dnadamage2/src/DetectorConstruction.cc

0001 //
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0025 //
0026 /// \file DetectorConstruction.cc
0027 /// \brief Implementation of the DetectorConstruction class
0028
0029 // This example is provided by the Geant4-DNA collaboration
0030 // dnadamage2 example is derived from the chem6 example
0031 // chem6 example authors: W. G. Shin and S. Incerti (CENBG, France)
0032 //
0033 // Any report or published results obtained using the Geant4-DNA software
0034 // shall cite the following Geant4-DNA collaboration publication:
0035 // J. Appl. Phys. 125 (2019) 104301
0036 // Med. Phys. 45 (2018) e722-e739
0037 // J. Comput. Phys. 274 (2014) 841-882
0038 // Med. Phys. 37 (2010) 4692-4708
0039 // Int. J. Model. Simul. Sci. Comput. 1 (2010) 157-178
0040 // The Geant4-DNA web site is available at http://geant4-dna.org
0041 //
0042 // Authors: J. Naoki D. Kondo (UCSF, US)
0043 //          J. Ramos-Mendez and B. Faddegon (UCSF, US)
0044 //
0045
0046 #include "DetectorConstruction.hh"
0047
0048 #include "ScoreLET.hh"
0049 #include "ScoreSpecies.hh"
0050 #include "ScoreStrandBreaks.hh"
0051
0052 #include "G4Box.hh"
0053 #include "G4GeometryManager.hh"
0054 #include "G4LogicalVolume.hh"
0055 #include "G4LogicalVolumeStore.hh"
0056 #include "G4MultiFunctionalDetector.hh"
0057 #include "G4NistManager.hh"
0058 #include "G4PVPlacement.hh"
0059 #include "G4PhysicalConstants.hh"
0060 #include "G4RunManager.hh"
0061 #include "G4SDManager.hh"
0062 #include "G4SystemOfUnits.hh"
0063 #include "G4VPrimitiveScorer.hh"
0064 #include "G4VisAttributes.hh"
0065
0066 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0067
0068 DetectorConstruction::DetectorConstruction() : G4VUserDetectorConstruction()
0069 {
0070   fDetDir = new G4UIdirectory("/det/");
0071   fDetDir->SetGuidance("Detector control.");
0072
0073   fSizeCmd = new G4UIcmdWithADoubleAndUnit("/det/setSize", this);
0074   fSizeCmd->SetDefaultUnit("um");
0075
0076   fpOffSetFileUI = new G4UIcmdWithAString("/det/OffSetFile", this);
0077   fpPlasmidNbUI = new G4UIcmdWithAnInteger("/det/NbOfPlasmids", this);
0078
0079   fpPlasmidFile = new G4UIcmdWithAString("/det/PlasmidFile", this);
0080   fpUseDNA = new G4UIcmdWithABool("/det/UseDNAVolumes", this);
0081 }
0082
0083 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0084
0085 DetectorConstruction::~DetectorConstruction()
0086 {
0087   delete fSizeCmd;
0088   delete fpOffSetFileUI;
0089   delete fpPlasmidFile;
0090   delete fpUseDNA;
0091 }
0092
0093 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0094
0095 void DetectorConstruction::SetNewValue(G4UIcommand* command, G4String newValue)
0096 {
0097   if (command == fSizeCmd) {
0098     G4double size = fSizeCmd->GetNewDoubleValue(newValue);
0099     SetSize(size);
0100   }
0101
0102   if (command == fpPlasmidNbUI) {
0103     fNbOfPlasmids = fpPlasmidNbUI->GetNewIntValue(newValue);
0104   }
0105
0106   if (command == fpOffSetFileUI) {
0107     G4String File = newValue;
0108     ReadOffsetFile(File);
0109   }
0110
0111   if (command == fpPlasmidFile) {
0112     fPlasmidFile = newValue;
0113   }
0114
0115   if (command == fpUseDNA) {
0116     fUseDNAVolumes = fpUseDNA->GetNewBoolValue(newValue);
0117   }
0118 }
0119
0120 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0121
0122 void DetectorConstruction::SetSize(G4double size)
0123 {
0124   G4GeometryManager::GetInstance()->OpenGeometry();
0125   fPlasmidEnvelope->SetRadius(size / 2);
0126   G4RunManager::GetRunManager()->GeometryHasBeenModified();
0127   G4cout << "#### the geometry has been modified " << G4endl;
0128 }
0129
0130 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0131
0132 G4VPhysicalVolume* DetectorConstruction::Construct()
0133 {
0134   // Clear DNA information Containers
0135   fSampleDNANames.clear();
0136   fSampleDNAPositions.clear();
0137   fSampleDNADetails.clear();
0138   fDNANames.clear();
0139   fDNAPositions.clear();
0140   fDNADetails.clear();
0141
0142   // Water is defined from NIST material database
0143   G4NistManager* man = G4NistManager::Instance();
0144   G4Material* normalWater = man->FindOrBuildMaterial("G4_WATER");
0145   G4Material* waterWorld =
0146     man->BuildMaterialWithNewDensity("G4_WATER_WORLD", "G4_WATER", 1.0 * g / cm / cm / cm);
0147
0148   //
0149   // World
0150   G4Box* solidWenvelope = new G4Box("SWorld", 1 * um, 1 * um, 1 * um);
0151   G4LogicalVolume* logicWorld = new G4LogicalVolume(solidWenvelope, waterWorld, "LWorld");
0152   G4VPhysicalVolume* physWorld =
0153     new G4PVPlacement(0, G4ThreeVector(), "PWorld", logicWorld, 0, false, 0);
0154
0155   // Molecule
0156   fPlasmidEnvelope = new G4Orb("plasmidEnvelope", 0.5 * fWorldSize);
0157
0158   G4LogicalVolume* tlogicPlasmid =
0159     new G4LogicalVolume(fPlasmidEnvelope, normalWater, "PlasmidVolume");
0160   new G4PVPlacement(0, G4ThreeVector(), tlogicPlasmid, "plasmid", logicWorld, false, 0);
0161
0162   // World Vis Attributes
0163   G4VisAttributes worldVis(G4Colour(0.0, 0.0, 1.0));
0164   logicWorld->SetVisAttributes(worldVis);
0165
0166   PhysGeoImport GeoImport = PhysGeoImport();
0167
0168   G4LogicalVolume* logicStraightVoxel;
0169
0170   logicStraightVoxel = GeoImport.CreateLogicVolumeXYZ(fPlasmidFile);
0171
0172   fSampleDNANames = GeoImport.GetMoleculesNames();
0173   fSampleDNAPositions = GeoImport.GetMoleculesPositions();
0174   fSampleDNADetails = GeoImport.GetMoleculesDetails();
0175
0176   for (int i = 0; i < fNbOfPlasmids; i++) {
0177     if (fUseDNAVolumes)
0178       new G4PVPlacement(0, fVOffset[i], logicStraightVoxel, "VoxelStraight", logicWorld, true, i);
0179     AddDNAInformation(i, fVOffset[i]);
0180   }
0181
0182   // always return the physical World
0183   return physWorld;
0184 }
0185
0186 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0187
0188 void DetectorConstruction::ConstructSDandField()
0189 {
0190   G4SDManager::GetSDMpointer()->SetVerboseLevel(1);
0191
0192   // declare World as a MultiFunctionalDetector scorer
0193   //
0194   G4MultiFunctionalDetector* mfDetector = new G4MultiFunctionalDetector("mfDetector");
0195
0196   // LET scorer:
0197   //  - scores restricted or unrestricted LET
0198
0199   ScoreLET* LET = new ScoreLET("LET");
0200   mfDetector->RegisterPrimitive(LET);
0201
0202   // Species scorer:
0203   //  - scores number of species over time
0204   //  - compute the radiochemical yields (G values)
0205
0206   G4VPrimitiveScorer* primitivSpecies = new ScoreSpecies("Species");
0207   mfDetector->RegisterPrimitive(primitivSpecies);
0208
0209   // SB Scorer: Requires access to Geometry
0210   //  - scores number of Direct SB
0211   //  - scores number of Indirect SB
0212
0213   G4VPrimitiveScorer* primitiveSB = new ScoreStrandBreaks("StrandBreaks", this, &fWorldSize);
0214   mfDetector->RegisterPrimitive(primitiveSB);
0215
0216   // Attach Detectors to Plasmid Volumes
0217   G4LogicalVolumeStore* theLogicalVolumes = G4LogicalVolumeStore::GetInstance();
0218   for (size_t t = 0; t < theLogicalVolumes->size(); t++) {
0219     G4String lVolumeName = (*theLogicalVolumes)[t]->GetName();
0220     if (lVolumeName != "LWorld") {
0221       (*theLogicalVolumes)[t]->SetSensitiveDetector(mfDetector);
0222     }
0223   }
0224   G4SDManager::GetSDMpointer()->AddNewDetector(mfDetector);
0225 }
0226
0227 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0228
0229 void DetectorConstruction::ReadOffsetFile(G4String file)
0230 {
0231   if (fVOffset.size() > 0) fVOffset.clear();
0232
0233   std::ifstream OffSetFile;
0234   OffSetFile.open(file);
0235   G4double x, y, z;
0236
0237   if (!OffSetFile) {
0238     G4cout << "Plasmid Offset positions file not found!!!" << G4endl;
0239     exit(1);
0240   }
0241
0242   else {
0243     while (OffSetFile >> x >> y >> z) {
0244       fVOffset.push_back(G4ThreeVector(x * nm, y * nm, z * nm));
0245     }
0246   }
0247 }
0248
0249 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....
0250
0251 void DetectorConstruction::AddDNAInformation(G4int copy, G4ThreeVector offset)
0252 {
0253   for (size_t i = 0; i < fSampleDNANames.size(); i++) {
0254     fDNANames.push_back(fSampleDNANames[i]);
0255     fDNAPositions.push_back(fSampleDNAPositions[i] + offset);
0256
0257     std::vector<G4int> Details = fSampleDNADetails[i];
0258     Details[0] = copy;
0259     fDNADetails.push_back(Details);
0260   }
0261 }
0262
0263 //....oooOO0OOooo........oooOO0OOooo........oooOO0OOooo........oooOO0OOooo.....