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25 // 25 //
26 /* 26 /*
27 * G4ReactionTableMessenger.cc 27 * G4ReactionTableMessenger.cc
28 * 28 *
29 * Created on: Sep 14, 2015 29 * Created on: Sep 14, 2015
30 * Author: mkaramit 30 * Author: mkaramit
31 */ 31 */
32 32
33 #include <G4ReactionTableMessenger.hh> 33 #include <G4ReactionTableMessenger.hh>
34 #include <G4DNAMolecularReactionTable.hh> 34 #include <G4DNAMolecularReactionTable.hh>
35 #include <G4UIcmdWithAString.hh> 35 #include <G4UIcmdWithAString.hh>
36 #include <G4UIcmdWithADoubleAndUnit.hh> 36 #include <G4UIcmdWithADoubleAndUnit.hh>
37 #include <G4UnitsTable.hh> 37 #include <G4UnitsTable.hh>
38 #include <G4SystemOfUnits.hh> 38 #include <G4SystemOfUnits.hh>
39 #include <G4UIcmdWithoutParameter.hh> 39 #include <G4UIcmdWithoutParameter.hh>
40 #include <G4UIcmdWithABool.hh> 40 #include <G4UIcmdWithABool.hh>
41 41
42 //-------------------------------------------- 42 //------------------------------------------------------------------------------
43 43
44 G4ReactionTableMessenger::G4ReactionTableMesse 44 G4ReactionTableMessenger::G4ReactionTableMessenger(G4DNAMolecularReactionTable* table)
45 : << 45 : G4UImessenger()
46 fpTable(table) << 46 , fpTable(table)
47 , fpActivateReactionUI(new G4UIcmdWithoutPar 47 , fpActivateReactionUI(new G4UIcmdWithoutParameter("/chem/reaction/UI", this))
48 { 48 {
49 fpNewDiffContReaction = new G4UIcmdWithAStri 49 fpNewDiffContReaction = new G4UIcmdWithAString("/chem/reaction/new", this);
50 fpAddReaction = new G4UIcmdWithAString("/che 50 fpAddReaction = new G4UIcmdWithAString("/chem/reaction/add", this);
51 fpPrintTable = new G4UIcmdWithoutParameter(" 51 fpPrintTable = new G4UIcmdWithoutParameter("/chem/reaction/print", this);
52 } 52 }
53 53
54 //-------------------------------------------- 54 //------------------------------------------------------------------------------
55 55
56 G4ReactionTableMessenger::~G4ReactionTableMess 56 G4ReactionTableMessenger::~G4ReactionTableMessenger()
57 { 57 {
58 delete fpNewDiffContReaction; << 58 if(fpNewDiffContReaction) delete fpNewDiffContReaction;
59 delete fpAddReaction; << 59 if(fpAddReaction) delete fpAddReaction;
60 delete fpPrintTable; << 60 if(fpPrintTable) delete fpPrintTable;
61 } 61 }
62 62
63 //-------------------------------------------- 63 //------------------------------------------------------------------------------
64 void G4ReactionTableMessenger::SetNewValue(G4U 64 void G4ReactionTableMessenger::SetNewValue(G4UIcommand* command,
65 G4S 65 G4String newValue)
66 { 66 {
67 if(command == fpActivateReactionUI.get()) 67 if(command == fpActivateReactionUI.get())
68 { 68 {
69 //assert(false); 69 //assert(false);
70 fpTable->Reset();//release reaction data 70 fpTable->Reset();//release reaction data
71 } 71 }
72 72
73 if(command == fpNewDiffContReaction) 73 if(command == fpNewDiffContReaction)
74 { 74 {
75 std::istringstream iss(newValue); 75 std::istringstream iss(newValue);
76 76
77 G4String species1; 77 G4String species1;
78 iss >> species1; 78 iss >> species1;
79 79
80 G4String species2; 80 G4String species2;
81 iss >> species2; 81 iss >> species2;
82 82
83 double reactionRate; 83 double reactionRate;
84 iss >> reactionRate; 84 iss >> reactionRate;
85 85
86 // G4String reactionRateUnit; 86 // G4String reactionRateUnit;
87 // iss >> reactionRateUnit; 87 // iss >> reactionRateUnit;
88 88
89 double dimensionedReactionRate = reactionR 89 double dimensionedReactionRate = reactionRate * (1e-3 * m3 / (mole * s));
90 // G4UIcmdWithADoubleAndUnit::ConvertTo 90 // G4UIcmdWithADoubleAndUnit::ConvertToDimensionedDouble((reactionRate
91 // + G4String(" ") + reactionRateUn 91 // + G4String(" ") + reactionRateUnit).c_str());
92 92
93 auto reactionData = 93 auto reactionData =
94 new G4DNAMolecularReactionData(dimensi 94 new G4DNAMolecularReactionData(dimensionedReactionRate,
95 species 95 species1,
96 species 96 species2);
97 97
98 // G4String productionRate; 98 // G4String productionRate;
99 // iss >> productionRate; 99 // iss >> productionRate;
100 // 100 //
101 // if(productionRate != "" && productionRat 101 // if(productionRate != "" && productionRate != "X")
102 // { 102 // {
103 // double prodRateReal = G4UIcommand::Con 103 // double prodRateReal = G4UIcommand::ConvertToDouble(productionRate);
104 // 104 //
105 // if(prodRateReal == 0 || isnan(prodRate 105 // if(prodRateReal == 0 || isnan(prodRateReal))
106 // { 106 // {
107 // G4Exception("G4ReactionTableMessenge 107 // G4Exception("G4ReactionTableMessenger",
108 // "WRONG_PRODUCTION_RATE", 108 // "WRONG_PRODUCTION_RATE",
109 // FatalException, ""); 109 // FatalException, "");
110 // } 110 // }
111 // 111 //
112 // double dimensionedProductionRate = pro 112 // double dimensionedProductionRate = prodRateReal
113 // * (1e-3 * m3 / (mole * s)); 113 // * (1e-3 * m3 / (mole * s));
114 // reactionData->SetProductionRate(dimens 114 // reactionData->SetProductionRate(dimensionedProductionRate);
115 // } 115 // }
116 116
117 while(!iss.eof()) << 117 while(iss.eof() == false)
118 { 118 {
119 G4String product; 119 G4String product;
120 iss >> product; 120 iss >> product;
121 121
122 if(!product.empty()) << 122 if(product != "")
123 { 123 {
124 reactionData->AddProduct(product); 124 reactionData->AddProduct(product);
125 } 125 }
126 else 126 else
127 { 127 {
128 break; 128 break;
129 } 129 }
130 }; 130 };
131 131
132 fpTable->SetReaction(reactionData); 132 fpTable->SetReaction(reactionData);
133 } 133 }
134 // else if(command == fpNewPartDiffContReacti 134 // else if(command == fpNewPartDiffContReactionByRadius)
135 // { 135 // {
136 // std::istringstream iss(newValue); 136 // std::istringstream iss(newValue);
137 // 137 //
138 // G4String species1; 138 // G4String species1;
139 // iss >> species1; 139 // iss >> species1;
140 // 140 //
141 // G4String species2; 141 // G4String species2;
142 // iss >> species2; 142 // iss >> species2;
143 // 143 //
144 // double reactionRate; 144 // double reactionRate;
145 // iss >> reactionRate; 145 // iss >> reactionRate;
146 // 146 //
147 //// G4String reactionRateUnit; 147 //// G4String reactionRateUnit;
148 //// iss >> reactionRateUnit; 148 //// iss >> reactionRateUnit;
149 // 149 //
150 //// G4String reactionRateUnit; 150 //// G4String reactionRateUnit;
151 //// iss >> reactionRateUnit; 151 //// iss >> reactionRateUnit;
152 // 152 //
153 // double reactionRadius; 153 // double reactionRadius;
154 // iss >> reactionRadius; 154 // iss >> reactionRadius;
155 // 155 //
156 //// G4String reactionRadiusUnit; 156 //// G4String reactionRadiusUnit;
157 //// iss >> reactionRadiusUnit; 157 //// iss >> reactionRadiusUnit;
158 // 158 //
159 // double dimensionedReactionRate = reactio 159 // double dimensionedReactionRate = reactionRate * (1e-3 * m3 / (mole * s));
160 // 160 //
161 //// double dimensionedReactionRate = 161 //// double dimensionedReactionRate =
162 //// G4UIcmdWithADoubleAndUnit::Convert 162 //// G4UIcmdWithADoubleAndUnit::ConvertToDimensionedDouble((reactionRate
163 //// + " " + reactionRateUnit).c_st 163 //// + " " + reactionRateUnit).c_str());
164 // 164 //
165 // double dimensionedReactionRadius = react 165 // double dimensionedReactionRadius = reactionRadius * nm;
166 //// G4UIcmdWithADoubleAndUnit::Convert 166 //// G4UIcmdWithADoubleAndUnit::ConvertToDimensionedDouble((reactionRadius
167 //// + " " + reactionRadiusUnit).c_ 167 //// + " " + reactionRadiusUnit).c_str());
168 // 168 //
169 // G4DNAMolecularReactionData* reactionData 169 // G4DNAMolecularReactionData* reactionData =
170 // new G4DNAMolecularReactionData(dimen 170 // new G4DNAMolecularReactionData(dimensionedReactionRate,
171 // speci 171 // species1,
172 // speci 172 // species2);
173 // reactionData->SetPartiallyDiffusionContr 173 // reactionData->SetPartiallyDiffusionControlledReaction(dimensionedReactionRate,
174 // 174 // dimensionedReactionRadius);
175 // 175 //
176 // while(iss.eof() == false) 176 // while(iss.eof() == false)
177 // { 177 // {
178 // G4String product; 178 // G4String product;
179 // iss >> product; 179 // iss >> product;
180 // 180 //
181 // if(product != "") 181 // if(product != "")
182 // { 182 // {
183 // reactionData->AddProduct(product); 183 // reactionData->AddProduct(product);
184 // } 184 // }
185 // else 185 // else
186 // { 186 // {
187 // break; 187 // break;
188 // } 188 // }
189 // } 189 // }
190 // 190 //
191 // fpTable->SetReaction(reactionData); 191 // fpTable->SetReaction(reactionData);
192 // } 192 // }
193 // else if(command == fpNewPartDiffContReacti 193 // else if(command == fpNewPartDiffContReactionByReactionRate)
194 // { 194 // {
195 // std::istringstream iss(newValue); 195 // std::istringstream iss(newValue);
196 // 196 //
197 // G4String species1; 197 // G4String species1;
198 // iss >> species1; 198 // iss >> species1;
199 // 199 //
200 // G4String species2; 200 // G4String species2;
201 // iss >> species2; 201 // iss >> species2;
202 // 202 //
203 // double reactionRate; 203 // double reactionRate;
204 // iss >> reactionRate; 204 // iss >> reactionRate;
205 // 205 //
206 // // G4String reactionRateUnit; 206 // // G4String reactionRateUnit;
207 // // iss >> reactionRateUnit; 207 // // iss >> reactionRateUnit;
208 // 208 //
209 // // G4String reactionRateUnit; 209 // // G4String reactionRateUnit;
210 // // iss >> reactionRateUnit; 210 // // iss >> reactionRateUnit;
211 // 211 //
212 // double activationRate; 212 // double activationRate;
213 // iss >> activationRate; 213 // iss >> activationRate;
214 // 214 //
215 // // G4String reactionRadiusUnit; 215 // // G4String reactionRadiusUnit;
216 // // iss >> reactionRadiusUnit; 216 // // iss >> reactionRadiusUnit;
217 // 217 //
218 // double dimensionedReactionRate = reactio 218 // double dimensionedReactionRate = reactionRate * (1e-3 * m3 / (mole * s));
219 // 219 //
220 // double dimensionedActivationRate = activ 220 // double dimensionedActivationRate = activationRate
221 // * (1e-3 * m3 / (mole * s)); 221 // * (1e-3 * m3 / (mole * s));
222 // 222 //
223 // G4DNAMolecularReactionData* reactionData 223 // G4DNAMolecularReactionData* reactionData =
224 // new G4DNAMolecularReactionData(dimen 224 // new G4DNAMolecularReactionData(dimensionedReactionRate,
225 // speci 225 // species1,
226 // speci 226 // species2);
227 // reactionData-> 227 // reactionData->
228 // SetPartiallyDiffusionControlledReactio 228 // SetPartiallyDiffusionControlledReactionByActivation(dimensionedReactionRate,
229 // 229 // dimensionedActivationRate);
230 // 230 //
231 // while(iss.eof() == false) 231 // while(iss.eof() == false)
232 // { 232 // {
233 // G4String product; 233 // G4String product;
234 // iss >> product; 234 // iss >> product;
235 // 235 //
236 // if(product != "") 236 // if(product != "")
237 // { 237 // {
238 // reactionData->AddProduct(product); 238 // reactionData->AddProduct(product);
239 // } 239 // }
240 // else 240 // else
241 // { 241 // {
242 // break; 242 // break;
243 // } 243 // }
244 // } 244 // }
245 // 245 //
246 // fpTable->SetReaction(reactionData); 246 // fpTable->SetReaction(reactionData);
247 // } 247 // }
248 else if(command == fpPrintTable) 248 else if(command == fpPrintTable)
249 { 249 {
250 fpTable->PrintTable(); 250 fpTable->PrintTable();
251 } 251 }
252 else if(command == fpAddReaction) 252 else if(command == fpAddReaction)
253 { 253 {
254 std::istringstream iss(newValue); 254 std::istringstream iss(newValue);
255 255
256 //---------------------------------------- 256 //--------------------------------------------------------------------------
257 // Reactants definition 257 // Reactants definition
258 258
259 G4String species1; 259 G4String species1;
260 iss >> species1; 260 iss >> species1;
261 261
262 G4String marker; 262 G4String marker;
263 iss >> marker; // peut etre +, ->, | 263 iss >> marker; // peut etre +, ->, |
264 264
265 G4String species2; 265 G4String species2;
266 266
267 if(marker == "+") 267 if(marker == "+")
268 { 268 {
269 iss >> species2; 269 iss >> species2;
270 iss >> marker; // peut etre ->, | 270 iss >> marker; // peut etre ->, |
271 } 271 }
272 272
273 //---------------------------------------- 273 //--------------------------------------------------------------------------
274 274
275 auto reactionData = << 275 G4DNAMolecularReactionData* reactionData =
276 new G4DNAMolecularReactionData 276 new G4DNAMolecularReactionData(0,
277 277 species1,
278 278 species2);
279 //fpTable->SetReaction(reactionData); 279 //fpTable->SetReaction(reactionData);
280 280
281 //---------------------------------------- 281 //--------------------------------------------------------------------------
282 // Add products 282 // Add products
283 if(marker == "->") 283 if(marker == "->")
284 { 284 {
285 iss >> marker; // doit etre = species na 285 iss >> marker; // doit etre = species name
286 286
287 while(marker!="|" 287 while(marker!="|"
288 //&& marker!="" 288 //&& marker!=""
289 && !iss.eof() << 289 && iss.eof() == false
290 ) 290 )
291 { 291 {
292 //G4cout << marker << G4endl; 292 //G4cout << marker << G4endl;
293 if(marker == "+") 293 if(marker == "+")
294 { 294 {
295 iss >> marker; // doit etre species 295 iss >> marker; // doit etre species name
296 continue; 296 continue;
297 } 297 }
298 if(marker != "H2O") 298 if(marker != "H2O")
299 { 299 {
300 reactionData->AddProduct(marker); 300 reactionData->AddProduct(marker);
301 } 301 }
302 302
303 iss >> marker; // peut etre species na 303 iss >> marker; // peut etre species name, +, |
304 }; 304 };
305 } 305 }
306 306
307 // G4cout << "out of 1st loop" << G4endl; 307 // G4cout << "out of 1st loop" << G4endl;
308 308
309 //---------------------------------------- 309 //--------------------------------------------------------------------------
310 // Add reaction rate method 310 // Add reaction rate method
311 G4String rateconst_method; 311 G4String rateconst_method;
312 iss >> rateconst_method; 312 iss >> rateconst_method;
313 if(rateconst_method == "Fix") 313 if(rateconst_method == "Fix")
314 { 314 {
315 iss >> marker; // must be | 315 iss >> marker; // must be |
316 double reactionRate; 316 double reactionRate;
317 iss >> reactionRate; 317 iss >> reactionRate;
318 318
319 double dimensionedReactionRate = reactio 319 double dimensionedReactionRate = reactionRate * (1e-3 * m3 / (mole * s));
320 reactionData->SetObservedReactionRateCon 320 reactionData->SetObservedReactionRateConstant(dimensionedReactionRate);
321 reactionData->ComputeEffectiveRadius(); 321 reactionData->ComputeEffectiveRadius();
322 G4String markerType; 322 G4String markerType;
323 iss >> markerType; // must be | 323 iss >> markerType; // must be |
324 if(markerType == "|") 324 if(markerType == "|")
325 { 325 {
326 G4int reactionType; 326 G4int reactionType;
327 iss >> reactionType; 327 iss >> reactionType;
328 if(reactionType == 1) 328 if(reactionType == 1)
329 { 329 {
330 reactionData->SetReactionType(reacti 330 reactionData->SetReactionType(reactionType);
331 } 331 }
332 } 332 }
333 333
334 334
335 // G4String productionRate; 335 // G4String productionRate;
336 // iss >> productionRate; 336 // iss >> productionRate;
337 // 337 //
338 // if(productionRate != "" && productionR 338 // if(productionRate != "" && productionRate != "X")
339 // { 339 // {
340 // double prodRateReal = G4UIcommand::C 340 // double prodRateReal = G4UIcommand::ConvertToDouble(productionRate);
341 // 341 //
342 // if(prodRateReal == 0 || isnan(prodRa 342 // if(prodRateReal == 0 || isnan(prodRateReal))
343 // { 343 // {
344 // G4Exception("G4ReactionTableMessen 344 // G4Exception("G4ReactionTableMessenger",
345 // "WRONG_PRODUCTION_RATE 345 // "WRONG_PRODUCTION_RATE",
346 // FatalException, 346 // FatalException,
347 // ""); 347 // "");
348 // } 348 // }
349 // 349 //
350 // double dimensionedProductionRate = p 350 // double dimensionedProductionRate = prodRateReal
351 // * (1e-3 * m3 / (mole * s)); 351 // * (1e-3 * m3 / (mole * s));
352 // reactionData->SetProductionRate(dime 352 // reactionData->SetProductionRate(dimensionedProductionRate);
353 // } 353 // }
354 } 354 }
355 else if(rateconst_method == "Arr") 355 else if(rateconst_method == "Arr")
356 { 356 {
357 iss >> marker; // must be | 357 iss >> marker; // must be |
358 double A0 = 0; 358 double A0 = 0;
359 double E_R = 0; 359 double E_R = 0;
360 360
361 iss >> A0; 361 iss >> A0;
362 iss >> E_R; 362 iss >> E_R;
363 reactionData->SetArrehniusParameterizati 363 reactionData->SetArrehniusParameterization(A0, E_R);
364 } 364 }
365 else if(rateconst_method == "Pol") 365 else if(rateconst_method == "Pol")
366 { 366 {
367 iss >> marker; // must be | 367 iss >> marker; // must be |
368 std::vector<double> P = {0, 0, 0, 0, 0}; 368 std::vector<double> P = {0, 0, 0, 0, 0};
369 369
370 size_t i = 0; 370 size_t i = 0;
371 while(i < 4) // could be changed to 5 on 371 while(i < 4) // could be changed to 5 only if marker is used as delimiter
372 { 372 {
373 double tmp; 373 double tmp;
374 iss >> tmp; 374 iss >> tmp;
375 P[i] = tmp; 375 P[i] = tmp;
376 // G4cout << newValue << G4endl; 376 // G4cout << newValue << G4endl;
377 // G4cout << tmp << G4endl; 377 // G4cout << tmp << G4endl;
378 // G4cout << P[i] << G4endl; 378 // G4cout << P[i] << G4endl;
379 ++i; 379 ++i;
380 }; 380 };
381 reactionData->SetPolynomialParameterizat 381 reactionData->SetPolynomialParameterization(P);
382 } 382 }
383 else if(rateconst_method == "Scale") 383 else if(rateconst_method == "Scale")
384 { 384 {
385 iss >> marker; // must be | 385 iss >> marker; // must be |
386 double temp_K; 386 double temp_K;
387 iss >> temp_K; 387 iss >> temp_K;
388 double reactionRateCste; 388 double reactionRateCste;
389 iss >> reactionRateCste; 389 iss >> reactionRateCste;
390 double dimensionedReactionRate = reactio 390 double dimensionedReactionRate = reactionRateCste * (1e-3 * m3 / (mole * s));
391 reactionData->SetObservedReactionRateCon 391 reactionData->SetObservedReactionRateConstant(dimensionedReactionRate);
392 reactionData->SetScaledParameterization( 392 reactionData->SetScaledParameterization(temp_K, dimensionedReactionRate);
393 } 393 }
394 394
395 // if(iss.eof() == false) 395 // if(iss.eof() == false)
396 // { 396 // {
397 // iss >> marker; 397 // iss >> marker;
398 // 398 //
399 // if(marker == "|") 399 // if(marker == "|")
400 // { 400 // {
401 // G4String productionRate ; 401 // G4String productionRate ;
402 // iss >> productionRate; 402 // iss >> productionRate;
403 // 403 //
404 //// G4cout << productionRate << G4endl 404 //// G4cout << productionRate << G4endl;
405 // 405 //
406 // double dimProductionRate = G4UIcomma 406 // double dimProductionRate = G4UIcommand::ConvertToDouble(productionRate)* (1e-3 * m3 / (mole * s));
407 // 407 //
408 // G4cout << " DIM PROD RATE = " << rea 408 // G4cout << " DIM PROD RATE = " << reactionData->GetReactant1()->GetName()
409 // << " + " << reactionData->GetRe 409 // << " + " << reactionData->GetReactant2()->GetName() << " = " << dimProductionRate << G4endl;
410 // 410 //
411 // reactionData->SetProductionRate(dimP 411 // reactionData->SetProductionRate(dimProductionRate);
412 // } 412 // }
413 // } 413 // }
414 fpTable->SetReaction(reactionData); 414 fpTable->SetReaction(reactionData);
415 // G4cout << "Reaction " << species1 << " + 415 // G4cout << "Reaction " << species1 << " + " << species2 << " added" << G4endl;
416 } 416 }
417 } 417 }
418 418