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