UHDR/src/ChemistryWorld.cc

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0025 //
0026 /// \file ChemistryWorld.cc
0027 /// \brief Implementation of the ChemistryWorld class
0028
0029 #include "ChemistryWorld.hh"
0030
0031 #include "G4DNABoundingBox.hh"
0032 #include "G4DNAMolecularReactionTable.hh"
0033 #include "G4MoleculeTable.hh"
0034 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0035
0036 ChemistryWorld::ChemistryWorld() : G4VChemistryWorld(), G4UImessenger()
0037 {
0038   fpChemWoldDir = std::make_unique<G4UIdirectory>("/UHDR/env/", false);
0039   fpChemWoldDir->SetGuidance("chemistry environment commands");
0040
0041   fpAddpH = std::make_unique<G4UIcmdWithADouble>("/UHDR/env/pH", this);
0042   fpAddpH->SetGuidance("Add pH for water.");
0043   fpAddpH->SetParameterName("pH", false);
0044   fpAddpH->SetToBeBroadcasted(false);
0045
0046   fpAddScavengerName = std::make_unique<G4UIcmdWithAString>("/UHDR/env/scavenger", this);
0047   fpAddScavengerName->SetToBeBroadcasted(false);
0048
0049   fpTargetVolume = std::make_unique<G4UIcmdWithADoubleAndUnit>("/UHDR/env/volume", this);
0050   fpTargetVolume->SetGuidance("Volume of water.");
0051   fpTargetVolume->SetParameterName("Volume", false);
0052   fpTargetVolume->AvailableForStates(G4State_PreInit);
0053   fpTargetVolume->SetToBeBroadcasted(false);
0054 }
0055 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0056
0057 void ChemistryWorld::ConstructChemistryBoundary()
0058 {
0059   fHalfBox = 1.6 * um;  // halfBox
0060   std::initializer_list<G4double> l{fHalfBox, -fHalfBox, fHalfBox, -fHalfBox, fHalfBox, -fHalfBox};
0061   fpChemistryBoundary = std::make_unique<G4DNABoundingBox>(l);
0062 }
0063 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0064
0065 void ChemistryWorld::SetNewValue(G4UIcommand* command, G4String newValue)
0066 {
0067   if (command == fpAddpH.get()) {
0068     fpH = fpAddpH->GetNewDoubleValue(newValue);
0069     ConstructChemistryComponents();
0070   }
0071   else if (command == fpAddScavengerName.get()) {
0072     std::istringstream iss(newValue);
0073     G4String species;
0074     iss >> species;
0075     auto scavengerConf = G4MoleculeTable::Instance()->GetConfiguration(species);
0076     G4double concentraion;
0077     iss >> concentraion;
0078     G4String unit;
0079     iss >> unit;
0080     if (unit == "M") {
0081       G4double ConcentrationInM = concentraion / (mole * liter);
0082       fpChemicalComponent[scavengerConf] = ConcentrationInM;
0083     }
0084     else if (unit == "mM") {
0085       G4double ConcentrationInM = concentraion / (mole * liter * 1e3);
0086       fpChemicalComponent[scavengerConf] = ConcentrationInM;
0087     }
0088     else if (unit == "uM") {
0089       G4double ConcentrationInM = concentraion / (mole * liter * 1e6);
0090       fpChemicalComponent[scavengerConf] = ConcentrationInM;
0091     }
0092     else if (unit == "%")  // only for O2 and CO2
0093     {
0094       G4double kH = 0.;
0095       if (species == "O2")
0096         kH = 0.0013;
0097       else if (species == "CO2")
0098         kH = 0.034;
0099       G4double ConcentrationInM = (concentraion / 100) * kH / (mole * liter);
0100       fpChemicalComponent[scavengerConf] = ConcentrationInM;
0101     }
0102     else {
0103       throw std::runtime_error("Unit should be in Molarity");
0104     }
0105   }
0106   else if (command == fpTargetVolume.get()) {
0107     fHalfBox = G4UIcmdWithADoubleAndUnit::GetNewDoubleValue(newValue);
0108     std::initializer_list<G4double> l{fHalfBox,  -fHalfBox, fHalfBox,
0109                                       -fHalfBox, fHalfBox,  -fHalfBox};
0110     fpChemistryBoundary = std::make_unique<G4DNABoundingBox>(l);
0111   }
0112 }
0113 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
0114
0115 void ChemistryWorld::ConstructChemistryComponents()
0116 {
0117   auto O2 = G4MoleculeTable::Instance()->GetConfiguration("O2");
0118   auto CO2 = G4MoleculeTable::Instance()->GetConfiguration("CO2");
0119   auto H2O = G4MoleculeTable::Instance()->GetConfiguration("H2O");
0120   auto H3Op = G4MoleculeTable::Instance()->GetConfiguration("H3Op(B)");
0121   auto OHm = G4MoleculeTable::Instance()->GetConfiguration("OHm(B)");
0122
0123   ////////////////////////////////////////////////////////////////////
0124   // Water is defined from NIST material database
0125   // water 55.3 M, 9.9x10-8 M, and 9.9x10-8 M
0126   // water density =  18.01528 g/mol * 55.3 M = 996.24498 g/l
0127   // H3OpB density = 1 g/mol * 9.9x10-8 M
0128   // OHmB density = 17.01528 g/mol * 9.9x10-8 M
0129   // O2B density = 15.999 g/mol * 2.58e-4 M
0130   /////////////////////////////////////////////////////////////////
0131   G4double pKw = 14;  // at 25°C pK of water is 14
0132   G4double waterMolarity = 55.3 / (mole * liter);  // 55.3 M
0133   fpChemicalComponent[H2O] = waterMolarity;
0134
0135   G4double H3OpBMolarity = std::pow(10, -fpH) / (mole * liter);  // pH = 7
0136   fpChemicalComponent[H3Op] = H3OpBMolarity;
0137
0138   G4double OHmBMolarity = std::pow(10, -(pKw - fpH)) / (mole * liter);  // pH = 7
0139   fpChemicalComponent[OHm] = OHmBMolarity;
0140   // oxygen
0141   G4double O2Molarity = (0. / 100) * 0.0013 / (mole * liter);
0142   fpChemicalComponent[O2] = O2Molarity;
0143
0144   // CO2 At 25°C,  kH  is approximately  3.3×10  −2   mol/(L·atm).
0145   G4double CO2Molarity = (0. / 100) * 0.034 / (mole * liter);
0146   fpChemicalComponent[CO2] = CO2Molarity;
0147 }
0148 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......