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