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25 // 25 //
26 // This example is provided by the Geant4-DNA 26 // This example is provided by the Geant4-DNA collaboration
27 // dnadamage2 example is derived from the chem 27 // dnadamage2 example is derived from the chem6 example
28 // chem6 example authors: W. G. Shin and S. In 28 // chem6 example authors: W. G. Shin and S. Incerti (CENBG, France)
29 // 29 //
30 // Any report or published results obtained us 30 // Any report or published results obtained using the Geant4-DNA software
31 // shall cite the following Geant4-DNA collabo 31 // shall cite the following Geant4-DNA collaboration publication:
32 // J. Appl. Phys. 125 (2019) 104301 32 // J. Appl. Phys. 125 (2019) 104301
33 // Med. Phys. 45 (2018) e722-e739 33 // Med. Phys. 45 (2018) e722-e739
34 // J. Comput. Phys. 274 (2014) 841-882 34 // J. Comput. Phys. 274 (2014) 841-882
35 // Med. Phys. 37 (2010) 4692-4708 35 // Med. Phys. 37 (2010) 4692-4708
36 // Int. J. Model. Simul. Sci. Comput. 1 (2010) 36 // Int. J. Model. Simul. Sci. Comput. 1 (2010) 157-178
37 // The Geant4-DNA web site is available at htt 37 // The Geant4-DNA web site is available at http://geant4-dna.org
38 // 38 //
39 // Authors: J. Naoki D. Kondo (UCSF, US) 39 // Authors: J. Naoki D. Kondo (UCSF, US)
40 // J. Ramos-Mendez and B. Faddegon (U 40 // J. Ramos-Mendez and B. Faddegon (UCSF, US)
41 // 41 //
42 /// \file DetectorConstruction.cc 42 /// \file DetectorConstruction.cc
43 /// \brief Implementation of the DetectorConst 43 /// \brief Implementation of the DetectorConstruction class
44 44
45 #include "DetectorConstruction.hh" 45 #include "DetectorConstruction.hh"
46 46
47 #include "ScoreLET.hh" << 47 #include "G4NistManager.hh"
48 #include "ScoreSpecies.hh" <<
49 #include "ScoreStrandBreaks.hh" <<
50 <<
51 #include "G4Box.hh" 48 #include "G4Box.hh"
52 #include "G4GeometryManager.hh" <<
53 #include "G4LogicalVolume.hh" 49 #include "G4LogicalVolume.hh"
54 #include "G4LogicalVolumeStore.hh" <<
55 #include "G4MultiFunctionalDetector.hh" <<
56 #include "G4NistManager.hh" <<
57 #include "G4PVPlacement.hh" 50 #include "G4PVPlacement.hh"
>> 51
>> 52 #include "G4VisAttributes.hh"
58 #include "G4PhysicalConstants.hh" 53 #include "G4PhysicalConstants.hh"
>> 54 #include "G4SystemOfUnits.hh"
>> 55 #include "G4GeometryManager.hh"
59 #include "G4RunManager.hh" 56 #include "G4RunManager.hh"
>> 57 #include "G4LogicalVolumeStore.hh"
>> 58
60 #include "G4SDManager.hh" 59 #include "G4SDManager.hh"
61 #include "G4SystemOfUnits.hh" << 60 #include "G4MultiFunctionalDetector.hh"
62 #include "G4VPrimitiveScorer.hh" 61 #include "G4VPrimitiveScorer.hh"
63 #include "G4VisAttributes.hh" << 62
>> 63 #include "ScoreSpecies.hh"
>> 64 #include "ScoreLET.hh"
>> 65 #include "ScoreStrandBreaks.hh"
64 66
65 //....oooOO0OOooo........oooOO0OOooo........oo 67 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
66 68
67 DetectorConstruction::DetectorConstruction() : << 69 DetectorConstruction::DetectorConstruction()
>> 70 : G4VUserDetectorConstruction()
68 { 71 {
69 fDetDir = new G4UIdirectory("/det/"); 72 fDetDir = new G4UIdirectory("/det/");
70 fDetDir->SetGuidance("Detector control."); 73 fDetDir->SetGuidance("Detector control.");
71 74
72 fSizeCmd = new G4UIcmdWithADoubleAndUnit("/d << 75 fSizeCmd = new G4UIcmdWithADoubleAndUnit("/det/setSize",this);
73 fSizeCmd->SetDefaultUnit("um"); 76 fSizeCmd->SetDefaultUnit("um");
74 77
75 fpOffSetFileUI = new G4UIcmdWithAString("/de 78 fpOffSetFileUI = new G4UIcmdWithAString("/det/OffSetFile", this);
76 fpPlasmidNbUI = new G4UIcmdWithAnInteger("/d << 79 fpPlasmidNbUI = new G4UIcmdWithAnInteger("/det/NbOfPlasmids", this);
77 80
78 fpPlasmidFile = new G4UIcmdWithAString("/det 81 fpPlasmidFile = new G4UIcmdWithAString("/det/PlasmidFile", this);
79 fpUseDNA = new G4UIcmdWithABool("/det/UseDNA << 82 fpUseDNA = new G4UIcmdWithABool("/det/UseDNAVolumes", this);
80 } 83 }
81 84
82 //....oooOO0OOooo........oooOO0OOooo........oo 85 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
83 86
84 DetectorConstruction::~DetectorConstruction() 87 DetectorConstruction::~DetectorConstruction()
85 { 88 {
86 delete fSizeCmd; 89 delete fSizeCmd;
87 delete fpOffSetFileUI; 90 delete fpOffSetFileUI;
88 delete fpPlasmidFile; 91 delete fpPlasmidFile;
89 delete fpUseDNA; 92 delete fpUseDNA;
90 } 93 }
91 94
92 //....oooOO0OOooo........oooOO0OOooo........oo 95 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
93 96
94 void DetectorConstruction::SetNewValue(G4UIcom 97 void DetectorConstruction::SetNewValue(G4UIcommand* command, G4String newValue)
95 { 98 {
96 if (command == fSizeCmd) { << 99 if(command == fSizeCmd)
>> 100 {
97 G4double size = fSizeCmd->GetNewDoubleValu 101 G4double size = fSizeCmd->GetNewDoubleValue(newValue);
98 SetSize(size); 102 SetSize(size);
99 } 103 }
100 104
101 if (command == fpPlasmidNbUI) { << 105 if (command == fpPlasmidNbUI)
>> 106 {
102 fNbOfPlasmids = fpPlasmidNbUI->GetNewIntVa 107 fNbOfPlasmids = fpPlasmidNbUI->GetNewIntValue(newValue);
103 } 108 }
104 109
105 if (command == fpOffSetFileUI) { << 110 if (command == fpOffSetFileUI)
>> 111 {
106 G4String File = newValue; 112 G4String File = newValue;
107 ReadOffsetFile(File); 113 ReadOffsetFile(File);
108 } 114 }
109 115
110 if (command == fpPlasmidFile) { << 116 if (command == fpPlasmidFile)
>> 117 {
111 fPlasmidFile = newValue; 118 fPlasmidFile = newValue;
112 } 119 }
113 120
114 if (command == fpUseDNA) { << 121 if (command == fpUseDNA)
>> 122 {
115 fUseDNAVolumes = fpUseDNA->GetNewBoolValue 123 fUseDNAVolumes = fpUseDNA->GetNewBoolValue(newValue);
116 } 124 }
117 } 125 }
118 126
119 //....oooOO0OOooo........oooOO0OOooo........oo 127 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
120 128
121 void DetectorConstruction::SetSize(G4double si 129 void DetectorConstruction::SetSize(G4double size)
122 { 130 {
>> 131
123 G4GeometryManager::GetInstance()->OpenGeomet 132 G4GeometryManager::GetInstance()->OpenGeometry();
124 fPlasmidEnvelope->SetRadius(size / 2); << 133 fPlasmidEnvelope->SetRadius(size/2);
125 G4RunManager::GetRunManager()->GeometryHasBe 134 G4RunManager::GetRunManager()->GeometryHasBeenModified();
126 G4cout << "#### the geometry has been modifi 135 G4cout << "#### the geometry has been modified " << G4endl;
127 } 136 }
128 137
129 //....oooOO0OOooo........oooOO0OOooo........oo 138 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
130 139
131 G4VPhysicalVolume* DetectorConstruction::Const 140 G4VPhysicalVolume* DetectorConstruction::Construct()
132 { 141 {
133 // Clear DNA information Containers 142 // Clear DNA information Containers
134 fSampleDNANames.clear(); 143 fSampleDNANames.clear();
135 fSampleDNAPositions.clear(); 144 fSampleDNAPositions.clear();
136 fSampleDNADetails.clear(); 145 fSampleDNADetails.clear();
137 fDNANames.clear(); 146 fDNANames.clear();
138 fDNAPositions.clear(); 147 fDNAPositions.clear();
139 fDNADetails.clear(); 148 fDNADetails.clear();
140 149
141 // Water is defined from NIST material datab 150 // Water is defined from NIST material database
142 G4NistManager* man = G4NistManager::Instance << 151 G4NistManager * man = G4NistManager::Instance();
143 G4Material* normalWater = man->FindOrBuildMa << 152 G4Material* normalWater = man->FindOrBuildMaterial("G4_WATER");
144 G4Material* waterWorld = << 153 G4Material* waterWorld = man->BuildMaterialWithNewDensity("G4_WATER_WORLD",
145 man->BuildMaterialWithNewDensity("G4_WATER << 154 "G4_WATER",
>> 155 1.0*g/cm/cm/cm);
146 156
147 // 157 //
148 // World 158 // World
149 G4Box* solidWenvelope = new G4Box("SWorld", << 159 G4Box* solidWenvelope = new G4Box("SWorld", 1 * um, 1 * um, 1 * um);
150 G4LogicalVolume* logicWorld = new G4LogicalV << 160 G4LogicalVolume* logicWorld = new G4LogicalVolume(solidWenvelope,
151 G4VPhysicalVolume* physWorld = << 161 waterWorld,
152 new G4PVPlacement(0, G4ThreeVector(), "PWo << 162 "LWorld");
>> 163 G4VPhysicalVolume* physWorld = new G4PVPlacement(0,
>> 164 G4ThreeVector(),
>> 165 "PWorld",
>> 166 logicWorld,
>> 167 0,
>> 168 false,
>> 169 0);
153 170
154 // Molecule 171 // Molecule
155 fPlasmidEnvelope = new G4Orb("plasmidEnvelop << 172 fPlasmidEnvelope = new G4Orb("plasmidEnvelope", 0.5*fWorldSize);
156 173
157 G4LogicalVolume* tlogicPlasmid = << 174 G4LogicalVolume* tlogicPlasmid = new G4LogicalVolume(fPlasmidEnvelope,
158 new G4LogicalVolume(fPlasmidEnvelope, norm << 175 normalWater,
159 new G4PVPlacement(0, G4ThreeVector(), tlogic << 176 "PlasmidVolume");
>> 177 new G4PVPlacement(0,
>> 178 G4ThreeVector(),
>> 179 tlogicPlasmid,
>> 180 "plasmid",
>> 181 logicWorld,
>> 182 false,
>> 183 0);
160 184
161 // World Vis Attributes 185 // World Vis Attributes
162 G4VisAttributes worldVis(G4Colour(0.0, 0.0, << 186 G4VisAttributes worldVis(G4Colour(0.0, 0.0, 1.0) );
163 logicWorld->SetVisAttributes(worldVis); 187 logicWorld->SetVisAttributes(worldVis);
164 188
165 PhysGeoImport GeoImport = PhysGeoImport(); 189 PhysGeoImport GeoImport = PhysGeoImport();
166 190
167 G4LogicalVolume* logicStraightVoxel; 191 G4LogicalVolume* logicStraightVoxel;
168 192
169 logicStraightVoxel = GeoImport.CreateLogicVo 193 logicStraightVoxel = GeoImport.CreateLogicVolumeXYZ(fPlasmidFile);
170 194
171 fSampleDNANames = GeoImport.GetMoleculesName << 195 fSampleDNANames = GeoImport.GetMoleculesNames();
172 fSampleDNAPositions = GeoImport.GetMolecules 196 fSampleDNAPositions = GeoImport.GetMoleculesPositions();
173 fSampleDNADetails = GeoImport.GetMoleculesDe << 197 fSampleDNADetails = GeoImport.GetMoleculesDetails();
174 198
175 for (int i = 0; i < fNbOfPlasmids; i++) { << 199 for ( int i = 0; i < fNbOfPlasmids; i++ ) {
176 if (fUseDNAVolumes) 200 if (fUseDNAVolumes)
177 new G4PVPlacement(0, fVOffset[i], logicS << 201 new G4PVPlacement(0,
178 AddDNAInformation(i, fVOffset[i]); << 202 fVOffset[i],
>> 203 logicStraightVoxel,
>> 204 "VoxelStraight",
>> 205 logicWorld,
>> 206 true,
>> 207 i);
>> 208 AddDNAInformation(i,fVOffset[i]);
179 } 209 }
180 210
181 // always return the physical World << 211 //always return the physical World
182 return physWorld; 212 return physWorld;
183 } 213 }
184 214
185 //....oooOO0OOooo........oooOO0OOooo........oo 215 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
186 216
187 void DetectorConstruction::ConstructSDandField 217 void DetectorConstruction::ConstructSDandField()
188 { 218 {
189 G4SDManager::GetSDMpointer()->SetVerboseLeve 219 G4SDManager::GetSDMpointer()->SetVerboseLevel(1);
190 220
191 // declare World as a MultiFunctionalDetecto 221 // declare World as a MultiFunctionalDetector scorer
192 // 222 //
193 G4MultiFunctionalDetector* mfDetector = new << 223 G4MultiFunctionalDetector* mfDetector =
>> 224 new G4MultiFunctionalDetector("mfDetector");
194 225
195 // LET scorer: 226 // LET scorer:
196 // - scores restricted or unrestricted LET 227 // - scores restricted or unrestricted LET
197 228
198 ScoreLET* LET = new ScoreLET("LET"); 229 ScoreLET* LET = new ScoreLET("LET");
199 mfDetector->RegisterPrimitive(LET); 230 mfDetector->RegisterPrimitive(LET);
200 231
201 // Species scorer: 232 // Species scorer:
202 // - scores number of species over time 233 // - scores number of species over time
203 // - compute the radiochemical yields (G va 234 // - compute the radiochemical yields (G values)
204 235
205 G4VPrimitiveScorer* primitivSpecies = new Sc 236 G4VPrimitiveScorer* primitivSpecies = new ScoreSpecies("Species");
206 mfDetector->RegisterPrimitive(primitivSpecie 237 mfDetector->RegisterPrimitive(primitivSpecies);
207 238
208 // SB Scorer: Requires access to Geometry 239 // SB Scorer: Requires access to Geometry
209 // - scores number of Direct SB 240 // - scores number of Direct SB
210 // - scores number of Indirect SB 241 // - scores number of Indirect SB
211 242
212 G4VPrimitiveScorer* primitiveSB = new ScoreS << 243 G4VPrimitiveScorer* primitiveSB = new ScoreStrandBreaks("StrandBreaks",
>> 244 this,&fWorldSize);
213 mfDetector->RegisterPrimitive(primitiveSB); 245 mfDetector->RegisterPrimitive(primitiveSB);
214 246
215 // Attach Detectors to Plasmid Volumes 247 // Attach Detectors to Plasmid Volumes
216 G4LogicalVolumeStore* theLogicalVolumes = G4 248 G4LogicalVolumeStore* theLogicalVolumes = G4LogicalVolumeStore::GetInstance();
217 for (size_t t = 0; t < theLogicalVolumes->si << 249 for ( size_t t = 0; t < theLogicalVolumes->size(); t++ ) {
218 G4String lVolumeName = (*theLogicalVolumes 250 G4String lVolumeName = (*theLogicalVolumes)[t]->GetName();
219 if (lVolumeName != "LWorld") { 251 if (lVolumeName != "LWorld") {
220 (*theLogicalVolumes)[t]->SetSensitiveDet 252 (*theLogicalVolumes)[t]->SetSensitiveDetector(mfDetector);
221 } 253 }
222 } 254 }
223 G4SDManager::GetSDMpointer()->AddNewDetector 255 G4SDManager::GetSDMpointer()->AddNewDetector(mfDetector);
>> 256
224 } 257 }
225 258
226 //....oooOO0OOooo........oooOO0OOooo........oo 259 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
227 260
228 void DetectorConstruction::ReadOffsetFile(G4St << 261 void DetectorConstruction::ReadOffsetFile(G4String file) {
229 { << 262 if (fVOffset.size() > 0)
230 if (fVOffset.size() > 0) fVOffset.clear(); << 263 fVOffset.clear();
231 264
232 std::ifstream OffSetFile; 265 std::ifstream OffSetFile;
233 OffSetFile.open(file); 266 OffSetFile.open(file);
234 G4double x, y, z; 267 G4double x, y, z;
235 268
236 if (!OffSetFile) { 269 if (!OffSetFile) {
237 G4cout << "Plasmid Offset positions file n 270 G4cout << "Plasmid Offset positions file not found!!!" << G4endl;
238 exit(1); 271 exit(1);
239 } 272 }
240 273
241 else { 274 else {
242 while (OffSetFile >> x >> y >> z) { 275 while (OffSetFile >> x >> y >> z) {
243 fVOffset.push_back(G4ThreeVector(x * nm, << 276 fVOffset.push_back(G4ThreeVector(x*nm,y*nm,z*nm));
244 } 277 }
245 } << 278 }
246 } 279 }
247 280
248 //....oooOO0OOooo........oooOO0OOooo........oo 281 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
249 282
250 void DetectorConstruction::AddDNAInformation(G << 283 void DetectorConstruction::AddDNAInformation(G4int copy, G4ThreeVector offset) {
251 { << 284 for(size_t i = 0; i < fSampleDNANames.size(); i++) {
252 for (size_t i = 0; i < fSampleDNANames.size( <<
253 fDNANames.push_back(fSampleDNANames[i]); 285 fDNANames.push_back(fSampleDNANames[i]);
254 fDNAPositions.push_back(fSampleDNAPosition 286 fDNAPositions.push_back(fSampleDNAPositions[i] + offset);
255 287
256 std::vector<G4int> Details = fSampleDNADet 288 std::vector<G4int> Details = fSampleDNADetails[i];
257 Details[0] = copy; 289 Details[0] = copy;
258 fDNADetails.push_back(Details); 290 fDNADetails.push_back(Details);
259 } 291 }
260 } 292 }
261 293
262 //....oooOO0OOooo........oooOO0OOooo........oo 294 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
263 295