dsbandrepair/src/TimeStepAction.cc

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0025 //
0026 //
0027 /// \file TimeStepAction.cc
0028 /// \brief Implementation of the TimeStepAction class
0029
0030 #include "TimeStepAction.hh"
0031 #include "G4UnitsTable.hh"
0032 #include "G4SystemOfUnits.hh"
0033
0034 #include "G4DNAChemistryManager.hh"
0035 #include "G4MoleculeCounter.hh"
0036 #include "G4MoleculeTable.hh"
0037 #include "G4Scheduler.hh"
0038 #include "UserMolecule.hh"
0039 #include "G4ChemTimeStepModel.hh"
0040 #include "G4EmParameters.hh"
0041 #include "Analysis.hh"
0042 #include "G4DNAMolecule.hh"
0043 #include "G4H3O.hh"
0044 #include "G4OH.hh"
0045 #include "G4H2O2.hh"
0046 #include "G4H2.hh"
0047 #include "G4Hydrogen.hh"
0048 #include "G4Electron_aq.hh"
0049 #include "G4ParticleTable.hh"
0050 #include "G4ParticleDefinition.hh"
0051 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0052
0053 TimeStepAction::TimeStepAction()
0054 : G4UserTimeStepAction()
0055 {
0056     auto param = G4EmParameters::Instance();
0057     if (param->GetTimeStepModel() == G4ChemTimeStepModel::SBS) {
0058         AddTimeStep(1*picosecond,0.1*picosecond);
0059         AddTimeStep(10*picosecond,1*picosecond);
0060         AddTimeStep(100*picosecond,3*picosecond);
0061         AddTimeStep(1000*picosecond,10*picosecond);
0062         AddTimeStep(10000*picosecond,100*picosecond);
0063     }
0064 }
0065
0066 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0067
0068
0069 TimeStepAction::TimeStepAction(const TimeStepAction& other)
0070 : G4UserTimeStepAction(other)
0071 {}
0072
0073 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0074
0075 TimeStepAction& TimeStepAction::operator=(const TimeStepAction& rhs)
0076 {
0077     if (this == &rhs) return *this; // handle self assignment
0078     //assignment operator
0079     return *this;
0080 }
0081
0082 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0083
0084 void TimeStepAction::StartProcessing()
0085 {
0086
0087     G4cout<<"Start chemistry "<<G4Scheduler::Instance()->GetGlobalTime()/s<<" s"<<G4endl;
0088     G4cout<<"Chemical endTime "<<G4Scheduler::Instance()->GetEndTime()/nanosecond<<" ns"<<G4endl;
0089 }
0090
0091 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0092
0093 void TimeStepAction::UserReactionAction(const G4Track& a, const G4Track& b,
0094     const std::vector<G4Track*>* products)
0095 {
0096
0097     // ***************************************
0098     // Flag Part
0099     // ***************************************
0100     //
0101     // set the flags
0102
0103     fReactif1 = 0;
0104     fReactif2 = 0;
0105     fProduct1 = 0;
0106     fProduct2 = 0;
0107
0108     fReactif1 = SetParticleFlag(a.GetDynamicParticle()->GetDefinition());
0109     fReactif2 = SetParticleFlag(b.GetDynamicParticle()->GetDefinition());
0110     if(products)
0111     {
0112         for(unsigned int i=0;i<products->size();++i)
0113         {
0114             switch(i)
0115             {
0116                 case 0:
0117                 fProduct1 = SetParticleFlag(((*products)[i])->GetDynamicParticle()->GetDefinition());
0118                 break;
0119                 case 1:
0120                 fProduct2 = SetParticleFlag(((*products)[i])->GetDynamicParticle()->GetDefinition());;
0121                 break;
0122                 default:
0123                 break;
0124             }
0125         }
0126     }
0127
0128     // ***************************************
0129     // Save Part
0130     // ***************************************
0131     // For DBScan
0132     G4int base;
0133
0134     if( (fReactif1==3 || fReactif2 ==3) // OH
0135         && (
0136             (fReactif1==8 || fReactif2 ==8) // Desoxyribose
0137                 || (fReactif1==9 || fReactif2 ==9) // Phosphate
0138         || (fReactif1==10|| fReactif2 ==10) // Adenine
0139             || (fReactif1==11|| fReactif2 ==11) // Thymine
0140             || (fReactif1==12|| fReactif2 ==12) // Guanine
0141             || (fReactif1==13|| fReactif2 ==13) // Cytosine
0142                 ) )
0143     {
0144         // Retrieve the dna molecule
0145         const G4Track* dnaMolecule = nullptr;
0146         const G4Track* radical = nullptr;
0147         //
0148         if (a.GetDynamicParticle()->GetDefinition() == G4OH::Definition()) {
0149             dnaMolecule = &b;
0150             radical = &a;
0151         }
0152         else {
0153             dnaMolecule = &a;
0154             radical = &b;
0155         }
0156
0157         auto _dnaMolecule = dynamic_cast<UserMolecule*> (dnaMolecule->GetUserInformation());
0158         if (_dnaMolecule) {
0159             G4int copyNo = _dnaMolecule->GetCopyNumber();
0160             G4int strand = _dnaMolecule->GetStrand();
0161
0162             if((fReactif1==8 || fReactif2 ==8) // Desoxyribose
0163                 || (fReactif1==9 || fReactif2 ==9)) // Phosphate
0164                 {
0165                     base=0;
0166                 }
0167             else
0168                 {
0169                     base=1;
0170                 }
0171
0172             // Retrieve the molecule coordinates
0173             auto analysisManager = Analysis::GetAnalysis()->GetAnalysisManager();
0174             analysisManager->FillNtupleIColumn(1, 0, strand);
0175             analysisManager->FillNtupleIColumn(1, 1, copyNo);
0176             analysisManager->FillNtupleDColumn(1, 2, radical->GetPosition().getX()/nm);
0177             analysisManager->FillNtupleDColumn(1, 3, radical->GetPosition().getY()/nm);
0178             analysisManager->FillNtupleDColumn(1, 4, radical->GetPosition().getZ()/nm);
0179             analysisManager->FillNtupleDColumn(1, 5, G4Scheduler::Instance()->GetGlobalTime()/ns );
0180             analysisManager->FillNtupleIColumn(1, 6, base);
0181             analysisManager->AddNtupleRow(1);
0182         } else {
0183             G4String msg = "Error in Downcasting";
0184             G4Exception("TimeStepAction::UserReactionAction", "", FatalException, msg);
0185         }
0186
0187     }
0188
0189 }
0190
0191 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0192
0193 G4int TimeStepAction::SetParticleFlag(const G4ParticleDefinition* partDef)
0194 {
0195     G4int flag (0);
0196
0197     if(partDef == G4H3O::Definition()) flag = 1;
0198     else if(partDef == G4OH::Definition()) flag = 3;
0199     else if(partDef == G4Electron_aq::Definition()) flag = 4;
0200     else if(partDef == G4Hydrogen::Definition()) flag = 5;
0201     else if(partDef == G4H2::Definition()) flag = 6;
0202     else if(partDef == G4H2O2::Definition()) flag = 7;
0203     else if(partDef == G4Deoxyribose::Definition()) flag = 8;
0204     else if(partDef == G4Phosphate::Definition()) flag = 9;
0205     else if(partDef == G4Adenine::Definition()) flag = 10;
0206     else if(partDef == G4Thymine::Definition()) flag = 11;
0207     else if(partDef == G4Guanine::Definition()) flag = 12;
0208     else if(partDef == G4Cytosine::Definition()) flag = 13;
0209     else if(partDef == G4Histone::Definition()) flag = 14;
0210     else if(partDef == G4DamagedDeoxyribose::Definition()) flag = 15;
0211     else if(partDef == G4DamagedAdenine::Definition()) flag = 16;
0212     else if(partDef == G4DamagedThymine::Definition()) flag = 17;
0213     else if(partDef == G4DamagedCytosine::Definition()) flag = 18;
0214     else if(partDef == G4DamagedGuanine::Definition()) flag = 19;
0215     else {
0216         G4ParticleDefinition* OHm =G4ParticleTable::GetParticleTable()->FindParticle("OHm");
0217         if (OHm && partDef == OHm) {
0218             flag = 2;
0219         }
0220     }
0221     return flag;
0222 }
0223
0224 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......