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25 // 25 //
26 // 26 //
27 // Author: Mathieu Karamitros (kara (AT) cenbg 27 // Author: Mathieu Karamitros (kara (AT) cenbg . in2p3 . fr)
28 // 28 //
29 // History: 29 // History:
30 // ----------- 30 // -----------
31 // 10 Oct 2011 M.Karamitros created 31 // 10 Oct 2011 M.Karamitros created
32 // 32 //
33 // ------------------------------------------- 33 // -------------------------------------------------------------------
34 34
35 #include "G4MolecularConfiguration.hh" 35 #include "G4MolecularConfiguration.hh"
36 #include "G4MoleculeDefinition.hh" 36 #include "G4MoleculeDefinition.hh"
37 #include "G4UIcommand.hh" 37 #include "G4UIcommand.hh"
38 #include "G4AllocatorList.hh" 38 #include "G4AllocatorList.hh"
39 #include "G4AutoLock.hh" 39 #include "G4AutoLock.hh"
40 #include "G4MoleculeTable.hh" 40 #include "G4MoleculeTable.hh"
41 #include "G4Serialize.hh" 41 #include "G4Serialize.hh"
42 #include <fstream> 42 #include <fstream>
43 43
44 using CLHEP::m2; 44 using CLHEP::m2;
45 using CLHEP::s; 45 using CLHEP::s;
46 using CLHEP::kelvin; 46 using CLHEP::kelvin;
47 47
48 using namespace std; 48 using namespace std;
49 49
50 #if defined ( WIN32 ) 50 #if defined ( WIN32 )
51 #define __func__ __FUNCTION__ 51 #define __func__ __FUNCTION__
52 #endif 52 #endif
53 53
54 /*G4ThreadLocal*/G4double G4MolecularConfigura 54 /*G4ThreadLocal*/G4double G4MolecularConfiguration::fgTemperature = 298; // 310*kelvin;
55 // 25°C, used to shoot an energy 55 // 25°C, used to shoot an energy
56 56
57 //____________________________________________ 57 //______________________________________________________________________________
58 // G4MolecularConfigurationManager 58 // G4MolecularConfigurationManager
59 using MolecularConfigurationManager = G4Molecu << 59 typedef G4MolecularConfiguration::G4MolecularConfigurationManager
>> 60 MolecularConfigurationManager;
60 61
61 MolecularConfigurationManager* G4MolecularConf << 62 MolecularConfigurationManager* G4MolecularConfiguration::fgManager = 0;
62 63
63 G4Mutex MolecularConfigurationManager::fManage 64 G4Mutex MolecularConfigurationManager::fManagerCreationMutex;
64 65
65 int G4MolecularConfiguration::GetNumberOfSpeci 66 int G4MolecularConfiguration::GetNumberOfSpecies()
66 { 67 {
67 return GetManager()->GetNumberOfCreatedSpeci 68 return GetManager()->GetNumberOfCreatedSpecies();
68 } 69 }
69 70
70 double G4MolecularConfiguration::ReturnDefault 71 double G4MolecularConfiguration::ReturnDefaultDiffCoeff(const G4Material*,
71 double, 72 double,
72 const G4M 73 const G4MolecularConfiguration*
73 molConf) 74 molConf)
74 { 75 {
75 return molConf->fDynDiffusionCoefficient; 76 return molConf->fDynDiffusionCoefficient;
76 } 77 }
77 78
78 G4MolecularConfiguration::G4MolecularConfigura 79 G4MolecularConfiguration::G4MolecularConfiguration(const G4MoleculeDefinition* moleculeDef,
79 80 const G4String& label,
80 81 int charge)
81 { 82 {
82 fMoleculeDefinition = moleculeDef; 83 fMoleculeDefinition = moleculeDef;
83 84
84 fLabel = new G4String(label); 85 fLabel = new G4String(label);
85 86
86 fMoleculeID = GetManager()->Insert(moleculeD 87 fMoleculeID = GetManager()->Insert(moleculeDef,
87 label, 88 label,
88 this); 89 this);
89 fElectronOccupancy = nullptr; << 90 fElectronOccupancy = 0;
90 91
91 fDynCharge = charge; 92 fDynCharge = charge;
92 93
93 fDynMass = fMoleculeDefinition->GetMass(); 94 fDynMass = fMoleculeDefinition->GetMass();
94 95
95 fDynDiffusionCoefficient = fMoleculeDefiniti 96 fDynDiffusionCoefficient = fMoleculeDefinition->GetDiffusionCoefficient();
96 fDynVanDerVaalsRadius = fMoleculeDefinition- 97 fDynVanDerVaalsRadius = fMoleculeDefinition->GetVanDerVaalsRadius();
97 fDynDecayTime = fMoleculeDefinition->GetDeca 98 fDynDecayTime = fMoleculeDefinition->GetDecayTime();
98 99
99 fName = fMoleculeDefinition->GetName(); 100 fName = fMoleculeDefinition->GetName();
100 fName += "^"; 101 fName += "^";
101 fName += G4UIcommand::ConvertToString(fDynCh 102 fName += G4UIcommand::ConvertToString(fDynCharge);
102 103
103 fFormatedName = fMoleculeDefinition->GetForm 104 fFormatedName = fMoleculeDefinition->GetFormatedName();
104 fFormatedName += "^"; 105 fFormatedName += "^";
105 fFormatedName += "{"; 106 fFormatedName += "{";
106 fFormatedName += G4UIcommand::ConvertToStrin 107 fFormatedName += G4UIcommand::ConvertToString(fDynCharge);
107 fFormatedName += "}"; 108 fFormatedName += "}";
108 109
109 fDiffParam = &G4MolecularConfiguration::Retu 110 fDiffParam = &G4MolecularConfiguration::ReturnDefaultDiffCoeff;
110 fIsFinalized = false; 111 fIsFinalized = false;
111 } 112 }
112 113
113 void G4MolecularConfiguration::MakeExceptionIf 114 void G4MolecularConfiguration::MakeExceptionIfFinalized()
114 { 115 {
115 if(fIsFinalized) 116 if(fIsFinalized)
116 { 117 {
117 G4ExceptionDescription errMsg; 118 G4ExceptionDescription errMsg;
118 errMsg << "This molecular configuration " 119 errMsg << "This molecular configuration " << GetName()
119 << " is already finalized. Therefor 120 << " is already finalized. Therefore its "
120 " properties cannot be changed."; 121 " properties cannot be changed.";
121 G4Exception("G4MolecularConfiguration::Mak 122 G4Exception("G4MolecularConfiguration::MakeExceptionIfFinalized",
122 "CONF_FINALIZED",FatalExceptio 123 "CONF_FINALIZED",FatalException,errMsg);
123 } 124 }
124 } 125 }
125 126
126 //____________________________________________ 127 //______________________________________________________________________________
127 128
128 G4MolecularConfiguration::G4MolecularConfigura 129 G4MolecularConfiguration::G4MolecularConfigurationManager*
129 G4MolecularConfiguration::GetManager() 130 G4MolecularConfiguration::GetManager()
130 { 131 {
131 if (fgManager == nullptr) << 132 if (!fgManager)
132 { 133 {
133 G4AutoLock lock(&MolecularConfigurationMan 134 G4AutoLock lock(&MolecularConfigurationManager::fManagerCreationMutex);
134 if (fgManager == nullptr) // double check << 135 if (!fgManager) // double check for MT
135 { 136 {
136 fgManager = new G4MolecularConfiguration 137 fgManager = new G4MolecularConfiguration::
137 G4MolecularConfigurationManager(); 138 G4MolecularConfigurationManager();
138 } 139 }
139 lock.unlock(); 140 lock.unlock();
140 } 141 }
141 142
142 return fgManager; 143 return fgManager;
143 } 144 }
144 145
145 //____________________________________________ 146 //______________________________________________________________________________
146 147
147 G4MolecularConfiguration:: 148 G4MolecularConfiguration::
148 G4MolecularConfigurationManager::~G4MolecularC 149 G4MolecularConfigurationManager::~G4MolecularConfigurationManager()
149 { 150 {
150 // G4cout << "Does G4AllocatorList exists= "; 151 // G4cout << "Does G4AllocatorList exists= ";
151 // G4cout << (G4AllocatorList::GetAllocatorLi 152 // G4cout << (G4AllocatorList::GetAllocatorListIfExist() ? "true":"false")
152 // << G4endl; 153 // << G4endl;
153 154
154 G4MolecularConfigurationManager::MolElectron 155 G4MolecularConfigurationManager::MolElectronConfTable::iterator it1;
155 G4MolecularConfigurationManager::ElectronOcc 156 G4MolecularConfigurationManager::ElectronOccupancyTable::
156 iterator it2; 157 iterator it2;
157 158
158 for (it1 = fElecOccTable.begin(); it1 != fEl 159 for (it1 = fElecOccTable.begin(); it1 != fElecOccTable.end(); it1++)
159 { 160 {
160 for (it2 = it1->second.begin(); it2 != it1 161 for (it2 = it1->second.begin(); it2 != it1->second.end(); it2++)
161 { 162 {
162 << 163 if (it2->second)
163 << 164 {
164 delete it2->second; 165 delete it2->second;
165 << 166 }
166 } 167 }
167 } 168 }
168 fElecOccTable.clear(); 169 fElecOccTable.clear();
169 fgManager = nullptr; << 170 fgManager = 0;
170 } 171 }
171 172
172 //____________________________________________ 173 //______________________________________________________________________________
173 // G4MolecularConfigurationManager 174 // G4MolecularConfigurationManager
174 G4int G4MolecularConfiguration:: 175 G4int G4MolecularConfiguration::
175 G4MolecularConfigurationManager:: 176 G4MolecularConfigurationManager::
176 Insert(const G4MoleculeDefinition* molDef, 177 Insert(const G4MoleculeDefinition* molDef,
177 const G4ElectronO 178 const G4ElectronOccupancy& eOcc,
178 G4MolecularConfig 179 G4MolecularConfiguration* molConf)
179 { 180 {
180 //G4AutoLock lock(&fMoleculeCreationMutex); 181 //G4AutoLock lock(&fMoleculeCreationMutex);
181 182
182 ElectronOccupancyTable& table2 = fElecOccTab 183 ElectronOccupancyTable& table2 = fElecOccTable[molDef];
183 auto it = table2.find(eOcc); << 184 ElectronOccupancyTable::iterator it = table2.find(eOcc);
184 185
185 if(it == table2.end()) 186 if(it == table2.end())
186 { 187 {
187 table2[eOcc] = molConf; 188 table2[eOcc] = molConf;
188 } 189 }
189 else 190 else
190 { 191 {
191 G4ExceptionDescription errMsg; 192 G4ExceptionDescription errMsg;
192 errMsg << "The same molecular configuratio 193 errMsg << "The same molecular configuration seemed to be recorded twice";
193 G4Exception("G4MolecularConfigurationManag 194 G4Exception("G4MolecularConfigurationManager::"
194 "SetMolecularConfiguration(con 195 "SetMolecularConfiguration(const G4MoleculeDefinition* molDef,"
195 "const G4ElectronOccupancy& eO 196 "const G4ElectronOccupancy& eOcc,"
196 "G4MolecularConfiguration* mol 197 "G4MolecularConfiguration* molConf)",
197 "", 198 "",
198 FatalException, 199 FatalException,
199 errMsg 200 errMsg
200 ); 201 );
201 } 202 }
202 203
203 fLastMoleculeID++; 204 fLastMoleculeID++;
204 205
205 fMolConfPerID.push_back(molConf); 206 fMolConfPerID.push_back(molConf);
206 207
207 //lock.unlock(); 208 //lock.unlock();
208 return fLastMoleculeID; 209 return fLastMoleculeID;
209 } 210 }
210 211
211 //____________________________________________ 212 //______________________________________________________________________________
212 213
213 const G4ElectronOccupancy* 214 const G4ElectronOccupancy*
214 G4MolecularConfiguration::G4MolecularConfigura 215 G4MolecularConfiguration::G4MolecularConfigurationManager::
215 FindCommonElectronOccupancy(const G4MoleculeDe 216 FindCommonElectronOccupancy(const G4MoleculeDefinition* molDef,
216 const G4ElectronOc 217 const G4ElectronOccupancy& eOcc)
217 { 218 {
218 //G4AutoLock lock(&fMoleculeCreationMutex); 219 //G4AutoLock lock(&fMoleculeCreationMutex);
219 220
220 auto it1 = fElecOccTable.find(molDef); << 221 MolElectronConfTable::iterator it1 = fElecOccTable.find(molDef);
221 222
222 if(it1 == fElecOccTable.end()) 223 if(it1 == fElecOccTable.end())
223 { 224 {
224 // TODO = handle exception ? 225 // TODO = handle exception ?
225 return nullptr; << 226 return 0;
226 } 227 }
227 228
228 ElectronOccupancyTable& table2 = it1->second 229 ElectronOccupancyTable& table2 = it1->second;
229 auto it2 = table2.find(eOcc); << 230 ElectronOccupancyTable::iterator it2 = table2.find(eOcc);
230 231
231 //lock.unlock(); 232 //lock.unlock();
232 233
233 if (it2 == table2.end()) 234 if (it2 == table2.end())
234 { 235 {
235 // TODO = handle exception ? 236 // TODO = handle exception ?
236 return nullptr; << 237 return 0;
237 } 238 }
238 239
239 return &(it2->first); 240 return &(it2->first);
240 } 241 }
241 242
242 //____________________________________________ 243 //______________________________________________________________________________
243 244
244 G4MolecularConfiguration* 245 G4MolecularConfiguration*
245 G4MolecularConfiguration::G4MolecularConfigura 246 G4MolecularConfiguration::G4MolecularConfigurationManager::
246 GetMolecularConfiguration(const G4MoleculeDefi 247 GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
247 const G4ElectronOccu 248 const G4ElectronOccupancy& eOcc)
248 { 249 {
249 auto it1 = fElecOccTable.find(molDef); << 250 MolElectronConfTable::iterator it1 = fElecOccTable.find(molDef);
250 251
251 if(it1 == fElecOccTable.end()) return nullpt << 252 if(it1 == fElecOccTable.end()) return 0;
252 253
253 ElectronOccupancyTable& table2 = it1->second 254 ElectronOccupancyTable& table2 = it1->second;
254 auto it = table2.find(eOcc); << 255 ElectronOccupancyTable::iterator it = table2.find(eOcc);
255 256
256 if(it == table2.end()) 257 if(it == table2.end())
257 { 258 {
258 return nullptr; << 259 return 0;
>> 260 }
>> 261 else
>> 262 {
>> 263 return it->second;
259 } 264 }
260 << 265
261 return it->second; << 266 return 0;
262 } 267 }
263 268
264 //____________________________________________ 269 //______________________________________________________________________________
265 270
266 G4int G4MolecularConfiguration::G4MolecularCon 271 G4int G4MolecularConfiguration::G4MolecularConfigurationManager::
267 Insert(const G4MoleculeDefinition* molDef, 272 Insert(const G4MoleculeDefinition* molDef,
268 int charge, 273 int charge,
269 G4MolecularConfiguration* molConf) 274 G4MolecularConfiguration* molConf)
270 { 275 {
271 276
272 //G4AutoLock lock(&fMoleculeCreationMutex); 277 //G4AutoLock lock(&fMoleculeCreationMutex);
273 ChargeTable& table2 = fChargeTable[molDef]; 278 ChargeTable& table2 = fChargeTable[molDef];
274 auto it = table2.find(charge); << 279 ChargeTable::iterator it = table2.find(charge);
275 280
276 if(it == table2.end()) 281 if(it == table2.end())
277 { 282 {
278 table2[charge] = molConf; 283 table2[charge] = molConf;
279 } 284 }
280 else 285 else
281 { 286 {
282 //lock.unlock(); 287 //lock.unlock();
283 G4ExceptionDescription errMsg; 288 G4ExceptionDescription errMsg;
284 errMsg << "The same molecular configuratio 289 errMsg << "The same molecular configuration seemed to be recorded twice";
285 G4Exception("G4MolecularConfigurationManag 290 G4Exception("G4MolecularConfigurationManager::"
286 "SetMolecularConfiguration(con 291 "SetMolecularConfiguration(const G4MoleculeDefinition* molDef,"
287 "int charge," 292 "int charge,"
288 "G4MolecularConfiguration* mol 293 "G4MolecularConfiguration* molConf)",
289 "", FatalException, errMsg); 294 "", FatalException, errMsg);
290 } 295 }
291 296
292 fLastMoleculeID++; 297 fLastMoleculeID++;
293 fMolConfPerID.push_back(molConf); 298 fMolConfPerID.push_back(molConf);
294 //lock.unlock(); 299 //lock.unlock();
295 return fLastMoleculeID; 300 return fLastMoleculeID;
296 } 301 }
297 302
298 //____________________________________________ 303 //______________________________________________________________________________
299 304
300 G4MolecularConfiguration* 305 G4MolecularConfiguration*
301 G4MolecularConfiguration::G4MolecularConfigura 306 G4MolecularConfiguration::G4MolecularConfigurationManager::
302 GetMolecularConfiguration(const G4MoleculeDefi 307 GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
303 int charge) 308 int charge)
304 { 309 {
305 //G4AutoLock lock(&fMoleculeCreationMutex); 310 //G4AutoLock lock(&fMoleculeCreationMutex);
306 311
307 auto it1 = fChargeTable.find(molDef); << 312 MolChargeConfTable::iterator it1 = fChargeTable.find(molDef);
308 313
309 if(it1 == fChargeTable.end()) return nullptr << 314 if(it1 == fChargeTable.end()) return 0;
310 315
311 ChargeTable& table2 = it1->second; 316 ChargeTable& table2 = it1->second;
312 auto it = table2.find(charge); << 317 ChargeTable::iterator it = table2.find(charge);
313 318
314 if(it == table2.end()) 319 if(it == table2.end())
315 { 320 {
316 return nullptr; << 321 return 0;
>> 322 }
>> 323 else
>> 324 {
>> 325 return it->second;
317 } 326 }
318 << 327
319 return it->second; << 328 return 0;
320 << 329
>> 330 //lock.unlock();
>> 331 return 0;
321 } 332 }
322 333
323 //____________________________________________ 334 //______________________________________________________________________________
324 // Static method in G4MolecularConfiguration 335 // Static method in G4MolecularConfiguration
325 G4MolecularConfiguration* 336 G4MolecularConfiguration*
326 G4MolecularConfiguration:: 337 G4MolecularConfiguration::
327 GetOrCreateMolecularConfiguration(const G4Mole 338 GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef)
328 { 339 {
329 if (molDef->GetGroundStateElectronOccupancy( << 340 if (molDef->GetGroundStateElectronOccupancy())
330 { 341 {
331 const G4ElectronOccupancy& elecOcc = 342 const G4ElectronOccupancy& elecOcc =
332 *molDef->GetGroundStateElectronOccupan 343 *molDef->GetGroundStateElectronOccupancy();
333 G4MolecularConfiguration* molConf = 344 G4MolecularConfiguration* molConf =
334 GetManager()->GetMolecularConfiguratio 345 GetManager()->GetMolecularConfiguration(molDef, elecOcc);
335 346
336 if (molConf != nullptr) << 347 if (molConf)
337 { 348 {
338 return molConf; 349 return molConf;
339 } 350 }
340 << 351 else
341 auto newConf = << 352 {
342 new G4MolecularConfiguration(molDef, << 353 G4MolecularConfiguration* newConf =
343 elecOcc); << 354 new G4MolecularConfiguration(molDef,
344 newConf->SetUserID(molDef->GetName()); << 355 elecOcc);
345 return newConf; << 356 newConf->SetUserID(molDef->GetName());
>> 357 return newConf;
>> 358 }
346 } 359 }
347 << 360 else
348 G4MolecularConfiguration* molConf = <<
349 GetManager()->GetMolecularConfiguration( <<
350 if(molConf != nullptr) <<
351 { 361 {
352 return molConf; << 362 G4MolecularConfiguration* molConf =
>> 363 GetManager()->GetMolecularConfiguration(molDef, molDef->GetCharge());
>> 364 if(molConf)
>> 365 {
>> 366 return molConf;
>> 367 }
>> 368 else
>> 369 {
>> 370 G4MolecularConfiguration* newConf =
>> 371 new G4MolecularConfiguration(molDef, molDef->GetCharge());
>> 372 newConf->SetUserID(molDef->GetName());
>> 373 return newConf;
>> 374 }
353 } 375 }
354 <<
355 auto newConf = <<
356 new G4MolecularConfiguration(molDef, mol <<
357 newConf->SetUserID(molDef->GetName()); <<
358 return newConf; <<
359 } 376 }
360 377
361 //____________________________________________ 378 //______________________________________________________________________________
362 379
363 G4MolecularConfiguration* 380 G4MolecularConfiguration*
364 G4MolecularConfiguration:: 381 G4MolecularConfiguration::
365 GetOrCreateMolecularConfiguration(const G4Mole 382 GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef,
366 const G4Elec 383 const G4ElectronOccupancy& elecOcc)
367 { 384 {
368 return GetManager()->GetOrCreateMolecularCon 385 return GetManager()->GetOrCreateMolecularConfiguration(molDef, elecOcc);
369 386
370 // G4MolecularConfiguration* molConf = 387 // G4MolecularConfiguration* molConf =
371 // GetManager()->GetMolecularConfiguratio 388 // GetManager()->GetMolecularConfiguration(molDef, elecOcc);
372 // 389 //
373 // if (molConf) 390 // if (molConf)
374 // { 391 // {
375 // return molConf; 392 // return molConf;
376 // } 393 // }
377 // else 394 // else
378 // { 395 // {
379 // G4MolecularConfiguration* newConf = 396 // G4MolecularConfiguration* newConf =
380 // new G4MolecularConfiguration(molDef, 397 // new G4MolecularConfiguration(molDef, elecOcc);
381 // return newConf; 398 // return newConf;
382 // } 399 // }
383 } 400 }
384 401
385 //____________________________________________ 402 //______________________________________________________________________________
386 403
387 G4MolecularConfiguration* 404 G4MolecularConfiguration*
388 G4MolecularConfiguration:: 405 G4MolecularConfiguration::
389 GetOrCreateMolecularConfiguration(const G4Mole 406 GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef,
390 int charge) 407 int charge)
391 { 408 {
392 G4MolecularConfiguration* molConf = 409 G4MolecularConfiguration* molConf =
393 GetManager()->GetMolecularConfiguration( 410 GetManager()->GetMolecularConfiguration(molDef, charge);
394 411
395 if(molConf != nullptr) << 412 if(molConf)
396 { 413 {
397 return molConf; 414 return molConf;
398 } 415 }
399 << 416 else
400 auto newConf = << 417 {
401 new G4MolecularConfiguration(molDef, cha << 418 G4MolecularConfiguration* newConf =
402 return newConf; << 419 new G4MolecularConfiguration(molDef, charge);
>> 420 return newConf;
>> 421 }
403 } 422 }
404 423
405 //____________________________________________ 424 //______________________________________________________________________________
406 425
407 void G4MolecularConfiguration::DeleteManager() 426 void G4MolecularConfiguration::DeleteManager()
408 { 427 {
409 G4AutoLock lock(&MolecularConfigurationManag 428 G4AutoLock lock(&MolecularConfigurationManager::fManagerCreationMutex);
410 delete fgManager; << 429 if (fgManager) delete fgManager;
411 fgManager = nullptr; << 430 fgManager = 0;
412 lock.unlock(); 431 lock.unlock();
413 } 432 }
414 433
415 //____________________________________________ 434 //______________________________________________________________________________
416 // G4MolecularConfiguration 435 // G4MolecularConfiguration
417 G4MolecularConfiguration:: 436 G4MolecularConfiguration::
418 G4MolecularConfiguration(const G4MoleculeDefin 437 G4MolecularConfiguration(const G4MoleculeDefinition* moleculeDef,
419 const G4ElectronOccup 438 const G4ElectronOccupancy& elecOcc,
420 const G4String& label 439 const G4String& label)
421 { 440 {
422 fMoleculeDefinition = moleculeDef; 441 fMoleculeDefinition = moleculeDef;
423 442
424 fMoleculeID = GetManager()->Insert(moleculeD 443 fMoleculeID = GetManager()->Insert(moleculeDef,
425 elecOcc, 444 elecOcc,
426 this); 445 this);
427 fElectronOccupancy = GetManager()->FindCommo 446 fElectronOccupancy = GetManager()->FindCommonElectronOccupancy(moleculeDef,
428 447 elecOcc);
429 448
430 /* 449 /*
431 fgManager->fTable[fMoleculeDefinition][elec 450 fgManager->fTable[fMoleculeDefinition][elecOcc] = this;
432 std::map<G4ElectronOccupancy, G4MolecularCo 451 std::map<G4ElectronOccupancy, G4MolecularConfiguration*, comparator>::iterator it ;
433 it = fgManager->fTable[moleculeDef].find(el 452 it = fgManager->fTable[moleculeDef].find(elecOcc);
434 fElectronOccupancy = &(it->first); 453 fElectronOccupancy = &(it->first);
435 */ 454 */
436 455
437 fDynCharge = fMoleculeDefinition->GetNbElect 456 fDynCharge = fMoleculeDefinition->GetNbElectrons()
438 - fElectronOccupancy->GetTotalOccupancy( 457 - fElectronOccupancy->GetTotalOccupancy()
439 + moleculeDef->GetCharge(); 458 + moleculeDef->GetCharge();
440 fDynMass = fMoleculeDefinition->GetMass(); 459 fDynMass = fMoleculeDefinition->GetMass();
441 460
442 fDynDiffusionCoefficient = fMoleculeDefiniti 461 fDynDiffusionCoefficient = fMoleculeDefinition->GetDiffusionCoefficient();
443 fDynVanDerVaalsRadius = fMoleculeDefinition- 462 fDynVanDerVaalsRadius = fMoleculeDefinition->GetVanDerVaalsRadius();
444 fDynDecayTime = fMoleculeDefinition->GetDeca 463 fDynDecayTime = fMoleculeDefinition->GetDecayTime();
445 464
446 fName = fMoleculeDefinition->GetName(); 465 fName = fMoleculeDefinition->GetName();
447 fName += "^"; 466 fName += "^";
448 fName += G4UIcommand::ConvertToString(fDynCh 467 fName += G4UIcommand::ConvertToString(fDynCharge);
449 468
450 fFormatedName = fMoleculeDefinition->GetForm 469 fFormatedName = fMoleculeDefinition->GetFormatedName();
451 fFormatedName += "^"; 470 fFormatedName += "^";
452 fFormatedName += "{"; 471 fFormatedName += "{";
453 fFormatedName += G4UIcommand::ConvertToStrin 472 fFormatedName += G4UIcommand::ConvertToString(fDynCharge);
454 fFormatedName += "}"; 473 fFormatedName += "}";
455 474
456 fLabel = nullptr; // let it here << 475 fLabel = 0; // let it here
457 476
458 if(!label.empty()) << 477 if(label != "")
459 { 478 {
460 SetLabel(label); 479 SetLabel(label);
461 } 480 }
462 481
463 fDiffParam = &G4MolecularConfiguration::Retu 482 fDiffParam = &G4MolecularConfiguration::ReturnDefaultDiffCoeff;
464 483
465 fIsFinalized = false; 484 fIsFinalized = false;
466 } 485 }
467 486
468 //____________________________________________ 487 //______________________________________________________________________________
469 488
470 G4MolecularConfiguration:: 489 G4MolecularConfiguration::
471 G4MolecularConfiguration(const G4MoleculeDefin 490 G4MolecularConfiguration(const G4MoleculeDefinition* moleculeDef,
472 int charge) 491 int charge)
473 { 492 {
474 fMoleculeDefinition = moleculeDef; 493 fMoleculeDefinition = moleculeDef;
475 494
476 fMoleculeID = GetManager()->Insert(moleculeD 495 fMoleculeID = GetManager()->Insert(moleculeDef,
477 charge, 496 charge,
478 this); 497 this);
479 fElectronOccupancy = nullptr; << 498 fElectronOccupancy = 0;
480 499
481 fDynCharge = charge; 500 fDynCharge = charge;
482 fDynMass = fMoleculeDefinition->GetMass(); 501 fDynMass = fMoleculeDefinition->GetMass();
483 502
484 fDynDiffusionCoefficient = fMoleculeDefiniti 503 fDynDiffusionCoefficient = fMoleculeDefinition->GetDiffusionCoefficient();
485 fDynVanDerVaalsRadius = fMoleculeDefinition- 504 fDynVanDerVaalsRadius = fMoleculeDefinition->GetVanDerVaalsRadius();
486 fDynDecayTime = fMoleculeDefinition->GetDeca 505 fDynDecayTime = fMoleculeDefinition->GetDecayTime();
487 506
488 fName = fMoleculeDefinition->GetName(); 507 fName = fMoleculeDefinition->GetName();
489 fName += "^"; 508 fName += "^";
490 fName += G4UIcommand::ConvertToString(fDynCh 509 fName += G4UIcommand::ConvertToString(fDynCharge);
491 510
492 fFormatedName = fMoleculeDefinition->GetForm 511 fFormatedName = fMoleculeDefinition->GetFormatedName();
493 fFormatedName += "^"; 512 fFormatedName += "^";
494 fFormatedName += "{"; 513 fFormatedName += "{";
495 fFormatedName += G4UIcommand::ConvertToStrin 514 fFormatedName += G4UIcommand::ConvertToString(fDynCharge);
496 fFormatedName += "}"; 515 fFormatedName += "}";
497 516
498 fLabel = nullptr; << 517 fLabel = 0;
499 518
500 fDiffParam = &G4MolecularConfiguration::Retu 519 fDiffParam = &G4MolecularConfiguration::ReturnDefaultDiffCoeff;
501 520
502 fIsFinalized = false; 521 fIsFinalized = false;
503 } 522 }
504 523
505 //____________________________________________ 524 //______________________________________________________________________________
506 525
507 G4MolecularConfiguration::~G4MolecularConfigur 526 G4MolecularConfiguration::~G4MolecularConfiguration()
508 { 527 {
509 if (fgManager != nullptr) fgManager->RemoveM << 528 if (fgManager) fgManager->RemoveMolecularConfigurationFromTable(this);
510 529
511 // if (G4AllocatorList::GetAllocatorListIfExi 530 // if (G4AllocatorList::GetAllocatorListIfExist())
512 // { 531 // {
513 // if (fElectronOccupancy) 532 // if (fElectronOccupancy)
514 // { 533 // {
515 // delete fElectronOccupancy; 534 // delete fElectronOccupancy;
516 // fElectronOccupancy = 0; 535 // fElectronOccupancy = 0;
517 // } 536 // }
518 // } 537 // }
519 } 538 }
520 539
521 //____________________________________________ 540 //______________________________________________________________________________
522 541
523 G4MolecularConfiguration* 542 G4MolecularConfiguration*
524 G4MolecularConfiguration:: 543 G4MolecularConfiguration::
525 ChangeConfiguration(const G4ElectronOccupancy& 544 ChangeConfiguration(const G4ElectronOccupancy& newElectronOccupancy) const
526 { 545 {
527 G4MolecularConfiguration* output = 546 G4MolecularConfiguration* output =
528 GetManager()->GetMolecularConfiguration( 547 GetManager()->GetMolecularConfiguration(fMoleculeDefinition,
529 548 newElectronOccupancy);
530 549
531 if (output == nullptr) << 550 if (!output)
532 { 551 {
533 output = new G4MolecularConfiguration(fMol 552 output = new G4MolecularConfiguration(fMoleculeDefinition,
534 newE 553 newElectronOccupancy);
535 } 554 }
536 return output; 555 return output;
537 } 556 }
538 557
539 //____________________________________________ 558 //______________________________________________________________________________
540 559
541 G4MolecularConfiguration* 560 G4MolecularConfiguration*
542 G4MolecularConfiguration::ChangeConfiguration( 561 G4MolecularConfiguration::ChangeConfiguration(int charge) const
543 { 562 {
544 G4MolecularConfiguration* output = 563 G4MolecularConfiguration* output =
545 GetManager()->GetMolecularConfiguration( 564 GetManager()->GetMolecularConfiguration(fMoleculeDefinition, charge);
546 565
547 if (output == nullptr) << 566 if (!output)
548 { 567 {
549 output = new G4MolecularConfiguration(fMol 568 output = new G4MolecularConfiguration(fMoleculeDefinition, charge);
550 } 569 }
551 return output; 570 return output;
552 } 571 }
553 572
554 //____________________________________________ 573 //______________________________________________________________________________
555 574
556 G4MolecularConfiguration& 575 G4MolecularConfiguration&
557 G4MolecularConfiguration::operator=(G4Molecula 576 G4MolecularConfiguration::operator=(G4MolecularConfiguration& /*right*/)
558 { 577 {
559 // if (&right == this) return *this; 578 // if (&right == this) return *this;
560 return *this; 579 return *this;
561 } 580 }
562 581
563 //____________________________________________ 582 //______________________________________________________________________________
564 583
565 /** Method used in Geant4-DNA to excite water 584 /** Method used in Geant4-DNA to excite water molecules
566 */ 585 */
567 G4MolecularConfiguration* 586 G4MolecularConfiguration*
568 G4MolecularConfiguration::ExciteMolecule(G4int 587 G4MolecularConfiguration::ExciteMolecule(G4int ExcitedLevel) const
569 { 588 {
570 // MakeExceptionIfFinalized(); 589 // MakeExceptionIfFinalized();
571 CheckElectronOccupancy(__func__); 590 CheckElectronOccupancy(__func__);
572 G4ElectronOccupancy newElectronOccupancy(*fE 591 G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
573 592
574 newElectronOccupancy.RemoveElectron(ExcitedL 593 newElectronOccupancy.RemoveElectron(ExcitedLevel, 1);
575 newElectronOccupancy.AddElectron(5, 1); 594 newElectronOccupancy.AddElectron(5, 1);
576 595
577 return ChangeConfiguration(newElectronOccupa 596 return ChangeConfiguration(newElectronOccupancy);
578 } 597 }
579 598
580 //____________________________________________ 599 //______________________________________________________________________________
581 600
582 /** Method used in Geant4-DNA to ionize water 601 /** Method used in Geant4-DNA to ionize water molecules
583 */ 602 */
584 G4MolecularConfiguration* 603 G4MolecularConfiguration*
585 G4MolecularConfiguration::IonizeMolecule(G4int 604 G4MolecularConfiguration::IonizeMolecule(G4int IonizedLevel) const
586 { 605 {
587 // MakeExceptionIfFinalized(); 606 // MakeExceptionIfFinalized();
588 CheckElectronOccupancy(__func__); 607 CheckElectronOccupancy(__func__);
589 G4ElectronOccupancy newElectronOccupancy(*fE 608 G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
590 609
591 if (newElectronOccupancy.GetOccupancy(Ionize 610 if (newElectronOccupancy.GetOccupancy(IonizedLevel) != 0)
592 { 611 {
593 newElectronOccupancy.RemoveElectron(Ionize 612 newElectronOccupancy.RemoveElectron(IonizedLevel, 1);
594 } 613 }
595 else 614 else
596 { 615 {
597 G4String errMsg = "There is no electron on 616 G4String errMsg = "There is no electron on the orbit "
598 + G4UIcommand::ConvertToString(Ionized 617 + G4UIcommand::ConvertToString(IonizedLevel)
599 + " you want to free. The molecule's n 618 + " you want to free. The molecule's name you want to ionized is "
600 + GetName(); 619 + GetName();
601 G4Exception("G4MolecularConfiguration::Ion 620 G4Exception("G4MolecularConfiguration::IonizeMolecule",
602 "", 621 "",
603 FatalErrorInArgument, 622 FatalErrorInArgument,
604 errMsg); 623 errMsg);
605 PrintState(); 624 PrintState();
606 } 625 }
607 626
608 // DEBUG 627 // DEBUG
609 // PrintState(); 628 // PrintState();
610 629
611 return ChangeConfiguration(newElectronOccupa 630 return ChangeConfiguration(newElectronOccupancy);
612 } 631 }
613 632
614 //____________________________________________ 633 //______________________________________________________________________________
615 634
616 G4MolecularConfiguration* G4MolecularConfigura 635 G4MolecularConfiguration* G4MolecularConfiguration::AddElectron(G4int orbit,
617 636 G4int number) const
618 { 637 {
619 // MakeExceptionIfFinalized(); 638 // MakeExceptionIfFinalized();
620 CheckElectronOccupancy(__func__); 639 CheckElectronOccupancy(__func__);
621 G4ElectronOccupancy newElectronOccupancy(*fE 640 G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
622 newElectronOccupancy.AddElectron(orbit, numb 641 newElectronOccupancy.AddElectron(orbit, number);
623 return ChangeConfiguration(newElectronOccupa 642 return ChangeConfiguration(newElectronOccupancy);
624 } 643 }
625 644
626 //____________________________________________ 645 //______________________________________________________________________________
627 646
628 G4MolecularConfiguration* 647 G4MolecularConfiguration*
629 G4MolecularConfiguration::RemoveElectron(G4int 648 G4MolecularConfiguration::RemoveElectron(G4int orbit,
630 G4int 649 G4int number) const
631 { 650 {
632 // MakeExceptionIfFinalized(); 651 // MakeExceptionIfFinalized();
633 CheckElectronOccupancy(__func__); 652 CheckElectronOccupancy(__func__);
634 G4ElectronOccupancy newElectronOccupancy(*fE 653 G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
635 654
636 if (newElectronOccupancy.GetOccupancy(orbit) 655 if (newElectronOccupancy.GetOccupancy(orbit) != 0)
637 { 656 {
638 newElectronOccupancy.RemoveElectron(orbit, 657 newElectronOccupancy.RemoveElectron(orbit, number);
639 } 658 }
640 else 659 else
641 { 660 {
642 G4String errMsg = "There is already no ele 661 G4String errMsg = "There is already no electron into the orbit "
643 + G4UIcommand::ConvertToString(orbit) 662 + G4UIcommand::ConvertToString(orbit)
644 + " you want to free. The molecule's n 663 + " you want to free. The molecule's name is " + GetName();
645 G4Exception("G4MolecularConfiguration::Rem 664 G4Exception("G4MolecularConfiguration::RemoveElectron",
646 "", 665 "",
647 JustWarning, 666 JustWarning,
648 errMsg); 667 errMsg);
649 PrintState(); 668 PrintState();
650 } 669 }
651 670
652 return ChangeConfiguration(newElectronOccupa 671 return ChangeConfiguration(newElectronOccupancy);
653 } 672 }
654 673
655 //____________________________________________ 674 //______________________________________________________________________________
656 675
657 G4MolecularConfiguration* 676 G4MolecularConfiguration*
658 G4MolecularConfiguration::MoveOneElectron(G4in 677 G4MolecularConfiguration::MoveOneElectron(G4int orbitToFree,
659 G4in 678 G4int orbitToFill) const
660 { 679 {
661 // MakeExceptionIfFinalized(); 680 // MakeExceptionIfFinalized();
662 CheckElectronOccupancy(__func__); 681 CheckElectronOccupancy(__func__);
663 G4ElectronOccupancy newElectronOccupancy(*fE 682 G4ElectronOccupancy newElectronOccupancy(*fElectronOccupancy);
664 683
665 if (newElectronOccupancy.GetOccupancy(orbitT 684 if (newElectronOccupancy.GetOccupancy(orbitToFree) >= 1)
666 { 685 {
667 newElectronOccupancy.RemoveElectron(orbitT 686 newElectronOccupancy.RemoveElectron(orbitToFree, 1);
668 newElectronOccupancy.AddElectron(orbitToFi 687 newElectronOccupancy.AddElectron(orbitToFill, 1);
669 } 688 }
670 else 689 else
671 { 690 {
672 G4String errMsg = "There is no electron on 691 G4String errMsg = "There is no electron on the orbit "
673 + G4UIcommand::ConvertToString(orbitTo 692 + G4UIcommand::ConvertToString(orbitToFree)
674 + " you want to free. The molecule's n 693 + " you want to free. The molecule's name is " + GetName();
675 G4Exception("G4MolecularConfiguration::Mov 694 G4Exception("G4MolecularConfiguration::MoveOneElectron",
676 "", 695 "",
677 FatalErrorInArgument, 696 FatalErrorInArgument,
678 errMsg); 697 errMsg);
679 PrintState(); 698 PrintState();
680 } 699 }
681 700
682 return ChangeConfiguration(newElectronOccupa 701 return ChangeConfiguration(newElectronOccupancy);
683 } 702 }
684 703
685 //____________________________________________ 704 //______________________________________________________________________________
686 705
687 const G4String& G4MolecularConfiguration::GetN 706 const G4String& G4MolecularConfiguration::GetName() const
688 { 707 {
>> 708 // if (fName.isNull())
>> 709 // {
>> 710 // fName = fMoleculeDefinition->GetName();
>> 711 // fName += "^";
>> 712 // // fName+= "{";
>> 713 // fName += G4UIcommand::ConvertToString(fDynCharge);
>> 714 // // fName+= "}";
>> 715 // }
689 return fName; 716 return fName;
690 } 717 }
691 718
692 //____________________________________________ 719 //______________________________________________________________________________
693 720
694 const G4String& G4MolecularConfiguration::GetF 721 const G4String& G4MolecularConfiguration::GetFormatedName() const
695 { 722 {
>> 723 // if (fFormatedName.isNull())
>> 724 // {
>> 725 // fFormatedName = fMoleculeDefinition->GetFormatedName();
>> 726 // fFormatedName += "^";
>> 727 // fFormatedName += "{";
>> 728 // fFormatedName += G4UIcommand::ConvertToString(fDynCharge);
>> 729 // fFormatedName += "}";
>> 730 // }
696 return fFormatedName; 731 return fFormatedName;
697 } 732 }
698 733
699 //____________________________________________ 734 //______________________________________________________________________________
700 735
701 G4int G4MolecularConfiguration::GetAtomsNumber 736 G4int G4MolecularConfiguration::GetAtomsNumber() const
702 { 737 {
703 return fMoleculeDefinition->GetAtomsNumber() 738 return fMoleculeDefinition->GetAtomsNumber();
704 } 739 }
705 740
706 //____________________________________________ 741 //______________________________________________________________________________
707 742
708 G4double G4MolecularConfiguration::GetNbElectr 743 G4double G4MolecularConfiguration::GetNbElectrons() const
709 { 744 {
710 CheckElectronOccupancy(__func__); 745 CheckElectronOccupancy(__func__);
711 return fElectronOccupancy->GetTotalOccupancy 746 return fElectronOccupancy->GetTotalOccupancy();
712 } 747 }
713 748
714 //____________________________________________ 749 //______________________________________________________________________________
715 750
716 void G4MolecularConfiguration::PrintState() co 751 void G4MolecularConfiguration::PrintState() const
717 { 752 {
718 G4cout << "-------------- Start Printing Sta 753 G4cout << "-------------- Start Printing State " << GetName()
719 << " ---------------" << G4endl; 754 << " ---------------" << G4endl;
720 755
721 if (fElectronOccupancy != nullptr) << 756 if (fElectronOccupancy)
722 { 757 {
723 G4cout << "--------------Print electronic 758 G4cout << "--------------Print electronic state of " << GetName()
724 << "---------------" << G4endl; 759 << "---------------" << G4endl;
725 fElectronOccupancy->DumpInfo(); 760 fElectronOccupancy->DumpInfo();
726 if(fElectronOccupancy==fMoleculeDefinition 761 if(fElectronOccupancy==fMoleculeDefinition->GetGroundStateElectronOccupancy())
727 { 762 {
728 G4cout<<"At ground state"<<G4endl; 763 G4cout<<"At ground state"<<G4endl;
729 } 764 }
730 } 765 }
731 else 766 else
732 { 767 {
733 G4cout << "--- No electron occupancy set u 768 G4cout << "--- No electron occupancy set up ---" << G4endl;
734 } 769 }
735 770
736 G4cout << "Charge :" 771 G4cout << "Charge :"
737 << fDynCharge 772 << fDynCharge
738 << G4endl; 773 << G4endl;
739 774
740 if(fLabel != nullptr) << 775 if(fLabel)
741 { 776 {
742 G4cout << "Label :" 777 G4cout << "Label :"
743 << GetLabel() 778 << GetLabel()
744 << G4endl; 779 << G4endl;
745 } 780 }
746 G4cout << "-------------- End Of State " << 781 G4cout << "-------------- End Of State " << GetName()
747 << " -----------------------" << G4e 782 << " -----------------------" << G4endl;
748 } 783 }
749 784
750 //____________________________________________ 785 //______________________________________________________________________________
751 786
752 // added - to be transformed in a "Decay metho 787 // added - to be transformed in a "Decay method"
753 const vector<const G4MolecularDissociationChan 788 const vector<const G4MolecularDissociationChannel*>*
754 G4MolecularConfiguration::GetDissociationCha 789 G4MolecularConfiguration::GetDissociationChannels() const
755 { 790 {
756 // if (fElectronOccupancy == 0) return 0; 791 // if (fElectronOccupancy == 0) return 0;
757 return fMoleculeDefinition->GetDecayChannels 792 return fMoleculeDefinition->GetDecayChannels(this);
758 } 793 }
759 794
760 //____________________________________________ 795 //______________________________________________________________________________
761 796
762 G4int G4MolecularConfiguration::GetFakeParticl 797 G4int G4MolecularConfiguration::GetFakeParticleID() const
763 { 798 {
764 if(fMoleculeDefinition != nullptr) return fM << 799 if(fMoleculeDefinition) return fMoleculeDefinition->GetPDGEncoding();
765 G4Exception("G4MolecularConfiguration::GetMo << 800 else G4Exception("G4MolecularConfiguration::GetMoleculeID",
766 "", 801 "",
767 FatalErrorInArgument, 802 FatalErrorInArgument,
768 "You should first enter a m 803 "You should first enter a molecule definition");
769 804
770 return INT_MAX; 805 return INT_MAX;
771 } 806 }
772 807
773 //____________________________________________ 808 //______________________________________________________________________________
774 809
775 const char* removePath(const char* path) 810 const char* removePath(const char* path)
776 { 811 {
777 const char* pDelimeter = strrchr(path, '\\') 812 const char* pDelimeter = strrchr(path, '\\');
778 if (pDelimeter != nullptr) path = pDelimeter << 813 if (pDelimeter) path = pDelimeter + 1;
779 814
780 pDelimeter = strrchr(path, '/'); 815 pDelimeter = strrchr(path, '/');
781 if (pDelimeter != nullptr) path = pDelimeter << 816 if (pDelimeter) path = pDelimeter + 1;
782 817
783 return path; 818 return path;
784 } 819 }
785 820
786 //____________________________________________ 821 //______________________________________________________________________________
787 822
788 void G4MolecularConfiguration::CheckElectronOc 823 void G4MolecularConfiguration::CheckElectronOccupancy(const char* function) const
789 { 824 {
790 if (fElectronOccupancy == nullptr) << 825 if (fElectronOccupancy == 0)
791 { 826 {
792 G4String functionName(function); 827 G4String functionName(function);
793 G4ExceptionDescription description; 828 G4ExceptionDescription description;
794 description 829 description
795 << "No G4ElectronOccupancy was defined 830 << "No G4ElectronOccupancy was defined for molecule definition : "
796 << fMoleculeDefinition->GetName() 831 << fMoleculeDefinition->GetName()
797 << ". The definition was probably defi 832 << ". The definition was probably defined using the charge state, "
798 "rather than electron state."; 833 "rather than electron state.";
799 834
800 G4Exception(functionName, "", FatalErrorIn 835 G4Exception(functionName, "", FatalErrorInArgument, description);
801 } 836 }
802 } 837 }
803 838
804 //____________________________________________ 839 //______________________________________________________________________________
805 840
806 void G4MolecularConfiguration::G4MolecularConf 841 void G4MolecularConfiguration::G4MolecularConfigurationManager::
807 RecordNewlyLabeledConfiguration(G4MolecularCon 842 RecordNewlyLabeledConfiguration(G4MolecularConfiguration* molConf)
808 { 843 {
809 //G4AutoLock lock(&fMoleculeCreationMutex); 844 //G4AutoLock lock(&fMoleculeCreationMutex);
810 845
811 LabelTable& tmpMap = fLabelTable[molConf->fM 846 LabelTable& tmpMap = fLabelTable[molConf->fMoleculeDefinition];
812 847
813 auto it = tmpMap.find(*molConf->fLabel); << 848 LabelTable::iterator it = tmpMap.find(*molConf->fLabel);
814 849
815 if(it == tmpMap.end()) 850 if(it == tmpMap.end())
816 { 851 {
817 tmpMap[*(molConf->fLabel)] = molConf; 852 tmpMap[*(molConf->fLabel)] = molConf;
818 } 853 }
819 else 854 else
820 { 855 {
821 G4ExceptionDescription errMsg; 856 G4ExceptionDescription errMsg;
822 errMsg << "The same molecular configuratio 857 errMsg << "The same molecular configuration seemed to be recorded twice";
823 G4Exception("G4MolecularConfigurationManag 858 G4Exception("G4MolecularConfigurationManager::"
824 "SetMolecularConfiguration(con 859 "SetMolecularConfiguration(const G4MoleculeDefinition* molDef,"
825 "const G4String& label," 860 "const G4String& label,"
826 "G4MolecularConfiguration* mol 861 "G4MolecularConfiguration* molConf)",
827 "", FatalException, errMsg); 862 "", FatalException, errMsg);
828 } 863 }
829 864
830 //lock.unlock(); 865 //lock.unlock();
831 } 866 }
832 867
833 void G4MolecularConfiguration::G4MolecularConf 868 void G4MolecularConfiguration::G4MolecularConfigurationManager::AddUserID(const G4String& userID,
834 869 G4MolecularConfiguration* molecule)
835 { 870 {
836 auto it = fUserIDTable.find(userID); << 871 UserIDTable::iterator it = fUserIDTable.find(userID);
837 872
838 if(it == fUserIDTable.end()) 873 if(it == fUserIDTable.end())
839 { 874 {
840 fUserIDTable[userID] = molecule; 875 fUserIDTable[userID] = molecule;
841 } 876 }
842 else if(molecule != it->second) 877 else if(molecule != it->second)
843 { 878 {
844 // TODO improve exception 879 // TODO improve exception
845 // exception 880 // exception
846 G4ExceptionDescription description; 881 G4ExceptionDescription description;
847 description << "The user identifier " << u 882 description << "The user identifier " << userID
848 << " was already given in anot 883 << " was already given in another configuration in the table"
849 << G4endl; 884 << G4endl;
850 G4Exception("G4MolecularConfiguration::G4Mol 885 G4Exception("G4MolecularConfiguration::G4MolecularConfigurationManager::AddUserID",
851 "CONF_ALREADY_RECORDED", 886 "CONF_ALREADY_RECORDED",
852 FatalException, 887 FatalException,
853 description); 888 description);
854 } 889 }
855 } 890 }
856 891
857 //____________________________________________ 892 //______________________________________________________________________________
858 893
859 void G4MolecularConfiguration::G4MolecularConf 894 void G4MolecularConfiguration::G4MolecularConfigurationManager::
860 RemoveMolecularConfigurationFromTable(G4Molecu 895 RemoveMolecularConfigurationFromTable(G4MolecularConfiguration* configuration)
861 { 896 {
862 auto it1 = << 897 MolElectronConfTable::iterator it1 =
863 fElecOccTable.find(configuration->GetDef 898 fElecOccTable.find(configuration->GetDefinition());
864 auto end = fElecOccTable.end(); << 899 MolElectronConfTable::iterator end = fElecOccTable.end();
865 900
866 if (it1 == end) return; 901 if (it1 == end) return;
867 902
868 auto it2 = << 903 std::map<G4ElectronOccupancy, G4MolecularConfiguration*, comparator>::
>> 904 iterator it2 =
869 it1->second.find(*configuration->GetElec 905 it1->second.find(*configuration->GetElectronOccupancy());
870 906
871 if (it2 == it1->second.end()) return; 907 if (it2 == it1->second.end()) return;
872 908
873 it2->second = 0; 909 it2->second = 0;
874 // it1->second.erase(it2); 910 // it1->second.erase(it2);
875 911
876 configuration->fElectronOccupancy = nullptr; << 912 configuration->fElectronOccupancy = 0;
877 } 913 }
878 914
879 //____________________________________________ 915 //______________________________________________________________________________
880 916
881 G4MolecularConfiguration* 917 G4MolecularConfiguration*
882 G4MolecularConfiguration::G4MolecularConfigura 918 G4MolecularConfiguration::G4MolecularConfigurationManager::
883 GetMolecularConfiguration(const G4MoleculeDefi 919 GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
884 const G4String& labe 920 const G4String& label)
885 { 921 {
886 //G4AutoLock lock(&fMoleculeCreationMutex); 922 //G4AutoLock lock(&fMoleculeCreationMutex);
887 923
888 auto it1 = fLabelTable.find(molDef); << 924 MolLabelConfTable::iterator it1 = fLabelTable.find(molDef);
889 925
890 if(it1 == fLabelTable.end()) return nullptr; << 926 if(it1 == fLabelTable.end()) return 0;
891 927
892 LabelTable& table2 = it1->second; 928 LabelTable& table2 = it1->second;
893 929
894 auto it2 = table2.find(label); << 930 LabelTable::iterator it2 = table2.find(label);
895 931
896 //lock.unlock(); 932 //lock.unlock();
897 933
898 if(it2 == table2.end()) return nullptr; << 934 if(it2 == table2.end()) return 0;
899 return it2->second; 935 return it2->second;
900 } 936 }
901 937
902 //____________________________________________ 938 //______________________________________________________________________________
903 939
904 G4MolecularConfiguration* 940 G4MolecularConfiguration*
905 G4MolecularConfiguration::G4MolecularConfigura 941 G4MolecularConfiguration::G4MolecularConfigurationManager::
906 GetMolecularConfiguration(int moleculeID) 942 GetMolecularConfiguration(int moleculeID)
907 { 943 {
908 if(moleculeID > (int) fMolConfPerID.size() | 944 if(moleculeID > (int) fMolConfPerID.size() ||
909 moleculeID < 0) return nullptr; << 945 moleculeID < 0) return 0;
910 946
911 return fMolConfPerID[moleculeID]; 947 return fMolConfPerID[moleculeID];
912 } 948 }
913 949
914 //____________________________________________ 950 //______________________________________________________________________________
915 951
916 G4int 952 G4int
917 G4MolecularConfiguration::G4MolecularConfigura 953 G4MolecularConfiguration::G4MolecularConfigurationManager::
918 Insert(const G4MoleculeDefinition* molDef, 954 Insert(const G4MoleculeDefinition* molDef,
919 const G4String& l 955 const G4String& label,
920 G4MolecularConfig 956 G4MolecularConfiguration* molConf)
921 { 957 {
922 G4AutoLock lock(&fMoleculeCreationMutex); 958 G4AutoLock lock(&fMoleculeCreationMutex);
923 LabelTable& tmpMap = fLabelTable[molDef]; 959 LabelTable& tmpMap = fLabelTable[molDef];
924 auto it = tmpMap.find(label); << 960 LabelTable::iterator it = tmpMap.find(label);
925 961
926 if(it == tmpMap.end()) 962 if(it == tmpMap.end())
927 { 963 {
928 fLastMoleculeID++; 964 fLastMoleculeID++;
929 tmpMap[label] = molConf; 965 tmpMap[label] = molConf;
930 lock.unlock(); 966 lock.unlock();
931 } 967 }
932 else 968 else
933 { 969 {
934 lock.unlock(); 970 lock.unlock();
935 G4ExceptionDescription errMsg; 971 G4ExceptionDescription errMsg;
936 errMsg << "The same molecular configuratio 972 errMsg << "The same molecular configuration seemed to be recorded twice";
937 G4Exception("G4MolecularConfigurationManag 973 G4Exception("G4MolecularConfigurationManager::"
938 "SetMolecularConfiguration(con 974 "SetMolecularConfiguration(const G4MoleculeDefinition* molDef,"
939 "const G4String& label," 975 "const G4String& label,"
940 "G4MolecularConfiguration* mol 976 "G4MolecularConfiguration* molConf)",
941 "", FatalException, errMsg); 977 "", FatalException, errMsg);
942 } 978 }
943 979
944 fMolConfPerID.push_back(molConf); 980 fMolConfPerID.push_back(molConf);
945 981
946 return fLastMoleculeID; 982 return fLastMoleculeID;
947 } 983 }
948 984
949 //____________________________________________ 985 //______________________________________________________________________________
950 986
951 G4MolecularConfiguration* 987 G4MolecularConfiguration*
952 G4MolecularConfiguration::GetMolecularConfigur 988 G4MolecularConfiguration::GetMolecularConfiguration(const G4MoleculeDefinition* molDef,
953 989 const G4String& label)
954 { 990 {
955 return GetManager()->GetMolecularConfigurati 991 return GetManager()->GetMolecularConfiguration(molDef, label);
956 } 992 }
957 993
958 //____________________________________________ 994 //______________________________________________________________________________
959 995
960 G4MolecularConfiguration* 996 G4MolecularConfiguration*
961 G4MolecularConfiguration::GetMolecularConfigur 997 G4MolecularConfiguration::GetMolecularConfiguration(int moleculeID)
962 { 998 {
963 return GetManager()->GetMolecularConfigurati 999 return GetManager()->GetMolecularConfiguration(moleculeID);
964 } 1000 }
965 1001
966 //____________________________________________ 1002 //______________________________________________________________________________
967 1003
968 G4MolecularConfiguration* 1004 G4MolecularConfiguration*
969 G4MolecularConfiguration::CreateMolecularConfi 1005 G4MolecularConfiguration::CreateMolecularConfiguration(const G4String& userIdentifier,
970 1006 const G4MoleculeDefinition* molDef,
971 1007 int charge,
972 1008 const G4String& label,
973 1009 bool& wasAlreadyCreated)
974 { 1010 {
975 wasAlreadyCreated = false; 1011 wasAlreadyCreated = false;
976 G4MolecularConfiguration* molConf = 1012 G4MolecularConfiguration* molConf =
977 GetManager()->GetMolecularConfiguration( 1013 GetManager()->GetMolecularConfiguration(molDef, charge);
978 1014
979 if (molConf != nullptr) << 1015 if (molConf)
980 { 1016 {
981 if(molConf->fLabel == nullptr) << 1017 if(molConf->fLabel == 0)
982 { 1018 {
983 molConf->SetLabel(label); 1019 molConf->SetLabel(label);
984 G4ExceptionDescription wMsg ; 1020 G4ExceptionDescription wMsg ;
985 wMsg << "The molecular configuration for 1021 wMsg << "The molecular configuration for the definition named "
986 << molDef->GetName() 1022 << molDef->GetName()
987 << " with charge " << charge << " 1023 << " with charge " << charge << " has already been created "
988 "but with NO label"; 1024 "but with NO label";
989 G4Exception("G4MolecularConfiguration::C 1025 G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
990 "DOUBLE_CREATION", 1026 "DOUBLE_CREATION",
991 JustWarning, 1027 JustWarning,
992 wMsg); 1028 wMsg);
993 } 1029 }
994 else if(molConf->fLabel->empty() ) << 1030 else if(*(molConf->fLabel) == "" )
995 { 1031 {
996 molConf->SetLabel(label); 1032 molConf->SetLabel(label);
997 } 1033 }
998 else if(*(molConf->fLabel) != label) 1034 else if(*(molConf->fLabel) != label)
999 { 1035 {
1000 G4ExceptionDescription errMsg ; 1036 G4ExceptionDescription errMsg ;
1001 errMsg << "The molecular configuration 1037 errMsg << "The molecular configuration for the definition named "
1002 << molDef->GetName() 1038 << molDef->GetName()
1003 << " with charge " << charge << 1039 << " with charge " << charge << " has already been created "
1004 "but with a different label 1040 "but with a different label :"
1005 << molConf->GetLabel(); 1041 << molConf->GetLabel();
1006 G4Exception("G4MolecularConfiguration:: 1042 G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
1007 "DOUBLE_CREATION", 1043 "DOUBLE_CREATION",
1008 FatalErrorInArgument, 1044 FatalErrorInArgument,
1009 errMsg); 1045 errMsg);
1010 // KILL APP 1046 // KILL APP
1011 } 1047 }
1012 1048
1013 if(molConf->fUserIdentifier.empty()) << 1049 if(molConf->fUserIdentifier == "")
1014 { 1050 {
1015 molConf->fUserIdentifier = userIdentifi 1051 molConf->fUserIdentifier = userIdentifier;
1016 1052
1017 G4ExceptionDescription wMsg ; 1053 G4ExceptionDescription wMsg ;
1018 wMsg << "The molecular configuration fo 1054 wMsg << "The molecular configuration for the definition named "
1019 << molDef->GetName() 1055 << molDef->GetName()
1020 << " with label " << label << " 1056 << " with label " << label << " has already been created.";
1021 G4Exception("G4MolecularConfiguration:: 1057 G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
1022 "DOUBLE_CREATION", 1058 "DOUBLE_CREATION",
1023 JustWarning, 1059 JustWarning,
1024 wMsg); 1060 wMsg);
1025 } 1061 }
1026 else if(molConf->fUserIdentifier != userI 1062 else if(molConf->fUserIdentifier != userIdentifier)
1027 { 1063 {
1028 G4ExceptionDescription errMsg ; 1064 G4ExceptionDescription errMsg ;
1029 errMsg << "The molecular configuration 1065 errMsg << "The molecular configuration for the definition named "
1030 << molDef->GetName() 1066 << molDef->GetName()
1031 << " with label " << label << " 1067 << " with label " << label << " has already been created "
1032 "BUT with a different user I 1068 "BUT with a different user ID :"
1033 << molConf->fUserIdentifier; 1069 << molConf->fUserIdentifier;
1034 G4Exception("G4MolecularConfiguration:: 1070 G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
1035 "DOUBLE_CREATION", 1071 "DOUBLE_CREATION",
1036 FatalErrorInArgument, 1072 FatalErrorInArgument,
1037 errMsg); 1073 errMsg);
1038 // KILL APP 1074 // KILL APP
1039 } 1075 }
1040 1076
1041 wasAlreadyCreated = true; 1077 wasAlreadyCreated = true;
1042 return molConf; 1078 return molConf;
1043 } 1079 }
1044 << 1080 else
1045 auto newConf = << 1081 {
1046 new G4MolecularConfiguration(molDef, la << 1082 G4MolecularConfiguration* newConf =
1047 newConf->fUserIdentifier = userIdentifier; << 1083 new G4MolecularConfiguration(molDef, label, charge);
>> 1084 newConf->fUserIdentifier = userIdentifier;
1048 1085
1049 GetManager()->AddUserID(userIdentifier, new << 1086 GetManager()->AddUserID(userIdentifier, newConf);
1050 1087
1051 // G4MoleculeTable::Instance()->RecordMole 1088 // G4MoleculeTable::Instance()->RecordMolecularConfiguration(userIdentifier,
1052 // 1089 // newConf);
1053 return newConf; << 1090 return newConf;
>> 1091 }
1054 } 1092 }
1055 1093
1056 //___________________________________________ 1094 //______________________________________________________________________________
1057 1095
1058 G4MolecularConfiguration* 1096 G4MolecularConfiguration*
1059 G4MolecularConfiguration:: 1097 G4MolecularConfiguration::
1060 CreateMolecularConfiguration(const G4String& 1098 CreateMolecularConfiguration(const G4String& userIdentifier,
1061 const G4Molecule 1099 const G4MoleculeDefinition* molDef,
1062 bool& wasAlready 1100 bool& wasAlreadyCreated)
1063 { 1101 {
1064 wasAlreadyCreated = false; 1102 wasAlreadyCreated = false;
1065 G4MolecularConfiguration* preRegisteredMolC 1103 G4MolecularConfiguration* preRegisteredMolConf =
1066 GetManager()->GetMolecularConfiguration 1104 GetManager()->GetMolecularConfiguration(userIdentifier);
1067 1105
1068 if(preRegisteredMolConf != nullptr) << 1106 if(preRegisteredMolConf)
1069 { 1107 {
1070 if(preRegisteredMolConf->GetDefinition() 1108 if(preRegisteredMolConf->GetDefinition() == molDef)
1071 { 1109 {
1072 wasAlreadyCreated = true; 1110 wasAlreadyCreated = true;
1073 return preRegisteredMolConf; 1111 return preRegisteredMolConf;
1074 } 1112 }
1075 } 1113 }
1076 1114
1077 if(molDef->GetGroundStateElectronOccupancy( << 1115 if(molDef->GetGroundStateElectronOccupancy())
1078 { 1116 {
1079 const G4ElectronOccupancy& elecOcc = *mol 1117 const G4ElectronOccupancy& elecOcc = *molDef
1080 ->GetGroundStateElectronOccupancy(); 1118 ->GetGroundStateElectronOccupancy();
1081 G4MolecularConfiguration* molConf = 1119 G4MolecularConfiguration* molConf =
1082 GetManager()->GetMolecularConfigurati 1120 GetManager()->GetMolecularConfiguration(molDef, elecOcc);
1083 1121
1084 if(molConf != nullptr) << 1122 if(molConf)
1085 { 1123 {
1086 if(molConf->fUserIdentifier.empty()) << 1124 if(molConf->fUserIdentifier == "")
1087 { 1125 {
1088 molConf->fUserIdentifier = userIdenti 1126 molConf->fUserIdentifier = userIdentifier;
1089 } 1127 }
1090 else if(molConf->fUserIdentifier != use 1128 else if(molConf->fUserIdentifier != userIdentifier)
1091 { 1129 {
1092 G4ExceptionDescription errMsg; 1130 G4ExceptionDescription errMsg;
1093 errMsg << "A molecular configuration 1131 errMsg << "A molecular configuration for the definition named "
1094 << molDef->GetName() << " has 1132 << molDef->GetName() << " has already been created "
1095 "and recorded with a different 1133 "and recorded with a different user ID "
1096 << molConf->fUserIdentifier; 1134 << molConf->fUserIdentifier;
1097 G4Exception("G4MolecularConfiguration 1135 G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
1098 "DOUBLE_CREATION", 1136 "DOUBLE_CREATION",
1099 FatalErrorInArgument, 1137 FatalErrorInArgument,
1100 errMsg); 1138 errMsg);
1101 } 1139 }
1102 // TODO exception 1140 // TODO exception
1103 G4ExceptionDescription errMsg; 1141 G4ExceptionDescription errMsg;
1104 errMsg << "A molecular configuration fo 1142 errMsg << "A molecular configuration for the definition named "
1105 << molDef->GetName() << " has al 1143 << molDef->GetName() << " has already been created.";
1106 G4Exception("G4MolecularConfiguration:: 1144 G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
1107 "DOUBLE_CREATION", 1145 "DOUBLE_CREATION",
1108 JustWarning, 1146 JustWarning,
1109 errMsg); 1147 errMsg);
1110 wasAlreadyCreated = true; 1148 wasAlreadyCreated = true;
1111 return molConf; 1149 return molConf;
1112 } 1150 }
1113 << 1151 else
1114 // G4cout << "Create molConf for " << mol << 1152 {
1115 auto newConf = new G4MolecularConfigurat << 1153 // G4cout << "Create molConf for " << molDef->GetName() << G4endl;
1116 << 1154 G4MolecularConfiguration* newConf = new G4MolecularConfiguration(molDef,
1117 newConf->fUserIdentifier = userIdentifier << 1155 elecOcc);
>> 1156 newConf->fUserIdentifier = userIdentifier;
1118 1157
1119 GetManager()->AddUserID(userIdentifier, n << 1158 GetManager()->AddUserID(userIdentifier, newConf);
1120 1159
1121 // G4MoleculeTable::Instance()->RecordMo 1160 // G4MoleculeTable::Instance()->RecordMolecularConfiguration(userIdentifier,
1122 // 1161 // newConf);
1123 return newConf; << 1162 return newConf;
>> 1163 }
>> 1164 }
>> 1165 else
>> 1166 {
>> 1167 return CreateMolecularConfiguration(userIdentifier,
>> 1168 molDef,
>> 1169 molDef->GetName(),
>> 1170 molDef->GetCharge(),
>> 1171 wasAlreadyCreated);
1124 } 1172 }
1125 <<
1126 return CreateMolecularConfiguration(userIde <<
1127 molDef, <<
1128 molDef- <<
1129 molDef- <<
1130 wasAlre <<
1131 } 1173 }
1132 1174
1133 //___________________________________________ 1175 //______________________________________________________________________________
1134 1176
1135 G4MolecularConfiguration* 1177 G4MolecularConfiguration*
1136 G4MolecularConfiguration:: 1178 G4MolecularConfiguration::
1137 CreateMolecularConfiguration(const G4String& 1179 CreateMolecularConfiguration(const G4String& userIdentifier,
1138 const G4Molecule 1180 const G4MoleculeDefinition* molDef,
1139 const G4String& 1181 const G4String& label,
1140 bool& wasAlready 1182 bool& wasAlreadyCreated)
1141 { 1183 {
1142 assert(label != ""); 1184 assert(label != "");
1143 wasAlreadyCreated = false; 1185 wasAlreadyCreated = false;
1144 1186
1145 G4MolecularConfiguration* molConf = 1187 G4MolecularConfiguration* molConf =
1146 GetManager()->GetMolecularConfiguration 1188 GetManager()->GetMolecularConfiguration(molDef, label);
1147 if(molConf != nullptr) << 1189 if(molConf)
1148 { 1190 {
1149 if((molConf->fLabel != nullptr) << 1191 if(molConf->fLabel
1150 && *molConf->fLabel == label) 1192 && *molConf->fLabel == label)
1151 { 1193 {
1152 wasAlreadyCreated = true; 1194 wasAlreadyCreated = true;
1153 return molConf; 1195 return molConf;
1154 } 1196 }
1155 if(molConf->fLabel == nullptr) << 1197 else if(molConf->fLabel == 0)
1156 { 1198 {
1157 wasAlreadyCreated = true; 1199 wasAlreadyCreated = true;
1158 molConf->SetLabel(label); 1200 molConf->SetLabel(label);
1159 return molConf; 1201 return molConf;
1160 } 1202 }
1161 if(molConf->fLabel->empty()) << 1203 else if(*molConf->fLabel == "")
1162 { 1204 {
1163 wasAlreadyCreated = true; 1205 wasAlreadyCreated = true;
1164 molConf->SetLabel(label); 1206 molConf->SetLabel(label);
1165 return molConf; 1207 return molConf;
1166 } 1208 }
1167 1209
1168 molConf->PrintState(); 1210 molConf->PrintState();
1169 G4ExceptionDescription errMsg ; 1211 G4ExceptionDescription errMsg ;
1170 errMsg << "A molecular configuration for 1212 errMsg << "A molecular configuration for the definition named "
1171 << molDef->GetName() 1213 << molDef->GetName()
1172 << " has already been created " 1214 << " has already been created "
1173 "with user ID " 1215 "with user ID "
1174 << molConf->fUserIdentifier << " a 1216 << molConf->fUserIdentifier << " and label "
1175 << molConf->GetLabel(); 1217 << molConf->GetLabel();
1176 G4Exception("G4MolecularConfiguration::Cr 1218 G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
1177 "DOUBLE_CREATION", 1219 "DOUBLE_CREATION",
1178 FatalErrorInArgument, 1220 FatalErrorInArgument,
1179 errMsg); 1221 errMsg);
1180 // KILL APP 1222 // KILL APP
1181 } 1223 }
1182 else 1224 else
1183 { 1225 {
1184 auto newConf = << 1226 G4MolecularConfiguration* newConf =
1185 new G4MolecularConfiguration(molDef, 1227 new G4MolecularConfiguration(molDef,
1186 label, 1228 label,
1187 molDef->Ge 1229 molDef->GetCharge());
1188 newConf->fUserIdentifier = userIdentifier 1230 newConf->fUserIdentifier = userIdentifier;
1189 1231
1190 GetManager()->AddUserID(userIdentifier, n 1232 GetManager()->AddUserID(userIdentifier, newConf);
1191 1233
1192 // G4MoleculeTable::Instance()-> 1234 // G4MoleculeTable::Instance()->
1193 // RecordMolecularConfiguration(userId 1235 // RecordMolecularConfiguration(userIdentifier, newConf);
1194 return newConf; 1236 return newConf;
1195 } 1237 }
1196 return molConf; 1238 return molConf;
1197 } 1239 }
1198 1240
1199 //___________________________________________ 1241 //______________________________________________________________________________
1200 1242
1201 G4MolecularConfiguration* 1243 G4MolecularConfiguration*
1202 G4MolecularConfiguration:: 1244 G4MolecularConfiguration::
1203 CreateMolecularConfiguration(const G4String& 1245 CreateMolecularConfiguration(const G4String& userIdentifier,
1204 const G4Molecule 1246 const G4MoleculeDefinition* molDef,
1205 const G4String& 1247 const G4String& label,
1206 const G4Electron 1248 const G4ElectronOccupancy& eOcc,
1207 bool& wasAlready 1249 bool& wasAlreadyCreated)
1208 { 1250 {
1209 assert(label != ""); 1251 assert(label != "");
1210 wasAlreadyCreated = false; 1252 wasAlreadyCreated = false;
1211 1253
1212 G4MolecularConfiguration* molConf = 1254 G4MolecularConfiguration* molConf =
1213 GetManager()->GetMolecularConfiguration 1255 GetManager()->GetMolecularConfiguration(molDef, eOcc);
1214 1256
1215 if(molConf != nullptr) << 1257 if(molConf)
1216 { 1258 {
1217 if(molConf->GetElectronOccupancy() != nul << 1259 if(molConf->GetElectronOccupancy())
1218 { 1260 {
1219 if(*molConf->GetElectronOccupancy() == 1261 if(*molConf->GetElectronOccupancy() == eOcc)
1220 { 1262 {
1221 if((molConf->fLabel != nullptr) && *m << 1263 if(molConf->fLabel && *molConf->fLabel == label)
1222 { 1264 {
1223 wasAlreadyCreated = true; 1265 wasAlreadyCreated = true;
1224 return molConf; 1266 return molConf;
1225 } 1267 }
1226 if(molConf->fLabel == nullptr) << 1268 else if(molConf->fLabel == 0)
1227 { 1269 {
1228 wasAlreadyCreated = true; 1270 wasAlreadyCreated = true;
1229 molConf->SetLabel(label); 1271 molConf->SetLabel(label);
1230 return molConf; 1272 return molConf;
1231 } 1273 }
1232 if(molConf->fLabel->empty()) << 1274 else if(*molConf->fLabel == "")
1233 { 1275 {
1234 wasAlreadyCreated = true; 1276 wasAlreadyCreated = true;
1235 molConf->SetLabel(label); 1277 molConf->SetLabel(label);
1236 return molConf; 1278 return molConf;
1237 } 1279 }
1238 } 1280 }
1239 } 1281 }
1240 1282
1241 1283
1242 molConf->PrintState(); 1284 molConf->PrintState();
1243 G4ExceptionDescription errMsg ; 1285 G4ExceptionDescription errMsg ;
1244 errMsg << "A molecular configuration for 1286 errMsg << "A molecular configuration for the definition named "
1245 << molDef->GetName() 1287 << molDef->GetName()
1246 << " has already been created " 1288 << " has already been created "
1247 "with user ID " 1289 "with user ID "
1248 << molConf->fUserIdentifier 1290 << molConf->fUserIdentifier
1249 << " and possible different electr 1291 << " and possible different electronic state";
1250 G4Exception("G4MolecularConfiguration::Cr 1292 G4Exception("G4MolecularConfiguration::CreateMolecularConfiguration",
1251 "DOUBLE_CREATION", 1293 "DOUBLE_CREATION",
1252 FatalErrorInArgument, 1294 FatalErrorInArgument,
1253 errMsg); 1295 errMsg);
1254 } 1296 }
1255 else 1297 else
1256 { 1298 {
1257 auto newConf = << 1299 G4MolecularConfiguration* newConf =
1258 new G4MolecularConfiguration(molDef, 1300 new G4MolecularConfiguration(molDef,
1259 eOcc, 1301 eOcc,
1260 label); 1302 label);
1261 newConf->fUserIdentifier = userIdentifier 1303 newConf->fUserIdentifier = userIdentifier;
1262 1304
1263 GetManager()->AddUserID(userIdentifier, n 1305 GetManager()->AddUserID(userIdentifier, newConf);
1264 1306
1265 // G4MoleculeTable::Instance()-> 1307 // G4MoleculeTable::Instance()->
1266 // RecordMolecularConfiguration(userId 1308 // RecordMolecularConfiguration(userIdentifier, newConf);
1267 return newConf; 1309 return newConf;
1268 } 1310 }
1269 return molConf; 1311 return molConf;
1270 } 1312 }
1271 1313
1272 1314
1273 //___________________________________________ 1315 //______________________________________________________________________________
1274 1316
1275 G4MolecularConfiguration* 1317 G4MolecularConfiguration*
1276 G4MolecularConfiguration::G4MolecularConfigur 1318 G4MolecularConfiguration::G4MolecularConfigurationManager::
1277 GetOrCreateMolecularConfiguration(const G4Mol 1319 GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef,
1278 const G4Ele 1320 const G4ElectronOccupancy& eOcc)
1279 { 1321 {
1280 auto it1 = fElecOccTable.find(molDef); << 1322 MolElectronConfTable::iterator it1 = fElecOccTable.find(molDef);
1281 1323
1282 if(it1 == fElecOccTable.end()) 1324 if(it1 == fElecOccTable.end())
1283 { 1325 {
1284 return new G4MolecularConfiguration(molDe 1326 return new G4MolecularConfiguration(molDef, eOcc);
1285 } 1327 }
1286 1328
1287 ElectronOccupancyTable& table2 = it1->secon 1329 ElectronOccupancyTable& table2 = it1->second;
1288 auto it = table2.find(eOcc); << 1330 ElectronOccupancyTable::iterator it = table2.find(eOcc);
1289 1331
1290 if(it == table2.end()) 1332 if(it == table2.end())
1291 { 1333 {
1292 auto molConf = << 1334 G4MolecularConfiguration* molConf =
1293 new G4MolecularConfiguration(molDef, 1335 new G4MolecularConfiguration(molDef, eOcc);
1294 // molConf->Finalize(); 1336 // molConf->Finalize();
1295 return molConf; 1337 return molConf;
1296 } 1338 }
1297 << 1339 else
1298 return it->second; << 1340 {
>> 1341 return it->second;
>> 1342 }
>> 1343
>> 1344 return 0;
1299 } 1345 }
1300 1346
1301 //___________________________________________ 1347 //______________________________________________________________________________
1302 1348
1303 G4MolecularConfiguration* 1349 G4MolecularConfiguration*
1304 G4MolecularConfiguration::G4MolecularConfigur 1350 G4MolecularConfiguration::G4MolecularConfigurationManager::
1305 GetOrCreateMolecularConfiguration(const G4Mol 1351 GetOrCreateMolecularConfiguration(const G4MoleculeDefinition* molDef,
1306 int charge) 1352 int charge)
1307 { 1353 {
1308 auto it1 = fChargeTable.find(molDef); << 1354 MolChargeConfTable::iterator it1 = fChargeTable.find(molDef);
1309 1355
1310 if(it1 == fChargeTable.end()) 1356 if(it1 == fChargeTable.end())
1311 { 1357 {
1312 G4AutoLock lock(&fMoleculeCreationMutex); 1358 G4AutoLock lock(&fMoleculeCreationMutex);
1313 1359
1314 auto newConf = new G4MolecularConfigurat << 1360 G4MolecularConfiguration* newConf = new G4MolecularConfiguration(molDef, charge);
1315 return newConf ; 1361 return newConf ;
1316 } 1362 }
1317 1363
1318 ChargeTable& table2 = it1->second; 1364 ChargeTable& table2 = it1->second;
1319 auto it = table2.find(charge); << 1365 ChargeTable::iterator it = table2.find(charge);
1320 1366
1321 if(it == table2.end()) 1367 if(it == table2.end())
1322 { 1368 {
1323 G4AutoLock lock(&fMoleculeCreationMutex); 1369 G4AutoLock lock(&fMoleculeCreationMutex);
1324 1370
1325 auto newConf = << 1371 G4MolecularConfiguration* newConf =
1326 new G4MolecularConfiguration(molDef, 1372 new G4MolecularConfiguration(molDef, charge);
1327 // newConf->Finalize(); 1373 // newConf->Finalize();
1328 return newConf ; 1374 return newConf ;
1329 } 1375 }
1330 << 1376 else
1331 return it->second; << 1377 {
>> 1378 return it->second;
>> 1379 }
>> 1380
>> 1381 return 0;
1332 } 1382 }
1333 1383
1334 //___________________________________________ 1384 //______________________________________________________________________________
1335 1385
1336 void G4MolecularConfiguration::Serialize(std: 1386 void G4MolecularConfiguration::Serialize(std::ostream& out)
1337 { 1387 {
1338 G4String moleculeName = fMoleculeDefinition 1388 G4String moleculeName = fMoleculeDefinition->GetName();
1339 WRITE(out, moleculeName); 1389 WRITE(out, moleculeName);
1340 1390
1341 // if(fLabel) 1391 // if(fLabel)
1342 // out << fLabel; 1392 // out << fLabel;
1343 // else 1393 // else
1344 // out << ""; 1394 // out << "";
1345 WRITE(out,fDynDiffusionCoefficient); 1395 WRITE(out,fDynDiffusionCoefficient);
1346 WRITE(out,fDynVanDerVaalsRadius); 1396 WRITE(out,fDynVanDerVaalsRadius);
1347 WRITE(out,fDynDecayTime); 1397 WRITE(out,fDynDecayTime);
1348 WRITE(out,fDynMass); 1398 WRITE(out,fDynMass);
1349 WRITE(out,fDynCharge); 1399 WRITE(out,fDynCharge);
1350 WRITE(out,fMoleculeID); 1400 WRITE(out,fMoleculeID);
1351 WRITE(out,fFormatedName); 1401 WRITE(out,fFormatedName);
1352 WRITE(out,fName); 1402 WRITE(out,fName);
1353 WRITE(out,fIsFinalized); 1403 WRITE(out,fIsFinalized);
1354 } 1404 }
1355 1405
1356 //___________________________________________ 1406 //______________________________________________________________________________
1357 1407
1358 void G4MolecularConfiguration::Unserialize(st 1408 void G4MolecularConfiguration::Unserialize(std::istream& in)
1359 { 1409 {
1360 G4String moleculeName; 1410 G4String moleculeName;
1361 READ(in, moleculeName); 1411 READ(in, moleculeName);
1362 fMoleculeDefinition = 1412 fMoleculeDefinition =
1363 G4MoleculeTable::Instance()->GetMolecul 1413 G4MoleculeTable::Instance()->GetMoleculeDefinition(moleculeName);
1364 1414
1365 // G4String label; 1415 // G4String label;
1366 // 1416 //
1367 // in.read((char*)(&label), sizeof(label)); 1417 // in.read((char*)(&label), sizeof(label));
1368 // 1418 //
1369 // if(label) 1419 // if(label)
1370 // fLabel = new G4String(label); 1420 // fLabel = new G4String(label);
1371 // else 1421 // else
1372 // fLabel = 0; 1422 // fLabel = 0;
1373 READ(in,fDynDiffusionCoefficient); 1423 READ(in,fDynDiffusionCoefficient);
1374 READ(in,fDynVanDerVaalsRadius); 1424 READ(in,fDynVanDerVaalsRadius);
1375 READ(in,fDynDecayTime); 1425 READ(in,fDynDecayTime);
1376 READ(in,fDynMass); 1426 READ(in,fDynMass);
1377 READ(in,fDynCharge); 1427 READ(in,fDynCharge);
1378 READ(in,fMoleculeID); 1428 READ(in,fMoleculeID);
1379 READ(in,fFormatedName); 1429 READ(in,fFormatedName);
1380 READ(in,fName); 1430 READ(in,fName);
1381 READ(in,fIsFinalized); 1431 READ(in,fIsFinalized);
1382 } 1432 }
1383 1433
1384 //___________________________________________ 1434 //______________________________________________________________________________
1385 1435
1386 G4MolecularConfiguration* G4MolecularConfigur 1436 G4MolecularConfiguration* G4MolecularConfiguration::Load(std::istream& in)
1387 { 1437 {
1388 return new G4MolecularConfiguration(in); 1438 return new G4MolecularConfiguration(in);
1389 } 1439 }
1390 1440
1391 //___________________________________________ 1441 //______________________________________________________________________________
1392 1442
1393 G4MolecularConfiguration::G4MolecularConfigur 1443 G4MolecularConfiguration::G4MolecularConfiguration(std::istream& in)
1394 { 1444 {
1395 fLabel = nullptr; // TODO: for now not seri << 1445 fLabel = 0; // TODO: for now not serialized
1396 Unserialize(in); 1446 Unserialize(in);
1397 fMoleculeDefinition = nullptr; << 1447 fMoleculeDefinition = 0;
1398 fElectronOccupancy = nullptr; << 1448 fElectronOccupancy = 0;
1399 if(fElectronOccupancy != nullptr) << 1449 if(fElectronOccupancy)
1400 { 1450 {
1401 GetManager()->Insert(fMoleculeDefinition, 1451 GetManager()->Insert(fMoleculeDefinition, *fElectronOccupancy, this);
1402 fElectronOccupancy = 1452 fElectronOccupancy =
1403 GetManager()->FindCommonElectronOccup 1453 GetManager()->FindCommonElectronOccupancy(fMoleculeDefinition,
1404 1454 *fElectronOccupancy);
1405 1455
1406 if(fLabel != nullptr) << 1456 if(fLabel)
1407 { 1457 {
1408 GetManager()->RecordNewlyLabeledConfigu 1458 GetManager()->RecordNewlyLabeledConfiguration(this);
1409 } 1459 }
1410 } 1460 }
1411 else if(fLabel != nullptr) << 1461 else if(fLabel)
1412 { 1462 {
1413 fMoleculeID = GetManager()->Insert(fMolec 1463 fMoleculeID = GetManager()->Insert(fMoleculeDefinition, *fLabel, this);
1414 } 1464 }
1415 else if(fDynCharge != 0) << 1465 else if(fDynCharge)
1416 { 1466 {
1417 fMoleculeID = GetManager()->Insert(fMolec 1467 fMoleculeID = GetManager()->Insert(fMoleculeDefinition, fDynCharge, this);
1418 } 1468 }
1419 } 1469 }
1420 1470
1421 //___________________________________________ 1471 //______________________________________________________________________________
1422 1472
1423 void G4MolecularConfiguration::SetUserID(cons 1473 void G4MolecularConfiguration::SetUserID(const G4String& userID)
1424 { 1474 {
1425 fUserIdentifier = userID; 1475 fUserIdentifier = userID;
1426 GetManager()->AddUserID(userID, this); 1476 GetManager()->AddUserID(userID, this);
1427 // G4MoleculeTable::Instance()->RecordMolecu 1477 // G4MoleculeTable::Instance()->RecordMolecularConfiguration(userID, this);
1428 } 1478 }
1429 1479
1430 //___________________________________________ 1480 //______________________________________________________________________________
1431 1481
1432 double G4MolecularConfiguration::DiffCoeffWat 1482 double G4MolecularConfiguration::DiffCoeffWater(double temperature_K)
1433 { 1483 {
1434 return pow(10, 4.311 1484 return pow(10, 4.311
1435 - 2.722e3/temperature_K 1485 - 2.722e3/temperature_K
1436 + 8.565e5/(temperature_K *temper 1486 + 8.565e5/(temperature_K *temperature_K)
1437 - 1.181e8/(temperature_K*tempera 1487 - 1.181e8/(temperature_K*temperature_K*temperature_K ))*1e-9*m2/s;
1438 } 1488 }
1439 1489
1440 //___________________________________________ 1490 //______________________________________________________________________________
1441 1491
1442 void 1492 void
1443 G4MolecularConfiguration:: 1493 G4MolecularConfiguration::
1444 ScaleAllDiffusionCoefficientsOnWater(double t 1494 ScaleAllDiffusionCoefficientsOnWater(double temperature_K)
1445 { 1495 {
1446 double D_water_0 = DiffCoeffWater(fgTempera 1496 double D_water_0 = DiffCoeffWater(fgTemperature);
1447 double D_water_f = DiffCoeffWater(temperatu 1497 double D_water_f = DiffCoeffWater(temperature_K);
1448 1498
1449 G4cout << "Scaling factor = " << D_water_f/ 1499 G4cout << "Scaling factor = " << D_water_f/D_water_0 << G4endl;
1450 1500
1451 G4ConfigurationIterator it = 1501 G4ConfigurationIterator it =
1452 G4MoleculeTable::Instance()->GetConfigu 1502 G4MoleculeTable::Instance()->GetConfigurationIterator();
1453 1503
1454 while(it()) 1504 while(it())
1455 { 1505 {
1456 G4MolecularConfiguration* conf = it.value 1506 G4MolecularConfiguration* conf = it.value();
1457 double D_0 = conf->GetDiffusionCoefficien 1507 double D_0 = conf->GetDiffusionCoefficient() ;
1458 double D_f = D_water_f * D_0 /D_water_0; 1508 double D_f = D_water_f * D_0 /D_water_0;
1459 conf->SetDiffusionCoefficient(D_f); 1509 conf->SetDiffusionCoefficient(D_f);
1460 }; 1510 };
1461 } 1511 }
1462 1512
1463 //___________________________________________ 1513 //______________________________________________________________________________
1464 1514
1465 void G4MolecularConfiguration::CreateDefaultD 1515 void G4MolecularConfiguration::CreateDefaultDiffCoeffParam()
1466 { 1516 {
1467 if(!static_cast<bool>(fDiffParam)) << 1517 if(bool(fDiffParam) == false)
1468 { 1518 {
1469 fDiffParam = &G4MolecularConfiguration::R 1519 fDiffParam = &G4MolecularConfiguration::ReturnDefaultDiffCoeff;
1470 } 1520 }
1471 } 1521 }
1472 1522
1473 //___________________________________________ 1523 //______________________________________________________________________________
1474 1524
1475 void G4MolecularConfiguration::SetGlobalTempe 1525 void G4MolecularConfiguration::SetGlobalTemperature(G4double temperature)
1476 { 1526 {
1477 ScaleAllDiffusionCoefficientsOnWater(temper 1527 ScaleAllDiffusionCoefficientsOnWater(temperature);
1478 fgTemperature = temperature; 1528 fgTemperature = temperature;
1479 } 1529 }
1480 1530
1481 //___________________________________________ 1531 //______________________________________________________________________________
1482 1532
1483 G4double G4MolecularConfiguration::GetGlobalT 1533 G4double G4MolecularConfiguration::GetGlobalTemperature()
1484 { 1534 {
1485 return fgTemperature; 1535 return fgTemperature;
1486 } 1536 }
1487 1537
1488 //___________________________________________ 1538 //______________________________________________________________________________
1489 1539
1490 G4MolecularConfiguration* 1540 G4MolecularConfiguration*
1491 G4MolecularConfiguration:: 1541 G4MolecularConfiguration::
1492 G4MolecularConfigurationManager::GetMolecular 1542 G4MolecularConfigurationManager::GetMolecularConfiguration(const G4String& userID)
1493 { 1543 {
1494 for(auto it : fMolConfPerID) 1544 for(auto it : fMolConfPerID)
1495 { 1545 {
1496 if(it->GetUserID() == userID) return it; 1546 if(it->GetUserID() == userID) return it;
1497 } 1547 }
1498 return nullptr; << 1548 return 0;
1499 } 1549 }
1500 1550
1501 //___________________________________________ 1551 //______________________________________________________________________________
1502 1552
1503 G4MolecularConfiguration* 1553 G4MolecularConfiguration*
1504 G4MolecularConfiguration::GetMolecularConfigu 1554 G4MolecularConfiguration::GetMolecularConfiguration(const G4String& userID)
1505 { 1555 {
1506 return GetManager()->GetMolecularConfigurat 1556 return GetManager()->GetMolecularConfiguration(userID);
1507 } 1557 }
1508 1558
1509 //___________________________________________ 1559 //______________________________________________________________________________
1510 1560
1511 void G4MolecularConfiguration::FinalizeAll() 1561 void G4MolecularConfiguration::FinalizeAll()
1512 { 1562 {
1513 const std::vector<G4MolecularConfiguration* 1563 const std::vector<G4MolecularConfiguration*>& species =
1514 GetManager()->GetAllSpecies(); 1564 GetManager()->GetAllSpecies();
1515 1565
1516 for(auto specie : species) << 1566 for(size_t i = 0; i < species.size() ; ++i)
1517 { 1567 {
1518 specie->Finalize(); << 1568 species[i]->Finalize();
1519 } <<
1520 <<
1521 } <<
1522 <<
1523 void G4MolecularConfiguration::PrintAll() //h <<
1524 { <<
1525 const std::vector<G4MolecularConfiguration* <<
1526 GetManager()->GetAllSpecies(); <<
1527 G4cout<<G4endl; <<
1528 G4cout<<"Molecular Config"<<std::setw(25)<< <<
1529 G4cout<<"__________________________________ <<
1530 "________________________________ <<
1531 for(auto specie : species) <<
1532 { <<
1533 G4cout<<specie->GetName() <<
1534 <<std::setw(G4int(30 - specie->Get <<
1535 <<right<<specie->GetDiffusionCoeff <<
1536 <<specie->GetVanDerVaalsRadius()/C <<
1537 G4cout<<"________________________________ <<
1538 "______________________________ <<
1539 } 1569 }
1540 1570
1541 } 1571 }
1542 1572