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25 // 25 //
>> 26 // $Id: G4DNASmoluchowskiReactionModel.cc 95948 2016-03-03 10:40:33Z gcosmo $
26 // 27 //
27 #include "G4DNASmoluchowskiReactionModel.hh" 28 #include "G4DNASmoluchowskiReactionModel.hh"
28 #include "Randomize.hh" 29 #include "Randomize.hh"
29 #include "G4Track.hh" 30 #include "G4Track.hh"
30 #include "G4DNAMolecularReactionTable.hh" 31 #include "G4DNAMolecularReactionTable.hh"
31 #include "G4UnitsTable.hh" 32 #include "G4UnitsTable.hh"
32 #include "G4Molecule.hh" 33 #include "G4Molecule.hh"
>> 34 //#include "G4Scheduler.hh"
33 #include "G4Exp.hh" 35 #include "G4Exp.hh"
34 36
35 G4DNASmoluchowskiReactionModel::G4DNASmoluchow << 37 G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel() :
>> 38 G4VDNAReactionModel()
>> 39 {
>> 40 fReactionData = 0;
>> 41 }
36 42
37 G4DNASmoluchowskiReactionModel::~G4DNASmolucho << 43 G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel(const G4DNASmoluchowskiReactionModel& __right) :
>> 44 G4VDNAReactionModel(__right)
>> 45 {
>> 46 fReactionData = 0;
>> 47 }
38 48
39 void G4DNASmoluchowskiReactionModel::Initialis << 49 G4DNASmoluchowskiReactionModel& G4DNASmoluchowskiReactionModel::operator=(const G4DNASmoluchowskiReactionModel& right)
>> 50 {
>> 51 if (this == &right) return *this;
>> 52 fReactionData = 0;
>> 53 return *this;
>> 54 }
>> 55
>> 56 G4DNASmoluchowskiReactionModel::~G4DNASmoluchowskiReactionModel()
>> 57 {
>> 58 fReactionData = 0;
>> 59 }
>> 60
>> 61 void G4DNASmoluchowskiReactionModel::Initialise(G4MolecularConfiguration* __molecule,
40 62 const G4Track&)
41 { 63 {
42 fpReactionData = fpReactionTable->GetReact << 64 fReactionData = fReactionTable->GetReactionData(__molecule);
43 } 65 }
44 66
45 void G4DNASmoluchowskiReactionModel::Initialis << 67 void
>> 68 G4DNASmoluchowskiReactionModel::
>> 69 InitialiseToPrint(G4MolecularConfiguration* __molecule)
46 { 70 {
47 fpReactionData = fpReactionTable->GetReact << 71 fReactionData = fReactionTable->GetReactionData(__molecule);
48 } 72 }
49 73
50 G4double G4DNASmoluchowskiReactionModel::GetRe << 74 G4double
51 << 75 G4DNASmoluchowskiReactionModel::GetReactionRadius(G4MolecularConfiguration* __mol1,
>> 76 G4MolecularConfiguration* __mol2)
52 { 77 {
53 G4double __output = fpReactionTable->GetRe << 78 G4double __output = fReactionTable->GetReactionData(__mol1, __mol2)
54 return __output; << 79 ->GetEffectiveReactionRadius();
>> 80 return __output;
55 } 81 }
56 82
57 G4double G4DNASmoluchowskiReactionModel::GetRe << 83 G4double G4DNASmoluchowskiReactionModel::GetReactionRadius(const G4int __i)
58 { 84 {
59 G4double __output = (*fpReactionData)[__i] << 85 G4double __output = (*fReactionData)[__i]->GetEffectiveReactionRadius();
60 return __output; << 86 return __output;
61 } 87 }
62 88
63 G4bool G4DNASmoluchowskiReactionModel::FindRea 89 G4bool G4DNASmoluchowskiReactionModel::FindReaction(const G4Track& __trackA,
64 90 const G4Track& __trackB,
65 << 91 const G4double __R,
66 << 92 G4double& __r,
67 93 const G4bool __alongStepReaction)
68 { 94 {
69 const G4double R2 = __reactionRadius * __r << 95 G4double postStepSeparation = 0;
70 G4double postStepSeparation = 0.; << 96 bool do_break = false;
71 bool do_break = false; << 97 G4double R2 = __R * __R;
72 int k = 0; << 98 int k = 0;
>> 99
>> 100 for (; k < 3; k++)
>> 101 {
>> 102 postStepSeparation += std::pow(
>> 103 __trackA.GetPosition()[k] - __trackB.GetPosition()[k], 2);
73 104
74 for (; k < 3; ++k) << 105 if (postStepSeparation > R2)
75 { 106 {
76 postStepSeparation += std::pow( << 107 do_break = true;
77 __trackA.GetPosition()[k] - __trac << 108 break;
78 <<
79 if (postStepSeparation > R2) <<
80 { <<
81 do_break = true; <<
82 break; <<
83 } <<
84 } 109 }
>> 110 }
85 111
86 if (!do_break) << 112 if (do_break == false)
>> 113 {
>> 114 // The loop was not break
>> 115 // => __r^2 < __R^2
>> 116 __r = std::sqrt(postStepSeparation);
>> 117 return true;
>> 118 }
>> 119 else if (__alongStepReaction == true)
>> 120 {
>> 121 //G4cout << "alongStepReaction==true" << G4endl;
>> 122 //Along step cheack and
>> 123 // the loop has break
>> 124
>> 125 // Continue loop
>> 126 for (; k < 3; k++)
87 { 127 {
88 // The loop was not break << 128 postStepSeparation += std::pow(
89 // => r^2 < R^2 << 129 __trackA.GetPosition()[k] - __trackB.GetPosition()[k], 2);
90 __separationDistance = std::sqrt(postS <<
91 return true; <<
92 } 130 }
93 if (__alongStepReaction) << 131 // Use Green approach : the Brownian bridge
94 { << 132 __r = (postStepSeparation = std::sqrt(postStepSeparation));
95 //Along step check and the loop has br << 133
>> 134 G4Molecule* __moleculeA = GetMolecule(__trackA);
>> 135 G4Molecule* __moleculeB = GetMolecule(__trackB);
>> 136
>> 137 G4double __D = __moleculeA->GetDiffusionCoefficient()
>> 138 + __moleculeB->GetDiffusionCoefficient();
>> 139
>> 140 G4ThreeVector __preStepPositionA = __trackA.GetStep()->GetPreStepPoint()
>> 141 ->GetPosition();
>> 142 G4ThreeVector __preStepPositionB = __trackB.GetStep()->GetPreStepPoint()
>> 143 ->GetPosition();
96 144
97 // Continue loop << 145 if (__preStepPositionA == __trackA.GetPosition())
98 for (; k < 3; ++k) << 146 {
99 { << 147 G4ExceptionDescription exceptionDescription;
100 postStepSeparation += std::pow( << 148 exceptionDescription << "The molecule : " << __moleculeA->GetName();
101 __trackA.GetPosition()[k] - __ << 149 exceptionDescription << " with track ID :" << __trackA.GetTrackID();
102 } << 150 exceptionDescription << " did not move since the previous step." << G4endl;
103 // Use Green approach : the Brownian b << 151 exceptionDescription << "Current position : "
104 __separationDistance = (postStepSepara << 152 << G4BestUnit(__trackA.GetPosition(), "Length")
105 << 153 << G4endl;
106 auto pMoleculeA = GetMolecule(__trackA << 154 exceptionDescription << "Previous position : "
107 auto pMoleculeB = GetMolecule(__trackB << 155 << G4BestUnit(__preStepPositionA, "Length") << G4endl;
108 << 156 G4Exception("G4DNASmoluchowskiReactionModel::FindReaction",
109 G4double D = pMoleculeA->GetDiffusionC << 157 "G4DNASmoluchowskiReactionModel", FatalErrorInArgument,
110 + pMoleculeB->GetDiffusio << 158 exceptionDescription);
111 <<
112 const auto& preStepPositionA = __track <<
113 const auto& preStepPositionB = __track <<
114 <<
115 G4double preStepSeparation = (preStepP <<
116 <<
117 //=================================== <<
118 // Brownian bridge <<
119 G4double __probabiltyOfEncounter = G4E <<
120 <<
121 <<
122 ); <<
123 G4double __selectedPOE = G4UniformRand <<
124 <<
125 if (__selectedPOE <= __probabiltyOfEnc <<
126 { <<
127 return true; <<
128 } <<
129 //=================================== <<
130 } 159 }
131 160
132 return false; << 161 G4double __preStepSeparation =
>> 162 (__preStepPositionA - __preStepPositionB).mag();
>> 163
>> 164 //===================================
>> 165 // Brownian bridge
>> 166
>> 167
>> 168 // if(G4Scheduler::Instance()->GetTimeStep() != __trackB.GetStep()->GetDeltaTime())
>> 169 // {
>> 170 // G4cout << G4Scheduler::Instance()->GetTimeStep() << G4endl;
>> 171 // G4cout << __trackB.GetStep()->GetDeltaTime() << G4endl;
>> 172 // assert(G4Scheduler::Instance()->GetTimeStep() == __trackB.GetStep()->GetDeltaTime());
>> 173 // }
>> 174
>> 175 G4double __probabiltyOfEncounter = G4Exp(
>> 176 -(__preStepSeparation - __R) * (postStepSeparation - __R) / (__D
>> 177 * (__trackB.GetStep()->GetDeltaTime())));
>> 178 G4double __selectedPOE = G4UniformRand();
>> 179
>> 180 if (__selectedPOE <= __probabiltyOfEncounter) return true;
>> 181 //===================================
>> 182 }
>> 183
>> 184 return false;
133 } 185 }
134 186