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Geant4/processes/electromagnetic/dna/models/src/G4DNASmoluchowskiReactionModel.cc

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Diff markup

Differences between /processes/electromagnetic/dna/models/src/G4DNASmoluchowskiReactionModel.cc (Version 11.3.0) and /processes/electromagnetic/dna/models/src/G4DNASmoluchowskiReactionModel.cc (Version 10.2.p3)


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 25 //                                                 25 //
                                                   >>  26 // $Id: G4DNASmoluchowskiReactionModel.cc 94218 2015-11-09 08:24:48Z 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"
 33 #include "G4Exp.hh"                            <<  34 //#include "G4Scheduler.hh"
 34                                                    35 
 35 G4DNASmoluchowskiReactionModel::G4DNASmoluchow <<  36 G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel() :
                                                   >>  37     G4VDNAReactionModel()
                                                   >>  38 {
                                                   >>  39   fReactionData = 0;
                                                   >>  40 }
 36                                                    41 
 37 G4DNASmoluchowskiReactionModel::~G4DNASmolucho <<  42 G4DNASmoluchowskiReactionModel::G4DNASmoluchowskiReactionModel(const G4DNASmoluchowskiReactionModel& __right) :
                                                   >>  43     G4VDNAReactionModel(__right)
                                                   >>  44 {
                                                   >>  45   fReactionData = 0;
                                                   >>  46 }
 38                                                    47 
 39 void G4DNASmoluchowskiReactionModel::Initialis <<  48 G4DNASmoluchowskiReactionModel& G4DNASmoluchowskiReactionModel::operator=(const G4DNASmoluchowskiReactionModel& right)
                                                   >>  49 {
                                                   >>  50   if (this == &right) return *this;
                                                   >>  51   fReactionData = 0;
                                                   >>  52   return *this;
                                                   >>  53 }
                                                   >>  54 
                                                   >>  55 G4DNASmoluchowskiReactionModel::~G4DNASmoluchowskiReactionModel()
                                                   >>  56 {
                                                   >>  57   fReactionData = 0;
                                                   >>  58 }
                                                   >>  59 
                                                   >>  60 void G4DNASmoluchowskiReactionModel::Initialise(G4MolecularConfiguration* __molecule,
 40                                                    61                                                 const G4Track&)
 41 {                                                  62 {
 42     fpReactionData = fpReactionTable->GetReact <<  63   fReactionData = fReactionTable->GetReactionData(__molecule);
 43 }                                                  64 }
 44                                                    65 
 45 void G4DNASmoluchowskiReactionModel::Initialis <<  66 void
                                                   >>  67 G4DNASmoluchowskiReactionModel::
                                                   >>  68 InitialiseToPrint(G4MolecularConfiguration* __molecule)
 46 {                                                  69 {
 47     fpReactionData = fpReactionTable->GetReact <<  70   fReactionData = fReactionTable->GetReactionData(__molecule);
 48 }                                                  71 }
 49                                                    72 
 50 G4double G4DNASmoluchowskiReactionModel::GetRe <<  73 G4double
 51                                                <<  74 G4DNASmoluchowskiReactionModel::GetReactionRadius(G4MolecularConfiguration* __mol1,
                                                   >>  75                                                   G4MolecularConfiguration* __mol2)
 52 {                                                  76 {
 53     G4double __output = fpReactionTable->GetRe <<  77   G4double __output = fReactionTable->GetReactionData(__mol1, __mol2)
 54     return __output;                           <<  78       ->GetEffectiveReactionRadius();
                                                   >>  79   return __output;
 55 }                                                  80 }
 56                                                    81 
 57 G4double G4DNASmoluchowskiReactionModel::GetRe <<  82 G4double G4DNASmoluchowskiReactionModel::GetReactionRadius(const G4int __i)
 58 {                                                  83 {
 59     G4double __output = (*fpReactionData)[__i] <<  84   G4double __output = (*fReactionData)[__i]->GetEffectiveReactionRadius();
 60     return __output;                           <<  85   return __output;
 61 }                                                  86 }
 62                                                    87 
 63 G4bool G4DNASmoluchowskiReactionModel::FindRea     88 G4bool G4DNASmoluchowskiReactionModel::FindReaction(const G4Track& __trackA,
 64                                                    89                                                     const G4Track& __trackB,
 65                                                <<  90                                                     const G4double __R,
 66                                                <<  91                                                     G4double& __r,
 67                                                    92                                                     const G4bool __alongStepReaction)
 68 {                                                  93 {
 69     const G4double R2 = __reactionRadius * __r <<  94   G4double postStepSeparation = 0;
 70     G4double postStepSeparation = 0.;          <<  95   bool do_break = false;
 71     bool do_break = false;                     <<  96   G4double R2 = __R * __R;
 72     int k = 0;                                 <<  97   int k = 0;
                                                   >>  98 
                                                   >>  99   for (; k < 3; k++)
                                                   >> 100   {
                                                   >> 101     postStepSeparation += std::pow(
                                                   >> 102         __trackA.GetPosition()[k] - __trackB.GetPosition()[k], 2);
 73                                                   103 
 74     for (; k < 3; ++k)                         << 104     if (postStepSeparation > R2)
 75     {                                             105     {
 76         postStepSeparation += std::pow(        << 106       do_break = true;
 77             __trackA.GetPosition()[k] - __trac << 107       break;
 78                                                << 
 79         if (postStepSeparation > R2)           << 
 80         {                                      << 
 81             do_break = true;                   << 
 82             break;                             << 
 83         }                                      << 
 84     }                                             108     }
                                                   >> 109   }
 85                                                   110 
 86     if (!do_break)                             << 111   if (do_break == false)
                                                   >> 112   {
                                                   >> 113     // The loop was not break
                                                   >> 114     // => __r^2 < __R^2
                                                   >> 115     __r = std::sqrt(postStepSeparation);
                                                   >> 116     return true;
                                                   >> 117   }
                                                   >> 118   else if (__alongStepReaction == true)
                                                   >> 119   {
                                                   >> 120     //G4cout << "alongStepReaction==true" << G4endl;
                                                   >> 121     //Along step cheack and
                                                   >> 122     // the loop has break
                                                   >> 123 
                                                   >> 124     // Continue loop
                                                   >> 125     for (; k < 3; k++)
 87     {                                             126     {
 88         // The loop was not break              << 127       postStepSeparation += std::pow(
 89         // => r^2 < R^2                        << 128           __trackA.GetPosition()[k] - __trackB.GetPosition()[k], 2);
 90         __separationDistance = std::sqrt(postS << 
 91         return true;                           << 
 92     }                                             129     }
 93     if (__alongStepReaction)                   << 130     // Use Green approach : the Brownian bridge
 94     {                                          << 131     __r = (postStepSeparation = std::sqrt(postStepSeparation));
 95         //Along step check and the loop has br << 132 
                                                   >> 133     G4Molecule* __moleculeA = GetMolecule(__trackA);
                                                   >> 134     G4Molecule* __moleculeB = GetMolecule(__trackB);
                                                   >> 135 
                                                   >> 136     G4double __D = __moleculeA->GetDiffusionCoefficient()
                                                   >> 137         + __moleculeB->GetDiffusionCoefficient();
                                                   >> 138 
                                                   >> 139     G4ThreeVector __preStepPositionA = __trackA.GetStep()->GetPreStepPoint()
                                                   >> 140         ->GetPosition();
                                                   >> 141     G4ThreeVector __preStepPositionB = __trackB.GetStep()->GetPreStepPoint()
                                                   >> 142         ->GetPosition();
 96                                                   143 
 97         // Continue loop                       << 144     if (__preStepPositionA == __trackA.GetPosition())
 98         for (; k < 3; ++k)                     << 145     {
 99         {                                      << 146       G4ExceptionDescription exceptionDescription;
100             postStepSeparation += std::pow(    << 147       exceptionDescription << "The molecule : " << __moleculeA->GetName();
101                 __trackA.GetPosition()[k] - __ << 148       exceptionDescription << " with track ID :" << __trackA.GetTrackID();
102         }                                      << 149       exceptionDescription << " did not move since the previous step." << G4endl;
103         // Use Green approach : the Brownian b << 150       exceptionDescription << "Current position : "
104         __separationDistance = (postStepSepara << 151                            << G4BestUnit(__trackA.GetPosition(), "Length")
105                                                << 152                            << G4endl;
106         auto pMoleculeA = GetMolecule(__trackA << 153       exceptionDescription << "Previous position : "
107         auto pMoleculeB = GetMolecule(__trackB << 154                            << G4BestUnit(__preStepPositionA, "Length") << G4endl;
108                                                << 155       G4Exception("G4DNASmoluchowskiReactionModel::FindReaction",
109         G4double D = pMoleculeA->GetDiffusionC << 156                   "G4DNASmoluchowskiReactionModel", FatalErrorInArgument,
110                      + pMoleculeB->GetDiffusio << 157                   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     }                                             158     }
131                                                   159 
132     return false;                              << 160     G4double __preStepSeparation =
                                                   >> 161         (__preStepPositionA - __preStepPositionB).mag();
                                                   >> 162 
                                                   >> 163     //===================================
                                                   >> 164     // Brownian bridge
                                                   >> 165 
                                                   >> 166 
                                                   >> 167 //    if(G4Scheduler::Instance()->GetTimeStep() != __trackB.GetStep()->GetDeltaTime())
                                                   >> 168 //    {
                                                   >> 169 //      G4cout << G4Scheduler::Instance()->GetTimeStep() << G4endl;
                                                   >> 170 //      G4cout << __trackB.GetStep()->GetDeltaTime() << G4endl;
                                                   >> 171 //      assert(G4Scheduler::Instance()->GetTimeStep() == __trackB.GetStep()->GetDeltaTime());
                                                   >> 172 //    }
                                                   >> 173 
                                                   >> 174     G4double __probabiltyOfEncounter = std::exp(
                                                   >> 175         -(__preStepSeparation - __R) * (postStepSeparation - __R) / (__D
                                                   >> 176             * (__trackB.GetStep()->GetDeltaTime())));
                                                   >> 177     G4double __selectedPOE = G4UniformRand();
                                                   >> 178 
                                                   >> 179     if (__selectedPOE <= __probabiltyOfEncounter) return true;
                                                   >> 180     //===================================
                                                   >> 181   }
                                                   >> 182 
                                                   >> 183   return false;
133 }                                                 184 }
134                                                   185