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25 //
26
27 #include "ChemistryWorld.hh"
28
29 #include "G4DNABoundingBox.hh"
30 #include "G4DNAMolecularReactionTable.hh"
31 #include "G4MoleculeTable.hh"
32 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
33
34 ChemistryWorld::ChemistryWorld() : G4VChemistryWorld(), G4UImessenger()
35 {
36 fpChemWoldDir = std::make_unique<G4UIdirectory>("/UHDR/env/", false);
37 fpChemWoldDir->SetGuidance("chemistry environment commands");
38
39 fpAddpH = std::make_unique<G4UIcmdWithADouble>("/UHDR/env/pH", this);
40 fpAddpH->SetGuidance("Add pH for water.");
41 fpAddpH->SetParameterName("pH", false);
42 fpAddpH->SetToBeBroadcasted(false);
43
44 fpAddScavengerName = std::make_unique<G4UIcmdWithAString>("/UHDR/env/scavenger", this);
45 fpAddScavengerName->SetToBeBroadcasted(false);
46
47 fpTargetVolume = std::make_unique<G4UIcmdWithADoubleAndUnit>("/UHDR/env/volume", this);
48 fpTargetVolume->SetGuidance("Volume of water.");
49 fpTargetVolume->SetParameterName("Volume", false);
50 fpTargetVolume->AvailableForStates(G4State_PreInit);
51 fpTargetVolume->SetToBeBroadcasted(false);
52 }
53 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
54
55 void ChemistryWorld::ConstructChemistryBoundary()
56 {
57 fHalfBox = 1.6 * um; // halfBox
58 std::initializer_list<G4double> l{fHalfBox, -fHalfBox, fHalfBox, -fHalfBox, fHalfBox, -fHalfBox};
59 fpChemistryBoundary = std::make_unique<G4DNABoundingBox>(l);
60 }
61 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
62
63 void ChemistryWorld::SetNewValue(G4UIcommand* command, G4String newValue)
64 {
65 if (command == fpAddpH.get()) {
66 fpH = fpAddpH->GetNewDoubleValue(newValue);
67 ConstructChemistryComponents();
68 }
69 else if (command == fpAddScavengerName.get()) {
70 std::istringstream iss(newValue);
71 G4String species;
72 iss >> species;
73 auto scavengerConf = G4MoleculeTable::Instance()->GetConfiguration(species);
74 G4double concentraion;
75 iss >> concentraion;
76 G4String unit;
77 iss >> unit;
78 if (unit == "M") {
79 G4double ConcentrationInM = concentraion / (mole * liter);
80 fpChemicalComponent[scavengerConf] = ConcentrationInM;
81 }
82 else if (unit == "mM") {
83 G4double ConcentrationInM = concentraion / (mole * liter * 1e3);
84 fpChemicalComponent[scavengerConf] = ConcentrationInM;
85 }
86 else if (unit == "uM") {
87 G4double ConcentrationInM = concentraion / (mole * liter * 1e6);
88 fpChemicalComponent[scavengerConf] = ConcentrationInM;
89 }
90 else if (unit == "%") // only for O2
91 {
92 G4double ConcentrationInM = (concentraion / 100) * 0.0013 / (mole * liter);
93 fpChemicalComponent[scavengerConf] = ConcentrationInM;
94 }
95 else {
96 throw std::runtime_error("Unit should be in Molarity");
97 }
98 }
99 else if (command == fpTargetVolume.get()) {
100 fHalfBox = G4UIcmdWithADoubleAndUnit::GetNewDoubleValue(newValue);
101 std::initializer_list<G4double> l{fHalfBox, -fHalfBox, fHalfBox,
102 -fHalfBox, fHalfBox, -fHalfBox};
103 fpChemistryBoundary = std::make_unique<G4DNABoundingBox>(l);
104 }
105 }
106 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
107
108 void ChemistryWorld::ConstructChemistryComponents()
109 {
110 auto O2 = G4MoleculeTable::Instance()->GetConfiguration("O2");
111 auto H2O = G4MoleculeTable::Instance()->GetConfiguration("H2O");
112 auto H3Op = G4MoleculeTable::Instance()->GetConfiguration("H3Op(B)");
113 auto OHm = G4MoleculeTable::Instance()->GetConfiguration("OHm(B)");
114
115 ////////////////////////////////////////////////////////////////////
116 // Water is defined from NIST material database
117 // water 55.3 M, 9.9x10-8 M, and 9.9x10-8 M
118 // water density = 18.01528 g/mol * 55.3 M = 996.24498 g/l
119 // H3OpB density = 1 g/mol * 9.9x10-8 M
120 // OHmB density = 17.01528 g/mol * 9.9x10-8 M
121 // O2B density = 15.999 g/mol * 2.58e-4 M
122 /////////////////////////////////////////////////////////////////
123 G4double pKw = 14; // at 25°C pK of water is 14
124 G4double waterMolarity = 55.3 / (mole * liter); // 55.3 M
125 fpChemicalComponent[H2O] = waterMolarity;
126
127 G4double H3OpBMolarity = std::pow(10, -fpH) / (mole * liter); // pH = 7
128 fpChemicalComponent[H3Op] = H3OpBMolarity;
129
130 G4double OHmBMolarity = std::pow(10, -(pKw - fpH)) / (mole * liter); // pH = 7
131 fpChemicalComponent[OHm] = OHmBMolarity;
132 // oxygen
133 G4double O2Molarity = (0. / 100) * 0.0013 / (mole * liter);
134 fpChemicalComponent[O2] = O2Molarity;
135 }
136 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo......
137