UHDR/src/ChemistryWorld.cc

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