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26 // 26 //
27 27
28 // Created by Z. Francis 28 // Created by Z. Francis
29 29
30 #include "G4DNASancheExcitationModel.hh" 30 #include "G4DNASancheExcitationModel.hh"
31 #include "G4SystemOfUnits.hh" 31 #include "G4SystemOfUnits.hh"
32 #include "G4DNAMolecularMaterial.hh" 32 #include "G4DNAMolecularMaterial.hh"
33 33
34 //....oooOO0OOooo........oooOO0OOooo........oo 34 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
35 35
36 using namespace std; 36 using namespace std;
37 37
38 //#define SANCHE_VERBOSE 38 //#define SANCHE_VERBOSE
39 39
40 //....oooOO0OOooo........oooOO0OOooo........oo 40 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
41 41
42 G4DNASancheExcitationModel::G4DNASancheExcitat 42 G4DNASancheExcitationModel::G4DNASancheExcitationModel(const G4ParticleDefinition*,
43 43 const G4String& nam) :
44 G4VEmModel(nam) << 44 G4VEmModel(nam), isInitialised(false)
45 { 45 {
46 fpWaterDensity = nullptr; << 46 fpWaterDensity = 0;
47 47
48 SetLowEnergyLimit(2.*eV); 48 SetLowEnergyLimit(2.*eV);
49 SetHighEnergyLimit(100*eV); 49 SetHighEnergyLimit(100*eV);
50 nLevels = 9; 50 nLevels = 9;
51 51
52 verboseLevel = 0; 52 verboseLevel = 0;
53 // Verbosity scale: 53 // Verbosity scale:
54 // 0 = nothing 54 // 0 = nothing
55 // 1 = warning for energy non-conservation 55 // 1 = warning for energy non-conservation
56 // 2 = details of energy budget 56 // 2 = details of energy budget
57 // 3 = calculation of cross sections, file o 57 // 3 = calculation of cross sections, file openings, sampling of atoms
58 // 4 = entering in methods 58 // 4 = entering in methods
59 59
60 #ifdef SANCHE_VERBOSE 60 #ifdef SANCHE_VERBOSE
61 if (verboseLevel > 0) 61 if (verboseLevel > 0)
62 { 62 {
63 G4cout << "Sanche Excitation model is cons 63 G4cout << "Sanche Excitation model is constructed "
64 << G4endl 64 << G4endl
65 << "Energy range: " 65 << "Energy range: "
66 << LowEnergyLimit() / eV << " eV - 66 << LowEnergyLimit() / eV << " eV - "
67 << HighEnergyLimit() / eV << " eV" 67 << HighEnergyLimit() / eV << " eV"
68 << G4endl; 68 << G4endl;
69 } 69 }
70 #endif 70 #endif
71 71
72 fParticleChangeForGamma = nullptr; << 72 fParticleChangeForGamma = 0;
73 fpWaterDensity = nullptr; << 73 fpWaterDensity = 0;
74 74
75 // Selection of stationary mode 75 // Selection of stationary mode
76 76
77 statCode = false; 77 statCode = false;
78 } 78 }
79 79
80 //....oooOO0OOooo........oooOO0OOooo........oo 80 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
81 81
82 G4DNASancheExcitationModel::~G4DNASancheExcita 82 G4DNASancheExcitationModel::~G4DNASancheExcitationModel()
83 = default; << 83 {
>> 84 }
84 85
85 //....oooOO0OOooo........oooOO0OOooo........oo 86 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
86 87
87 void 88 void
88 G4DNASancheExcitationModel:: 89 G4DNASancheExcitationModel::
89 Initialise(const G4ParticleDefinition* /*parti 90 Initialise(const G4ParticleDefinition* /*particle*/,
90 const G4DataVector& /*cuts*/) 91 const G4DataVector& /*cuts*/)
91 { 92 {
92 93
93 #ifdef SANCHE_VERBOSE 94 #ifdef SANCHE_VERBOSE
94 if (verboseLevel > 3) 95 if (verboseLevel > 3)
95 { 96 {
96 G4cout << "Calling G4DNASancheExcitationMo 97 G4cout << "Calling G4DNASancheExcitationModel::Initialise()"
97 << G4endl; 98 << G4endl;
98 } 99 }
99 #endif 100 #endif
100 101
101 // Energy limits 102 // Energy limits
102 103
103 if (LowEnergyLimit() < 2.*eV) 104 if (LowEnergyLimit() < 2.*eV)
104 { 105 {
105 G4Exception("*** WARNING : the G4DNASanche 106 G4Exception("*** WARNING : the G4DNASancheExcitationModel class is not "
106 "validated below 2 eV !", 107 "validated below 2 eV !",
107 "", JustWarning, ""); 108 "", JustWarning, "");
108 } 109 }
109 110
110 if (HighEnergyLimit() > 100.*eV) 111 if (HighEnergyLimit() > 100.*eV)
111 { 112 {
112 G4cout << "G4DNASancheExcitationModel: hig 113 G4cout << "G4DNASancheExcitationModel: high energy limit decreased from " <<
113 HighEnergyLimit()/eV << " eV to " << 100. 114 HighEnergyLimit()/eV << " eV to " << 100. << " eV" << G4endl;
114 SetHighEnergyLimit(100.*eV); 115 SetHighEnergyLimit(100.*eV);
115 } 116 }
116 117
117 // 118 //
118 #ifdef SANCHE_VERBOSE 119 #ifdef SANCHE_VERBOSE
119 if (verboseLevel > 0) 120 if (verboseLevel > 0)
120 { 121 {
121 G4cout << "Sanche Excitation model is init 122 G4cout << "Sanche Excitation model is initialized " << G4endl
122 << "Energy range: " 123 << "Energy range: "
123 << LowEnergyLimit() / eV << " eV - " 124 << LowEnergyLimit() / eV << " eV - "
124 << HighEnergyLimit() / eV << " eV" 125 << HighEnergyLimit() / eV << " eV"
125 << G4endl; 126 << G4endl;
126 } 127 }
127 #endif 128 #endif
128 129
129 // Initialize water density pointer 130 // Initialize water density pointer
130 fpWaterDensity = G4DNAMolecularMaterial::Ins 131 fpWaterDensity = G4DNAMolecularMaterial::Instance()->
131 GetNumMolPerVolTableFor(G4Material::GetM 132 GetNumMolPerVolTableFor(G4Material::GetMaterial("G4_WATER"));
132 133
133 if (isInitialised) {return;} 134 if (isInitialised) {return;}
134 135
135 fParticleChangeForGamma = GetParticleChangeF 136 fParticleChangeForGamma = GetParticleChangeForGamma();
136 isInitialised = true; 137 isInitialised = true;
137 138
138 const char *path = G4FindDataDir("G4LEDATA") << 139 char *path = getenv("G4LEDATA");
139 std::ostringstream eFullFileName; 140 std::ostringstream eFullFileName;
140 eFullFileName << path << "/dna/sigma_excitat 141 eFullFileName << path << "/dna/sigma_excitationvib_e_sanche.dat";
141 std::ifstream input(eFullFileName.str().c_st 142 std::ifstream input(eFullFileName.str().c_str());
142 143
143 if (!input) 144 if (!input)
144 { 145 {
145 G4Exception("G4DNASancheExcitationModel::I 146 G4Exception("G4DNASancheExcitationModel::Initialise","em0003",
146 FatalException,"Missing data file:/dna 147 FatalException,"Missing data file:/dna/sigma_excitationvib_e_sanche.dat");
147 } 148 }
148 149
149 // March 25th, 2014 - Vaclav Stepan, Sebasti 150 // March 25th, 2014 - Vaclav Stepan, Sebastien Incerti
150 // Added clear for MT 151 // Added clear for MT
151 tdummyVec.clear(); 152 tdummyVec.clear();
152 // 153 //
153 154
154 G4double t; 155 G4double t;
155 G4double xs; 156 G4double xs;
156 157
157 while(!input.eof()) 158 while(!input.eof())
158 { 159 {
159 input>>t; 160 input>>t;
160 tdummyVec.push_back(t); 161 tdummyVec.push_back(t);
161 162
162 fEnergyLevelXS.emplace_back(); << 163 fEnergyLevelXS.push_back(std::vector<G4double>());
163 fEnergyTotalXS.push_back(0); 164 fEnergyTotalXS.push_back(0);
164 std::vector<G4double>& levelXS = fEnergyLe 165 std::vector<G4double>& levelXS = fEnergyLevelXS.back();
165 levelXS.reserve(9); 166 levelXS.reserve(9);
166 167
167 // G4cout<<t; 168 // G4cout<<t;
168 169
169 for(size_t i = 0 ; i < 9 ;++i) 170 for(size_t i = 0 ; i < 9 ;++i)
170 { 171 {
171 input>>xs; 172 input>>xs;
172 levelXS.push_back(xs); 173 levelXS.push_back(xs);
173 fEnergyTotalXS.back() += xs; 174 fEnergyTotalXS.back() += xs;
174 // G4cout <<" " << levelXS[i]; 175 // G4cout <<" " << levelXS[i];
175 } 176 }
176 177
177 // G4cout << G4endl; 178 // G4cout << G4endl;
178 } 179 }
179 } 180 }
180 181
181 //....oooOO0OOooo........oooOO0OOooo........oo 182 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
182 183
183 G4double G4DNASancheExcitationModel::CrossSect 184 G4double G4DNASancheExcitationModel::CrossSectionPerVolume(const G4Material* material,
184 185 const G4ParticleDefinition*
185 #ifdef SANCHE_VERBOSE 186 #ifdef SANCHE_VERBOSE
186 187 particleDefinition
187 #endif 188 #endif
188 189 ,
189 190 G4double ekin,
190 191 G4double,
191 192 G4double)
192 { 193 {
193 #ifdef SANCHE_VERBOSE 194 #ifdef SANCHE_VERBOSE
194 if (verboseLevel > 3) 195 if (verboseLevel > 3)
195 { 196 {
196 G4cout << "Calling CrossSectionPerVolume() 197 G4cout << "Calling CrossSectionPerVolume() of G4DNASancheExcitationModel"
197 << G4endl; 198 << G4endl;
198 } 199 }
199 #endif 200 #endif
200 201
201 // Calculate total cross section for model 202 // Calculate total cross section for model
202 203
203 G4double sigma = 0.; 204 G4double sigma = 0.;
204 205
205 G4double waterDensity = (*fpWaterDensity)[ma 206 G4double waterDensity = (*fpWaterDensity)[material->GetIndex()];
206 207
207 if (ekin >= LowEnergyLimit() && ekin <= High 208 if (ekin >= LowEnergyLimit() && ekin <= HighEnergyLimit())
208 sigma = TotalCrossSection(ekin); 209 sigma = TotalCrossSection(ekin);
209 210
210 #ifdef SANCHE_VERBOSE 211 #ifdef SANCHE_VERBOSE
211 if (verboseLevel > 2) 212 if (verboseLevel > 2)
212 { 213 {
213 G4cout << "_______________________________ 214 G4cout << "__________________________________" << G4endl;
214 G4cout << "=== G4DNASancheExcitationModel 215 G4cout << "=== G4DNASancheExcitationModel - XS INFO START" << G4endl;
215 G4cout << "=== Kinetic energy(eV)=" << eki 216 G4cout << "=== Kinetic energy(eV)=" << ekin/eV << " particle : " << particleDefinition->GetParticleName() << G4endl;
216 G4cout << "=== Cross section per water mol 217 G4cout << "=== Cross section per water molecule (cm^2)=" << sigma/cm/cm << G4endl;
217 G4cout << "=== Cross section per water mol 218 G4cout << "=== Cross section per water molecule (cm^-1)=" << sigma*waterDensity/(1./cm) << G4endl;
218 G4cout << "=== G4DNASancheExcitationModel 219 G4cout << "=== G4DNASancheExcitationModel - XS INFO END" << G4endl;
219 } 220 }
220 #endif 221 #endif
221 222
222 return sigma*2.*waterDensity; 223 return sigma*2.*waterDensity;
223 // see papers for factor 2 description (liqu 224 // see papers for factor 2 description (liquid phase)
224 } 225 }
225 226
226 //....oooOO0OOooo........oooOO0OOooo........oo 227 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
227 228
228 void G4DNASancheExcitationModel::SampleSeconda 229 void G4DNASancheExcitationModel::SampleSecondaries(std::vector<
229 230 G4DynamicParticle*>*,
230 231 const G4MaterialCutsCouple*,
231 232 const G4DynamicParticle* aDynamicElectron,
232 233 G4double,
233 234 G4double)
234 { 235 {
235 #ifdef SANCHE_VERBOSE 236 #ifdef SANCHE_VERBOSE
236 if (verboseLevel > 3) 237 if (verboseLevel > 3)
237 { 238 {
238 G4cout << "Calling SampleSecondaries() of 239 G4cout << "Calling SampleSecondaries() of G4DNASancheExcitationModel"
239 << G4endl; 240 << G4endl;
240 } 241 }
241 #endif 242 #endif
242 243
243 G4double electronEnergy0 = aDynamicElectron- 244 G4double electronEnergy0 = aDynamicElectron->GetKineticEnergy();
244 G4int level = RandomSelect(electronEnergy0); 245 G4int level = RandomSelect(electronEnergy0);
245 G4double excitationEnergy = VibrationEnergy( 246 G4double excitationEnergy = VibrationEnergy(level); // levels go from 0 to 8
246 G4double newEnergy = electronEnergy0 - excit 247 G4double newEnergy = electronEnergy0 - excitationEnergy;
247 248
248 /* 249 /*
249 if (electronEnergy0 < highEnergyLimit) 250 if (electronEnergy0 < highEnergyLimit)
250 { 251 {
251 if (newEnergy >= lowEnergyLimit) 252 if (newEnergy >= lowEnergyLimit)
252 { 253 {
253 fParticleChangeForGamma->ProposeMomentu 254 fParticleChangeForGamma->ProposeMomentumDirection(aDynamicElectron->GetMomentumDirection());
254 fParticleChangeForGamma->SetProposedKin 255 fParticleChangeForGamma->SetProposedKineticEnergy(newEnergy);
255 fParticleChangeForGamma->ProposeLocalEn 256 fParticleChangeForGamma->ProposeLocalEnergyDeposit(excitationEnergy);
256 } 257 }
257 258
258 else 259 else
259 { 260 {
260 fParticleChangeForGamma->ProposeTrackSt 261 fParticleChangeForGamma->ProposeTrackStatus(fStopAndKill);
261 fParticleChangeForGamma->ProposeLocalEn 262 fParticleChangeForGamma->ProposeLocalEnergyDeposit(electronEnergy0);
262 } 263 }
263 } 264 }
264 */ 265 */
265 266
266 if (electronEnergy0 <= HighEnergyLimit() && 267 if (electronEnergy0 <= HighEnergyLimit() && newEnergy>0.)
267 { 268 {
268 269
269 if (!statCode) 270 if (!statCode)
270 { 271 {
271 fParticleChangeForGamma->ProposeMomentum 272 fParticleChangeForGamma->ProposeMomentumDirection(aDynamicElectron->GetMomentumDirection());
272 fParticleChangeForGamma->SetProposedKine 273 fParticleChangeForGamma->SetProposedKineticEnergy(newEnergy);
273 fParticleChangeForGamma->ProposeLocalEne 274 fParticleChangeForGamma->ProposeLocalEnergyDeposit(excitationEnergy);
274 } 275 }
275 276
276 else 277 else
277 { 278 {
278 fParticleChangeForGamma->ProposeMomentum 279 fParticleChangeForGamma->ProposeMomentumDirection(aDynamicElectron->GetMomentumDirection());
279 fParticleChangeForGamma->SetProposedKine 280 fParticleChangeForGamma->SetProposedKineticEnergy(electronEnergy0);
280 fParticleChangeForGamma->ProposeLocalEne 281 fParticleChangeForGamma->ProposeLocalEnergyDeposit(excitationEnergy);
281 } 282 }
282 283
283 } 284 }
284 285
285 // 286 //
286 } 287 }
287 288
288 //....oooOO0OOooo........oooOO0OOooo........oo 289 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
289 290
290 G4double G4DNASancheExcitationModel::PartialCr 291 G4double G4DNASancheExcitationModel::PartialCrossSection(G4double t,
291 292 G4int level)
292 { 293 {
293 // Protection against out of boundary access 294 // Protection against out of boundary access
294 if (t/eV==tdummyVec.back()) t=t*(1.-1e-12); 295 if (t/eV==tdummyVec.back()) t=t*(1.-1e-12);
295 // 296 //
296 297
297 auto t2 = std::upper_bound(tdummyVec.begin() << 298 std::vector<G4double>::iterator t2 = std::upper_bound(tdummyVec.begin(),
298 299 tdummyVec.end(), t / eV);
299 auto t1 = t2 - 1; << 300 std::vector<G4double>::iterator t1 = t2 - 1;
300 301
301 size_t i1 = t1 - tdummyVec.begin(); 302 size_t i1 = t1 - tdummyVec.begin();
302 size_t i2 = t2 - tdummyVec.begin(); 303 size_t i2 = t2 - tdummyVec.begin();
303 304
304 G4double sigma = LinInterpolate((*t1), (*t2) 305 G4double sigma = LinInterpolate((*t1), (*t2),
305 t / eV, 306 t / eV,
306 fEnergyLevelXS 307 fEnergyLevelXS[i1][level],
307 fEnergyLevelXS 308 fEnergyLevelXS[i2][level]);
308 309
309 static const G4double conv_factor = 1e-16 * 310 static const G4double conv_factor = 1e-16 * cm * cm;
310 311
311 sigma *= conv_factor; 312 sigma *= conv_factor;
312 if (sigma == 0.) sigma = 1e-30; 313 if (sigma == 0.) sigma = 1e-30;
313 return (sigma); 314 return (sigma);
314 } 315 }
315 316
316 //....oooOO0OOooo........oooOO0OOooo........oo 317 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
317 318
318 G4double G4DNASancheExcitationModel::TotalCros 319 G4double G4DNASancheExcitationModel::TotalCrossSection(G4double t)
319 { 320 {
320 // Protection against out of boundary access 321 // Protection against out of boundary access
321 if (t/eV==tdummyVec.back()) t=t*(1.-1e-12); 322 if (t/eV==tdummyVec.back()) t=t*(1.-1e-12);
322 // 323 //
323 324
324 auto t2 = std::upper_bound(tdummyVec.begin() << 325 std::vector<G4double>::iterator t2 = std::upper_bound(tdummyVec.begin(),
325 326 tdummyVec.end(), t / eV);
326 auto t1 = t2 - 1; << 327 std::vector<G4double>::iterator t1 = t2 - 1;
327 328
328 size_t i1 = t1 - tdummyVec.begin(); 329 size_t i1 = t1 - tdummyVec.begin();
329 size_t i2 = t2 - tdummyVec.begin(); 330 size_t i2 = t2 - tdummyVec.begin();
330 331
331 G4double sigma = LinInterpolate((*t1), (*t2) 332 G4double sigma = LinInterpolate((*t1), (*t2),
332 t / eV, 333 t / eV,
333 fEnergyTotalXS 334 fEnergyTotalXS[i1],
334 fEnergyTotalXS 335 fEnergyTotalXS[i2]);
335 336
336 static const G4double conv_factor = 1e-16 * 337 static const G4double conv_factor = 1e-16 * cm * cm;
337 338
338 sigma *= conv_factor; 339 sigma *= conv_factor;
339 if (sigma == 0.) sigma = 1e-30; 340 if (sigma == 0.) sigma = 1e-30;
340 return (sigma); 341 return (sigma);
341 } 342 }
342 343
343 //....oooOO0OOooo........oooOO0OOooo........oo 344 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
344 345
345 G4double G4DNASancheExcitationModel::Vibration 346 G4double G4DNASancheExcitationModel::VibrationEnergy(G4int level)
346 { 347 {
347 static G4double energies[9] = { 0.01, 0.024, 348 static G4double energies[9] = { 0.01, 0.024, 0.061, 0.092, 0.204, 0.417, 0.460,
348 0.500, 0.835 }; 349 0.500, 0.835 };
349 return (energies[level] * eV); 350 return (energies[level] * eV);
350 } 351 }
351 352
352 //....oooOO0OOooo........oooOO0OOooo........oo 353 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
353 354
354 G4int G4DNASancheExcitationModel::RandomSelect 355 G4int G4DNASancheExcitationModel::RandomSelect(G4double k)
355 { 356 {
356 357
357 // Level Selection Counting can be done here 358 // Level Selection Counting can be done here !
358 359
359 G4int i = nLevels; 360 G4int i = nLevels;
360 G4double value = 0.; 361 G4double value = 0.;
361 std::deque<G4double> values; 362 std::deque<G4double> values;
362 363
363 while (i > 0) 364 while (i > 0)
364 { 365 {
365 i--; 366 i--;
366 G4double partial = PartialCrossSection(k, 367 G4double partial = PartialCrossSection(k, i);
367 values.push_front(partial); 368 values.push_front(partial);
368 value += partial; 369 value += partial;
369 } 370 }
370 371
371 value *= G4UniformRand(); 372 value *= G4UniformRand();
372 373
373 i = nLevels; 374 i = nLevels;
374 375
375 while (i > 0) 376 while (i > 0)
376 { 377 {
377 i--; 378 i--;
378 if (values[i] > value) 379 if (values[i] > value)
379 { 380 {
380 //outcount<<i<<" "<<VibrationEnergy(i)< 381 //outcount<<i<<" "<<VibrationEnergy(i)<<G4endl;
381 return i; 382 return i;
382 } 383 }
383 value -= values[i]; 384 value -= values[i];
384 } 385 }
385 386
386 //outcount<<0<<" "<<VibrationEnergy(0)<<G4e 387 //outcount<<0<<" "<<VibrationEnergy(0)<<G4endl;
387 388
388 return 0; 389 return 0;
389 } 390 }
390 391
391 //....oooOO0OOooo........oooOO0OOooo........oo 392 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
392 393
393 G4double G4DNASancheExcitationModel::Sum(G4dou 394 G4double G4DNASancheExcitationModel::Sum(G4double k)
394 { 395 {
395 G4double totalCrossSection = 0.; 396 G4double totalCrossSection = 0.;
396 397
397 for (G4int i = 0; i < nLevels; i++) 398 for (G4int i = 0; i < nLevels; i++)
398 { 399 {
399 totalCrossSection += PartialCrossSection(k 400 totalCrossSection += PartialCrossSection(k, i);
400 } 401 }
401 402
402 return totalCrossSection; 403 return totalCrossSection;
403 } 404 }
404 405
405 //....oooOO0OOooo........oooOO0OOooo........oo 406 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
406 407
407 G4double G4DNASancheExcitationModel::LinInterp 408 G4double G4DNASancheExcitationModel::LinInterpolate(G4double e1,
408 409 G4double e2,
409 410 G4double e,
410 411 G4double xs1,
411 412 G4double xs2)
412 { 413 {
413 G4double a = (xs2 - xs1) / (e2 - e1); 414 G4double a = (xs2 - xs1) / (e2 - e1);
414 G4double b = xs2 - a * e2; 415 G4double b = xs2 - a * e2;
415 G4double value = a * e + b; 416 G4double value = a * e + b;
416 // G4cout<<"interP >> "<<e1<<" "<<e2<<" " 417 // G4cout<<"interP >> "<<e1<<" "<<e2<<" "<<e<<" "
417 // <<xs1<<" "<<xs2<<" "<<a<<" "<<b<<" "< 418 // <<xs1<<" "<<xs2<<" "<<a<<" "<<b<<" "<<value<<G4endl;
418 419
419 return value; 420 return value;
420 } 421 }
421 422
422 423