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25
26 #include "G4DNAGillespieDirectMethod.hh"
27 #include "Randomize.hh"
28 #include "G4PhysicalConstants.hh"
29 #include <memory>
30 #include <tuple>
31 #include "G4DNAEventSet.hh"
32 #include "G4UnitsTable.hh"
33 #include "G4DNAScavengerMaterial.hh"
34 #include "G4Scheduler.hh"
35 #include "G4DNAMolecularReactionTable.hh"
36 #include "G4ChemEquilibrium.hh"
37
38 G4DNAGillespieDirectMethod::G4DNAGillespieDire
39 : fMolecularReactions(G4DNAMolecularReaction
40 {}
41
42 G4DNAGillespieDirectMethod::~G4DNAGillespieDir
43
44 void G4DNAGillespieDirectMethod::SetEventSet(G
45 {
46 fpEventSet = pEventSet;
47 }
48
49 //#define DEBUG 1
50
51 G4double G4DNAGillespieDirectMethod::VolumeOfN
52 {
53 auto box = std::get<1>(voxel);
54 auto LengthY = box.Getyhi() - box.Getylo();
55 auto LengthX = box.Getxhi() - box.Getxlo();
56 auto LengthZ = box.Getzhi() - box.Getzlo();
57 G4double V = LengthY * LengthX * LengthZ;
58 if(V <= 0)
59 {
60 G4ExceptionDescription exceptionDescriptio
61 exceptionDescription << "V > 0 !! ";
62 G4Exception("G4DNAGillespieDirectMethod::V
63 "G4DNAGillespieDirectMethod03"
64 exceptionDescription);
65 }
66 return V;
67 }
68 G4double G4DNAGillespieDirectMethod::Propensit
69
70 {
71 if(moleType->GetDiffusionCoefficient() == 0)
72 {
73 return 0.;
74 }
75 const auto& node = std::get<2>(voxel);
76 const auto& box = std::get<1>(voxel);
77
78 G4double alpha = 0;
79 auto it = node.find(moleType);
80 if(it != node.end())
81 {
82 auto LengthY = box.Getyhi() - box.Getylo()
83 G4double d = it->first->GetDiffusionCoef
84 alpha = d * it->second;
85
86 #ifdef DEBUG
87 G4cout << it->first->GetName() << " " << i
88 << " D : " << it->first->GetDiffusi
89 << " LengthY : " << LengthY << " Pr
90 << G4endl;
91 #endif
92 }
93 return alpha;
94 }
95
96 G4double G4DNAGillespieDirectMethod::Propensit
97
98 {
99 G4double value;
100 auto ConfA = data->GetReactant
101 auto ConfB = data->GetReactant
102 G4double scavengerNumber = 0;
103 auto typeANumber = FindScavenging(vo
104 ? scavengerNumb
105 : ComputeNumber
106
107 auto typeBNumber = FindScavenging(voxel, Con
108 ? scavengerNumber
109 : ComputeNumberInNode(v
110
111 if(typeANumber == 0 || typeBNumber == 0)
112 {
113 return 0;
114 }
115
116 auto k =
117 data->GetObservedReactionRateConstant() /
118 if(ConfA == ConfB)
119 {
120 value = typeANumber * (typeBNumber - 1) *
121 }
122 else
123 {
124 value = typeANumber * typeBNumber * k;
125 }
126
127 if(value < 0)
128 {
129 G4ExceptionDescription exceptionDescriptio
130 exceptionDescription
131 << "G4DNAGillespieDirectMethod::Propensi
132 << ConfA->GetName() << "(" << typeANumbe
133 << "(" << typeBNumber << ") : propensity
134 << " GetObservedReactionRateConstant : "
135 << data->GetObservedReactionRateConstant
136 << " GetEffectiveReactionRadius : "
137 << G4BestUnit(data->GetEffectiveReaction
138 << " k : " << k << " volume : " << Volum
139 G4Exception("G4DNAGillespieDirectMethod::P
140 "G4DNAGillespieDirectMethod013
141 exceptionDescription);
142 }
143
144 #ifdef DEBUG
145 if(value > 0)
146 G4cout << "G4DNAGillespieDirectMethod::Pro
147 << ConfA->GetName() << "(" << typeA
148 << ConfB->GetName() << "(" << typeB
149 << ") : propensity : " << value
150 << " Time to Reaction : " << G4Bes
151 << " k : " << k << " Index : " << i
152 #endif
153
154 return value;
155 }
156
157 void G4DNAGillespieDirectMethod::Initialize()
158 {
159 // for Scavenger
160 fpScavengerMaterial = dynamic_cast<G4DNAScav
161 G4Scheduler::Instance()->GetScavengerMater
162 fEquilibriumProcesses.emplace(
163 std::make_pair(6, std::make_unique<G4ChemE
164 fEquilibriumProcesses.emplace(
165 std::make_pair(7, std::make_unique<G4ChemE
166 fEquilibriumProcesses.emplace(
167 std::make_pair(8, std::make_unique<G4ChemE
168 for(auto& it : fEquilibriumProcesses)
169 {
170 it.second->Initialize();
171 it.second->SetVerbose(fVerbose);
172 }
173 }
174
175 void G4DNAGillespieDirectMethod::CreateEvents(
176 {
177 auto begin = fpMesh->begin();
178 auto end = fpMesh->end();
179 for(; begin != end; begin++)
180 {
181 auto index = std::get<0>(*begin);
182 #ifdef DEBUG
183 fpMesh->PrintVoxel(index);
184 #endif
185 CreateEvent(index);
186 }
187 }
188
189 void G4DNAGillespieDirectMethod::SetTimeStep(c
190 {
191 fTimeStep = stepTime;
192 }
193 void G4DNAGillespieDirectMethod::CreateEvent(c
194 {
195 const auto& voxel = fpMesh->GetVoxel(index);
196 if(std::get<2>(voxel).empty())
197 {
198 G4ExceptionDescription exceptionDescriptio
199 exceptionDescription << "This voxel : " <<
200 << " is not ready to
201 G4Exception("G4DNAGillespieDirectMethod::C
202 "G4DNAGillespieDirectMethod05"
203 exceptionDescription);
204 }
205 G4double r1 = G4UniformRand();
206 G4double r2 = G4UniformRand();
207 G4double dAlpha0 = DiffusiveJumping(voxel
208 G4double rAlpha0 = Reaction(voxel);
209 G4double alphaTotal = dAlpha0 + rAlpha0;
210
211 if(alphaTotal == 0)
212 {
213 return;
214 }
215 auto timeStep = ((1.0 / (alphaTotal)) * std:
216
217 #ifdef DEBUG
218 G4cout << "r2 : " << r2 << " rAlpha0 : " <<
219 << " dAlpha0 : " << dAlpha0 << " r
220 << rAlpha0 / (dAlpha0 + rAlpha0) << G
221 #endif
222 if(r2 < rAlpha0 / alphaTotal)
223 {
224 if(fVerbose > 1)
225 {
226 G4cout << "=>>>>reaction at : " << timeS
227 << G4BestUnit(((1.0 / alphaTotal)
228 << G4endl;
229 }
230 auto rSelectedIter = fReactionDataMap.uppe
231 fpEventSet->CreateEvent(timeStep, index, r
232 }
233 else if(dAlpha0 > 0)
234 {
235 if(fVerbose > 1)
236 {
237 G4cout << "=>>>>jumping at : " << timeSt
238 << G4BestUnit(((1.0 / alphaTotal)
239 << G4endl;
240 }
241
242 auto dSelectedIter = fJumpingDataMap.upper
243 auto pDSelected =
244 std::make_unique<std::pair<MolType, Inde
245 fpEventSet->CreateEvent(timeStep, index, s
246 }
247 #ifdef DEBUG
248 G4cout << G4endl;
249 #endif
250 }
251
252 G4double G4DNAGillespieDirectMethod::Reaction(
253 {
254 fReactionDataMap.clear();
255 G4double alpha0 = 0;
256 const auto& dataList =
257 fMolecularReactions->GetVectorOfReactionDa
258 if(dataList.empty())
259 {
260 G4ExceptionDescription exceptionDescriptio
261 exceptionDescription << "MolecularReaction
262 G4Exception("G4DNAGillespieDirectMethod::R
263 "G4DNAGillespieDirectMethod01"
264 exceptionDescription);
265 }
266
267 for(const auto& it : dataList)
268 {
269 if(!IsEquilibrium(it->GetReactionType()))
270 {
271 continue;
272 }
273 auto propensity = PropensityFunction(voxel
274 if(propensity == 0)
275 {
276 continue;
277 }
278 alpha0 += propensity;
279 fReactionDataMap[alpha0] = it;
280 }
281 #ifdef DEBUG
282 G4cout << "Reaction :alpha0 : " << alpha0 <
283 #endif
284 return alpha0;
285 }
286
287 G4double G4DNAGillespieDirectMethod::Diffusive
288 {
289 fJumpingDataMap.clear();
290 G4double alpha0 = 0;
291 auto index = std::get<0>(voxel);
292 auto NeighboringVoxels = fpMesh->FindNeighbo
293 if(NeighboringVoxels.empty())
294 {
295 return 0;
296 }
297 auto iter = G4MoleculeTable::Instance()->Get
298 while(iter())
299 {
300 const auto* conf = iter.value();
301 auto propensity = PropensityFunction(voxe
302 if(propensity == 0)
303 {
304 continue;
305 }
306 for(const auto& it_Neighbor : NeighboringV
307 {
308 alpha0 += propensity;
309 fJumpingDataMap[alpha0] = std::make_pair
310 #ifdef DEBUG
311 G4cout << "mole : " << conf->GetName()
312 << " number : " << ComputeNumberI
313 << " propensity : " << propensity
314 << G4endl;
315 #endif
316 }
317 }
318 #ifdef DEBUG
319 G4cout << "DiffusiveJumping :alpha0 : " <<
320 #endif
321 return alpha0;
322 }
323
324 G4double G4DNAGillespieDirectMethod::ComputeNu
325 const Voxel& voxel, MolType type) // depend
326 {
327 if(type->GetDiffusionCoefficient() != 0)
328 {
329 const auto& node = std::get<2>(voxel);
330 const auto& it = node.find(type);
331 return (it != node.end()) ? (it->second) :
332 }
333 return 0;
334 }
335
336 G4bool G4DNAGillespieDirectMethod::FindScaveng
337
338
339 {
340 numberOfScavenger = 0;
341 if(fpScavengerMaterial == nullptr)
342 {
343 return false;
344 }
345 auto volumeOfNode = VolumeOfNode(voxel);
346 if(G4MoleculeTable::Instance()->GetConfigura
347 {
348 auto factor = Avogadro * volumeOfNod
349 numberOfScavenger = factor;
350 return true;
351 }
352
353 G4double totalNumber =
354 fpScavengerMaterial->GetNumberMoleculePerV
355 moletype);
356 if(totalNumber == 0)
357 {
358 return false;
359 }
360
361 G4double numberInDouble = volumeOfNode * std
362 fpMesh->GetBoundin
363 auto numberInInterg = (int64_t) (std::floor(
364 G4double change = numberInDouble - numbe
365 G4UniformRand() > change ? numberOfScavenger
366 : numberOfScave
367 return true;
368 }
369
370 G4bool G4DNAGillespieDirectMethod::IsEquilibri
371 {
372 auto reaction = fEquilibriumProcesses.find(r
373 if(reaction == fEquilibriumProcesses.end())
374 {
375 return true;
376 }else
377 {
378 return (reaction->second->GetEquilibriumSt
379 }
380
381 }
382
383 G4bool G4DNAGillespieDirectMethod::SetEquilibr
384 {
385 for(auto& it : fEquilibriumProcesses)
386 {
387 it.second->SetGlobalTime(fTimeStep);
388 it.second->SetEquilibrium(pReaction);
389 if(it.second->IsStatusChanged()) return tr
390 }
391 return false;
392 }
393
394 void G4DNAGillespieDirectMethod::ResetEquilibr
395 {
396 for(auto& it : fEquilibriumProcesses)
397 {
398 it.second->Reset();
399 }
400 }
401
402
403
404