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Geant4/examples/extended/medical/dna/dnadamage2/src/DetectorConstruction.cc

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Diff markup

Differences between /examples/extended/medical/dna/dnadamage2/src/DetectorConstruction.cc (Version 11.3.0) and /examples/extended/medical/dna/dnadamage2/src/DetectorConstruction.cc (Version 8.3.p2)


  1 //                                                  1 
  2 // *******************************************    
  3 // * License and Disclaimer                       
  4 // *                                              
  5 // * The  Geant4 software  is  copyright of th    
  6 // * the Geant4 Collaboration.  It is provided    
  7 // * conditions of the Geant4 Software License    
  8 // * LICENSE and available at  http://cern.ch/    
  9 // * include a list of copyright holders.         
 10 // *                                              
 11 // * Neither the authors of this software syst    
 12 // * institutes,nor the agencies providing fin    
 13 // * work  make  any representation or  warran    
 14 // * regarding  this  software system or assum    
 15 // * use.  Please see the license in the file     
 16 // * for the full disclaimer and the limitatio    
 17 // *                                              
 18 // * This  code  implementation is the result     
 19 // * technical work of the GEANT4 collaboratio    
 20 // * By using,  copying,  modifying or  distri    
 21 // * any work based  on the software)  you  ag    
 22 // * use  in  resulting  scientific  publicati    
 23 // * acceptance of all terms of the Geant4 Sof    
 24 // *******************************************    
 25 //                                                
 26 // This example is provided by the Geant4-DNA     
 27 // dnadamage2 example is derived from the chem    
 28 // chem6 example authors: W. G. Shin and S. In    
 29 //                                                
 30 // Any report or published results obtained us    
 31 // shall cite the following Geant4-DNA collabo    
 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)    
 37 // The Geant4-DNA web site is available at htt    
 38 //                                                
 39 // Authors: J. Naoki D. Kondo (UCSF, US)          
 40 //          J. Ramos-Mendez and B. Faddegon (U    
 41 //                                                
 42 /// \file DetectorConstruction.cc                 
 43 /// \brief Implementation of the DetectorConst    
 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........oo    
 66                                                   
 67 DetectorConstruction::DetectorConstruction() :    
 68 {                                                 
 69   fDetDir = new G4UIdirectory("/det/");           
 70   fDetDir->SetGuidance("Detector control.");      
 71                                                   
 72   fSizeCmd = new G4UIcmdWithADoubleAndUnit("/d    
 73   fSizeCmd->SetDefaultUnit("um");                 
 74                                                   
 75   fpOffSetFileUI = new G4UIcmdWithAString("/de    
 76   fpPlasmidNbUI = new G4UIcmdWithAnInteger("/d    
 77                                                   
 78   fpPlasmidFile = new G4UIcmdWithAString("/det    
 79   fpUseDNA = new G4UIcmdWithABool("/det/UseDNA    
 80 }                                                 
 81                                                   
 82 //....oooOO0OOooo........oooOO0OOooo........oo    
 83                                                   
 84 DetectorConstruction::~DetectorConstruction()     
 85 {                                                 
 86   delete fSizeCmd;                                
 87   delete fpOffSetFileUI;                          
 88   delete fpPlasmidFile;                           
 89   delete fpUseDNA;                                
 90 }                                                 
 91                                                   
 92 //....oooOO0OOooo........oooOO0OOooo........oo    
 93                                                   
 94 void DetectorConstruction::SetNewValue(G4UIcom    
 95 {                                                 
 96   if (command == fSizeCmd) {                      
 97     G4double size = fSizeCmd->GetNewDoubleValu    
 98     SetSize(size);                                
 99   }                                               
100                                                   
101   if (command == fpPlasmidNbUI) {                 
102     fNbOfPlasmids = fpPlasmidNbUI->GetNewIntVa    
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    
116   }                                               
117 }                                                 
118                                                   
119 //....oooOO0OOooo........oooOO0OOooo........oo    
120                                                   
121 void DetectorConstruction::SetSize(G4double si    
122 {                                                 
123   G4GeometryManager::GetInstance()->OpenGeomet    
124   fPlasmidEnvelope->SetRadius(size / 2);          
125   G4RunManager::GetRunManager()->GeometryHasBe    
126   G4cout << "#### the geometry has been modifi    
127 }                                                 
128                                                   
129 //....oooOO0OOooo........oooOO0OOooo........oo    
130                                                   
131 G4VPhysicalVolume* DetectorConstruction::Const    
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 datab    
142   G4NistManager* man = G4NistManager::Instance    
143   G4Material* normalWater = man->FindOrBuildMa    
144   G4Material* waterWorld =                        
145     man->BuildMaterialWithNewDensity("G4_WATER    
146                                                   
147   //                                              
148   // World                                        
149   G4Box* solidWenvelope = new G4Box("SWorld",     
150   G4LogicalVolume* logicWorld = new G4LogicalV    
151   G4VPhysicalVolume* physWorld =                  
152     new G4PVPlacement(0, G4ThreeVector(), "PWo    
153                                                   
154   // Molecule                                     
155   fPlasmidEnvelope = new G4Orb("plasmidEnvelop    
156                                                   
157   G4LogicalVolume* tlogicPlasmid =                
158     new G4LogicalVolume(fPlasmidEnvelope, norm    
159   new G4PVPlacement(0, G4ThreeVector(), tlogic    
160                                                   
161   // World Vis Attributes                         
162   G4VisAttributes worldVis(G4Colour(0.0, 0.0,     
163   logicWorld->SetVisAttributes(worldVis);         
164                                                   
165   PhysGeoImport GeoImport = PhysGeoImport();      
166                                                   
167   G4LogicalVolume* logicStraightVoxel;            
168                                                   
169   logicStraightVoxel = GeoImport.CreateLogicVo    
170                                                   
171   fSampleDNANames = GeoImport.GetMoleculesName    
172   fSampleDNAPositions = GeoImport.GetMolecules    
173   fSampleDNADetails = GeoImport.GetMoleculesDe    
174                                                   
175   for (int i = 0; i < fNbOfPlasmids; i++) {       
176     if (fUseDNAVolumes)                           
177       new G4PVPlacement(0, fVOffset[i], logicS    
178     AddDNAInformation(i, fVOffset[i]);            
179   }                                               
180                                                   
181   // always return the physical World             
182   return physWorld;                               
183 }                                                 
184                                                   
185 //....oooOO0OOooo........oooOO0OOooo........oo    
186                                                   
187 void DetectorConstruction::ConstructSDandField    
188 {                                                 
189   G4SDManager::GetSDMpointer()->SetVerboseLeve    
190                                                   
191   // declare World as a MultiFunctionalDetecto    
192   //                                              
193   G4MultiFunctionalDetector* mfDetector = new     
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 va    
204                                                   
205   G4VPrimitiveScorer* primitivSpecies = new Sc    
206   mfDetector->RegisterPrimitive(primitivSpecie    
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 ScoreS    
213   mfDetector->RegisterPrimitive(primitiveSB);     
214                                                   
215   // Attach Detectors to Plasmid Volumes          
216   G4LogicalVolumeStore* theLogicalVolumes = G4    
217   for (size_t t = 0; t < theLogicalVolumes->si    
218     G4String lVolumeName = (*theLogicalVolumes    
219     if (lVolumeName != "LWorld") {                
220       (*theLogicalVolumes)[t]->SetSensitiveDet    
221     }                                             
222   }                                               
223   G4SDManager::GetSDMpointer()->AddNewDetector    
224 }                                                 
225                                                   
226 //....oooOO0OOooo........oooOO0OOooo........oo    
227                                                   
228 void DetectorConstruction::ReadOffsetFile(G4St    
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 n    
238     exit(1);                                      
239   }                                               
240                                                   
241   else {                                          
242     while (OffSetFile >> x >> y >> z) {           
243       fVOffset.push_back(G4ThreeVector(x * nm,    
244     }                                             
245   }                                               
246 }                                                 
247                                                   
248 //....oooOO0OOooo........oooOO0OOooo........oo    
249                                                   
250 void DetectorConstruction::AddDNAInformation(G    
251 {                                                 
252   for (size_t i = 0; i < fSampleDNANames.size(    
253     fDNANames.push_back(fSampleDNANames[i]);      
254     fDNAPositions.push_back(fSampleDNAPosition    
255                                                   
256     std::vector<G4int> Details = fSampleDNADet    
257     Details[0] = copy;                            
258     fDNADetails.push_back(Details);               
259   }                                               
260 }                                                 
261                                                   
262 //....oooOO0OOooo........oooOO0OOooo........oo    
263