometry" << G4endl;
447 } 459 }
448 460
449 G4GeometryManager* pGeomManager = G4Ge 461 G4GeometryManager* pGeomManager = G4GeometryManager::GetInstance();
450 pGeomManager->OpenGeometry(); 462 pGeomManager->OpenGeometry();
451 pGeomManager->CloseGeometry(true, true 463 pGeomManager->CloseGeometry(true, true);
452 fGeometryClosed = true; 464 fGeometryClosed = true;
453 } 465 }
454 466
455 fPhysicsTableBuilt = true; 467 fPhysicsTableBuilt = true;
456 } 468 }
457 469
458 //-------------------------------------------- 470 //------------------------------------------------------------------------------
459 471
460 void G4DNAChemistryManager::InitializeThread() 472 void G4DNAChemistryManager::InitializeThread()
461 { 473 {
462 if (fpThreadData->fThreadInitialized && !f 474 if (fpThreadData->fThreadInitialized && !fForceThreadReinitialization)
463 { 475 {
464 return; 476 return;
465 } 477 }
466 478
467 if (fpUserChemistryList == nullptr) 479 if (fpUserChemistryList == nullptr)
468 { 480 {
469 G4ExceptionDescription description; 481 G4ExceptionDescription description;
470 description << "No user chemistry list 482 description << "No user chemistry list has been provided.";
471 G4Exception("G4DNAChemistryManager::In 483 G4Exception("G4DNAChemistryManager::InitializeThread", "NO_CHEM_LIST",
472 FatalException, descriptio 484 FatalException, description);
473 }else 485 }else
474 { 486 {
475 HandleStandaloneInitialization();// To 487 HandleStandaloneInitialization();// To make coverty happy
476 fpUserChemistryList->ConstructTimeStep 488 fpUserChemistryList->ConstructTimeStepModel(G4DNAMolecularReactionTable::GetReactionTable());
477 } 489 }
478 490
479 if (fVerbose != 0) << 491 if (fVerbose)
480 { 492 {
481 G4cout << "G4DNAChemistryManager::Init 493 G4cout << "G4DNAChemistryManager::InitializeThread() is called"
482 << G4endl; 494 << G4endl;
483 } 495 }
484 496
485 G4Scheduler::Instance()->Initialize(); 497 G4Scheduler::Instance()->Initialize();
486 498
487 fpThreadData->fThreadInitialized = true; 499 fpThreadData->fThreadInitialized = true;
488 500
489 G4VMoleculeCounter::InitializeInstance(); 501 G4VMoleculeCounter::InitializeInstance();
490 502
491 InitializeFile(); 503 InitializeFile();
492 } 504 }
493 505
494 //-------------------------------------------- 506 //------------------------------------------------------------------------------
495 507
496 void G4DNAChemistryManager::InitializeFile() 508 void G4DNAChemistryManager::InitializeFile()
497 { 509 {
498 if (fVerbose != 0) << 510 if (fVerbose)
499 { 511 {
500 G4cout << "G4DNAChemistryManager::Init 512 G4cout << "G4DNAChemistryManager::InitializeFile() is called"
501 << G4endl; 513 << G4endl;
502 } 514 }
503 515
504 if (fpThreadData->fpPhysChemIO) 516 if (fpThreadData->fpPhysChemIO)
505 { 517 {
506 fpThreadData->fpPhysChemIO->Initialize 518 fpThreadData->fpPhysChemIO->InitializeFile();
507 } 519 }
508 } 520 }
509 521
510 //-------------------------------------------- 522 //------------------------------------------------------------------------------
511 523
512 G4bool G4DNAChemistryManager::IsActivated() 524 G4bool G4DNAChemistryManager::IsActivated()
513 { 525 {
514 return fgInstance != nullptr ? fgInstance- << 526 return fgInstance ? fgInstance->IsChemistryActivated() : false;
515 } 527 }
516 528
517 //-------------------------------------------- 529 //------------------------------------------------------------------------------
518 530
519 G4bool G4DNAChemistryManager::IsChemistryActiv 531 G4bool G4DNAChemistryManager::IsChemistryActivated()
520 { 532 {
521 return fActiveChemistry; 533 return fActiveChemistry;
522 } 534 }
523 535
524 //-------------------------------------------- 536 //------------------------------------------------------------------------------
525 537
526 void G4DNAChemistryManager::SetChemistryActiva 538 void G4DNAChemistryManager::SetChemistryActivation(G4bool flag)
527 { 539 {
528 fActiveChemistry = flag; 540 fActiveChemistry = flag;
529 } 541 }
530 542
531 //-------------------------------------------- 543 //------------------------------------------------------------------------------
532 544
533 void G4DNAChemistryManager::WriteInto(const G4 545 void G4DNAChemistryManager::WriteInto(const G4String& output,
534 std::ios 546 std::ios_base::openmode mode)
535 { 547 {
536 if (fVerbose != 0) << 548 if (fVerbose)
537 { 549 {
538 G4cout << "G4DNAChemistryManager: Writ 550 G4cout << "G4DNAChemistryManager: Write chemical stage into "
539 << output.data() << G4endl; 551 << output.data() << G4endl;
540 } 552 }
541 553
542 if (!fpThreadData->fpPhysChemIO) 554 if (!fpThreadData->fpPhysChemIO)
543 { 555 {
544 fpThreadData->fpPhysChemIO = std::make << 556 fpThreadData->fpPhysChemIO.reset(new G4PhysChemIO::FormattedText());
545 } 557 }
546 558
547 fpThreadData->fpPhysChemIO->WriteInto(outp 559 fpThreadData->fpPhysChemIO->WriteInto(output, mode);
548 560
549 } 561 }
550 562
551 //-------------------------------------------- 563 //------------------------------------------------------------------------------
552 564
553 void G4DNAChemistryManager::AddEmptyLineInOutp 565 void G4DNAChemistryManager::AddEmptyLineInOutputFile()
554 { 566 {
555 if (fpThreadData->fpPhysChemIO) 567 if (fpThreadData->fpPhysChemIO)
556 { 568 {
557 fpThreadData->fpPhysChemIO->AddEmptyLi 569 fpThreadData->fpPhysChemIO->AddEmptyLineInOutputFile();
558 } 570 }
559 } 571 }
560 572
561 //-------------------------------------------- 573 //------------------------------------------------------------------------------
562 574
563 void G4DNAChemistryManager::CloseFile() 575 void G4DNAChemistryManager::CloseFile()
564 { 576 {
565 if (fpThreadData->fpPhysChemIO) 577 if (fpThreadData->fpPhysChemIO)
566 { 578 {
567 fpThreadData->fpPhysChemIO->CloseFile( 579 fpThreadData->fpPhysChemIO->CloseFile();
568 } 580 }
569 } 581 }
570 582
571 //-------------------------------------------- 583 //------------------------------------------------------------------------------
572 584
573 G4DNAWaterExcitationStructure* G4DNAChemistryM 585 G4DNAWaterExcitationStructure* G4DNAChemistryManager::GetExcitationLevel()
574 { 586 {
575 if (!fpExcitationLevel) 587 if (!fpExcitationLevel)
576 { 588 {
577 fpExcitationLevel = std::make_unique<G << 589 fpExcitationLevel.reset(new G4DNAWaterExcitationStructure);
578 } 590 }
579 return fpExcitationLevel.get(); 591 return fpExcitationLevel.get();
580 } 592 }
581 593
582 //-------------------------------------------- 594 //------------------------------------------------------------------------------
583 595
584 G4DNAWaterIonisationStructure* G4DNAChemistryM 596 G4DNAWaterIonisationStructure* G4DNAChemistryManager::GetIonisationLevel()
585 { 597 {
586 if (!fpIonisationLevel) 598 if (!fpIonisationLevel)
587 { 599 {
588 fpIonisationLevel = std::make_unique<G << 600 fpIonisationLevel.reset(new G4DNAWaterIonisationStructure);
589 } 601 }
590 return fpIonisationLevel.get(); 602 return fpIonisationLevel.get();
591 } 603 }
592 604
593 //-------------------------------------------- 605 //------------------------------------------------------------------------------
594 606
595 void G4DNAChemistryManager::CreateWaterMolecul 607 void G4DNAChemistryManager::CreateWaterMolecule(ElectronicModification modification,
596 608 G4int electronicLevel,
597 609 const G4Track* pIncomingTrack)
598 { 610 {
599 if (fpThreadData->fpPhysChemIO) 611 if (fpThreadData->fpPhysChemIO)
600 { 612 {
601 G4double energy = -1.; 613 G4double energy = -1.;
602 614
603 switch (modification) 615 switch (modification)
604 { 616 {
605 case eDissociativeAttachment: 617 case eDissociativeAttachment:
606 energy = 0.; 618 energy = 0.;
607 break; 619 break;
608 case eExcitedMolecule: 620 case eExcitedMolecule:
609 energy = GetExcitationLevel()->Exc 621 energy = GetExcitationLevel()->ExcitationEnergy(electronicLevel);
610 break; 622 break;
611 case eIonizedMolecule: 623 case eIonizedMolecule:
612 energy = GetIonisationLevel()->Ion 624 energy = GetIonisationLevel()->IonisationEnergy(electronicLevel);
613 break; 625 break;
614 } 626 }
615 627
616 fpThreadData->fpPhysChemIO->CreateWate 628 fpThreadData->fpPhysChemIO->CreateWaterMolecule(modification,
617 629 4 - electronicLevel,
618 630 energy,
619 631 pIncomingTrack);
620 } 632 }
621 633
622 if (fActiveChemistry) 634 if (fActiveChemistry)
623 { 635 {
624 auto pH2OMolecule = new G4Molecule(G4 << 636 G4Molecule* pH2OMolecule = new G4Molecule(G4H2O::Definition());
625 637
626 switch (modification) 638 switch (modification)
627 { 639 {
628 case eDissociativeAttachment: 640 case eDissociativeAttachment:
629 pH2OMolecule->AddElectron(5, 1); 641 pH2OMolecule->AddElectron(5, 1);
630 break; 642 break;
631 case eExcitedMolecule: 643 case eExcitedMolecule:
632 pH2OMolecule->ExciteMolecule(4 - e 644 pH2OMolecule->ExciteMolecule(4 - electronicLevel);
633 break; 645 break;
634 case eIonizedMolecule: 646 case eIonizedMolecule:
635 pH2OMolecule->IonizeMolecule(4 - e 647 pH2OMolecule->IonizeMolecule(4 - electronicLevel);
636 break; 648 break;
637 } 649 }
638 650
639 G4double delayedTime = 0.; << 651 G4Track* pH2OTrack = pH2OMolecule->BuildTrack(picosecond,
640 if(pIncomingTrack->GetUserInformation( <<
641 { <<
642 auto pPulseInfo = dynamic_cast<G4V <<
643 (pIncomingTrack->GetUserInformat <<
644 if(pPulseInfo != nullptr) <<
645 { <<
646 delayedTime = pPulseInfo->GetD <<
647 } <<
648 } <<
649 <<
650 G4Track* pH2OTrack = pH2OMolecule->Bui <<
651 652 pIncomingTrack->GetPosition());
652 653
653 pH2OTrack->SetParentID(pIncomingTrack- 654 pH2OTrack->SetParentID(pIncomingTrack->GetTrackID());
654 pH2OTrack->SetTrackStatus(fStopButAliv 655 pH2OTrack->SetTrackStatus(fStopButAlive);
655 pH2OTrack->SetKineticEnergy(0.); 656 pH2OTrack->SetKineticEnergy(0.);
656 PushTrack(pH2OTrack); 657 PushTrack(pH2OTrack);
657 } 658 }
658 } 659 }
659 660
660 //-------------------------------------------- 661 //------------------------------------------------------------------------------
661 // pFinalPosition is optional 662 // pFinalPosition is optional
662 void G4DNAChemistryManager::CreateSolvatedElec 663 void G4DNAChemistryManager::CreateSolvatedElectron(const G4Track* pIncomingTrack,
663 664 G4ThreeVector* pFinalPosition)
664 { 665 {
665 if (fpThreadData->fpPhysChemIO) 666 if (fpThreadData->fpPhysChemIO)
666 { 667 {
667 fpThreadData->fpPhysChemIO->CreateSolv 668 fpThreadData->fpPhysChemIO->CreateSolvatedElectron(pIncomingTrack,
668 669 pFinalPosition);
669 } 670 }
670 671
671 if (fActiveChemistry) 672 if (fActiveChemistry)
672 { 673 {
673 G4double delayedTime = 0.; << 674 PushMolecule(std::unique_ptr<G4Molecule>(new G4Molecule(G4Electron_aq::Definition())),
674 if(pIncomingTrack->GetUserInformation( << 675 picosecond,
675 { << 676 pFinalPosition ? *pFinalPosition : pIncomingTrack->GetPosition(),
676 auto pPulseInfo = dynamic_cast<G4V <<
677 (pIncomingTrack->GetUserInformat <<
678 if(pPulseInfo != nullptr) <<
679 { <<
680 delayedTime = pPulseInfo->GetD <<
681 } <<
682 } <<
683 <<
684 PushMolecule(std::make_unique<G4Molecu <<
685 picosecond + delayedTime, <<
686 pFinalPosition != nullptr <<
687 pIncomingTrack->GetTrackI 677 pIncomingTrack->GetTrackID());
688 } 678 }
689 } 679 }
690 680
691 //-------------------------------------------- 681 //------------------------------------------------------------------------------
692 682
693 void G4DNAChemistryManager::PushMolecule(std:: 683 void G4DNAChemistryManager::PushMolecule(std::unique_ptr<G4Molecule> pMolecule,
694 doubl 684 double time,
695 const 685 const G4ThreeVector& position,
696 int p 686 int parentID)
697 { 687 {
698 assert(fActiveChemistry 688 assert(fActiveChemistry
699 && "To inject chemical species, the 689 && "To inject chemical species, the chemistry must be activated. "
700 "Check chemistry activation befo 690 "Check chemistry activation before injecting species.");
701 G4Track* pTrack = pMolecule->BuildTrack(ti 691 G4Track* pTrack = pMolecule->BuildTrack(time, position);
702 pTrack->SetTrackStatus(fAlive); 692 pTrack->SetTrackStatus(fAlive);
703 pTrack->SetParentID(parentID); 693 pTrack->SetParentID(parentID);
704 pMolecule.release(); 694 pMolecule.release();
705 PushTrack(pTrack); 695 PushTrack(pTrack);
706 } 696 }
707 697
708 //-------------------------------------------- 698 //------------------------------------------------------------------------------
709 699
710 void G4DNAChemistryManager::SetGlobalTemperatu 700 void G4DNAChemistryManager::SetGlobalTemperature(G4double temp_K)
711 { 701 {
712 G4MolecularConfiguration::SetGlobalTempera 702 G4MolecularConfiguration::SetGlobalTemperature(temp_K);
713 G4DNAMolecularReactionTable::Instance()->S 703 G4DNAMolecularReactionTable::Instance()->ScaleReactionRateForNewTemperature(temp_K);
714 } 704 }
715 705
716 //-------------------------------------------- 706 //------------------------------------------------------------------------------
717 // [[deprecated]] : chemistry list should neve 707 // [[deprecated]] : chemistry list should never be nullptr
718 void G4DNAChemistryManager::SetChemistryList(G 708 void G4DNAChemistryManager::SetChemistryList(G4VUserChemistryList* pChemistryList)
719 { 709 {
720 fpUserChemistryList.reset(pChemistryList); 710 fpUserChemistryList.reset(pChemistryList);
721 fOwnChemistryList = false; 711 fOwnChemistryList = false;
722 SetChemistryActivation(true); 712 SetChemistryActivation(true);
723 } 713 }
724 714
725 void G4DNAChemistryManager::SetChemistryList(G 715 void G4DNAChemistryManager::SetChemistryList(G4VUserChemistryList& chemistryList)
726 { 716 {
727 fpUserChemistryList.reset(&chemistryList); 717 fpUserChemistryList.reset(&chemistryList);
728 fOwnChemistryList = false; 718 fOwnChemistryList = false;
729 SetChemistryActivation(true); 719 SetChemistryActivation(true);
730 } 720 }
731 721
732 void G4DNAChemistryManager::SetChemistryList(s 722 void G4DNAChemistryManager::SetChemistryList(std::unique_ptr<G4VUserChemistryList> pChemistryList)
733 { 723 {
734 fpUserChemistryList = std::move(pChemistry 724 fpUserChemistryList = std::move(pChemistryList);
735 fOwnChemistryList = true; 725 fOwnChemistryList = true;
736 SetChemistryActivation(true); 726 SetChemistryActivation(true);
737 } 727 }
738 728
739 //-------------------------------------------- 729 //------------------------------------------------------------------------------
740 730
741 void G4DNAChemistryManager::Deregister(G4VUser 731 void G4DNAChemistryManager::Deregister(G4VUserChemistryList& chemistryList)
742 { 732 {
743 if (fpUserChemistryList.get() == &chemistr 733 if (fpUserChemistryList.get() == &chemistryList)
744 { 734 {
745 if (!fpUserChemistryList->IsPhysicsCon 735 if (!fpUserChemistryList->IsPhysicsConstructor() || fOwnChemistryList)
746 { 736 {
747 fpUserChemistryList.reset(); 737 fpUserChemistryList.reset();
748 } 738 }
749 739
750 fpUserChemistryList.release(); 740 fpUserChemistryList.release();
751 } 741 }
752 } 742 }
753 743
754 //-------------------------------------------- 744 //------------------------------------------------------------------------------
755 745
756 void G4DNAChemistryManager::PushTrack(G4Track* 746 void G4DNAChemistryManager::PushTrack(G4Track* pTrack)
757 { 747 {
758 G4ITTrackHolder::Instance()->Push(pTrack); 748 G4ITTrackHolder::Instance()->Push(pTrack);
759 } 749 }
760 750
761 //-------------------------------------------- 751 //------------------------------------------------------------------------------
762 752
763 void G4DNAChemistryManager::SetVerbose(G4int v 753 void G4DNAChemistryManager::SetVerbose(G4int verbose)
764 { 754 {
765 fVerbose = verbose; 755 fVerbose = verbose;
766 } 756 }
767 757
768 //-------------------------------------------- 758 //------------------------------------------------------------------------------
769 759
770 G4bool G4DNAChemistryManager::IsCounterResetWh 760 G4bool G4DNAChemistryManager::IsCounterResetWhenRunEnds() const
771 { 761 {
772 return fResetCounterWhenRunEnds; 762 return fResetCounterWhenRunEnds;
773 } 763 }
774 764
775 //-------------------------------------------- 765 //------------------------------------------------------------------------------
776 766
777 void G4DNAChemistryManager::ResetCounterWhenRu 767 void G4DNAChemistryManager::ResetCounterWhenRunEnds(G4bool resetCounterWhenRunEnds)
778 { 768 {
779 fResetCounterWhenRunEnds = resetCounterWhe 769 fResetCounterWhenRunEnds = resetCounterWhenRunEnds;
780 } 770 }
781 771
782 //-------------------------------------------- 772 //------------------------------------------------------------------------------
783 773
784 void G4DNAChemistryManager::ForceRebuildingPhy 774 void G4DNAChemistryManager::ForceRebuildingPhysicsTable()
785 { 775 {
786 fPhysicsTableBuilt = false; 776 fPhysicsTableBuilt = false;
787 } 777 }
788 778
789 //-------------------------------------------- 779 //------------------------------------------------------------------------------
790 780
791 void G4DNAChemistryManager::ForceMasterReiniti 781 void G4DNAChemistryManager::ForceMasterReinitialization()
792 { 782 {
793 fMasterInitialized = false; 783 fMasterInitialized = false;
794 InitializeMaster(); 784 InitializeMaster();
795 } 785 }
796 786
797 //-------------------------------------------- 787 //------------------------------------------------------------------------------
798 788
799 void G4DNAChemistryManager::ForceThreadReiniti 789 void G4DNAChemistryManager::ForceThreadReinitialization()
800 { 790 {
801 fForceThreadReinitialization = true; 791 fForceThreadReinitialization = true;
802 } 792 }
803 793
804 //-------------------------------------------- 794 //------------------------------------------------------------------------------
805 795
806 void G4DNAChemistryManager::TagThreadForReinit 796 void G4DNAChemistryManager::TagThreadForReinitialization()
807 { 797 {
808 fpThreadData->fThreadInitialized = false; 798 fpThreadData->fThreadInitialized = false;
809 } 799 }
810 800