| Geant4 Cross Reference |
1 // 1
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17 // *
18 // * This code implementation is the result
19 // * technical work of the GEANT4 collaboratio
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23 // * acceptance of all terms of the Geant4 Sof
24 // *******************************************
25 //
26
27 #include "ChemistryWorld.hh"
28
29 #include "G4DNABoundingBox.hh"
30 #include "G4DNAMolecularReactionTable.hh"
31 #include "G4MoleculeTable.hh"
32 //....oooOO0OOooo........oooOO0OOooo........oo
33
34 ChemistryWorld::ChemistryWorld() : G4VChemistr
35 {
36 fpChemWoldDir = std::make_unique<G4UIdirecto
37 fpChemWoldDir->SetGuidance("chemistry enviro
38
39 fpAddpH = std::make_unique<G4UIcmdWithADoubl
40 fpAddpH->SetGuidance("Add pH for water.");
41 fpAddpH->SetParameterName("pH", false);
42 fpAddpH->SetToBeBroadcasted(false);
43
44 fpAddScavengerName = std::make_unique<G4UIcm
45 fpAddScavengerName->SetToBeBroadcasted(false
46
47 fpTargetVolume = std::make_unique<G4UIcmdWit
48 fpTargetVolume->SetGuidance("Volume of water
49 fpTargetVolume->SetParameterName("Volume", f
50 fpTargetVolume->AvailableForStates(G4State_P
51 fpTargetVolume->SetToBeBroadcasted(false);
52 }
53 //....oooOO0OOooo........oooOO0OOooo........oo
54
55 void ChemistryWorld::ConstructChemistryBoundar
56 {
57 fHalfBox = 1.6 * um; // halfBox
58 std::initializer_list<G4double> l{fHalfBox,
59 fpChemistryBoundary = std::make_unique<G4DNA
60 }
61 //....oooOO0OOooo........oooOO0OOooo........oo
62
63 void ChemistryWorld::SetNewValue(G4UIcommand*
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::Inst
74 G4double concentraion;
75 iss >> concentraion;
76 G4String unit;
77 iss >> unit;
78 if (unit == "M") {
79 G4double ConcentrationInM = concentraion
80 fpChemicalComponent[scavengerConf] = Con
81 }
82 else if (unit == "mM") {
83 G4double ConcentrationInM = concentraion
84 fpChemicalComponent[scavengerConf] = Con
85 }
86 else if (unit == "uM") {
87 G4double ConcentrationInM = concentraion
88 fpChemicalComponent[scavengerConf] = Con
89 }
90 else if (unit == "%") // only for O2
91 {
92 G4double ConcentrationInM = (concentraio
93 fpChemicalComponent[scavengerConf] = Con
94 }
95 else {
96 throw std::runtime_error("Unit should be
97 }
98 }
99 else if (command == fpTargetVolume.get()) {
100 fHalfBox = G4UIcmdWithADoubleAndUnit::GetN
101 std::initializer_list<G4double> l{fHalfBox
102 -fHalfBo
103 fpChemistryBoundary = std::make_unique<G4D
104 }
105 }
106 //....oooOO0OOooo........oooOO0OOooo........oo
107
108 void ChemistryWorld::ConstructChemistryCompone
109 {
110 auto O2 = G4MoleculeTable::Instance()->GetCo
111 auto H2O = G4MoleculeTable::Instance()->GetC
112 auto H3Op = G4MoleculeTable::Instance()->Get
113 auto OHm = G4MoleculeTable::Instance()->GetC
114
115 ////////////////////////////////////////////
116 // Water is defined from NIST material datab
117 // water 55.3 M, 9.9x10-8 M, and 9.9x10-8 M
118 // water density = 18.01528 g/mol * 55.3 M
119 // H3OpB density = 1 g/mol * 9.9x10-8 M
120 // OHmB density = 17.01528 g/mol * 9.9x10-8
121 // O2B density = 15.999 g/mol * 2.58e-4 M
122 ////////////////////////////////////////////
123 G4double pKw = 14; // at 25°C pK of water
124 G4double waterMolarity = 55.3 / (mole * lite
125 fpChemicalComponent[H2O] = waterMolarity;
126
127 G4double H3OpBMolarity = std::pow(10, -fpH)
128 fpChemicalComponent[H3Op] = H3OpBMolarity;
129
130 G4double OHmBMolarity = std::pow(10, -(pKw -
131 fpChemicalComponent[OHm] = OHmBMolarity;
132 // oxygen
133 G4double O2Molarity = (0. / 100) * 0.0013 /
134 fpChemicalComponent[O2] = O2Molarity;
135 }
136 //....oooOO0OOooo........oooOO0OOooo........oo
137