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25 //
26 //
27 // Author: Mathieu Karamitros (kara@cenbg.in2p3.fr)
28 //
29 // WARNING : This class is released as a prototype.
30 // It might strongly evolve or even disapear in the next releases.
31 //
32 // History:
33 // -----------
34 // 10 Oct 2011 M.Karamitros created
35 //
36 // -------------------------------------------------------------------
37
38 #include "G4DNAMolecularReaction.hh"
39 #include "G4DNAMolecularReactionTable.hh"
40 #include "G4VDNAReactionModel.hh"
41 #include "G4MolecularConfiguration.hh"
42 #include "G4Molecule.hh"
43 #include "G4MoleculeFinder.hh"
44 #include "G4ITReactionChange.hh"
45 #include "G4ITReaction.hh"
46
47 #include "G4ITTrackHolder.hh"
48
49 G4DNAMolecularReaction::G4DNAMolecularReaction()
50 :
51 fMolReactionTable(reference_cast<const G4DNAMolecularReactionTable*>(fpReactionTable))
52 , fpReactionModel(nullptr)
53 {
54 }
55
56 G4DNAMolecularReaction::G4DNAMolecularReaction(G4VDNAReactionModel* pReactionModel)
57 : G4DNAMolecularReaction()
58 {
59 fpReactionModel = pReactionModel;
60 }
61
62 G4bool G4DNAMolecularReaction::TestReactibility(const G4Track &trackA,
63 const G4Track &trackB,
64 double currentStepTime,
65 bool userStepTimeLimit) /*const*/
66 {
67 const auto pMoleculeA = GetMolecule(trackA)->GetMolecularConfiguration();
68 const auto pMoleculeB = GetMolecule(trackB)->GetMolecularConfiguration();
69
70 const G4double reactionRadius = fpReactionModel->GetReactionRadius(pMoleculeA, pMoleculeB);
71
72 G4double separationDistance = -1.;
73
74 if (currentStepTime == 0.)
75 {
76 userStepTimeLimit = false;
77 }
78
79 G4bool output = fpReactionModel->FindReaction(trackA, trackB, reactionRadius,
80 separationDistance, userStepTimeLimit);
81 return output;
82 }
83
84 std::unique_ptr<G4ITReactionChange> G4DNAMolecularReaction::MakeReaction(const G4Track &trackA,
85 const G4Track &trackB)
86 {
87 std::unique_ptr<G4ITReactionChange> pChanges(new G4ITReactionChange());
88 pChanges->Initialize(trackA, trackB);
89
90 const auto pMoleculeA = GetMolecule(trackA)->GetMolecularConfiguration();
91 const auto pMoleculeB = GetMolecule(trackB)->GetMolecularConfiguration();
92
93 const auto pReactionData = fMolReactionTable->GetReactionData(pMoleculeA, pMoleculeB);
94
95 const G4int nbProducts = pReactionData->GetNbProducts();
96
97 if (nbProducts != 0)
98 {
99 const G4double D1 = pMoleculeA->GetDiffusionCoefficient();
100 const G4double D2 = pMoleculeB->GetDiffusionCoefficient();
101 const G4double sqrD1 = D1 == 0. ? 0. : std::sqrt(D1);
102 const G4double sqrD2 = D2 == 0. ? 0. : std::sqrt(D2);
103 const G4double inv_numerator = 1./(sqrD1 + sqrD2);
104 const G4ThreeVector reactionSite = sqrD2 * inv_numerator * trackA.GetPosition()
105 + sqrD1 * inv_numerator * trackB.GetPosition();
106
107 for (G4int j = 0; j < nbProducts; ++j)
108 {
109 auto pProduct = new G4Molecule(pReactionData->GetProduct(j));
110 auto pProductTrack = pProduct->BuildTrack(trackA.GetGlobalTime(), reactionSite);
111
112 pProductTrack->SetTrackStatus(fAlive);
113
114 G4ITTrackHolder::Instance()->Push(pProductTrack);
115
116 pChanges->AddSecondary(pProductTrack);
117 G4MoleculeFinder::Instance()->Push(pProductTrack);
118 }
119 }
120
121 pChanges->KillParents(true);
122 return pChanges;
123 }
124
125 void G4DNAMolecularReaction::SetReactionModel(G4VDNAReactionModel* pReactionModel)
126 {
127 fpReactionModel = pReactionModel;
128 }
129
130 std::vector<std::unique_ptr<G4ITReactionChange>> G4DNAMolecularReaction::FindReaction(
131 G4ITReactionSet* pReactionSet,
132 const double currentStepTime,
133 const double /*fGlobalTime*/,
134 const bool reachedUserStepTimeLimit)
135 {
136 std::vector<std::unique_ptr<G4ITReactionChange>> fReactionInfo;
137 fReactionInfo.clear();
138
139 if (pReactionSet == nullptr)
140 {
141 return fReactionInfo;
142 }
143
144 G4ITReactionPerTrackMap& reactionPerTrackMap = pReactionSet->GetReactionMap();
145 for (auto tracks_i = reactionPerTrackMap.cbegin();
146 tracks_i != reactionPerTrackMap.cend();
147 tracks_i = reactionPerTrackMap.cbegin())
148 {
149 G4Track* pTrackA = tracks_i->first;
150 if (pTrackA->GetTrackStatus() == fStopAndKill)
151 {
152 continue;
153 }
154
155 G4ITReactionPerTrackPtr reactionPerTrack = tracks_i->second;
156 G4ITReactionList& reactionList = reactionPerTrack->GetReactionList();
157
158 assert(reactionList.cbegin() != reactionList.cend());
159
160 for (auto it = reactionList.cbegin(); it != reactionList.cend(); it = reactionList.cbegin())
161 {
162 G4ITReactionPtr reaction(*it);
163 G4Track* pTrackB = reaction->GetReactant(pTrackA);
164 if (pTrackB->GetTrackStatus() == fStopAndKill)
165 {
166 continue;
167 }
168
169 if (pTrackB == pTrackA)
170 {
171 G4ExceptionDescription exceptionDescription;
172 exceptionDescription
173 << "The IT reaction process sent back a reaction between trackA and trackB. ";
174 exceptionDescription << "The problem is trackA == trackB";
175 G4Exception("G4ITModelProcessor::FindReaction",
176 "ITModelProcessor005",
177 FatalErrorInArgument,
178 exceptionDescription);
179 }
180
181 pReactionSet->SelectThisReaction(std::move(reaction));
182
183 if (TestReactibility(*pTrackA, *pTrackB, currentStepTime, reachedUserStepTimeLimit))
184 {
185 auto pReactionChange = MakeReaction(*pTrackA, *pTrackB);
186
187 if (pReactionChange)
188 {
189 fReactionInfo.push_back(std::move(pReactionChange));
190 break;
191 }
192 }
193 }
194 }
195
196 pReactionSet->CleanAllReaction();
197 return fReactionInfo;
198 }
199