| Geant4 Cross Reference |
1 // 1 //
2 // ******************************************* 2 // ********************************************************************
3 // * License and Disclaimer 3 // * License and Disclaimer *
4 // * 4 // * *
5 // * The Geant4 software is copyright of th 5 // * The Geant4 software is copyright of the Copyright Holders of *
6 // * the Geant4 Collaboration. It is provided 6 // * the Geant4 Collaboration. It is provided under the terms and *
7 // * conditions of the Geant4 Software License 7 // * conditions of the Geant4 Software License, included in the file *
8 // * LICENSE and available at http://cern.ch/ 8 // * LICENSE and available at http://cern.ch/geant4/license . These *
9 // * include a list of copyright holders. 9 // * include a list of copyright holders. *
10 // * 10 // * *
11 // * Neither the authors of this software syst 11 // * Neither the authors of this software system, nor their employing *
12 // * institutes,nor the agencies providing fin 12 // * institutes,nor the agencies providing financial support for this *
13 // * work make any representation or warran 13 // * work make any representation or warranty, express or implied, *
14 // * regarding this software system or assum 14 // * regarding this software system or assume any liability for its *
15 // * use. Please see the license in the file 15 // * use. Please see the license in the file LICENSE and URL above *
16 // * for the full disclaimer and the limitatio 16 // * for the full disclaimer and the limitation of liability. *
17 // * 17 // * *
18 // * This code implementation is the result 18 // * This code implementation is the result of the scientific and *
19 // * technical work of the GEANT4 collaboratio 19 // * technical work of the GEANT4 collaboration. *
20 // * By using, copying, modifying or distri 20 // * By using, copying, modifying or distributing the software (or *
21 // * any work based on the software) you ag 21 // * any work based on the software) you agree to acknowledge its *
22 // * use in resulting scientific publicati 22 // * use in resulting scientific publications, and indicate your *
23 // * acceptance of all terms of the Geant4 Sof 23 // * acceptance of all terms of the Geant4 Software license. *
24 // ******************************************* 24 // ********************************************************************
25 // 25 //
26 26
27 #include "ChemistryWorld.hh" 27 #include "ChemistryWorld.hh"
28 <<
29 #include "G4DNABoundingBox.hh" 28 #include "G4DNABoundingBox.hh"
30 #include "G4DNAMolecularReactionTable.hh" 29 #include "G4DNAMolecularReactionTable.hh"
31 #include "G4MoleculeTable.hh" 30 #include "G4MoleculeTable.hh"
32 //....oooOO0OOooo........oooOO0OOooo........oo <<
33 31
34 ChemistryWorld::ChemistryWorld() : G4VChemistr << 32 ChemistryWorld::ChemistryWorld() : G4VChemistryWorld(), G4UImessenger() {
35 { <<
36 fpChemWoldDir = std::make_unique<G4UIdirecto 33 fpChemWoldDir = std::make_unique<G4UIdirectory>("/UHDR/env/", false);
37 fpChemWoldDir->SetGuidance("chemistry enviro 34 fpChemWoldDir->SetGuidance("chemistry environment commands");
38 35
39 fpAddpH = std::make_unique<G4UIcmdWithADoubl 36 fpAddpH = std::make_unique<G4UIcmdWithADouble>("/UHDR/env/pH", this);
40 fpAddpH->SetGuidance("Add pH for water."); 37 fpAddpH->SetGuidance("Add pH for water.");
41 fpAddpH->SetParameterName("pH", false); 38 fpAddpH->SetParameterName("pH", false);
42 fpAddpH->SetToBeBroadcasted(false); 39 fpAddpH->SetToBeBroadcasted(false);
43 40
44 fpAddScavengerName = std::make_unique<G4UIcm << 41 fpAddScavengerName =
>> 42 std::make_unique<G4UIcmdWithAString>("/UHDR/env/scavenger", this);
45 fpAddScavengerName->SetToBeBroadcasted(false 43 fpAddScavengerName->SetToBeBroadcasted(false);
46 44
47 fpTargetVolume = std::make_unique<G4UIcmdWit 45 fpTargetVolume = std::make_unique<G4UIcmdWithADoubleAndUnit>("/UHDR/env/volume", this);
48 fpTargetVolume->SetGuidance("Volume of water 46 fpTargetVolume->SetGuidance("Volume of water.");
49 fpTargetVolume->SetParameterName("Volume", f 47 fpTargetVolume->SetParameterName("Volume", false);
50 fpTargetVolume->AvailableForStates(G4State_P 48 fpTargetVolume->AvailableForStates(G4State_PreInit);
51 fpTargetVolume->SetToBeBroadcasted(false); 49 fpTargetVolume->SetToBeBroadcasted(false);
52 } 50 }
53 //....oooOO0OOooo........oooOO0OOooo........oo <<
54 51
55 void ChemistryWorld::ConstructChemistryBoundar << 52 void ChemistryWorld::ConstructChemistryBoundary() {
56 { << 53 fHalfBox = 1.6 * um; // halfBox
57 fHalfBox = 1.6 * um; // halfBox << 54 std::initializer_list<G4double> l{fHalfBox, -fHalfBox, fHalfBox,
58 std::initializer_list<G4double> l{fHalfBox, << 55 -fHalfBox, fHalfBox, -fHalfBox};
59 fpChemistryBoundary = std::make_unique<G4DNA 56 fpChemistryBoundary = std::make_unique<G4DNABoundingBox>(l);
60 } 57 }
61 //....oooOO0OOooo........oooOO0OOooo........oo <<
62 58
63 void ChemistryWorld::SetNewValue(G4UIcommand* << 59 void ChemistryWorld::SetNewValue(G4UIcommand *command, G4String newValue) {
64 { <<
65 if (command == fpAddpH.get()) { 60 if (command == fpAddpH.get()) {
66 fpH = fpAddpH->GetNewDoubleValue(newValue) 61 fpH = fpAddpH->GetNewDoubleValue(newValue);
67 ConstructChemistryComponents(); 62 ConstructChemistryComponents();
68 } << 63 } else if (command == fpAddScavengerName.get()) {
69 else if (command == fpAddScavengerName.get() <<
70 std::istringstream iss(newValue); 64 std::istringstream iss(newValue);
71 G4String species; 65 G4String species;
72 iss >> species; 66 iss >> species;
73 auto scavengerConf = G4MoleculeTable::Inst 67 auto scavengerConf = G4MoleculeTable::Instance()->GetConfiguration(species);
74 G4double concentraion; 68 G4double concentraion;
75 iss >> concentraion; 69 iss >> concentraion;
76 G4String unit; 70 G4String unit;
77 iss >> unit; 71 iss >> unit;
78 if (unit == "M") { 72 if (unit == "M") {
79 G4double ConcentrationInM = concentraion 73 G4double ConcentrationInM = concentraion / (mole * liter);
80 fpChemicalComponent[scavengerConf] = Con 74 fpChemicalComponent[scavengerConf] = ConcentrationInM;
81 } << 75 } else if (unit == "mM") {
82 else if (unit == "mM") { <<
83 G4double ConcentrationInM = concentraion 76 G4double ConcentrationInM = concentraion / (mole * liter * 1e3);
84 fpChemicalComponent[scavengerConf] = Con 77 fpChemicalComponent[scavengerConf] = ConcentrationInM;
85 } << 78 } else if (unit == "uM") {
86 else if (unit == "uM") { <<
87 G4double ConcentrationInM = concentraion 79 G4double ConcentrationInM = concentraion / (mole * liter * 1e6);
88 fpChemicalComponent[scavengerConf] = Con 80 fpChemicalComponent[scavengerConf] = ConcentrationInM;
89 } << 81 } else if (unit == "%") // only for O2
90 else if (unit == "%") // only for O2 <<
91 { 82 {
92 G4double ConcentrationInM = (concentraio << 83 G4double ConcentrationInM =
>> 84 (concentraion / 100) * 0.0013 / (mole * liter);
93 fpChemicalComponent[scavengerConf] = Con 85 fpChemicalComponent[scavengerConf] = ConcentrationInM;
94 } << 86 } else {
95 else { <<
96 throw std::runtime_error("Unit should be 87 throw std::runtime_error("Unit should be in Molarity");
97 } 88 }
98 } << 89 }else if (command == fpTargetVolume.get()) {
99 else if (command == fpTargetVolume.get()) { <<
100 fHalfBox = G4UIcmdWithADoubleAndUnit::GetN 90 fHalfBox = G4UIcmdWithADoubleAndUnit::GetNewDoubleValue(newValue);
101 std::initializer_list<G4double> l{fHalfBox 91 std::initializer_list<G4double> l{fHalfBox, -fHalfBox, fHalfBox,
102 -fHalfBo 92 -fHalfBox, fHalfBox, -fHalfBox};
103 fpChemistryBoundary = std::make_unique<G4D 93 fpChemistryBoundary = std::make_unique<G4DNABoundingBox>(l);
104 } 94 }
>> 95
105 } 96 }
106 //....oooOO0OOooo........oooOO0OOooo........oo <<
107 97
108 void ChemistryWorld::ConstructChemistryCompone << 98 void ChemistryWorld::ConstructChemistryComponents() {
109 { <<
110 auto O2 = G4MoleculeTable::Instance()->GetCo 99 auto O2 = G4MoleculeTable::Instance()->GetConfiguration("O2");
111 auto H2O = G4MoleculeTable::Instance()->GetC 100 auto H2O = G4MoleculeTable::Instance()->GetConfiguration("H2O");
112 auto H3Op = G4MoleculeTable::Instance()->Get 101 auto H3Op = G4MoleculeTable::Instance()->GetConfiguration("H3Op(B)");
113 auto OHm = G4MoleculeTable::Instance()->GetC 102 auto OHm = G4MoleculeTable::Instance()->GetConfiguration("OHm(B)");
114 103
115 //////////////////////////////////////////// << 104 ////////////////////////////////////////////////////////////////////
116 // Water is defined from NIST material datab << 105 // Water is defined from NIST material database
117 // water 55.3 M, 9.9x10-8 M, and 9.9x10-8 M << 106 // water 55.3 M, 9.9x10-8 M, and 9.9x10-8 M
118 // water density = 18.01528 g/mol * 55.3 M << 107 // water density = 18.01528 g/mol * 55.3 M = 996.24498 g/l
119 // H3OpB density = 1 g/mol * 9.9x10-8 M << 108 // H3OpB density = 1 g/mol * 9.9x10-8 M
120 // OHmB density = 17.01528 g/mol * 9.9x10-8 << 109 // OHmB density = 17.01528 g/mol * 9.9x10-8 M
121 // O2B density = 15.999 g/mol * 2.58e-4 M << 110 // O2B density = 15.999 g/mol * 2.58e-4 M
122 //////////////////////////////////////////// << 111 /////////////////////////////////////////////////////////////////
123 G4double pKw = 14; // at 25°C pK of water << 112 G4double pKw = 14; // at 25°C pK of water is 14
124 G4double waterMolarity = 55.3 / (mole * lite << 113 G4double waterMolarity = 55.3 / (mole * liter); // 55.3 M
125 fpChemicalComponent[H2O] = waterMolarity; 114 fpChemicalComponent[H2O] = waterMolarity;
126 115
127 G4double H3OpBMolarity = std::pow(10, -fpH) << 116 G4double H3OpBMolarity = std::pow(10, -fpH) / (mole * liter); // pH = 7
128 fpChemicalComponent[H3Op] = H3OpBMolarity; 117 fpChemicalComponent[H3Op] = H3OpBMolarity;
129 118
130 G4double OHmBMolarity = std::pow(10, -(pKw - << 119 G4double OHmBMolarity = std::pow(10, -(pKw - fpH)) / (mole * liter); // pH = 7
131 fpChemicalComponent[OHm] = OHmBMolarity; 120 fpChemicalComponent[OHm] = OHmBMolarity;
132 // oxygen 121 // oxygen
133 G4double O2Molarity = (0. / 100) * 0.0013 / 122 G4double O2Molarity = (0. / 100) * 0.0013 / (mole * liter);
134 fpChemicalComponent[O2] = O2Molarity; 123 fpChemicalComponent[O2] = O2Molarity;
135 } << 124 }
136 //....oooOO0OOooo........oooOO0OOooo........oo <<
137